1
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Apps R, Biancotto A, Candia J, Kotliarov Y, Perl S, Cheung F, Farmer R, Mulè MP, Rachmaninoff N, Chen J, Martins AJ, Shi R, Zhou H, Bansal N, Schum P, Olnes MJ, Milanez-Almeida P, Han KL, Sellers B, Cortese M, Hagan T, Rouphael N, Pulendran B, King L, Manischewitz J, Khurana S, Golding H, van der Most RG, Dickler HB, Germain RN, Schwartzberg PL, Tsang JS. Acute and persistent responses after H5N1 vaccination in humans. Cell Rep 2024; 43:114706. [PMID: 39235945 DOI: 10.1016/j.celrep.2024.114706] [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: 01/16/2024] [Revised: 04/14/2024] [Accepted: 08/16/2024] [Indexed: 09/07/2024] Open
Abstract
To gain insight into how an adjuvant impacts vaccination responses, we use systems immunology to study human H5N1 influenza vaccination with or without the adjuvant AS03, longitudinally assessing 14 time points including multiple time points within the first day after prime and boost. We develop an unsupervised computational framework to discover high-dimensional response patterns, which uncover adjuvant- and immunogenicity-associated early response dynamics, including some that differ post prime versus boost. With or without adjuvant, some vaccine-induced transcriptional patterns persist to at least 100 days after initial vaccination. Single-cell profiling of surface proteins, transcriptomes, and chromatin accessibility implicates transcription factors in the erythroblast-transformation-specific (ETS) family as shaping these long-lasting signatures, primarily in classical monocytes but also in CD8+ naive-like T cells. These cell-type-specific signatures are elevated at baseline in high-antibody responders in an independent vaccination cohort, suggesting that antigen-agnostic baseline immune states can be modulated by vaccine antigens alone to enhance future responses.
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Affiliation(s)
- Richard Apps
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | | | - Julián Candia
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA; Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, MD, USA
| | - Shira Perl
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; NIH Oxford-Cambridge Scholars Program, Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, UCB2 0QQ Cambridge, UK
| | - Nicholas Rachmaninoff
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Rongye Shi
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Huizhi Zhou
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Paula Schum
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Matthew J Olnes
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | | | - Kyu Lee Han
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Brian Sellers
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA
| | - Mario Cortese
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Thomas Hagan
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Decatur, GA 30030, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA; Hope Clinic of the Emory Vaccine Center, Decatur, GA 30030, USA
| | - Lisa King
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20993 USA
| | - Jody Manischewitz
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20993 USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20993 USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD 20993 USA
| | | | | | - Ronald N Germain
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Pamela L Schwartzberg
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA; Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - John S Tsang
- NIH Center for Human Immunology, NIH, Bethesda, MD 20892, USA; Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Center for Systems and Engineering Immunology, Departments of Immunobiology and Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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2
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Pelletier AN, Sanchez GP, Izmirly A, Watson M, Di Pucchio T, Carvalho KI, Filali-Mouhim A, Paramithiotis E, Timenetsky MDCST, Precioso AR, Kalil J, Diamond MS, Haddad EK, Kallas EG, Sekaly RP. A pre-vaccination immune metabolic interplay determines the protective antibody response to a dengue virus vaccine. Cell Rep 2024; 43:114370. [PMID: 38900640 PMCID: PMC11404042 DOI: 10.1016/j.celrep.2024.114370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 02/05/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Protective immunity to dengue virus (DENV) requires antibody response to all four serotypes. Systems vaccinology identifies a multi-OMICs pre-vaccination signature and mechanisms predictive of broad antibody responses after immunization with a tetravalent live attenuated DENV vaccine candidate (Butantan-DV/TV003). Anti-inflammatory pathways, including TGF-β signaling expressed by CD68low monocytes, and the metabolites phosphatidylcholine (PC) and phosphatidylethanolamine (PE) positively correlate with broadly neutralizing antibody responses against DENV. In contrast, expression of pro-inflammatory pathways and cytokines (IFN and IL-1) in CD68hi monocytes and primary and secondary bile acids negatively correlates with broad DENV-specific antibody responses. Induction of TGF-β and IFNs is done respectively by PC/PE and bile acids in CD68low and CD68hi monocytes. The inhibition of viral sensing by PC/PE-induced TGF-β is confirmed in vitro. Our studies show that the balance between metabolites and the pro- or anti-inflammatory state of innate immune cells drives broad and protective B cell response to a live attenuated dengue vaccine.
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Affiliation(s)
- Adam-Nicolas Pelletier
- RPM Bioinfo Solutions, Sainte-Thérèse, QC, Canada; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Gabriela Pacheco Sanchez
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Abdullah Izmirly
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Tiziana Di Pucchio
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Karina Inacio Carvalho
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Abdelali Filali-Mouhim
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | | | | | | | - Jorge Kalil
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, SP, Brazil; Institute for Investigation in Immunology-Instituto Nacional de Ciência e Tecnologia-iii-INCT, São Paulo, SP, Brazil
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elias K Haddad
- Department of Medicine and Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Esper G Kallas
- Instituto Butantan, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, Hospital das Clínicas, School of Medicine, University of Sao Paulo, São Paulo 01246-903, Brazil
| | - Rafick Pierre Sekaly
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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3
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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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4
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Azees AS, Fasiku MM, Isa A, Ezenwoko AZ, Ahmed A, Temitayo-Oboh AO, Utulu R, Adeniyi MA, Musa A, Alo C, Ibrahim UM, Imhonopi GB, Adesoye OO, Okeke IM, John GT, Ayinla AY. Vaccine Safety: Assessing the Prevalence and Severity of Adverse Events Following COVID-19 Vaccination amongst Healthcare Workers in Tertiary Health Facilities in Nigeria. Niger Postgrad Med J 2024; 31:1-7. [PMID: 38321791 DOI: 10.4103/npmj.npmj_227_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Vaccines, including COVID-19 vaccines, are known to be cost-effective interventions for disease prevention and control. However, adverse events following immunisation (AEFI) may challenge the acceptance of these vaccines. This study assessed the prevalence and severity of COVID-19-related AEFI amongst healthcare workers at tertiary health facilities in Nigeria. MATERIALS AND METHODS This descriptive, cross-sectional study was conducted among healthcare workers who had received the COVID-19 vaccine. A multi-stage sampling technique was used to select participants from six Tertiary Health Facilities in Nigeria. Ethical approval (NHREC/01/01/2007-19/07/2021) was obtained from NHREC. Data were analysed using IBM® SPSS version 25 and categorical variables were presented in tables/charts using frequencies and proportions. RESULTS A total of 2130 respondents participated in the study, with a mean age of 37.4 ± 9.1 years. Most of the respondents, 1674 (78.6%), had two doses of the vaccine, and the overall prevalence of AEFI was 813 (38.2%). Common among the AEFI reported following the administration of the first dose of the vaccine were fever 649 (30.5%) and pain at the injection site 644 (30.2%), while it was pain at the injection site 216 (10.1%) and fever 173 (8.1%) for second dose. The higher proportions of AEFI were mostly mild to moderate. CONCLUSION The study observed a relatively low prevalence of AEFI, with the commonly reported ones being fever and injection site pain. It is crucial that countries continuously collect the data on AEFI and establish causality as a way to improve quality and guarantee vaccine safety.
