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Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers BA, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint. Immunity 2024; 57:1160-1176.e7. [PMID: 38697118 DOI: 10.1016/j.immuni.2024.04.009] [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: 03/28/2023] [Revised: 01/21/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
Abstract
Multimodal single-cell profiling methods can capture immune cell variations unfolding over time at the molecular, cellular, and population levels. Transforming these data into biological insights remains challenging. Here, we introduce a framework to integrate variations at the human population and single-cell levels in vaccination responses. Comparing responses following AS03-adjuvanted versus unadjuvanted influenza vaccines with CITE-seq revealed AS03-specific early (day 1) response phenotypes, including a B cell signature of elevated germinal center competition. A correlated network of cell-type-specific transcriptional states defined the baseline immune status associated with high antibody responders to the unadjuvanted vaccine. Certain innate subsets in the network appeared "naturally adjuvanted," with transcriptional states resembling those induced uniquely by AS03-adjuvanted vaccination. Consistently, CD14+ monocytes from high responders at baseline had elevated phospho-signaling responses to lipopolysaccharide stimulation. Our findings link baseline immune setpoints to early vaccine responses, with positive implications for adjuvant development and immune response engineering.
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Affiliation(s)
- Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA; NIH-Oxford-Cambridge Scholars Program, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juan A Quiel
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Arjun Jain
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Pamela L Schwartzberg
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Cell Signaling and Immunity Section, NIAID, NIH, Bethesda, MD, USA
| | - John S 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.
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2
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Peng X, Yang L, Yuan P, Ding X. Hybrid Cell Membrane-Based Nanoplatforms for Enhanced Immunotherapy against Cancer and Infectious Diseases. Adv Healthc Mater 2024:e2304477. [PMID: 38709914 DOI: 10.1002/adhm.202304477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/20/2024] [Indexed: 05/08/2024]
Abstract
Immunotherapy based on nanoplatforms is a promising approach to treat cancer and infectious diseases, and it has achieved considerable progress in clinical practices. Cell membrane-based nanoplatforms endow nanoparticles with versatile characteristics, such as half-life extension, targeting ability, and immune-system regulation. However, monotypic cell membrane usually fails to provoke strong immune response for immunotherapy while maintaining good biosafety. The integration of different cell-membrane types provides a promising approach to construct multifunctional nanoplatforms for improved immunotherapeutic efficacy by enhancing immunogenicity or targeting function, evading immune clearance, or combining with other therapeutic modalities. In this review, the design principles, preparation strategies, and applications of hybrid cell membrane-based nanoplatforms for cancer and infection immunotherapy are first discussed. Furthermore, the challenges and prospects for the potential clinical translation of hybrid cell membrane-based nanoplatforms are discussed.
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Affiliation(s)
- Xinran Peng
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Li Yang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Peiyan Yuan
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Xin Ding
- School of Medicine, Sun Yat-sen University, Shenzhen, 518107, China
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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3
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Haralambieva IH, Chen J, Quach HQ, Ratishvili T, Warner ND, Ovsyannikova IG, Poland GA, Kennedy RB. Early B cell transcriptomic markers of measles-specific humoral immunity following a 3 rd dose of MMR vaccine. Front Immunol 2024; 15:1358477. [PMID: 38633249 PMCID: PMC11021587 DOI: 10.3389/fimmu.2024.1358477] [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: 12/19/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
B cell transcriptomic signatures hold promise for the early prediction of vaccine-induced humoral immunity and vaccine protective efficacy. We performed a longitudinal study in 232 healthy adult participants before/after a 3rd dose of MMR (MMR3) vaccine. We assessed baseline and early transcriptional patterns in purified B cells and their association with measles-specific humoral immunity after MMR vaccination using two analytical methods ("per gene" linear models and joint analysis). Our study identified distinct early transcriptional signatures/genes following MMR3 that were associated with measles-specific neutralizing antibody titer and/or binding antibody titer. The most significant genes included: the interleukin 20 receptor subunit beta/IL20RB gene (a subunit receptor for IL-24, a cytokine involved in the germinal center B cell maturation/response); the phorbol-12-myristate-13-acetate-induced protein 1/PMAIP1, the brain expressed X-linked 2/BEX2 gene and the B cell Fas apoptotic inhibitory molecule/FAIM, involved in the selection of high-affinity B cell clones and apoptosis/regulation of apoptosis; as well as IL16 (encoding the B lymphocyte-derived IL-16 ligand of CD4), involved in the crosstalk between B cells, dendritic cells and helper T cells. Significantly enriched pathways included B cell signaling, apoptosis/regulation of apoptosis, metabolic pathways, cell cycle-related pathways, and pathways associated with viral infections, among others. In conclusion, our study identified genes/pathways linked to antigen-induced B cell proliferation, differentiation, apoptosis, and clonal selection, that are associated with, and impact measles virus-specific humoral immunity after MMR vaccination.
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Affiliation(s)
- Iana H. Haralambieva
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Jun Chen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Huy Quang Quach
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Tamar Ratishvili
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Nathaniel D. Warner
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
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4
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Sugrue JA, Duffy D. Systems vaccinology studies - achievements and future potential. Microbes Infect 2024:105318. [PMID: 38460935 DOI: 10.1016/j.micinf.2024.105318] [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: 07/02/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Human immune responses to vaccination are variable both within and between populations. Systems vaccinology, which is the application of multi-omics technologies to vaccine studies, seeks to understand such variation and predict responses to optimise vaccine strategies. Here, we outline new approaches to systems vaccinology, focusing on the incorporation of additional cohorts, endpoints and technologies.
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Affiliation(s)
- Jamie A Sugrue
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France.
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Plaça DR, Fonseca DLM, Marques AHC, Zaki Pour S, Usuda JN, Baiocchi GC, Prado CADS, Salgado RC, Filgueiras IS, Freire PP, Rocha V, Camara NOS, Catar R, Moll G, Jurisica I, Calich VLG, Giil LM, Rivino L, Ochs HD, Cabral-Miranda G, Schimke LF, Cabral-Marques O. Immunological signatures unveiled by integrative systems vaccinology characterization of dengue vaccination trials and natural infection. Front Immunol 2024; 15:1282754. [PMID: 38444851 PMCID: PMC10912564 DOI: 10.3389/fimmu.2024.1282754] [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: 08/24/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Introduction Dengue virus infection is a global health problem lacking specific therapy, requiring an improved understanding of DENV immunity and vaccine responses. Considering the recent emerging of new dengue vaccines, here we performed an integrative systems vaccinology characterization of molecular signatures triggered by the natural DENV infection (NDI) and attenuated dengue virus infection models (DVTs). Methods and results We analyzed 955 samples of transcriptomic datasets of patients with NDI and attenuated dengue virus infection trials (DVT1, DVT2, and DVT3) using a systems vaccinology approach. Differential expression analysis identified 237 common differentially expressed genes (DEGs) between DVTs and NDI. Among them, 28 and 60 DEGs were up or downregulated by dengue vaccination during DVT2 and DVT3, respectively, with 20 DEGs intersecting across all three DVTs. Enriched biological processes of these genes included type I/II interferon signaling, cytokine regulation, apoptosis, and T-cell differentiation. Principal component analysis based on 20 common DEGs (overlapping between DVTs and our NDI validation dataset) distinguished dengue patients by disease severity, particularly in the late acute phase. Machine learning analysis ranked the ten most critical predictors of disease severity in NDI, crucial for the anti-viral immune response. Conclusion This work provides insights into the NDI and vaccine-induced overlapping immune response and suggests molecular markers (e.g., IFIT5, ISG15, and HERC5) for anti-dengue-specific therapies and effective vaccination development.
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Affiliation(s)
- Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Dennyson Leandro M. Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - Alexandre H. C. Marques
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Shahab Zaki Pour
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Júlia Nakanishi Usuda
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Gabriela Crispim Baiocchi
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ranieri Coelho Salgado
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Igor Salerno Filgueiras
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Paula Paccielli Freire
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Vanderson Rocha
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology and Cell Therapy, Hospital das Clínicas, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
- Instituto D’Or de Ensino e Pesquisa, São Paulo, Brazil
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
- Department of Hematology, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Niels Olsen Saraiva Camara
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Rusan Catar
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Guido Moll
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
- Berlin Institute of Health (BIH) Center for Regenerative Therapies (BCRT) and Berlin-Brandenburg School for Regenerative Therapies (BSRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vera Lúcia Garcia Calich
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lasse M. Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Laura Rivino
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Emerging Infectious Diseases, Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Hans D. Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children’s Research Institute, Seattle, WA, United States
| | - Gustavo Cabral-Miranda
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lena F. Schimke
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, Berlin, Germany
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil
| | - Otavio Cabral-Marques
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Instituto D’Or de Ensino e Pesquisa, São Paulo, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, Berlin, Germany
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil
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6
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Hurissi EA, Abuallut II, Dibaji MQ, Jaly A, Alhazmi AH, Abuageelah BM, Alameer KM, Alyami YM. Ocular Complications after COVID-19 Vaccination: A Systematic Review. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:249. [PMID: 38399537 PMCID: PMC10890211 DOI: 10.3390/medicina60020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/07/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024]
Abstract
Background and Objectives: The COVID-19 pandemic affects various populations worldwide. The discovery of vaccinations was necessary for the prevention and elimination of the disease. Despite the high importance of these vaccinations, they may cause some complications, such as ocular complications. This study aims to draw attention to the possible complications of the vaccination and highlight its importance. Materials and Methods: Systematic review of the literature from January 2021 to January 2023. A total of 20 published articles were included and reported cases of ocular complications in patients who received COVID-19 vaccines. Results: A total of 243 patients with verified ocular complications following the COVID-19 vaccination were included, ranging in age from 18 to 84 years. The most common ocular complications reported in the current study were ocular inflammatory complications, which represented 47.3%, followed by optic neuritis (24.3%). Retinal artery occlusion, retinal vein occlusion, acute macular neuroretinopathy, and paracentral acute middle maculopathy represented 10.7%. Herpetic ocular infections and herpetic eye disease (14%). Nearly half (42%) of the patients with ocular problems received the Pfizer-BioNTech vaccination. Conclusions: Despite the high importance of the COVID-19 vaccination, it was found that it is associated with the occurrence of some ocular complications. Future projects should come with more extensive prospective studies to further elucidate the underlying mechanisms and risk factors associated with ocular complications following COVID-19 vaccination, thereby enhancing our understanding and guiding appropriate management strategies.