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Affiliation(s)
- Ayotunde Sherif Azees
- Department of Community Medicine and Primary Care, Federal Medical Center, Abeokuta, Ogun State, Nigeria
| | - Mojirola Martina Fasiku
- Department of Epidemiology and Community Health, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Abdulfattah Isa
- Department of Public Health, Federal Medical Centre, Birnin Kebbi, Nigeria
| | - Ahuna Zainab Ezenwoko
- Department of Community Medicine, Usmanu Danfodiyo University Teaching Hospital, Argungu, Kebbi State, Nigeria
| | - Abdullahi Ahmed
- Department of Community Medicine and Primary Care, Federal Medical Center, Abeokuta, Ogun State, Nigeria
| | | | - Rowland Utulu
- Department of Community Medicine, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Makinde Adebayo Adeniyi
- Department of Community Medicine and Primary Care, Federal Medical Center, Abeokuta, Ogun State, Nigeria
| | - Abubakar Musa
- Department of Community Medicine, Abubakar Tafawa Balewa University Teaching Hospital, Bauchi, Nigeria
| | - Chihurumnanya Alo
- Department of Community Medicine, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Usman Muhammed Ibrahim
- Department of Community Medicine, Federal University Dutse, Dutse, Jigawa State, Nigeria
| | - Gloria Bosede Imhonopi
- Department of Community Medicine and Primary Care, Federal Medical Center, Abeokuta, Ogun State, Nigeria
| | - Oluwaseun Opeyemi Adesoye
- Department of Community Medicine, Medicine Delta State University Teaching Hospital, Oghara, Nigeria
| | - Ifeyinwa Maureen Okeke
- Department of Community Medicine, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Godwin ThankGod John
- Department of Epidemiology and Community Health, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Abdulquadri Yeketi Ayinla
- Department of Epidemiology and Community Health, University of Ilorin Teaching Hospital, Ilorin, Nigeria
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5
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Buscher K, Rixen R, Schütz P, Hüchtmann B, Van Marck V, Heitplatz B, Jehn U, Braun DA, Gabriëls G, Pavenstädt H, Reuter S. Plasma protein signatures reflect systemic immunity and allograft function in kidney transplantation. Transl Res 2023; 262:35-43. [PMID: 37507006 DOI: 10.1016/j.trsl.2023.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/20/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023]
Abstract
Kidney transplantation causes large perturbations of the immune system. While many studies focus on the allograft, insights into systemic effects are largely missing. Here, we analyzed the systemic immune response in 3 cohorts of kidney transplanted patients. Using serum proteomics, laboratory values, mass cytometry, histological and clinical parameters, inter-patient heterogeneity was leveraged for multi-omic co-variation analysis. We identified circulating immune modules (CIM) that describe extra-renal signatures of co-regulated plasma proteins. CIM are present in nontransplanted controls, in transplant conditions and during rejection. They are enriched in pathways linked to kidney function, extracellular matrix, signaling, and cellular activation. A complex leukocyte response in the blood during allograft quiescence and rejection is associated with CIM activity and CIM-specific cytokines. CIM activity correlates with kidney function including a 2-month prediction. Together, the data suggest a systemic and multi-layered response of transplant immunity that might be insightful for understanding allograft dysfunction and developing translational biomarkers.
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Affiliation(s)
- Konrad Buscher
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Münster, Münster, Germany.
| | - Rebecca Rixen
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Münster, Münster, Germany
| | - Paula Schütz
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Münster, Münster, Germany
| | - Birte Hüchtmann
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Münster, Münster, Germany
| | - Veerle Van Marck
- Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Barbara Heitplatz
- Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Ulrich Jehn
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Münster, Münster, Germany
| | - Daniela A Braun
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Münster, Münster, Germany
| | - Gert Gabriëls
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Münster, Münster, Germany
| | - Hermann Pavenstädt
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Münster, Münster, Germany
| | - Stefan Reuter
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Münster, Münster, Germany
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6
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Pichichero ME. Variability of vaccine responsiveness in early life. Cell Immunol 2023; 393-394:104777. [PMID: 37866234 DOI: 10.1016/j.cellimm.2023.104777] [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: 06/15/2023] [Revised: 09/18/2023] [Accepted: 10/14/2023] [Indexed: 10/24/2023]
Abstract
Vaccinations in early life elicit variable antibody and cellular immune responses, sometimes leaving fully vaccinated children unprotected against life-threatening infectious diseases. Specific immune cell populations and immune networks may have a critical period of development and calibration in a window of opportunity occurring during the first 100 days of early life. Among the early life determinants of vaccine responses, this review will focus on modifiable factors involving development of the infant microbiota and metabolome: antibiotic exposure, breast versus formula feeding, and Caesarian section versus vaginal delivery of newborns. How microbiota may serve as natural adjuvants for vaccine responses and how microbiota-derived metabolites influence vaccine responses are also reviewed. Early life poor vaccine responsiveness can be linked to increased infection susceptibility because both phenotypes share similar immunity dysregulation profiles. An early life pre-vaccination endotype, when interventions have the highest potential for success, should be sought that predicts vaccine response trajectories.
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Affiliation(s)
- Michael E Pichichero
- Center for Infectious Diseases and Immunology, Research Institute, Rochester General Hospital, 1425 Portland Ave, Rochester, NY 14621, USA.
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7
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Strulovici-Barel Y, Rostami MR, Kaner RJ, Mezey JG, Crystal RG. Serial Sampling of the Small Airway Epithelium to Identify Persistent Smoking-dysregulated Genes. Am J Respir Crit Care Med 2023; 208:780-790. [PMID: 37531632 PMCID: PMC10563181 DOI: 10.1164/rccm.202204-0786oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/02/2023] [Indexed: 08/04/2023] Open
Abstract
Rationale: The small airway epithelium (beyond the sixth generation), the initiation site of smoking-induced airway disorders, is highly sensitive to the stress of smoking. Because of variations over time in smoking habits, the small airway epithelium transcriptome is dynamic, fluctuating not only among smokers but also within each smoker. Objectives: To perform accurate assessment of the smoking-related dysregulation of the human small airway epithelium despite the variation of smoking within the same individual and of the effects of smoking cessation on the dysregulated transcriptome. Methods: We conducted serial sampling of the same smokers and nonsmoker control subjects over time to identify persistent smoking dysregulation of the biology of the small airway epithelium over 1 year. We conducted serial sampling of smokers who quit smoking, before and after smoking cessation, to assess the effect of smoking cessation on the smoking-dysregulated genes. Measurements and Main Results: Repeated measures ANOVA of the small airway epithelium transcriptome sampled four times in the same individuals over 1 year enabled the identification of 475 persistent smoking-dysregulated genes. Most genes were normalized after 12 months of smoking cessation; however, 53 (11%) genes, including CYP1B1, PIR, ME1, and TRIM16, remained persistently abnormally expressed. Dysregulated pathways enriched with the nonreversible genes included xenobiotic metabolism signaling, bupropion degradation, and nicotine degradation. Conclusions: Analysis of repetitive sampling of the same individuals identified persistent smoking-induced dysregulation of the small airway epithelium transcriptome and the effect of smoking cessation. These results help identify targets for the development of therapies that can be applicable to smoking-related airway diseases.
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Affiliation(s)
| | | | - Robert J. Kaner
- Department of Genetic Medicine and
- Department of Medicine, Weill Cornell Medical College, New York, New York; and
| | - Jason G. Mezey
- Department of Genetic Medicine and
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York
| | - Ronald G. Crystal
- Department of Genetic Medicine and
- Department of Medicine, Weill Cornell Medical College, New York, New York; and
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8
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Kalyakulina A, Yusipov I, Kondakova E, Bacalini MG, Franceschi C, Vedunova M, Ivanchenko M. Small immunological clocks identified by deep learning and gradient boosting. Front Immunol 2023; 14:1177611. [PMID: 37691946 PMCID: PMC10485620 DOI: 10.3389/fimmu.2023.1177611] [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: 03/01/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
Background The aging process affects all systems of the human body, and the observed increase in inflammatory components affecting the immune system in old age can lead to the development of age-associated diseases and systemic inflammation. Results We propose a small clock model SImAge based on a limited number of immunological biomarkers. To regress the chronological age from cytokine data, we first use a baseline Elastic Net model, gradient-boosted decision trees models, and several deep neural network architectures. For the full dataset of 46 immunological parameters, DANet, SAINT, FT-Transformer and TabNet models showed the best results for the test dataset. Dimensionality reduction of these models with SHAP values revealed the 10 most age-associated immunological parameters, taken to construct the SImAge small immunological clock. The best result of the SImAge model shown by the FT-Transformer deep neural network model has mean absolute error of 6.94 years and Pearson ρ = 0.939 on the independent test dataset. Explainable artificial intelligence methods allow for explaining the model solution for each individual participant. Conclusions We developed an approach to construct a model of immunological age based on just 10 immunological parameters, coined SImAge, for which the FT-Transformer deep neural network model had proved to be the best choice. The model shows competitive results compared to the published studies on immunological profiles, and takes a smaller number of features as an input. Neural network architectures outperformed gradient-boosted decision trees, and can be recommended in the further analysis of immunological profiles.
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Affiliation(s)
- Alena Kalyakulina
- Research Center for Trusted Artificial Intelligence, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, Russia
| | - Igor Yusipov
- Research Center for Trusted Artificial Intelligence, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, Russia
| | - Elena Kondakova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, Russia
- Institute of Neuroscience, Lobachevsky State University, Nizhny Novgorod, Russia
| | | | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, Russia
| | - Maria Vedunova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, Russia
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9
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Hirota M, Tamai M, Yukawa S, Taira N, Matthews MM, Toma T, Seto Y, Yoshida M, Toguchi S, Miyagi M, Mori T, Tomori H, Tamai O, Kina M, Sakihara E, Yamashiro C, Miyagi M, Tamaki K, Wolf M, Collins MK, Kitano H, Ishikawa H. Human immune and gut microbial parameters associated with inter-individual variations in COVID-19 mRNA vaccine-induced immunity. Commun Biol 2023; 6:368. [PMID: 37081096 PMCID: PMC10119155 DOI: 10.1038/s42003-023-04755-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/24/2023] [Indexed: 04/22/2023] Open
Abstract
COVID-19 mRNA vaccines induce protective adaptive immunity against SARS-CoV-2 in most individuals, but there is wide variation in levels of vaccine-induced antibody and T-cell responses. However, the mechanisms underlying this inter-individual variation remain unclear. Here, using a systems biology approach based on multi-omics analyses of human blood and stool samples, we identified several factors that are associated with COVID-19 vaccine-induced adaptive immune responses. BNT162b2-induced T cell response is positively associated with late monocyte responses and inversely associated with baseline mRNA expression of activation protein 1 (AP-1) transcription factors. Interestingly, the gut microbial fucose/rhamnose degradation pathway is positively correlated with mRNA expression of AP-1, as well as a gene encoding an enzyme producing prostaglandin E2 (PGE2), which promotes AP-1 expression, and inversely correlated with BNT162b2-induced T-cell responses. These results suggest that baseline AP-1 expression, which is affected by commensal microbial activity, is a negative correlate of BNT162b2-induced T-cell responses.
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Affiliation(s)
- Masato Hirota
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Miho Tamai
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Sachie Yukawa
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
- Integrated Open Systems Unit, OIST, Onna-son, Okinawa, Japan
| | - Naoyuki Taira
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | | | - Takeshi Toma
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Yu Seto
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Makiko Yoshida
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Sakura Toguchi
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Mio Miyagi
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Tomoari Mori
- Research Support Division, Occupational Health and Safety, OIST, Onna-son, Okinawa, Japan
| | | | | | | | - Eishin Sakihara
- Health Care Center of the Naha Medical Association, Naha-city, Okinawa, Japan
| | - Chiaki Yamashiro
- Yamashiro Orthopedic Surgery Ophthalmology Clinic, Naha-city, Okinawa, Japan
| | | | - Kentaro Tamaki
- Naha-Nishi Clinic, Department of Breast Surgery, Naha-city, Okinawa, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, OIST, Onna-son, Okinawa, Japan
| | - Mary K Collins
- Research Support Division, Office of the Provost, OIST, Onna-son, Okinawa, Japan
| | - Hiroaki Kitano
- Integrated Open Systems Unit, OIST, Onna-son, Okinawa, Japan
| | - Hiroki Ishikawa
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan.
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10
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Giles ML, Sing Way S, Marchant A, Aghaepour N, James T, Schaltz-Buchholzer F, Zazara D, Arck P, Kollmann TR. Maternal vaccination to prevent adverse pregnancy outcomes: An underutilized molecular immunological intervention? J Mol Biol 2023; 435:168097. [PMID: 37080422 DOI: 10.1016/j.jmb.2023.168097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 04/22/2023]
Abstract
Adverse pregnancy outcomes including maternal mortality, stillbirth, preterm birth, intrauterine growth restriction cause millions of deaths each year. More effective interventions are urgently needed. Maternal immunization could be one such intervention protecting the mother and newborn from infection through its pathogen-specific effects. However, many adverse pregnancy outcomes are not directly linked to the infectious pathogens targeted by existing maternal vaccines but rather are linked to pathological inflammation unfolding during pregnancy. The underlying pathogenesis driving such unfavourable outcomes have only partially been elucidated but appear to relate to altered immune regulation by innate as well as adaptive immune responses, ultimately leading to aberrant maternal immune activation. Maternal immunization, like all immunization, impacts the immune system beyond pathogen-specific immunity. This raises the possibility that maternal vaccination could potentially be utilised as a pathogen-agnostic immune modulatory intervention to redirect abnormal immune trajectories towards a more favourable phenotype providing pregnancy protection. In this review we describe the epidemiological evidence surrounding this hypothesis, along with the mechanistic plausibility and present a possible path forward to accelerate addressing the urgent need of adverse pregnancy outcomes.