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Affiliation(s)
- Eman A. Hurissi
- Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia; (E.A.H.); (K.M.A.)
| | - Ismail I. Abuallut
- Department of Surgery, Ophthalmology Division, Jazan University, Jazan 45142, Saudi Arabia;
| | | | - Abdulaziz Jaly
- Pharmacy, Jazan University Hospital, Jazan 45142, Saudi Arabia;
| | - Abdulaziz H. Alhazmi
- Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia; (E.A.H.); (K.M.A.)
| | - Bandar M. Abuageelah
- Department of Medicine and Surgery, Batterjee Medical College, Abha 62451, Saudi Arabia; (B.M.A.); (Y.M.A.)
| | - Khalid M. Alameer
- Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia; (E.A.H.); (K.M.A.)
| | - Yousef M. Alyami
- Department of Medicine and Surgery, Batterjee Medical College, Abha 62451, Saudi Arabia; (B.M.A.); (Y.M.A.)
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7
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Zhang Y, Zhao L, Zhang J, Zhang X, Han S, Sun Q, Yao M, Pang B, Duan Q, Jiang X. Antibody and transcription landscape in peripheral blood mononuclear cells of elderly adults over 70 years of age with third dose of COVID-19 BBIBP-CorV and ZF2001 booster vaccine. Immun Ageing 2024; 21:11. [PMID: 38280989 PMCID: PMC10821575 DOI: 10.1186/s12979-023-00408-x] [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: 08/22/2023] [Accepted: 12/20/2023] [Indexed: 01/29/2024]
Abstract
BACKGROUND In the context of the COVID-19 pandemic and extensive vaccination, it is important to explore the immune response of elderly adults to homologous and heterologous booster vaccines of COVID-19. At this point, we detected serum IgG antibodies and PBMC sample transcriptome profiles in 46 participants under 70 years old and 25 participants over 70 years old who received the third dose of the BBIBP-CorV and ZF2001 vaccines. RESULTS On day 7, the antibody levels of people over 70 years old after the third dose of booster vaccine were lower than those of young people, and the transcriptional responses of innate and adaptive immunity were also weak. The age of the participants showed a significant negative correlation with functions related to T-cell differentiation and costimulation. Nevertheless, 28 days after the third dose, the IgG antibodies of elderly adults reached equivalence to those of younger adults, and immune-related transcriptional regulation was significantly improved. The age showed a significant positive correlation with functions related to "chemokine receptor binding", "chemokine activity", and "chemokine-mediated signaling pathway". CONCLUSIONS Our results document that the response of elderly adults to the third dose of the vaccine was delayed, but still able to achieve comparable immune effects compared to younger adults, in regard to antibody responses as well as at the transcript level.
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Affiliation(s)
- Yuwei Zhang
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Lianxiang Zhao
- School of Public Health and Management, Binzhou Medical University, Yantai , Shandong Province, China
| | - Jinzhong Zhang
- Liaocheng Center for Disease Control and Prevention, Liaocheng, Shandong Province, China
| | - Xiaomei Zhang
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Shanshan Han
- School of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Qingshuai Sun
- School of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Mingxiao Yao
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Bo Pang
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Qing Duan
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Xiaolin Jiang
- School of Public Health and Management, Binzhou Medical University, Yantai , Shandong Province, China.
- School of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong Province, China.
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road , Jinan, 250014, Shandong Province, China.
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Pathak RK, Kim JM. Veterinary systems biology for bridging the phenotype-genotype gap via computational modeling for disease epidemiology and animal welfare. Brief Bioinform 2024; 25:bbae025. [PMID: 38343323 PMCID: PMC10859662 DOI: 10.1093/bib/bbae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Veterinary systems biology is an innovative approach that integrates biological data at the molecular and cellular levels, allowing for a more extensive understanding of the interactions and functions of complex biological systems in livestock and veterinary science. It has tremendous potential to integrate multi-omics data with the support of vetinformatics resources for bridging the phenotype-genotype gap via computational modeling. To understand the dynamic behaviors of complex systems, computational models are frequently used. It facilitates a comprehensive understanding of how a host system defends itself against a pathogen attack or operates when the pathogen compromises the host's immune system. In this context, various approaches, such as systems immunology, network pharmacology, vaccinology and immunoinformatics, can be employed to effectively investigate vaccines and drugs. By utilizing this approach, we can ensure the health of livestock. This is beneficial not only for animal welfare but also for human health and environmental well-being. Therefore, the current review offers a detailed summary of systems biology advancements utilized in veterinary sciences, demonstrating the potential of the holistic approach in disease epidemiology, animal welfare and productivity.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
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9
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Zhu H, Chelysheva I, Pollard AJ, O'Connor D. Spotlight on systems vaccinology: a novel approach to elucidate correlates of protection. Genes Immun 2023:10.1038/s41435-023-00247-2. [PMID: 38148341 DOI: 10.1038/s41435-023-00247-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Affiliation(s)
- Henderson Zhu
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
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10
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Equils O, Bakaj A, Wilson-Mifsud B, Chatterjee A. Restoring Trust: The Need for Precision Medicine in Infectious Diseases, Public Health and Vaccines. Hum Vaccin Immunother 2023; 19:2234787. [PMID: 37465958 PMCID: PMC10361134 DOI: 10.1080/21645515.2023.2234787] [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: 04/04/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
There are limited data on precision medicine in infectious diseases and vaccines; however, precise management of infectious diseases plays a critical role in trust for government, health-care organizations, science, and pharma. The improvement in biomedical technologies, availability of large clinical and -omic data and appropriate application of artificial intelligence may allow precision in vaccines and public health and restore trust. This is an invited editorial on the role of precision medicine in infectious diseases and vaccines.
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Affiliation(s)
- Ozlem Equils
- Public Health Non-Profit, MiOra, Los Angeles, CA, USA
- Clinical Development, Cidara Therapeutics, San Diego, CA, USA
| | - Angela Bakaj
- Public Health Non-Profit, MiOra, Los Angeles, CA, USA
| | - Brittany Wilson-Mifsud
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Archana Chatterjee
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 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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Lykins WR, Fox CB. Practical Considerations for Next-Generation Adjuvant Development and Translation. Pharmaceutics 2023; 15:1850. [PMID: 37514037 PMCID: PMC10385070 DOI: 10.3390/pharmaceutics15071850] [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: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Over the last several years, there has been increased interest from academia and the pharmaceutical/biotech industry in the development of vaccine adjuvants for new and emerging vaccine modalities. Despite this, vaccine adjuvant development still has some of the longest timelines in the pharmaceutical space, from discovery to clinical approval. The reasons for this are manyfold and range from complexities in translation from animal to human models, concerns about safety or reactogenicity, to challenges in sourcing the necessary raw materials at scale. In this review, we will describe the current state of the art for many adjuvant technologies and how they should be approached or applied in the development of new vaccine products. We postulate that there are many factors to be considered and tools to be applied earlier on in the vaccine development pipeline to improve the likelihood of clinical success. These recommendations may require a modified approach to some of the common practices in new product development but would result in more accessible and practical adjuvant-containing products.
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13
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Siddiqa A, Wang Y, Thapa M, Martin DE, Cadar AN, Bartley JM, Li S. A pilot metabolomic study of drug interaction with the immune response to seasonal influenza vaccination. NPJ Vaccines 2023; 8:92. [PMID: 37308481 PMCID: PMC10261085 DOI: 10.1038/s41541-023-00682-2] [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: 01/05/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
Many human diseases, including metabolic diseases, are intertwined with the immune system. The understanding of how the human immune system interacts with pharmaceutical drugs is still limited, and epidemiological studies only start to emerge. As the metabolomics technology matures, both drug metabolites and biological responses can be measured in the same global profiling data. Therefore, a new opportunity presents itself to study the interactions between pharmaceutical drugs and immune system in the high-resolution mass spectrometry data. We report here a double-blinded pilot study of seasonal influenza vaccination, where half of the participants received daily metformin administration. Global metabolomics was measured in the plasma samples at six timepoints. Metformin signatures were successfully identified in the metabolomics data. Statistically significant metabolite features were found both for the vaccination effect and for the drug-vaccine interactions. This study demonstrates the concept of using metabolomics to investigate drug interaction with the immune response in human samples directly at molecular levels.
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Affiliation(s)
- Amnah Siddiqa
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Yating Wang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Maheshwor Thapa
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Dominique E Martin
- Department of Immunology and Center on Aging, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Andreia N Cadar
- Department of Immunology and Center on Aging, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Jenna M Bartley
- Department of Immunology and Center on Aging, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT, 06030, USA.
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
- Department of Immunology and Center on Aging, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT, 06030, USA.
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14
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Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers B, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. Multiscale integration of human and single-cell variations reveals unadjuvanted vaccine high responders are naturally adjuvanted. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.20.23287474. [PMID: 37090674 PMCID: PMC10120791 DOI: 10.1101/2023.03.20.23287474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Advances in multimodal single cell analysis can empower high-resolution dissection of human vaccination responses. The resulting data capture multiple layers of biological variations, including molecular and cellular states, vaccine formulations, inter- and intra-subject differences, and responses unfolding over time. Transforming such data into biological insight remains a major challenge. Here we present a systematic framework applied to multimodal single cell data obtained before and after influenza vaccination without adjuvants or pandemic H5N1 vaccination with the AS03 adjuvant. Our approach pinpoints responses shared across or unique to specific cell types and identifies adjuvant specific signatures, including pro-survival transcriptional states in B lymphocytes that emerged one day after vaccination. We also reveal that high antibody responders to the unadjuvanted vaccine have a distinct baseline involving a rewired network of cell type specific transcriptional states. Remarkably, the status of certain innate immune cells in this network in high responders of the unadjuvanted vaccine appear "naturally adjuvanted": they resemble phenotypes induced early in the same cells only by vaccination with AS03. Furthermore, these cell subsets have elevated frequency in the blood at baseline and increased cell-intrinsic phospho-signaling responses after LPS stimulation ex vivo in high compared to low responders. Our findings identify how variation in the status of multiple immune cell types at baseline may drive robust differences in innate and adaptive responses to vaccination and thus open new avenues for vaccine development and immune response engineering in humans.
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Affiliation(s)
- Matthew P. Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Brian Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juan A. Quiel
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Arjun Jain
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Pamela L. Schwartzberg
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Cell Signaling and Immunity Section, NIAID, NIH, Bethesda, MD, USA
| | - John S. 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
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15
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Cheung F, Apps R, Dropulic L, Kotliarov Y, Chen J, Jordan T, Langweiler M, Candia J, Biancotto A, Han KL, Rachmaninoff N, Pietz H, Wang K, Tsang JS, Cohen JI. Sex and prior exposure jointly shape innate immune responses to a live herpesvirus vaccine. eLife 2023; 12:80652. [PMID: 36648132 PMCID: PMC9844983 DOI: 10.7554/elife.80652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 12/02/2022] [Indexed: 01/11/2023] Open
Abstract
Background Both sex and prior exposure to pathogens are known to influence responses to immune challenges, but their combined effects are not well established in humans, particularly in early innate responses critical for shaping subsequent outcomes. Methods We employed systems immunology approaches to study responses to a replication-defective, herpes simplex virus (HSV) 2 vaccine in men and women either naive or previously exposed to HSV. Results Blood transcriptomic and cell population profiling showed substantial changes on day 1 after vaccination, but the responses depended on sex and whether the vaccinee was naive or previously exposed to HSV. The magnitude of early transcriptional responses was greatest in HSV naive women where type I interferon (IFN) signatures were prominent and associated negatively with vaccine-induced neutralizing antibody titers, suggesting that a strong early antiviral response reduced the uptake of this replication-defective virus vaccine. While HSV seronegative vaccine recipients had upregulation of gene sets in type I IFN (IFN-α/β) responses, HSV2 seropositive vaccine recipients tended to have responses focused more on type II IFN (IFN-γ) genes. Conclusions These results together show that prior exposure and sex interact to shape early innate responses that then impact subsequent adaptive immune phenotypes. Funding Intramural Research Program of the NIH, the National Institute of Allergy and Infectious Diseases, and other institutes supporting the Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation. The vaccine trial was supported through a clinical trial agreement between the National Institute of Allergy and Infectious Diseases and Sanofi Pasteur. Clinical trial number: NCT01915212.
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Affiliation(s)
- Foo Cheung
- Center for Human Immunology, National Institutes of HealthBethesdaUnited States
| | - Richard Apps
- Center for Human Immunology, National Institutes of HealthBethesdaUnited States
| | - Lesia Dropulic
- Medical Virology Section, Laboratory of Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Yuri Kotliarov
- Center for Human Immunology, National Institutes of HealthBethesdaUnited States
| | - Jinguo Chen
- Center for Human Immunology, National Institutes of HealthBethesdaUnited States
| | - Tristan Jordan
- Medical Virology Section, Laboratory of Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Marc Langweiler
- Center for Human Immunology, National Institutes of HealthBethesdaUnited States
| | - Julian Candia
- Center for Human Immunology, National Institutes of HealthBethesdaUnited States
| | - Angelique Biancotto
- Center for Human Immunology, National Institutes of HealthBethesdaUnited States
| | - Kyu Lee Han
- Center for Human Immunology, National Institutes of HealthBethesdaUnited States
| | - Nicholas Rachmaninoff
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institutes of HealthBethesdaUnited States
| | - Harlan Pietz
- Medical Virology Section, Laboratory of Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Kening Wang
- Medical Virology Section, Laboratory of Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - John S Tsang
- Center for Human Immunology, National Institutes of HealthBethesdaUnited States
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institutes of HealthBethesdaUnited States
| | - Jeffrey I Cohen
- Medical Virology Section, Laboratory of Infectious Diseases, National Institutes of HealthBethesdaUnited States
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16
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Lacasta A, Kim HC, Kepl E, Gachogo R, Chege N, Ojuok R, Muriuki C, Mwalimu S, Touboul G, Stiber A, Poole EJ, Ndiwa N, Fiala B, King NP, Nene V. Design and immunological evaluation of two-component protein nanoparticle vaccines for East Coast fever. Front Immunol 2023; 13:1015840. [PMID: 36713406 PMCID: PMC9880323 DOI: 10.3389/fimmu.2022.1015840] [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: 08/10/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
Nanoparticle vaccines usually prime stronger immune responses than soluble antigens. Within this class of subunit vaccines, the recent development of computationally designed self-assembling two-component protein nanoparticle scaffolds provides a powerful and versatile platform for displaying multiple copies of one or more antigens. Here we report the generation of three different nanoparticle immunogens displaying 60 copies of p67C, an 80 amino acid polypeptide from a candidate vaccine antigen of Theileria parva, and their immunogenicity in cattle. p67C is a truncation of p67, the major surface protein of the sporozoite stage of T. parva, an apicomplexan parasite that causes an often-fatal bovine disease called East Coast fever (ECF) in sub-Saharan Africa. Compared to I32-19 and I32-28, we found that I53-50 nanoparticle scaffolds displaying p67C had the best biophysical characteristics. p67C-I53-50 also outperformed the other two nanoparticles in stimulating p67C-specific IgG1 and IgG2 antibodies and CD4+ T-cell responses, as well as sporozoite neutralizing capacity. In experimental cattle vaccine trials, p67C-I53-50 induced significant immunity to ECF, suggesting that the I53-50 scaffold is a promising candidate for developing novel nanoparticle vaccines. To our knowledge this is the first application of computationally designed nanoparticles to the development of livestock vaccines.
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Affiliation(s)
- Anna Lacasta
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya,*Correspondence: Anna Lacasta, ; Neil P. King,
| | - Hyung Chan Kim
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Rachael Gachogo
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Naomi Chege
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Rose Ojuok
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Charity Muriuki
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Stephen Mwalimu
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Gilad Touboul
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Ariel Stiber
- Summer Undergraduate Research Fellowship Program, Caltech, Pasadena, CA, United States
| | - Elizabeth Jane Poole
- Research Methods Group, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Nicholas Ndiwa
- Research Methods Group, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States,*Correspondence: Anna Lacasta, ; Neil P. King,
| | - Vishvanath Nene
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
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17
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Fong Y, Huang Y, Borate B, van der Laan LWP, Zhang W, Carpp LN, Cho I, Glenn G, Fries L, Gottardo R, Gilbert PB. Antibody Correlates of Protection From Severe Respiratory Syncytial Virus Disease in a Vaccine Efficacy Trial. Open Forum Infect Dis 2023; 10:ofac693. [PMID: 36655191 PMCID: PMC9835761 DOI: 10.1093/ofid/ofac693] [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: 03/22/2022] [Indexed: 01/13/2023] Open
Abstract
Background Respiratory syncytial virus (RSV) can cause serious lung infections in young children and there is currently no available vaccine. Methods We used complementary statistical frameworks to analyze 4 RSV serology measurements in mothers and their infants in South Africa who participated in a phase 3 maternal immunization trial of an RSV F protein nanoparticle vaccine as correlates of risk and of protection against different RSV disease endpoints. Results We found evidence to support each antibody measurement-encompassing RSV-neutralizing antibodies and F surface glycoprotein-binding antibodies-as an inverse correlate of risk of RSV-associated acute lower respiratory tract infection with severe hypoxia in at least 1 framework, with vaccine-induced fold-rise from the maternal enrollment to day 14 samples of anti-F immunoglobulin G (IgG) binding antibodies having the most consistent evidence. This evidence includes a significant association of fold-rise anti-F IgG with vaccine efficacy (VE); achieving a baseline covariate-adjusted VE of 75% requires a vaccine-induced maternal anti-F IgG fold-rise of around 16. Neither multivariable logistic regression nor superlearning analyses showed benefit to including multiple time points or assays in the same model, suggesting a parsimonious correlate. Post hoc exploratory analyses supported adherence of vaccine-induced maternal anti-F IgG fold-rise to the Prentice criteria for a valid surrogate endpoint. Conclusions Our results suggest that the vaccine induced protective anti-F antibody responses. If this finding is confirmed, VE could potentially be augmented by increasing these responses.
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Affiliation(s)
- Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA,Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA,Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Bhavesh Borate
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lars W P van der Laan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Wenbo Zhang
- Present affiliations: Department of Statistics, University of California, Irvine, Irvine, California, USA
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Iksung Cho
- Novavax, Inc, Gaithersburg, Maryland, USA
| | - Greg Glenn
- Novavax, Inc, Gaithersburg, Maryland, USA
| | | | - Raphael Gottardo
- Present affiliations: University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Peter B Gilbert
- Correspondence: Peter B. Gilbert, PhD, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA 98109, USA ()
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18
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A systems biology approach to better understand human tick-borne diseases. Trends Parasitol 2023; 39:53-69. [PMID: 36400674 DOI: 10.1016/j.pt.2022.10.006] [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: 08/11/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022]
Abstract
Tick-borne diseases (TBDs) are a growing global health concern. Despite extensive studies, ill-defined tick-associated pathologies remain with unknown aetiologies. Human immunological responses after tick bite, and inter-individual variations of immune-response phenotypes, are not well characterised. Current reductive experimental methodologies limit our understanding of more complex tick-associated illness, which results from the interactions between the host, tick, and microbes. An unbiased, systems-level integration of clinical metadata and biological host data - obtained via transcriptomics, proteomics, and metabolomics - offers to drive the data-informed generation of testable hypotheses in TBDs. Advanced computational tools have rendered meaningful analysis of such large data sets feasible. This review highlights the advantages of integrative system biology approaches as essential for understanding the complex pathobiology of TBDs.
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19
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Hagan T, Gerritsen B, Tomalin LE, Fourati S, Mulè MP, Chawla DG, Rychkov D, Henrich E, Miller HER, Diray-Arce J, Dunn P, Lee A, Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Sékaly RP, Kleinstein SH, Pulendran B. Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses. Nat Immunol 2022; 23:1788-1798. [PMID: 36316475 PMCID: PMC9869360 DOI: 10.1038/s41590-022-01328-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/12/2022] [Indexed: 11/27/2022]
Abstract
Systems vaccinology has defined molecular signatures and mechanisms of immunity to vaccination. However, comparative analysis of immunity to different vaccines is lacking. We integrated transcriptional data of over 3,000 samples, from 820 adults across 28 studies of 13 vaccines and analyzed vaccination-induced signatures of antibody responses. Most vaccines induced signatures of innate immunity and plasmablasts at days 1 and 7, respectively, after vaccination. However, the yellow fever vaccine induced an early transient signature of T and B cell activation at day 1, followed by delayed antiviral/interferon and plasmablast signatures that peaked at days 7 and 14-21, respectively. Thus, there was no evidence for a 'universal signature' that predicted antibody response to all vaccines. However, accounting for the asynchronous nature of responses, we defined a time-adjusted signature that predicted antibody responses across vaccines. These results provide a transcriptional atlas of immunity to vaccination and define a common, time-adjusted signature of antibody responses.