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Affiliation(s)
| | - Sing Sing Way
- Center for Inflammation and Tolerance; Cincinnati Children's Hospital, Cincinnati USA
| | | | - Nima Aghaepour
- Stanford University School of Medicine, Stanford, CA, USA
| | - Tomin James
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Dimitra Zazara
- Division of Experimental Feto-Maternal Medicine, Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg, Hamburg, Germany
| | - Petra Arck
- Division of Experimental Feto-Maternal Medicine, Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg, Hamburg, Germany
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11
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Rodriguez L, Pou C, Lakshmikanth T, Zhang J, Mugabo CH, Wang J, Mikes J, Olin A, Chen Y, Rorbach J, Juto JE, Li TQ, Julin P, Brodin P. Achieving symptom relief in patients with myalgic encephalomyelitis by targeting the neuro-immune interface and optimizing disease tolerance. OXFORD OPEN IMMUNOLOGY 2023; 4:iqad003. [PMID: 37255930 PMCID: PMC10148714 DOI: 10.1093/oxfimm/iqad003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/05/2023] [Accepted: 03/24/2023] [Indexed: 06/01/2023] Open
Abstract
Myalgic encephalomyelitis (ME) previously also known as chronic fatigue syndrome is a heterogeneous, debilitating syndrome of unknown etiology responsible for long-lasting disability in millions of patients worldwide. The most well-known symptom of ME is post-exertional malaise, but many patients also experience autonomic dysregulation, cranial nerve dysfunction and signs of immune system activation. Many patients also report a sudden onset of disease following an infection. The brainstem is a suspected focal point in ME pathogenesis and patients with structural impairment to the brainstem often show ME-like symptoms. The brainstem is also where the vagus nerve originates, a critical neuro-immune interface and mediator of the inflammatory reflex which regulate systemic inflammation. Here, we report the results of a randomized, placebo-controlled trial using intranasal mechanical stimulation targeting nerve endings in the nasal cavity, likely from the trigeminal nerve, possibly activating additional centers in the brainstem of ME patients and correlating with a ∼30% reduction in overall symptom scores after 8 weeks of treatment. By performing longitudinal, systems-level monitoring of the blood immune system in these patients, we uncover signs of chronic immune activation in ME, as well as immunological correlates of improvement that center around gut-homing immune cells and reduced inflammation. The mechanisms of symptom relief remain to be determined, but transcriptional analyses suggest an upregulation of disease tolerance mechanisms. We believe that these results are suggestive of ME as a condition explained by a maladaptive disease tolerance response following infection.
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Affiliation(s)
- Lucie Rodriguez
- Department of Women’s and Children’s Health, Karolinska Institutet, Solna 17121, Sweden
| | | | | | - Jingdian Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna 17176, Sweden
- Max Planck Institute Biology of Ageing—Karolinska Institutet Laboratory, Karolinska Institutet, Solna 17176, Sweden
| | | | - Jun Wang
- Department of Women’s and Children’s Health, Karolinska Institutet, Solna 17121, Sweden
| | - Jaromir Mikes
- Department of Women’s and Children’s Health, Karolinska Institutet, Solna 17121, Sweden
| | - Axel Olin
- Department of Women’s and Children’s Health, Karolinska Institutet, Solna 17121, Sweden
| | - Yang Chen
- Department of Women’s and Children’s Health, Karolinska Institutet, Solna 17121, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna 17176, Sweden
- Max Planck Institute Biology of Ageing—Karolinska Institutet Laboratory, Karolinska Institutet, Solna 17176, Sweden
| | - Jan-Erik Juto
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Solna 17177, Sweden
| | - Tie Qiang Li
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Solna 17177, Sweden
- Department of Medical Radiation Physics and Nuclear Medicine, Karolinska University Hospital, Solna 17176, Sweden
| | - Per Julin
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna 17176, Sweden
- Neurological Rehabilitation Clinic, Stora Sköndal, Sköndal 12864, Sweden
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12
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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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13
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Sparks R, Lau WW, Liu C, Han KL, Vrindten KL, Sun G, Cox M, Andrews SF, Bansal N, Failla LE, Manischewitz J, Grubbs G, King LR, Koroleva G, Leimenstoll S, Snow L, Chen J, Tang J, Mukherjee A, Sellers BA, Apps R, McDermott AB, Martins AJ, Bloch EM, Golding H, Khurana S, Tsang JS. Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19. Nature 2023; 614:752-761. [PMID: 36599369 PMCID: PMC10481789 DOI: 10.1038/s41586-022-05670-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023]
Abstract
Acute viral infections can have durable functional impacts on the immune system long after recovery, but how they affect homeostatic immune states and responses to future perturbations remain poorly understood1-4. Here we use systems immunology approaches, including longitudinal multimodal single-cell analysis (surface proteins, transcriptome and V(D)J sequences) to comparatively assess baseline immune statuses and responses to influenza vaccination in 33 healthy individuals after recovery from mild, non-hospitalized COVID-19 (mean, 151 days after diagnosis) and 40 age- and sex-matched control individuals who had never had COVID-19. At the baseline and independent of time after COVID-19, recoverees had elevated T cell activation signatures and lower expression of innate immune genes including Toll-like receptors in monocytes. Male individuals who had recovered from COVID-19 had coordinately higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared with healthy male individuals and female individuals who had recovered from COVID-19, in part because male recoverees had monocytes with higher IL-15 responses early after vaccination coupled with elevated prevaccination frequencies of 'virtual memory'-like CD8+ T cells poised to produce more IFNγ after IL-15 stimulation. Moreover, the expression of the repressed innate immune genes in monocytes increased by day 1 to day 28 after vaccination in recoverees, therefore moving towards the prevaccination baseline of the healthy control individuals. By contrast, these genes decreased on day 1 and returned to the baseline by day 28 in the control individuals. Our study reveals sex-dimorphic effects of previous mild COVID-19 and suggests that viral infections in humans can establish new immunological set-points that affect future immune responses in an antigen-agnostic manner.
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Affiliation(s)
- Rachel Sparks
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - William W Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- Graduate Program in Biological Sciences, University of Maryland, College Park, MD, USA
| | - Kyu Lee Han
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Kiera L Vrindten
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Guangping Sun
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Milann Cox
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | | | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Laura E Failla
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jody Manischewitz
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Gabrielle Grubbs
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Lisa R King
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Galina Koroleva
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | | | - LaQuita Snow
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juanjie Tang
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | | | - Brian A Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Richard Apps
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | | | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, 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.
- Yale Center for Systems and Engineering Immunology and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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14
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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:e80652. [PMID: 36648132 PMCID: PMC9844983 DOI: 10.7554/elife.80652] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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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15
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Sparks R, Lau WW, Liu C, Han KL, Vrindten KL, Sun G, Cox M, Andrews SF, Bansal N, Failla LE, Manischewitz J, Grubbs G, King LR, Koroleva G, Leimenstoll S, Snow L, Chen J, Tang J, Mukherjee A, Sellers BA, Apps R, McDermott AB, Martins AJ, Bloch EM, Golding H, Khurana S, Tsang JS. Influenza vaccination and single cell multiomics reveal sex dimorphic immune imprints of prior mild COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.17.22271138. [PMID: 35233581 PMCID: PMC8887138 DOI: 10.1101/2022.02.17.22271138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Viral infections can have profound and durable functional impacts on the immune system. There is an urgent need to characterize the long-term immune effects of SARS-CoV-2 infection given the persistence of symptoms in some individuals and the continued threat of novel variants. Here we use systems immunology, including longitudinal multimodal single cell analysis (surface proteins, transcriptome, and V(D)J sequences) from 33 previously healthy individuals after recovery from mild, non-hospitalized COVID-19 and 40 age- and sex-matched healthy controls with no history of COVID-19 to comparatively assess the post-infection immune status (mean: 151 days after diagnosis) and subsequent innate and adaptive responses to seasonal influenza vaccination. Identification of both sex-specific and -independent temporally stable changes, including signatures of T-cell activation and repression of innate defense/immune receptor genes (e.g., Toll-like receptors) in monocytes, suggest that mild COVID-19 can establish new post-recovery immunological set-points. COVID-19-recovered males had higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared to healthy males and COVID-19-recovered females, partly attributable to elevated pre-vaccination frequencies of a GPR56 expressing CD8+ T-cell subset in male recoverees that are "poised" to produce higher levels of IFNγ upon inflammatory stimulation. Intriguingly, by day 1 post-vaccination in COVID-19-recovered subjects, the expression of the repressed genes in monocytes increased and moved towards the pre-vaccination baseline of healthy controls, suggesting that the acute inflammation induced by vaccination could partly reset the immune states established by mild COVID-19. Our study reveals sex-dimorphic immune imprints and in vivo functional impacts of mild COVID-19 in humans, suggesting that prior COVID-19, and possibly respiratory viral infections in general, could change future responses to vaccination and in turn, vaccines could help reset the immune system after COVID-19, both in an antigen-agnostic manner.