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Affiliation(s)
- Thomas Hagan
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bram Gerritsen
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lewis E Tomalin
- Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Slim Fourati
- Emory University School of Medicine, Atlanta, GA, 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
| | - Daniel G Chawla
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Dmitri Rychkov
- Division of Transplant Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Evan Henrich
- Fred Hutchinson Cancer Research Center, Seattle, WA, 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
| | - Audrey Lee
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Raphael Gottardo
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Minne 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
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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20
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Distinct immunological and molecular signatures underpinning influenza vaccine responsiveness in the elderly. Nat Commun 2022; 13:6894. [PMID: 36371426 PMCID: PMC9653450 DOI: 10.1038/s41467-022-34487-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Seasonal influenza outbreaks, especially in high-risk groups such as the elderly, represent an important public health problem. Prevailing inadequate efficacy of seasonal vaccines is a crucial bottleneck. Understanding the immunological and molecular mechanisms underpinning differential influenza vaccine responsiveness is essential to improve vaccination strategies. Here we show comprehensive characterization of the immune response of randomly selected elderly participants (≥ 65 years), immunized with the adjuvanted influenza vaccine Fluad. In-depth analyses by serology, multi-parametric flow cytometry, multiplex and transcriptome analysis, coupled to bioinformatics and mathematical modelling, reveal distinguishing immunological and molecular features between responders and non-responders defined by vaccine-induced seroconversion. Non-responders are specifically characterized by multiple suppressive immune mechanisms. The generated comprehensive high dimensional dataset enables the identification of putative mechanisms and nodes responsible for vaccine non-responsiveness independently of confounding age-related effects, with the potential to facilitate development of tailored vaccination strategies for the elderly.
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21
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Diray-Arce J, Miller HER, Henrich E, Gerritsen B, Mulè MP, Fourati S, Gygi J, Hagan T, Tomalin L, Rychkov D, Kazmin D, Chawla DG, Meng H, Dunn P, Campbell J, Sarwal M, Tsang JS, Levy O, Pulendran B, Sekaly R, Floratos A, Gottardo R, Kleinstein SH, Suárez-Fariñas M. The Immune Signatures data resource, a compendium of systems vaccinology datasets. Sci Data 2022; 9:635. [PMID: 36266291 PMCID: PMC9584267 DOI: 10.1038/s41597-022-01714-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/22/2022] [Indexed: 01/04/2023] Open
Abstract
Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern 'omic profiling techniques and computational modeling to promote rapid and transformative advances in vaccinology and vaccine discovery. The NIH/NIAID Human Immunology Project Consortium (HIPC) has leveraged systems immunology approaches to identify molecular signatures associated with the immunogenicity of many vaccines. However, comparative analyses have been limited by the distributed nature of some data, potential batch effects across studies, and the absence of multiple relevant studies from non-HIPC groups in ImmPort. To support comparative analyses across different vaccines, we have created the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets. This data resource is available through ImmuneSpace, along with code to reproduce the processing and batch normalization starting from the underlying study data in ImmPort and the Gene Expression Omnibus (GEO). The current release comprises 1405 participants from 53 cohorts profiling the response to 24 different vaccines. This novel systems vaccinology data release represents a valuable resource for comparative and meta-analyses that will accelerate our understanding of mechanisms underlying vaccine responses.
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Affiliation(s)
- Joann Diray-Arce
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Helen E R Miller
- Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Evan Henrich
- Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID NIH Center for Human Immunology, NIH, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program, Department of Medicine, Cambridge University, Atlanta, GA, USA
| | - Slim Fourati
- Emory University School of Medicine, Atlanta, GA, USA
| | - Jeremy Gygi
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Thomas Hagan
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lewis Tomalin
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dmitry Rychkov
- University of California, San Francisco, San Francisco, CA, USA
| | - Dmitri Kazmin
- The Jackson Laboratory for Genomic Medicine, Farmington CT, Rockville, MD, USA
| | - Daniel G Chawla
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | | | - Patrick Dunn
- ImmPort Curation Team, NG Health Solutions, Rockville, MD, USA
| | - John Campbell
- ImmPort Curation Team, NG Health Solutions, Rockville, MD, USA
| | - Minnie Sarwal
- University of California, San Francisco, San Francisco, CA, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID NIH Center for Human Immunology, NIH, Bethesda, MD, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Bali Pulendran
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Rafick Sekaly
- Emory University School of Medicine, Atlanta, GA, USA
| | - Aris Floratos
- Columbia University Medical Center, New York, NY, USA
| | - Raphael Gottardo
- Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland
| | | | - Mayte Suárez-Fariñas
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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22
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Zhang J, Askenase P, Crumpacker CS. Systems Vaccinology in HIV Vaccine Development. Vaccines (Basel) 2022; 10:vaccines10101624. [PMID: 36298489 PMCID: PMC9611490 DOI: 10.3390/vaccines10101624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Themes of discussions in the Special Issue of T Cell Immunity and HIV-1 Pathogenicity are outlined here [...]
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23
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Vitallé J, Pérez-Gómez A, Ostos FJ, Gasca-Capote C, Jiménez-Leon MR, Bachiller S, Rivas-Jeremías I, Silva-Sánchez MDM, Ruiz-Mateos AM, Martín-Sánchez MÁ, López-Cortes LF, Rafii El Idrissi Benhnia M, Ruiz-Mateos E. Immune defects associated with lower SARS-CoV-2 BNT162b2 mRNA vaccine response in elderly people. JCI Insight 2022; 7:161045. [PMID: 35943812 PMCID: PMC9536264 DOI: 10.1172/jci.insight.161045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
The immune factors associated with impaired SARS-CoV-2 vaccine response in the elderly are mostly unknown. We studied >60 and <60 years old people vaccinated with SARS-CoV-2 BNT162b2 mRNA before and after the first and second dose. Aging was associated with a lower anti-RBD IgG levels and a decreased magnitude and polyfunctionality of SARS-CoV-2 specific T cell response. The dramatic decrease in thymic function in aged people with >60 years of age, which fueled alteration in T cell homeostasis, and lower CD161+ T cell levels were associated with decreased T cell response two months after vaccination. Additionally, a deficient dendritic cell (DC) homing, activation and Toll like receptor (TLR)-mediated function, along with a proinflammatory functional profile in monocytes, were observed in the >60 years old group, which was also related to lower specific T cell response after vaccination. These findings might be relevant for the improvement of the current vaccination strategies and for the development of new vaccine prototypes.
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Affiliation(s)
- Joana Vitallé
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Alberto Pérez-Gómez
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Francisco José Ostos
- Department of Medical Biochemistry, Molecular Biology, and Immunology, University of Seville School of Medicine, Seville, Spain
| | - Carmen Gasca-Capote
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Maria Reyes Jiménez-Leon
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Sara Bachiller
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Inmaculada Rivas-Jeremías
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Maria Del Mar Silva-Sánchez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Anabel M Ruiz-Mateos
- Centro de Salud Pinillo Chico, Centro de Salud Pinillo Chico, El Puerto de Santa María, Seville, Spain
| | - María Ángeles Martín-Sánchez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Luis Fernando López-Cortes
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Mohammed Rafii El Idrissi Benhnia
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
| | - Ezequiel Ruiz-Mateos
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, Seville, Spain
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24
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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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25
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Lipsit S, Facciuolo A, Scruten E, Griebel P, Napper S. Plasma Cytokines and Birth Weight as Biomarkers of Vaccine-Induced Humoral Responses in Piglets. Front Vet Sci 2022; 9:922992. [PMID: 35903142 PMCID: PMC9325413 DOI: 10.3389/fvets.2022.922992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
Failure to mount an effective immune response to vaccination leaves individuals at risk for infection and can compromise herd immunity. Vaccine unresponsiveness can range from poor responses “low responders” to a failure to seroconvert “non-responders.” Biomarkers of vaccine unresponsiveness, particularly those measured at the time of vaccination, could facilitate more strategic vaccination programs. We previously reported that pro-inflammatory cytokine signaling within peripheral blood mononuclear cells, elevated plasma interferon-gamma (IFNγ), and low birth weight correlated with vaccine-induced serum IgG titers in piglets that were below the threshold of detectable seroconversion (vaccine non-responders). These observations suggested that plasma IFNγ concentration and birth weight might serve as pre-vaccination biomarkers of vaccine unresponsiveness. To test this hypothesis, piglets (n = 67) from a different production facility were vaccinated with the same commercial Mycoplasma hyopneumoniae bacterin (RespiSure-One) to determine if there was a consistent and significant association between vaccine-induced serum IgG titers and either plasma cytokine concentrations or birth weight. All piglets seroconverted following vaccination with significantly less variability in vaccine-induced serum IgG titers than observed in the previous vaccine trial. Piglets exhibited highly variable birth weights and plasma cytokine concentrations prior to vaccination, but there were no significant associations (p > 0.05) between these variables and vaccine-induced serum IgG titers. There were significant (p < 0.001) differences in plasma IFNγ concentrations among individual litters (n = 6), and plasma IFNγ concentrations decreased in all pigs from birth to 63-days of age. One of the six litters (n = 11 piglets) exhibited significantly elevated plasma IFNγ concentrations during the first 3 weeks of life (p < 0.001) and at the time of vaccination (p < 0.01). This litter, however, had similar vaccine-induced serum IgG titers when compared to the other piglets in this study. Collectively the two studies indicate that while plasma cytokines and birth weight can be associated with vaccine non-responsiveness, their temporal and individual variation, as well as the complexity of the vaccine responsiveness phenotype, make them inconsistent biomarkers for predicting the less extreme phenotype of vaccine low responders.