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Affiliation(s)
- Rachel Sparks
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA,These authors contributed equally
| | - William W. Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA,These authors contributed equally
| | - Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA,Graduate Program in Biological Sciences, University of Maryland, College Park, MD, USA,These authors contributed equally
| | - Kyu Lee Han
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Kiera L. Vrindten
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Guangping Sun
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA,Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Milann Cox
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | | | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Laura E. Failla
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jody Manischewitz
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Gabrielle Grubbs
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Lisa R. King
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Galina Koroleva
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | | | - LaQuita Snow
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | | | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juanjie Tang
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | | | | | - Richard Apps
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | | | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Evan M. Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, 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,Correspondence:
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16
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Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) accelerated development of messenger RNA (mRNA) vaccines, which have proven to be highly effective against COVID-19. However, antibody responses vary widely and wane over time. This study evaluated the range and kinetics of the primary antibody response to SARS-CoV-2 mRNA-based vaccination in parallel with the B cells that are involved in generating and maintaining this response. These include plasmablasts, the antibody-secreting cells that arise rapidly yet transiently following immunization, and memory B cells, a heterogeneous population that can provide long-lasting immunity. Our results show that the antibody response was tightly linked to early plasmablasts, while the cellular response was sustained by a distinct population of memory B cells. Messenger RNA (mRNA) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are highly effective at inducing protective immunity. However, weak antibody responses are seen in some individuals, and cellular correlates of immunity remain poorly defined, especially for B cells. Here we used unbiased approaches to longitudinally dissect primary antibody, plasmablast, and memory B cell (MBC) responses to the two-dose mRNA-1273 vaccine in SARS-CoV-2–naive adults. Coordinated immunoglobulin A (IgA) and IgG antibody responses were preceded by bursts of spike-specific plasmablasts after both doses but earlier and more intensely after dose 2. While antibody and B cell cellular responses were generally robust, they also varied within the cohort and decreased over time after a dose-2 peak. Both antigen-nonspecific postvaccination plasmablast frequency after dose 1 and their spike-specific counterparts early after dose 2 correlated with subsequent antibody levels. This correlation between early plasmablasts and antibodies remained for titers measured at 6 months after vaccination. Several distinct antigen-specific MBC populations emerged postvaccination with varying kinetics, including two MBC populations that correlated with 2- and 6-month antibody titers. Both were IgG-expressing MBCs: one less mature, appearing as a correlate after the first dose, while the other MBC correlate showed a more mature and resting phenotype, emerging as a correlate later after dose 2. This latter MBC was also a major contributor to the sustained spike-specific MBC response observed at month 6. Thus, these plasmablasts and MBCs that emerged after both the first and second doses with distinct kinetics are potential determinants of the magnitude and durability of antibodies in response to mRNA-based vaccination.
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17
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Szittner Z, Péter B, Kurunczi S, Székács I, Horváth R. Functional blood cell analysis by label-free biosensors and single-cell technologies. Adv Colloid Interface Sci 2022; 308:102727. [DOI: 10.1016/j.cis.2022.102727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 11/01/2022]
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18
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Abstract
"The Primate Malarias" book has been a uniquely important resource for multiple generations of scientists, since its debut in 1971, and remains pertinent to the present day. Indeed, nonhuman primates (NHPs) have been instrumental for major breakthroughs in basic and pre-clinical research on malaria for over 50 years. Research involving NHPs have provided critical insights and data that have been essential for malaria research on many parasite species, drugs, vaccines, pathogenesis, and transmission, leading to improved clinical care and advancing research goals for malaria control, elimination, and eradication. Whilst most malaria scientists over the decades have been studying Plasmodium falciparum, with NHP infections, in clinical studies with humans, or using in vitro culture or rodent model systems, others have been dedicated to advancing research on Plasmodium vivax, as well as on phylogenetically related simian species, including Plasmodium cynomolgi, Plasmodium coatneyi, and Plasmodium knowlesi. In-depth study of these four phylogenetically related species over the years has spawned the design of NHP longitudinal infection strategies for gathering information about ongoing infections, which can be related to human infections. These Plasmodium-NHP infection model systems are reviewed here, with emphasis on modern systems biological approaches to studying longitudinal infections, pathogenesis, immunity, and vaccines. Recent discoveries capitalizing on NHP longitudinal infections include an advanced understanding of chronic infections, relapses, anaemia, and immune memory. With quickly emerging new technological advances, more in-depth research and mechanistic discoveries can be anticipated on these and additional critical topics, including hypnozoite biology, antigenic variation, gametocyte transmission, bone marrow dysfunction, and loss of uninfected RBCs. New strategies and insights published by the Malaria Host-Pathogen Interaction Center (MaHPIC) are recapped here along with a vision that stresses the importance of educating future experts well trained in utilizing NHP infection model systems for the pursuit of innovative, effective interventions against malaria.
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Affiliation(s)
- Mary R Galinski
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Vaccine Center, Emory University, Atlanta, GA, USA.
- Emory National Primate Research Center (Yerkes National Primate Research Center), Emory University, Atlanta, GA, USA.
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19
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Moorlag SJCFM, Taks E, ten Doesschate T, van der Vaart TW, Janssen AB, Müller L, Ostermann P, Dijkstra H, Lemmers H, Simonetti E, Mazur M, Schaal H, ter Heine R, van de Veerdonk FL, Bleeker-Rovers CP, van Crevel R, ten Oever J, de Jonge MI, Bonten MJ, van Werkhoven CH, Netea MG. Efficacy of BCG Vaccination Against Respiratory Tract Infections in Older Adults During the Coronavirus Disease 2019 Pandemic. Clin Infect Dis 2022; 75:e938-e946. [PMID: 35247264 PMCID: PMC8903481 DOI: 10.1093/cid/ciac182] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Older age is associated with increased severity and death from respiratory infections, including coronavirus disease 2019 (COVID-19). The tuberculosis BCG vaccine may provide heterologous protection against nontuberculous infections and has been proposed as a potential preventive strategy against COVID-19. METHODS In this multicenter, placebo-controlled trial, we randomly assigned older adults (aged ≥60 years; n = 2014) to intracutaneous vaccination with BCG vaccine (n = 1008) or placebo (n = 1006). The primary end point was the cumulative incidence of respiratory tract infections (RTIs) that required medical intervention, during 12 months of follow-up. Secondary end points included the incidence of COVID-19, and the effect of BCG vaccination on the cellular and humoral immune responses. RESULTS The cumulative incidence of RTIs requiring medical intervention was 0.029 in the BCG-vaccinated group and 0.024 in the control group (subdistribution hazard ratio, 1.26 [98.2% confidence interval, .65-2.44]). In the BCG vaccine and placebo groups, 51 and 48 individuals, respectively tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with polymerase chain reaction (subdistribution hazard ratio, 1.053 [95% confidence interval, .71-1.56]). No difference was observed in the frequency of adverse events. BCG vaccination was associated with enhanced cytokine responses after influenza, and also partially associated after SARS-CoV-2 stimulation. In patients diagnosed with COVID-19, antibody responses after infection were significantly stronger if the volunteers had previously received BCG vaccine. CONCLUSIONS BCG vaccination had no effect on the incidence of RTIs, including SARS-CoV-2 infection, in older adult volunteers. However, it improved cytokine responses stimulated by influenza and SARS-CoV-2 and induced stronger antibody titers after COVID-19 infection. CLINICAL TRIALS REGISTRATION EU Clinical Trials Register 2020-001591-15 ClinicalTrials.gov NCT04417335.