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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
| | - Philip Griebel
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- School of Public Health, 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
- *Correspondence: Scott Napper
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26
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O'Connor D. The omics strategy: the use of systems vaccinology to characterise immune responses to childhood immunisation. Expert Rev Vaccines 2022; 21:1205-1214. [PMID: 35786291 DOI: 10.1080/14760584.2022.2093193] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Vaccines have had a transformative impact on child health. Despite this impact the immunological processes involved in protective responses are not entirely understood and vaccine development has been largely empirical. Recent technological advances offer the opportunity to reveal the immunology underlying vaccine response at an unprecedented resolution. These data could revolutionise the way vaccines are developed and tested and further augment their role in securing the health of children around the world. AREAS COVERED Systems level information and the tools are now being deployed by vaccinologists at all stages of the vaccine development pathway; however, this review will specifically describe some of the key findings that have be gleaned from multi-omics datasets collected in the context of childhood immunisation. EXPERT OPINION Despite the success of vaccines there remains hard-to-target pathogens, refractory to current vaccination strategies. Moreover, zoonotic diseases with pandemic potential are a threat to global health, as recently illustrated by COVID-19. Systems vaccinology holds a great deal of promise in revealing a greater understanding of vaccine responses and consequently modernising vaccinology. However, there is a need for future studies -particularly in vulnerable populations that are targets for vaccination programmes - if this potential is to be fulfilled.
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Affiliation(s)
- Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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27
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Clarkson KA, Porter CK, Talaat KR, Kapulu MC, Chen WH, Frenck RW, Bourgeois AL, Kaminski RW, Martin LB. Shigella-Controlled Human Infection Models: Current and Future Perspectives. Curr Top Microbiol Immunol 2022. [PMID: 35616717 DOI: 10.1007/82_2021_248] [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] [Indexed: 10/18/2022]
Abstract
Shigella-controlled human infection models (CHIMs) are an invaluable tool utilized by the vaccine community to combat one of the leading global causes of infectious diarrhea, which affects infants, children and adults regardless of socioeconomic status. The impact of shigellosis disproportionately affects children in low- and middle-income countries (LMICs) resulting in cognitive and physical stunting, perpetuating a cycle that must be halted. Shigella-CHIMs not only facilitate the early evaluation of enteric countermeasures and up-selection of the most promising products but also provide insight into mechanisms of infection and immunity that are not possible utilizing animal models or in vitro systems. The greater understanding of shigellosis obtained in CHIMs builds and empowers the development of new generation solutions to global health issues which are unattainable in the conventional laboratory and clinical settings. Therefore, refining, mining and expansion of safe and reproducible infection models hold the potential to create effective means to end diarrheal disease and associated co-morbidities associated with Shigella infection.
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Affiliation(s)
- Kristen A Clarkson
- Department of Diarrheal Disease Research, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Chad K Porter
- Enteric Disease Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Kawsar R Talaat
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, 624 North Broadway Street Hampton House, Baltimore, MD, 21205, USA
| | - Melissa C Kapulu
- Department of Biosciences, KEMRI-Wellcome Trust Research Programme, Kilifi County Hospital, Off Bofa Road, Kilifi, 80108, Kenya
| | - Wilbur H Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Robert W Frenck
- Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - A Louis Bourgeois
- PATH Center for Vaccine Innovation and Access, 455 Massachusetts Avenue NW, Washington, DC, 20001, USA
| | - Robert W Kaminski
- Department of Diarrheal Disease Research, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Laura B Martin
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100, Siena, Italy.
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Lesueur J, Walachowski S, Barbey S, Cebron N, Lefebvre R, Launay F, Boichard D, Germon P, Corbiere F, Foucras G. Standardized Whole Blood Assay and Bead-Based Cytokine Profiling Reveal Commonalities and Diversity of the Response to Bacteria and TLR Ligands in Cattle. Front Immunol 2022; 13:871780. [PMID: 35677047 PMCID: PMC9169910 DOI: 10.3389/fimmu.2022.871780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/13/2022] [Indexed: 11/15/2022] Open
Abstract
Recent developments in multiplex technologies enable the determination of a large nu\mber of soluble proteins such as cytokines in various biological samples. More than a one-by-one determination of the concentration of immune mediators, they permit the establishment of secretion profiles for a more accurate description of conditions related to infectious diseases or vaccination. Cytokine profiling has recently been made available for bovine species with the development of a Luminex® technology-based 15-plex assay. Independently from the manufacturer, we evaluated the bovine cytokine/chemokine multiplex assay for limits of detection, recovery rate, and reproducibility. Furthermore, we assessed cytokine secretion in blood samples from 107 cows upon stimulation with heat-killed bacteria and TLR2/4 ligands compared to a null condition. Secretion patterns were analyzed either using the absolute concentration of cytokines or using their relative concentration with respect to the overall secretion level induced by each stimulus. Using Partial Least Square-Discriminant Analysis, we show that the 15-cytokine profile is different under Escherichia coli, Staphylococcus aureus, and Streptococcus uberis conditions, and that IFN-γ, IL-1β, and TNF-α contribute the most to differentiate these conditions. LPS and E. coli induced largely overlapping biological responses, but S. aureus and S. uberis were associated with distinct cytokine profiles than their respective TLR ligands. Finally, results based on adjusted or absolute cytokine levels yielded similar discriminative power, but led to different stimuli-related signatures.
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Affiliation(s)
- Jérémy Lesueur
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Sarah Barbey
- Unité Expérimentale du Pin, INRAE, Borculo, Le Pin au Haras, France
| | - Nathan Cebron
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Rachel Lefebvre
- GABI, Université de Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Frédéric Launay
- Unité Expérimentale du Pin, INRAE, Borculo, Le Pin au Haras, France
| | - Didier Boichard
- GABI, Université de Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | | | | | - Gilles Foucras
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
- *Correspondence: Gilles Foucras,
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Watkins RR. Using Precision Medicine for the Diagnosis and Treatment of Viral Pneumonia. Adv Ther 2022; 39:3061-3071. [PMID: 35596912 PMCID: PMC9123616 DOI: 10.1007/s12325-022-02180-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/04/2022] [Indexed: 01/06/2023]
Abstract
The COVID-19 pandemic has drawn considerable attention to viral pneumonia from clinicians, public health authorities, and the general public. With dozens of viruses able to cause pneumonia in humans, differentiating viral from bacterial pneumonia can be very challenging in clinical practice using traditional diagnostic methods. Precision medicine is a medical model in which decisions, practices, interventions, and therapies are adapted to the individual patient on the basis of their predicted response or risk of disease. Precision medicine approaches hold promise as a way to improve outcomes for patients with viral pneumonia. This review describes the latest advances in the use of precision medicine for diagnosing and treating viral pneumonia in adults and discusses areas where further research is warranted.
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Affiliation(s)
- Richard R Watkins
- Department of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA.
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30
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Bing X, Lovelace T, Bunea F, Wegkamp M, Kasturi SP, Singh H, Benos PV, Das J. Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets. PATTERNS (NEW YORK, N.Y.) 2022; 3:100473. [PMID: 35607614 PMCID: PMC9122954 DOI: 10.1016/j.patter.2022.100473] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/17/2021] [Accepted: 03/01/2022] [Indexed: 01/19/2023]
Abstract
High-dimensional cellular and molecular profiling of biological samples highlights the need for analytical approaches that can integrate multi-omic datasets to generate prioritized causal inferences. Current methods are limited by high dimensionality of the combined datasets, the differences in their data distributions, and their integration to infer causal relationships. Here, we present Essential Regression (ER), a novel latent-factor-regression-based interpretable machine-learning approach that addresses these problems by identifying latent factors and their likely cause-effect relationships with system-wide outcomes/properties of interest. ER can integrate many multi-omic datasets without structural or distributional assumptions regarding the data. It outperforms a range of state-of-the-art methods in terms of prediction. ER can be coupled with probabilistic graphical modeling, thereby strengthening the causal inferences. The utility of ER is demonstrated using multi-omic system immunology datasets to generate and validate novel cellular and molecular inferences in a wide range of contexts including immunosenescence and immune dysregulation.
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Affiliation(s)
- Xin Bing
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Tyler Lovelace
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Carnegie Mellon – University of Pittsburgh, Pittsburgh, PA, USA
| | - Florentina Bunea
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Marten Wegkamp
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
- Department of Mathematics, Cornell University, Ithaca, NY, USA
| | - Sudhir Pai Kasturi
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Harinder Singh
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Panayiotis V. Benos
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Klasse PJ, Moore JP. Reappraising the Value of HIV-1 Vaccine Correlates of Protection Analyses. J Virol 2022; 96:e0003422. [PMID: 35384694 PMCID: PMC9044961 DOI: 10.1128/jvi.00034-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2022] [Indexed: 01/09/2023] Open
Abstract
With the much-debated exception of the modestly reduced acquisition reported for the RV144 efficacy trial, HIV-1 vaccines have not protected humans against infection, and a vaccine of similar design to that tested in RV144 was not protective in a later trial, HVTN 702. Similar vaccine regimens have also not consistently protected nonhuman primates (NHPs) against viral acquisition. Conversely, experimental vaccines of different designs have protected macaques from viral challenges but then failed to protect humans, while many other HIV-1 vaccine candidates have not protected NHPs. While efficacy varies more in NHPs than humans, vaccines have failed to protect in the most stringent NHP model. Intense investigations have aimed to identify correlates of protection (CoPs), even in the absence of net protection. Unvaccinated animals and humans vary vastly in their susceptibility to infection and in their innate and adaptive responses to the vaccines; hence, merely statistical associations with factors that do not protect are easily found. Systems biological analyses, including artificial intelligence, have identified numerous candidate CoPs but with no clear consistency within or between species. Proposed CoPs sometimes have only tenuous mechanistic connections to immune protection. In contrast, neutralizing antibodies (NAbs) are a central mechanistic CoP for vaccines that succeed against other viruses, including SARS-CoV-2. No HIV-1 vaccine candidate has yet elicited potent and broadly active NAbs in NHPs or humans, but narrow-specificity NAbs against the HIV-1 isolate corresponding to the immunogen do protect against infection by the autologous virus. Here, we analyze why so many HIV-1 vaccines have failed, summarize the outcomes of vaccination in NHPs and humans, and discuss the value and pitfalls of hunting for CoPs other than NAbs. We contrast the failure to find a consistent CoP for HIV-1 vaccines with the identification of NAbs as the principal CoP for SARS-CoV-2.
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Affiliation(s)
- P. J. Klasse
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | - John P. Moore
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
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Fulop T, Larbi A, Pawelec G, Cohen AA, Provost G, Khalil A, Lacombe G, Rodrigues S, Desroches M, Hirokawa K, Franceschi C, Witkowski JM. Immunosenescence and Altered Vaccine Efficiency in Older Subjects: A Myth Difficult to Change. Vaccines (Basel) 2022; 10:vaccines10040607. [PMID: 35455356 PMCID: PMC9030923 DOI: 10.3390/vaccines10040607] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 12/14/2022] Open
Abstract
Organismal ageing is associated with many physiological changes, including differences in the immune system of most animals. These differences are often considered to be a key cause of age-associated diseases as well as decreased vaccine responses in humans. The most often cited vaccine failure is seasonal influenza, but, while it is usually the case that the efficiency of this vaccine is lower in older than younger adults, this is not always true, and the reasons for the differential responses are manifold. Undoubtedly, changes in the innate and adaptive immune response with ageing are associated with failure to respond to the influenza vaccine, but the cause is unclear. Moreover, recent advances in vaccine formulations and adjuvants, as well as in our understanding of immune changes with ageing, have contributed to the development of vaccines, such as those against herpes zoster and SARS-CoV-2, that can protect against serious disease in older adults just as well as in younger people. In the present article, we discuss the reasons why it is a myth that vaccines inevitably protect less well in older individuals, and that vaccines represent one of the most powerful means to protect the health and ensure the quality of life of older adults.
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Affiliation(s)
- Tamas Fulop
- Research Center on Aging, Geriatric Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.K.); (G.L.)
- Correspondence: (T.F.); (S.R.)
| | - Anis Larbi
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore;
| | - Graham Pawelec
- Department of Immunology, University of Tübingen, 72072 Tübingen, Germany;
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada
| | - Alan A. Cohen
- Groupe de Recherche PRIMUS, Department of Family Medicine, University of Sherbrooke, 3001 12e Ave N, Sherbrooke, QC J1H 5N4, Canada;
| | | | - Abedelouahed Khalil
- Research Center on Aging, Geriatric Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.K.); (G.L.)
| | - Guy Lacombe
- Research Center on Aging, Geriatric Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.K.); (G.L.)
| | - Serafim Rodrigues
- Ikerbasque, The Basque Foundation for Science, 48009 Bilbao, Spain;
- BCAM—The Basque Center for Applied Mathematics, 48009 Bilbao, Spain
- Correspondence: (T.F.); (S.R.)
| | - Mathieu Desroches
- MathNeuro Team, Inria Sophia Antipolis Méditerranée, CEDEX, 06902 Sophia Antipolis, France;
- The Jean Alexandre Dieudonné Laboratory, Université Côte d’Azur, CEDEX 2, 06108 Nice, France
| | - Katsuiku Hirokawa
- Institute of Health and Life Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan;
| | - Claudio Franceschi
- IRCCS Institute of Neurological Sciences of Bologna, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy;
- Department of Applied Mathematics and Laboratory of Systems Biology of Healthy Aging, Lobachevsky State University, 603000 Nizhny Novgorod, Russia
| | - Jacek M. Witkowski
- Department of Pathophysiology, Medical University of Gdansk, 80-210 Gdansk, Poland;
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Taslimi Y, Masoudzadeh N, Bahrami F, Rafati S. Cutaneous leishmaniasis: multiomics approaches to unravel the role of immune cells checkpoints. Expert Rev Proteomics 2022; 19:213-225. [PMID: 36191333 DOI: 10.1080/14789450.2022.2131545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Cutaneous leishmaniasis (CL) is the most frequent form of leishmaniases, associated with skin inflammation and ulceration. Understanding the interaction of different phagocytic cells in the recognition and uptake of different Leishmania species is critical for controlling the infection. Phagocytic cells have a pivotal role as professional antigen-presenting cells that bridge the innate and adaptive immunity and shape the outcome of the disease. AREAS COVERED Here we reviewed new technologies with high-throughput data collection capabilities along with systems biology approaches which are recently being used to decode the paradox of CL immunology. EXPERT OPINION We emphasized on the crosstalk between DC and T-cells while focusing on the immune checkpoints interactions between the human immune system and the Leishmania species. Further, we discussed omics technologies including bulk RNA sequencing, reverse transcriptase-multiplex ligation dependent probe amplification (RT-MLPA), and proximity extension assay (PEA) in studies on human blood or tissue-driven samples from CL patients in which we have so far been involved.
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Affiliation(s)
- Yasaman Taslimi
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran Iran
| | - Nasrin Masoudzadeh
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran Iran
| | - Fariborz Bahrami
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran Iran
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BNT162b2 vaccination enhances interferon-JAK-STAT-regulated antiviral programs in COVID-19 patients infected with the SARS-CoV-2 Beta variant. COMMUNICATIONS MEDICINE 2022; 2. [PMID: 35465056 PMCID: PMC9029844 DOI: 10.1038/s43856-022-00083-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background SARS-CoV-2 infection activates interferon-controlled signaling pathways and elicits a wide spectrum of immune responses and clinical manifestations in human patients. Methods Here, we investigate the impact of prior vaccination on the innate immune response of hospitalized COVID-19 patients infected with the SARS-CoV-2 Beta variant through RNA sequencing of peripheral blood immune cells. Four patients had received the first dose of BNT162b2 about 11 days prior to the onset of COVID-19 symptoms and five patients were unvaccinated. Patients had received dexamethasone treatment. Immune transcriptomes were obtained at days 7-13, 20-32 and 42-60 after first symptomology. Results RNA-seq reveals an enhanced JAK-STAT-mediated immune transcriptome response at day 10 in vaccinated patients as compared to unvaccinated ones. This increase subsides by day 35. Expression of the gene encoding the antiviral protein oligoadenylate synthetase (OAS) 1, which is inversely correlated with disease severity, and other key antiviral proteins increases in the vaccinated group. We also investigate the immune transcriptome in naïve individuals receiving their first dose of BNT162b2 and identify a gene signature shared with the vaccinated COVID-19 patients. Conclusions Our study demonstrates that RNA-seq can be used to monitor molecular immune responses elicited by the BNT162b2 vaccine, both in naïve individuals and in COVID-19 patients, and it provides a biomarker-based approach to systems vaccinology. The human body’s immune response can be triggered by infection or vaccination. Vaccination provides exposure to microbial proteins and trains the immune system in creating a healthy and stronger immune response to subsequent infection. This study looked at changes in the immune response in three groups of individuals, those infected with the Beta SARS-CoV-2 variant following BNT162b2 mRNA vaccination, those infected with Beta SARS-CoV-2 without prior vaccination, and uninfected individuals receiving the BNT162b2 vaccine. It focused on a group of proteins, the JAK-STAT pathway, that plays an important role in the immune response. In previously vaccinated infected individuals JAK-STAT genes were more highly expressed than in unvaccinated infected individuals. JAK-STAT genes were also induced by vaccination alone. This study defines a molecular mechanism for how vaccination strengthens immune responses. Knabl and Lee et al. use RNA sequencing to assess the impact of vaccination with BNT162b2 on the peripheral innate immune response of a small cohort of COVID-19 patients infected with the SARS-CoV-2 Beta variant. They show an increased JAK-STAT-mediated immune response in vaccinated patients as compared to unvaccinated ones.
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Progress towards the Elusive Mastitis Vaccines. Vaccines (Basel) 2022; 10:vaccines10020296. [PMID: 35214754 PMCID: PMC8876843 DOI: 10.3390/vaccines10020296] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 01/25/2023] Open
Abstract
Mastitis is a major problem in dairy farming. Vaccine prevention of mammary bacterial infections is of particular interest in helping to deal with this issue, all the more so as antibacterial drug inputs in dairy farms must be reduced. Unfortunately, the effectiveness of current vaccines is not satisfactory. In this review, we examine the possible reasons for the current shortcomings of mastitis vaccines. Some reasons stem from the peculiarities of the mammary gland immunobiology, others from the pathogens adapted to the mammary gland niche. Infection does not induce sterilizing protection, and recurrence is common. Efficacious vaccines will have to elicit immune mechanisms different from and more effective than those induced by infection. We propose focusing our research on a few points pertaining to either the current immune knowledge or vaccinology approaches to get out of the current deadlock. A possible solution is to focus on the contribution of cell-mediated immunity to udder protection based on the interactions of T cells with the mammary epithelium. On the vaccinology side, studies on the orientation of the immune response by adjuvants, the route of vaccine administration and the delivery systems are among the keys to success.
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Appelberg S, John L, Pardi N, Végvári Á, Bereczky S, Ahlén G, Monteil V, Abdurahman S, Mikaeloff F, Beattie M, Tam Y, Sällberg M, Neogi U, Weissman D, Mirazimi A. Nucleoside-Modified mRNA Vaccines Protect IFNAR -/- Mice against Crimean-Congo Hemorrhagic Fever Virus Infection. J Virol 2022; 96:e0156821. [PMID: 34817199 PMCID: PMC8826901 DOI: 10.1128/jvi.01568-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/13/2021] [Indexed: 01/11/2023] Open
Abstract
Crimean-Congo hemorrhagic fever (CCHF), caused by Crimean-Congo hemorrhagic fever virus (CCHFV), is on the World Health Organizations' list of prioritized diseases and pathogens. With global distribution, high fatality rate, and no approved vaccine or effective treatment, CCHF constitutes a threat against global health. In the current study, we demonstrate that vaccination with nucleoside-modified mRNA-lipid nanoparticles (mRNA-LNP), encoding for the CCHFV nucleoprotein (N) or glycoproteins (GcGn) protect IFNAR-/- mice against lethal CCHFV infection. In addition, we found that both mRNA-LNP induced strong humoral and cellular immune responses in IFNAR-/- and immunocompetent mice and that neutralizing antibodies are not necessary for protection. When evaluating immune responses induced by immunization including CCHFV Gc and Gn antigens, we found the Gc protein to be more immunogenic compared with the Gn protein. Hepatic injury is prevalent in CCHF and contributes to the severity and mortality of the disease in humans. Thus, to understand the immune response in the liver after infection and the potential effect of the vaccine, we performed a proteomic analysis on liver samples from vaccinated and control mice after CCHFV infection. Similar to observations in humans, vaccination affected the metabolic pathways. In conclusion, this study shows that a CCHFV mRNA-LNP vaccine, based on viral nucleo- or glycoproteins, mediate protection against CCHFV induced disease. Consequently, genetic immunization is an attractive approach to prevent disease caused by CCHFV and we believe we have necessary evidence to bring this vaccine platform to the next step in the development of a vaccine against CCHFV infection. IMPORTANCE Crimean-Congo hemorrhagic fever virus (CCHFV) is a zoonotic pathogen causing Crimean-Congo hemorrhagic fever (CCHF), a severe fever disease. CCHFV has a wide distribution and is endemic in several areas around the world. Cases of CCHF are also being reported in new areas, indicating an expansion of the disease, which is of high concern. Dispersion of the disease, high fatality rate, and no approved vaccine makes CCHF a threat to global health. The development of a vaccine is thus of great importance. Here we show 100% protection against lethal CCHFV infection in mice immunized with mRNA-LNP encoding for different CCHFV proteins. The vaccination showed both robust humoral and cellular immunity. mRNA-LNP vaccines combine the ability to induce an effective immune response, the safety of a transient carrier, and the flexibility of genetic vaccines. This and our results from the current study support the development of a mRNA-LNP based vaccine against CCHFV.