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Affiliation(s)
| | | | | | | | - Axel B Janssen
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lisa Müller
- Department for Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University Duesseldorf, Germany
| | - Philipp Ostermann
- Department for Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University Duesseldorf, Germany
| | - Helga Dijkstra
- Department of Internal Medicine Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Heidi Lemmers
- Department of Internal Medicine Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elles Simonetti
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands,Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marc Mazur
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Heiner Schaal
- Department for Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University Duesseldorf, Germany
| | - Rob ter Heine
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlandsand
| | - Frank L van de Veerdonk
- Department of Internal Medicine Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Chantal P Bleeker-Rovers
- Department of Internal Medicine Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jaap ten Oever
- Department of Internal Medicine Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marien I de Jonge
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands,Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marc J Bonten
- University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Mihai G Netea
- Correspondence: Mihai G. Netea, Department of Medicine (463), Radboud University Nijmegen Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, the Netherlands ()
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20
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Aevermann BD, Shannon CP, Novotny M, Ben-Othman R, Cai B, Zhang Y, Ye JC, Kobor MS, Gladish N, Lee AHY, Blimkie TM, Hancock RE, Llibre A, Duffy D, Koff WC, Sadarangani M, Tebbutt SJ, Kollmann TR, Scheuermann RH. Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response. Front Immunol 2021; 12:690470. [PMID: 34777332 PMCID: PMC8588842 DOI: 10.3389/fimmu.2021.690470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/25/2021] [Indexed: 01/23/2023] Open
Abstract
Vaccination to prevent infectious disease is one of the most successful public health interventions ever developed. And yet, variability in individual vaccine effectiveness suggests that a better mechanistic understanding of vaccine-induced immune responses could improve vaccine design and efficacy. We have previously shown that protective antibody levels could be elicited in a subset of recipients with only a single dose of the hepatitis B virus (HBV) vaccine and that a wide range of antibody levels were elicited after three doses. The immune mechanisms responsible for this vaccine response variability is unclear. Using single cell RNA sequencing of sorted innate immune cell subsets, we identified two distinct myeloid dendritic cell subsets (NDRG1-expressing mDC2 and CDKN1C-expressing mDC4), the ratio of which at baseline (pre-vaccination) correlated with the immune response to a single dose of HBV vaccine. Our results suggest that the participants in our vaccine study were in one of two different dendritic cell dispositional states at baseline – an NDRG2-mDC2 state in which the vaccine elicited an antibody response after a single immunization or a CDKN1C-mDC4 state in which the vaccine required two or three doses for induction of antibody responses. To explore this correlation further, genes expressed in these mDC subsets were used for feature selection prior to the construction of predictive models using supervised canonical correlation machine learning. The resulting models showed an improved correlation with serum antibody titers in response to full vaccination. Taken together, these results suggest that the propensity of circulating dendritic cells toward either activation or suppression, their “dispositional endotype” at pre-vaccination baseline, could dictate response to vaccination.
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Affiliation(s)
- Brian D Aevermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Mark Novotny
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Rym Ben-Othman
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Bing Cai
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Jamie C Ye
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Michael S Kobor
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Gladish
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Travis M Blimkie
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Robert E Hancock
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Alba Llibre
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Wayne C Koff
- Human Vaccines Project, New York, NY, United States
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tobias R Kollmann
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States.,Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
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21
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Immunological Trajectories of White Blood Cells from Adolescence to Adulthood: Description and Determinants. Diagnostics (Basel) 2021; 11:diagnostics11112063. [PMID: 34829410 PMCID: PMC8625023 DOI: 10.3390/diagnostics11112063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 01/03/2023] Open
Abstract
Background: The immune system gradually matures early in life in the face of internal and external stimuli. Whether the immune responses are lasting and stable during the course of life is still unclear. Methods: As part of the EPITeen cohort, 1183 adolescents were prospectively evaluated at the ages of 13, 17, 21, 24 and 27. Sociodemographic, behavioral and clinical data were collected by self- and face-to-face-administered questionnaires, along with a physical examination comprising anthropometric measurements and blood sample collections. Mixed-effects models were used to identify individual trajectories of white blood cells (WBC) and finite Gaussian mixture models were used to identify the clusters of individual trajectories. Results: Participants were allocated into six clusters based on the individual trajectories of WBC distribution. Higher Inflammatory Activation Cluster (11.4%) had the highest total WBC count and neutrophils percentage, as well as the lowest percentage of lymphocytes. These participants had significantly higher odds of being overweight [OR = 2.44, 95%CI:1.51–3.92]. Lowest Levels of WBC Cluster (24.1%) had the lowest total WBC count, being characterized by a higher participation on sports [OR = 1.54, 95%CI:1.12–2.13]. Highest Proportion of Eosinophils Cluster (20.1%) had the highest eosinophils percentage and the highest likelihood of having been diagnosed with a chronic disease [OR = 2.11, 95%CI:1.43–3.13], namely “asthma or allergies” [OR = 14.0 (1.73, 112.2]. Lowest Proportion of Eosinophils Cluster (29.1%) had the lowest percentage of eosinophils and basophils, as well as the highest lymphocyte proportion. Participants in the Undefined Cluster (13.8%) showed the highest percentage of monocytes and basophils and were also characterized by significant lower odds of having parents with 7–9 years of schooling [OR = 0.56, (0.32, 0.99]. Conclusions: In this study we identified distinct immunological trajectories of WBC from adolescence to adulthood that were associated with social, clinical and behavioral determinants. These results suggest that these immunological trajectories are defined early in life, being dependent on the exposures.
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22
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Buscher K, Heitplatz B, van Marck V, Song J, Loismann S, Rixen R, Hüchtmann B, Kurian S, Ehinger E, Wolf D, Ley K, Pavenstädt H, Reuter S. Data-Driven Kidney Transplant Phenotyping as a Histology-Independent Framework for Biomarker Discovery. J Am Soc Nephrol 2021; 32:1933-1945. [PMID: 34078665 PMCID: PMC8455252 DOI: 10.1681/asn.2020121685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/15/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND In transplant medicine, clinical decision making largely relies on histology of biopsy specimens. However, histology suffers from low specificity, sensitivity, and reproducibility, leading to suboptimal stratification of patients. We developed a histology-independent immune framework of kidney graft homeostasis and rejection. METHODS We applied tailored RNA deconvolution for leukocyte enumeration and coregulated gene network analysis to published bulk human kidney transplant RNA transcriptomes as input for unsupervised, high-dimensional phenotype clustering. We used framework-based graft survival analysis to identify a biomarker that was subsequently characterized in independent transplant biopsy specimens. RESULTS We found seven immune phenotypes that confirm known rejection types and uncovered novel signatures. The molecular phenotypes allow for improved graft survival analysis compared with histology, and identify a high-risk group in nonrejecting transplants. Two fibrosis-related phenotypes with distinct immune features emerged with reduced graft survival. We identified lysyl oxidase-like 2 (LOXL2)-expressing peritubular CD68+ macrophages as a framework-derived biomarker of impaired allograft function. These cells precede graft fibrosis, as demonstrated in longitudinal biopsy specimens, and may be clinically useful as a biomarker for early fibrogenesis. CONCLUSIONS This study provides a comprehensive, data-driven atlas of human kidney transplant phenotypes and demonstrates its utility to identify novel clinical biomarkers.
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Affiliation(s)
- Konrad Buscher
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany,Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California
| | - Barbara Heitplatz
- Institute of Pathology, University Hospital Muenster, Muenster, Germany
| | - Veerle van Marck
- Institute of Pathology, University Hospital Muenster, Muenster, Germany
| | - Jian Song
- Institute of Physiological Chemistry and Pathobiochemistry, University of Muenster, Muenster, Germany,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Sophie Loismann
- Institute of Physiological Chemistry and Pathobiochemistry, University of Muenster, Muenster, Germany,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Rebecca Rixen
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
| | - Birte Hüchtmann
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
| | - Sunil Kurian
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | - Erik Ehinger
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California
| | - Dennis Wolf
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California,Department of Cardiology and Angiology I, University Heart Center, and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus Ley
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California
| | - Hermann Pavenstädt
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
| | - Stefan Reuter
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
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23
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Kardava L, Rachmaninoff N, Lau WW, Buckner CM, Trihemasava K, de Assis FL, Wang W, Zhang X, Wang Y, Chiang CI, Narpala S, Reger R, McCormack GE, Seamon CA, Childs RW, Suffredini AF, Strich JR, Chertow DS, Davey RT, Sneller MC, O’Connell S, Li Y, McDermott A, Chun TW, Fauci AS, Tsang JS, Moir S. Pre-vaccination and early B cell signatures predict antibody response to SARS-CoV-2 mRNA vaccine. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.07.06.21259528. [PMID: 34268520 PMCID: PMC8282109 DOI: 10.1101/2021.07.06.21259528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 mRNA vaccines are highly effective, although weak antibody responses are seen in some individuals with correlates of immunity that remain poorly understood. Here we longitudinally dissected antibody, plasmablast, and memory B cell (MBC) responses to the two-dose Moderna mRNA vaccine in SARS-CoV-2-uninfected adults. Robust, coordinated IgA and IgG antibody responses were preceded by bursts of spike-specific plasmablasts after both doses, but earlier and more intensely after dose two. Distinct antigen-specific MBC populations also emerged post-vaccination with varying kinetics. We identified antigen non-specific pre-vaccination MBC and post-vaccination plasmablasts after dose one and their spike-specific counterparts early after dose two that correlated with subsequent antibody levels. These baseline and response signatures can thus provide early indicators of serological efficacy and explain response variability in the population.
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Affiliation(s)
- Lela Kardava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nicholas Rachmaninoff
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - William W. Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Clarisa M. Buckner
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Krittin Trihemasava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Felipe Lopes de Assis
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Wei Wang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Xiaozhen Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yimeng Wang
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | | | - Robert Reger
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Genevieve E. McCormack
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Catherine A. Seamon
- Critical Care Medicine Department, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Richard W. Childs
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
- United States Public Health Service Commissioned Corps, Rockville, MD, USA
| | - Anthony F. Suffredini
- Critical Care Medicine Department, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Jeffrey R. Strich
- Critical Care Medicine Department, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
- United States Public Health Service Commissioned Corps, Rockville, MD, USA
| | - Daniel S. Chertow
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Critical Care Medicine Department, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
- United States Public Health Service Commissioned Corps, Rockville, MD, USA
| | - Richard T. Davey
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Michael C. Sneller
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Department of Microbiology and Immunology and Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Anthony S. Fauci
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (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
| | - Susan Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
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24
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Khatri I, Berkowska MA, van den Akker EB, Teodosio C, Reinders MJT, van Dongen JJM. Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations. Genes Immun 2021; 22:172-186. [PMID: 34120151 PMCID: PMC8196923 DOI: 10.1038/s41435-021-00143-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023]
Abstract
Immunoglobulin (IG) loci harbor inter-individual allelic variants in many different germline IG variable, diversity and joining genes of the IG heavy (IGH), kappa (IGK) and lambda (IGL) loci, which together form the genetic basis of the highly diverse antigen-specific B-cell receptors. These allelic variants can be shared between or be specific to human populations. The current immunogenetics resources gather the germline alleles, however, lack the population specificity of the alleles which poses limitations for disease-association studies related to immune responses in different human populations. Therefore, we systematically identified germline alleles from 26 different human populations around the world, profiled by "1000 Genomes" data. We identified 409 IGHV, 179 IGKV, and 199 IGLV germline alleles supported by at least seven haplotypes. The diversity of germline alleles is the highest in Africans. Remarkably, the variants in the identified novel alleles show strikingly conserved patterns, the same as found in other IG databases, suggesting over-time evolutionary selection processes. We could relate the genetic variants to population-specific immune responses, e.g. IGHV1-69 for flu in Africans. The population matched IG (pmIG) resource will enhance our understanding of the SHM-related B-cell receptor selection processes in (infectious) diseases and vaccination within and between different human populations.
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Affiliation(s)
- Indu Khatri
- Department Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Erik B van den Akker
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Department Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Cristina Teodosio
- Department Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel J T Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
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Gonçalves E, Guillén Y, Lama JR, Sanchez J, Brander C, Paredes R, Combadière B. Host Transcriptome and Microbiota Signatures Prior to Immunization Profile Vaccine Humoral Responsiveness. Front Immunol 2021; 12:657162. [PMID: 34040607 PMCID: PMC8141841 DOI: 10.3389/fimmu.2021.657162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
The identification of new biomarkers is essential to predict responsiveness to vaccines. We investigated the whole-blood transcriptome and microbiome prior to immunization, in order to assess their involvement in induction of humoral responses two months later. We based our analyses on stool and skin microbiota, and blood transcriptome prior to immunization, in a randomized clinical study in which participants were vaccinated with the MVA-HIV clade B vaccine (MVA-B). We found that the levels of neutralizing antibody responses were correlated with abundance of Eubacterium in stool and Prevotella in skin. In addition, genus diversity and bacterial species abundance were also correlated with the expression of genes involved in B cell development prior to immunization and forecast strong responders to MVA-B. To our knowledge, this is the first study integrating host blood gene expression and microbiota that might open an avenue of research in this field and to optimize vaccination strategies and predict responsiveness to vaccines.
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Affiliation(s)
- Elena Gonçalves
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Yolanda Guillén
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Javier R Lama
- Asociacion Civil Impacta Salud y Educacion, Lima, Peru
| | - Jorge Sanchez
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Christian Brander
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain.,Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), Vic, Spain.,Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Roger Paredes
- Infectious Diseases Department, Hospital Universitari Germans Trias, Barcelona, Spain
| | - Behazine Combadière
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
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Sadarangani M, Kollmann T, Bjornson G, Heath P, Clarke E, Marchant A, Levy O, Leuridan E, Ulloa-Gutierrez R, Cutland CL, Kampmann B, Chaithongwongwatthana S, Dinleyici E, van Damme P, Munoz FM. The Fifth International Neonatal and Maternal Immunization Symposium (INMIS 2019): Securing Protection for the Next Generation. mSphere 2021; 6:e00862-20. [PMID: 33504658 PMCID: PMC7885317 DOI: 10.1128/msphere.00862-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Despite significant progress in reaching some milestones of the United Nations Sustainable Development Goals, neonatal and early infant morbidity and mortality remain high, and maternal health remains suboptimal in many countries. Novel and improved preventative strategies with the potential to benefit pregnant women and their infants are needed, with maternal and neonatal immunization representing effective approaches. Experts from immunology, vaccinology, infectious diseases, clinicians, industry, public health, and vaccine-related social sciences convened at the 5th International Neonatal and Maternal Immunization Symposium (INMIS) in Vancouver, Canada, from 15 to 17 September 2019. We critically evaluated the lessons learned from recent clinical studies, presented cutting-edge scientific progress in maternal and neonatal immunology and vaccine development, and discussed maternal and neonatal immunization in the broader context of infectious disease epidemiology and public health. Focusing on practical aspects of research and implementation, we also discussed the safety, awareness, and perception of maternal immunization as an existing strategy to address the need to improve maternal and neonatal health worldwide. The symposium provided a comprehensive scientific and practical primer as well as an update for all those with an interest in maternal and neonatal infection, immunity, and vaccination. The summary presented here provides an update of the current status of progress in maternal and neonatal immunization.