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MESH Headings
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Computational Biology/methods
- Disease Models, Animal
- Dose-Response Relationship, Immunologic
- Female
- Hemorrhagic Fever Virus, Crimean-Congo/immunology
- Hemorrhagic Fever, Crimean/prevention & control
- High-Throughput Screening Assays
- Immunization
- Immunogenicity, Vaccine
- Liposomes
- Mice
- Mice, Knockout
- Nanoparticles
- Proteomics/methods
- Receptor, Interferon alpha-beta/deficiency
- Vaccination
- Vaccines, Synthetic/immunology
- mRNA Vaccines/immunology
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Affiliation(s)
| | - Lijo John
- National Veterinary Institute, Uppsala, Sweden
| | - Norbert Pardi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Gustaf Ahlén
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Vanessa Monteil
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Flora Mikaeloff
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Ying Tam
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Matti Sällberg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Drew Weissman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ali Mirazimi
- Public Health Agency of Sweden, Solna, Sweden
- National Veterinary Institute, Uppsala, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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AI and Immunoinformatics. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Long non-coding RNAs associated with infection and vaccine-induced immunity. Essays Biochem 2021; 65:657-669. [PMID: 34528687 DOI: 10.1042/ebc20200072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 08/01/2021] [Accepted: 08/10/2021] [Indexed: 12/31/2022]
Abstract
The immune system responds to infection or vaccination through a dynamic and complex process that involves several molecular and cellular factors. Among these factors, long non-coding RNAs (lncRNAs) have emerged as significant players in all areas of biology, particularly in immunology. Most of the mammalian genome is transcribed in a highly regulated manner, generating a diversity of lncRNAs that impact the differentiation and activation of immune cells and affect innate and adaptive immunity. Here, we have reviewed the range of functions and mechanisms of lncRNAs in response to infectious disease, including pathogen recognition, interferon (IFN) response, and inflammation. We describe examples of lncRNAs exploited by pathogenic agents during infection, which indicate that lncRNAs are a fundamental part of the arms race between hosts and pathogens. We also discuss lncRNAs potentially implicated in vaccine-induced immunity and present examples of lncRNAs associated with the antibody response of subjects receiving Influenza or Yellow Fever vaccines. Elucidating the widespread involvement of lncRNAs in the immune system will improve our understanding of the factors affecting immune response to different pathogenic agents, to better prevent and treat disease.
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Immune Responses against SARS-CoV-2-Questions and Experiences. Biomedicines 2021; 9:biomedicines9101342. [PMID: 34680460 PMCID: PMC8533170 DOI: 10.3390/biomedicines9101342] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/07/2023] Open
Abstract
Understanding immune reactivity against SARS-CoV-2 is essential for coping with the COVID-19 pandemic. Herein, we discuss experiences and open questions about the complex immune responses to SARS-CoV-2. Some people react excellently without experiencing any clinical symptoms, they do not get sick, and they do not pass the virus on to anyone else ("sterilizing" immunity). Others produce antibodies and do not get COVID-19 but transmit the virus to others ("protective" immunity). Some people get sick but recover. A varying percentage develops respiratory failure, systemic symptoms, clotting disorders, cytokine storms, or multi-organ failure; they subsequently decease. Some develop long COVID, a new pathologic entity similar to fatigue syndrome or autoimmunity. In reality, COVID-19 is considered more of a systemic immune-vascular disease than a pulmonic disease, involving many tissues and the central nervous system. To fully comprehend the complex clinical manifestations, a profound understanding of the immune responses to SARS-CoV-2 is a good way to improve clinical management of COVID-19. Although neutralizing antibodies are an established approach to recognize an immune status, cellular immunity plays at least an equivalent or an even more important role. However, reliable methods to estimate the SARS-CoV-2-specific T cell capacity are not available for clinical routines. This deficit is important because an unknown percentage of people may exist with good memory T cell responsibility but a low number of or completely lacking peripheral antibodies against SARS-CoV-2. Apart from natural immune responses, vaccination against SARS-CoV-2 turned out to be very effective and much safer than naturally acquired immunity. Nevertheless, besides unwanted side effects of the currently available vector and mRNA preparations, concerns remain whether these vaccines will be strong enough to defeat the pandemic. Altogether, herein we discuss important questions, and try to give answers based on the current knowledge and preliminary data from our laboratories.
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Bocharov G, Grebennikov D, Argilaguet J, Meyerhans A. Examining the cooperativity mode of antibody and CD8 + T cell immune responses for vaccinology. Trends Immunol 2021; 42:852-855. [PMID: 34561159 DOI: 10.1016/j.it.2021.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/03/2023]
Abstract
A fundamental unsolved issue in vaccine design is how neutralizing antibodies and cytotoxic CD8+ T cells cooperate numerically in controlling virus infections. We hypothesize on a viewpoint for the multiplicative cooperativity between neutralizing antibodies and CD8+ T cells and propose how this might be exploited for improving vaccine-induced protective immunity.
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Affiliation(s)
- Gennady Bocharov
- Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences, 119333 Moscow, Russia; Moscow Center for Fundamental and Applied Mathematics at INM RAS, 119333 Moscow, Russia; Sechenov First Moscow State Medical University, 119991 Moscow, Russia.
| | - Dmitry Grebennikov
- Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences, 119333 Moscow, Russia; Moscow Center for Fundamental and Applied Mathematics at INM RAS, 119333 Moscow, Russia; Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Jordi Argilaguet
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Andreas Meyerhans
- Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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42
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Nakaya HI. Hidden in plain sight: uncovering the role of CREB1 in HIV-1 vaccine-induced immunity. Nat Immunol 2021; 22:1199-1200. [PMID: 34556875 DOI: 10.1038/s41590-021-01018-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil. .,Scientific Platform Pasteur-University of São Paulo, São Paulo, Brazil. .,Hospital Israelita Albert Einstein, São Paulo, Brazil.
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Weng NP, Pawelec G. Validation of the effectiveness of SARS-CoV-2 vaccines in older adults in "real-world" settings. Immun Ageing 2021; 18:36. [PMID: 34551812 PMCID: PMC8455805 DOI: 10.1186/s12979-021-00248-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/10/2021] [Indexed: 01/06/2023]
Abstract
The rapidity of SARS-CoV-2 vaccination around the world has substantially reduced the number of new cases of COVID-19 and their severity in highly vaccinated countries. The unanticipated efficacy of SARS-CoV-2 vaccines in older adults has been very encouraging but the longevity of vaccine immunity is currently unknown and protection against emerging variants may be lower. Adoptive immunotherapy with neutralizing mAb may offer an alternative for poor vaccine responders, while the mechanisms underlying failure to respond are still unclear. Further studies of B and T cell responses and their regulation particularly in older populations will provide a more solid foundation to develop suitable approaches to optimize vaccine responses of older adults who fail to mount a durable response.
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Affiliation(s)
- Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA.
| | - Graham Pawelec
- Department of Immunology, University of Tübingen, Tübingen, Germany.
- Health Sciences North Research Institute, Sudbury, ON, Canada.
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Wimmers F, Donato M, Kuo A, Ashuach T, Gupta S, Li C, Dvorak M, Foecke MH, Chang SE, Hagan T, De Jong SE, Maecker HT, van der Most R, Cheung P, Cortese M, Bosinger SE, Davis M, Rouphael N, Subramaniam S, Yosef N, Utz PJ, Khatri P, Pulendran B. The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination. Cell 2021; 184:3915-3935.e21. [PMID: 34174187 PMCID: PMC8316438 DOI: 10.1016/j.cell.2021.05.039] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/15/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022]
Abstract
Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we mapped the epigenomic and transcriptional landscape of immunity to influenza vaccination in humans at the single-cell level. Vaccination against seasonal influenza induced persistently diminished H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to Toll-like receptor stimulation. Single-cell ATAC-seq analysis revealed an epigenomically distinct subcluster of monocytes with reduced chromatin accessibility at AP-1-targeted loci after vaccination. Similar effects were observed in response to vaccination with the AS03-adjuvanted H5N1 pandemic influenza vaccine. However, this vaccine also stimulated persistently increased chromatin accessibility at interferon response factor (IRF) loci in monocytes and mDCs. This was associated with elevated expression of antiviral genes and heightened resistance to the unrelated Zika and Dengue viruses. These results demonstrate that vaccination stimulates persistent epigenomic remodeling of the innate immune system and reveal AS03's potential as an epigenetic adjuvant.
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Affiliation(s)
- Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alex Kuo
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shakti Gupta
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mariko Hinton Foecke
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Hagan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sanne E De Jong
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Peggie Cheung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mario Cortese
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mark Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Shigella-Specific Immune Profiles Induced after Parenteral Immunization or Oral Challenge with Either Shigella flexneri 2a or Shigella sonnei. mSphere 2021; 6:e0012221. [PMID: 34259559 PMCID: PMC8386581 DOI: 10.1128/msphere.00122-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shigella spp. are a leading cause of diarrhea-associated global morbidity and mortality. Development and widespread implementation of an efficacious vaccine remain the best option to reduce Shigella-specific morbidity. Unfortunately, the lack of a well-defined correlate of protection for shigellosis continues to hinder vaccine development efforts. Shigella controlled human infection models (CHIM) are often used in the early stages of vaccine development to provide preliminary estimates of vaccine efficacy; however, CHIMs also provide the opportunity to conduct in-depth immune response characterizations pre- and postvaccination or pre- and postinfection. In the current study, principal-component analyses were used to examine immune response data from two recent Shigella CHIMs in order to characterize immune response profiles associated with parenteral immunization, oral challenge with Shigella flexneri 2a, or oral challenge with Shigella sonnei. Although parenteral immunization induced an immune profile characterized by robust systemic antibody responses, it also included mucosal responses. Interestingly, oral challenge with S. flexneri 2a induced a distinctively different profile compared to S. sonnei, characterized by a relatively balanced systemic and mucosal response. In contrast, S. sonnei induced robust increases in mucosal antibodies with no differences in systemic responses across shigellosis outcomes postchallenge. Furthermore, S. flexneri 2a challenge induced significantly higher levels of intestinal inflammation compared to S. sonnei, suggesting that both serotypes may also differ in how they trigger induction and activation of innate immunity. These findings could have important implications for Shigella vaccine development as protective immune mechanisms may differ across Shigella serotypes. IMPORTANCE Although immune correlates of protection have yet to be defined for shigellosis, prior studies have demonstrated that Shigella infection provides protection against reinfection in a serotype-specific manner. Therefore, it is likely that subjects with moderate to severe disease post-oral challenge would be protected from a homologous rechallenge, and investigating immune responses in these subjects may help identify immune markers associated with the development of protective immunity. This is the first study to describe distinct innate and adaptive immune profiles post-oral challenge with two different Shigella serotypes. Analyses conducted here provide essential insights into the potential of different immune mechanisms required to elicit protective immunity, depending on the Shigella serotype. Such differences could have significant impacts on vaccine design and development within the Shigella field and should be further investigated across multiple Shigella serotypes.
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Shah NJ, Aloysius MM, Sharma NR, Pallav K. Advances in treatment and prevention of hepatitis B. World J Gastrointest Pharmacol Ther 2021. [DOI: 10.4292/wjg.v12.i4.56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Shah NJ, Aloysius MM, Sharma NR, Pallav K. Advances in treatment and prevention of hepatitis B. World J Gastrointest Pharmacol Ther 2021; 12:56-78. [PMID: 34316384 PMCID: PMC8290928 DOI: 10.4292/wjgpt.v12.i4.56] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/22/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis B (CHB) continues to contribute to worldwide morbidity and mortality significantly. Scientists, clinicians, pharmaceutical companies, and health organizations have dedicated substantial Intellectual and monetary resources to finding a cure, increasing immunization rates, and reducing the global burden of CHB. National and international health-related organizations including the center for disease control, the national institute of health, the American Association for the study of liver disease (AASLD), The European association for the study of the Liver (EASL), The Asia Pacific association for the study of the Liver (APASL) and the world health organization release periodic recommendations for disease prevention and treatment. Our review of the most recent guidelines by EASL, AASLD, APASL, and Taiwan Association for the Study of the Liver revealed that an overwhelming majority of cited studies were published before 2018. We reviewed Hepatitis B-related literature published 2018 onwards to identify recent developments and current barriers that will likely direct future efforts towards eradicating hepatitis B. The breakthrough in our understanding of the hepatitis B virus life cycle and resulting drug development is encouraging with significant room for further progress. Data from high-risk populations, most vulnerable to the devastating effects of hepatitis B infection and reactivation remain sparse. Utilization of systems approach, optimization of experimental models, identification and validation of next-generation biomarkers, and precise modulation of the human immune response will be critical for future innovation. Within the foreseeable future, new treatments will likely complement conventional therapies rather than replace them. Most Importantly, pragmatic management of CHB related population health challenges must be prioritized to produce real-world results.
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Affiliation(s)
- Niraj James Shah
- Department of Internal Medicine, Digestive Disease, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Mark M Aloysius
- Department of Internal Medicine, The Wright Center for Graduate Medical Education, Scranton, PA 18505, United States
| | - Neil Rohit Sharma
- Department of Internal Medicine, Interventional Oncology and Surgical Endoscopy, Parkview Regional Medical Center, Parkview Cancer Institute, Fort Wayne, IN 46845, United States
| | - Kumar Pallav
- Department of Internal Medicine, Interventional Oncology and Surgical Endoscopy, Parkview Regional Medical Center, Parkview Cancer Institute, Fort Wayne, IN 46845, United States
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48
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Coyle PK, Gocke A, Vignos M, Newsome SD. Vaccine Considerations for Multiple Sclerosis in the COVID-19 Era. Adv Ther 2021; 38:3550-3588. [PMID: 34075554 PMCID: PMC8169434 DOI: 10.1007/s12325-021-01761-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/24/2021] [Indexed: 02/06/2023]
Abstract
People with multiple sclerosis (MS) are at risk for infections that can result in amplification of baseline symptoms and possibly trigger clinical relapses. Vaccination can prevent infection through the activation of humoral and cellular immune responses. This is particularly pertinent in the era of emerging novel vaccines against severe acute respiratory syndrome coronavirus 2, the virus that causes coronavirus disease 2019 (COVID-19). MS disease-modifying therapies (DMTs), which affect the immune system, may impact immune responses to COVID-19 vaccines in people with MS. The objective of this article is to provide information on immune system responses to vaccinations and review previous studies of vaccine responses in people with MS to support the safety and importance of receiving currently available and emerging COVID-19 vaccines. Immunological studies have shown that coordinated interactions between T and B lymphocytes of the adaptive immune system are key to successful generation of immunological memory and production of neutralizing antibodies following recognition of vaccine antigens by innate immune cells. CD4+ T cells are essential to facilitate CD8+ T cell and B cell activation, while B cells drive and sustain T cell memory. Data suggest that some classes of DMT, including type 1 interferons and glatiramer acetate, may not significantly impair the response to vaccination. DMTs-such as sphingosine-1-phosphate receptor modulators, which sequester lymphocytes from circulation; alemtuzumab; and anti-CD20 therapies, which rely on depleting populations of immune cells-have been shown to attenuate responses to conventional vaccines. Currently, three COVID-19 vaccines have been granted emergency use authorization in the USA on the basis of promising interim findings of ongoing trials. Because analyses of these vaccines in people with MS are not available, decisions regarding COVID-19 vaccination and DMT choice should be informed by data and expert consensus, and personalized with considerations for disease burden, risk of infection, and other factors.
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Affiliation(s)
- Patricia K Coyle
- Department of Neurology, Stony Brook University Medical Center, Stony Brook, NY, USA
| | | | - Megan Vignos
- Biogen, Cambridge, MA, USA.
- US Medical MS Franchise and Interferons, Biogen, 133 Boston Post Rd, Weston, MA, 20493, USA.
| | - Scott D Newsome
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
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49
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Kroes MM, Miranda-Bedate A, Hovingh ES, Jacobi R, Schot C, Pupo E, Raeven RHM, van der Ark AAJ, van Putten JPM, de Wit J, Mariman R, Pinelli E. Naturally circulating pertactin-deficient Bordetella pertussis strains induce distinct gene expression and inflammatory signatures in human dendritic cells. Emerg Microbes Infect 2021; 10:1358-1368. [PMID: 34132167 PMCID: PMC8259873 DOI: 10.1080/22221751.2021.1943537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Respiratory infections caused by Bordetella pertussis are reemerging despite high pertussis vaccination coverage. Since the introduction of the acellular pertussis vaccine in the late twentieth century, circulating B. pertussis strains increasingly lack expression of the vaccine component pertactin (Prn). In some countries, up to 90% of the circulating B. pertussis strains are deficient in Prn. To better understand the resurgence of pertussis, we investigated the response of human monocyte-derived dendritic cells (moDCs) to naturally circulating Prn-expressing (Prn-Pos) and Prn-deficient (Prn-Neg) B. pertussis strains from 2016 in the Netherlands. Transcriptome analysis of moDC showed enriched IFNα response-associated gene expression after exposure to Prn-Pos B. pertussis strains, whereas the Prn-Neg strains induced enriched expression of interleukin- and TNF-signaling genes, as well as other genes involved in immune activation. Multiplex immune assays confirmed enhanced proinflammatory cytokine secretion by Prn-Neg stimulated moDC. Comparison of the proteomes from the Prn-Pos and Prn-Neg strains revealed, next to the difference in Prn, differential expression of a number of other proteins including several proteins involved in metabolic processes. Our findings indicate that Prn-deficient B. pertussis strains induce a distinct and stronger immune activation of moDCs than the Prn-Pos strains. These findings highlight the role of pathogen adaptation in the resurgence of pertussis as well as the effects that vaccine pressure can have on a bacterial population.
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Affiliation(s)
- Michiel M Kroes
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Alberto Miranda-Bedate
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Elise S Hovingh
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Ronald Jacobi
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Corrie Schot
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Elder Pupo
- Institute for Translational Vaccinology (Intravacc), Bilthoven, Netherlands
| | - René H M Raeven
- Institute for Translational Vaccinology (Intravacc), Bilthoven, Netherlands
| | | | - Jos P M van Putten
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Jelle de Wit
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Rob Mariman
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Elena Pinelli
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
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50
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Cortese M, Sherman AC, Rouphael NG, Pulendran B. Systems Biological Analysis of Immune Response to Influenza Vaccination. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038596. [PMID: 32152245 DOI: 10.1101/cshperspect.a038596] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The last decade has witnessed tremendous progress in immunology and vaccinology, owing to several scientific and technological breakthroughs. Systems vaccinology is a field that has emerged at the forefront of vaccine research and development and provides a unique way to probe immune responses to vaccination in humans. The goals of systems vaccinology are to use systems-based approaches to define signatures that can be used to predict vaccine immunogenicity and efficacy and to delineate the molecular mechanisms driving protective immunity. The application of systems biological approaches in influenza vaccination studies has enabled the discovery of early signatures that predict immunogenicity to vaccination and yielded novel mechanistic insights about vaccine-induced immunity. Here we review the contributions of systems vaccinology to influenza vaccine development and critically examine the potential of systems vaccinology toward enabling the development of a universal influenza vaccine that provides robust and durable immunity against diverse influenza viruses.
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Affiliation(s)
- Mario Cortese
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Amy C Sherman
- Hope Clinic of the Emory Vaccine Center, Decatur, Georgia 30030, USA
| | - Nadine G Rouphael
- Hope Clinic of the Emory Vaccine Center, Decatur, Georgia 30030, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California 94305, USA.,Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA.,Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA
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