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Affiliation(s)
- Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Division of Infectious Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tobias Kollmann
- Telethon Kids Institute, Perth Children's Hospital, University of Western Perth, Perth, Australia
| | - Gordean Bjornson
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Paul Heath
- St. George's University of London, London, United Kingdom
| | - Ed Clarke
- Vaccines & Immunity Theme, Medical Research Council Unit, The Gambia, London School of Hygiene and Tropical Medicine (MRCG at LSHTM), Banjul, The Gambia
| | - Arnaud Marchant
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT & Harvard, Cambridge, Massachusetts, USA
| | - Elke Leuridan
- Centre for the Evaluation of Vaccination, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Rolando Ulloa-Gutierrez
- Hospital Nacional de Niños Dr. Carlos Sáenz Herrera, Centro de Ciencias Médicas C.C.S.S., San José, Costa Rica
| | - Clare L Cutland
- African Leadership in Vaccinology Expertise (ALIVE), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Beate Kampmann
- Vaccines & Immunity Theme, Medical Research Council Unit, The Gambia, London School of Hygiene and Tropical Medicine (MRCG at LSHTM), Banjul, The Gambia
- The Vaccine Centre, Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Surasith Chaithongwongwatthana
- Division of Infectious Disease in Gynecology and Obstetrics (InDiGO), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ener Dinleyici
- Eskisehir Osmangazi University, Faculty of Medicine, Eskisehir, Turkey
| | - Pierre van Damme
- Centre for the Evaluation of Vaccination, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Flor M Munoz
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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Mo AXY, Pesce J, Augustine AD, Bodmer JL, Breen J, Leitner W, Hall BF. Understanding vaccine-elicited protective immunity against pre-erythrocytic stage malaria in endemic regions. Vaccine 2020; 38:7569-7577. [PMID: 33071001 DOI: 10.1016/j.vaccine.2020.09.071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/26/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022]
Abstract
Recent malaria vaccine trials in endemic areas have yielded disparate results compared to studies conducted in non-endemic areas. A workshop was organized to discuss the differential pre-erythrocytic stage malaria vaccine (Pre-E-Vac) efficacies and underlying protective immunity under various conditions. It was concluded that many factors, including vaccine technology platforms, host genetics or physiologic conditions, and parasite and mosquito vector variations, may all contribute to Pre-E-Vac efficacy. Cross-disciplinary approaches are needed to decipher the multi-dimensional variables that contribute to the observed vaccine hypo-responsiveness. The malaria vaccine community has an opportunity to leverage recent advances in immunology, systems vaccinology, and high dimensionality data science methodologies to generate new clinical datasets with unprecedented levels of functional resolution as well as capitalize on existing datasets for comprehensive and aggregate analyses. These approaches would help to unlock our understanding of Pre-E-Vac immunology and to translate new candidates from the laboratory to the field more predictably.
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Affiliation(s)
- Annie X Y Mo
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA.
| | - John Pesce
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
| | - Alison Deckhut Augustine
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
| | | | - Joseph Breen
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
| | - Wolfgang Leitner
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
| | - B Fenton Hall
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
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Soni D, Van Haren SD, Idoko OT, Evans JT, Diray-Arce J, Dowling DJ, Levy O. Towards Precision Vaccines: Lessons From the Second International Precision Vaccines Conference. Front Immunol 2020; 11:590373. [PMID: 33178222 PMCID: PMC7593811 DOI: 10.3389/fimmu.2020.590373] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/23/2020] [Indexed: 12/16/2022] Open
Abstract
Other than clean drinking water, vaccines have been the most effective public health intervention in human history, yet their full potential is still untapped. To date, vaccine development has been largely limited to empirical approaches focused on infectious diseases and has targeted entire populations, potentially disregarding distinct immunity in vulnerable populations such as infants, elders, and the immunocompromised. Over the past few decades innovations in genetic engineering, adjuvant discovery, formulation science, and systems biology have fueled rapid advances in vaccine research poised to consider demographic factors (e.g., age, sex, genetics, and epigenetics) in vaccine discovery and development. Current efforts are focused on leveraging novel approaches to vaccine discovery and development to optimize vaccinal antigen and, as needed, adjuvant systems to enhance vaccine immunogenicity while maintaining safety. These approaches are ushering in an era of precision vaccinology aimed at tailoring immunization for vulnerable populations with distinct immunity. To foster collaboration among leading vaccinologists, government, policy makers, industry partners, and funders from around the world, the Precision Vaccines Program at Boston Children's Hospital hosted the 2nd International Precision Vaccines Conference (IPVC) at Harvard Medical School on the 17th-18th October 2019. The conference convened experts in vaccinology, including vaccine formulation and adjuvantation, immunology, cell signaling, systems biology, biostatistics, bioinformatics, as well as vaccines for non-infectious indications such as cancer and opioid use disorder. Herein we review highlights from the 2nd IPVC and discuss key concepts in the field of precision vaccines.
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Affiliation(s)
- Dheeraj Soni
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Simon D. Van Haren
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Olubukola T. Idoko
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jay T. Evans
- Center for Translational Medicine, University of Montana, Missoula, MT, United States
| | - Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT & Harvard, Cambridge, MA, United States
| | - David J. Dowling
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT & Harvard, Cambridge, MA, United States
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Rozot V, Nemes E, Geldenhuys H, Musvosvi M, Toefy A, Rantangee F, Makhethe L, Erasmus M, Bilek N, Mabwe S, Finak G, Fulp W, Ginsberg AM, Hokey DA, Shey M, Gurunathan S, DiazGranados C, Bekker LG, Hatherill M, Scriba TJ. Multidimensional analyses reveal modulation of adaptive and innate immune subsets by tuberculosis vaccines. Commun Biol 2020; 3:563. [PMID: 33037320 PMCID: PMC7547090 DOI: 10.1038/s42003-020-01288-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
We characterize the breadth, function and phenotype of innate and adaptive cellular responses in a prevention of Mycobacterium tuberculosis infection trial. Responses are measured by whole blood intracellular cytokine staining at baseline and 70 days after vaccination with H4:IC31 (subunit vaccine containing Ag85B and TB10.4), Bacille Calmette-Guerin (BCG, a live attenuated vaccine) or placebo (n = ~30 per group). H4:IC31 vaccination induces Ag85B and TB10.4-specific CD4 T cells, and an unexpected NKTlike subset, that expresses IFN-γ, TNF and/or IL-2. BCG revaccination increases frequencies of CD4 T cell subsets that either express Th1 cytokines or IL-22, and modestly increases IFNγ-producing NK cells. In vitro BCG re-stimulation also triggers responses by donor-unrestricted T cells, which may contribute to host responses against mycobacteria. BCG, which demonstrated efficacy against sustained Mycobacterium tuberculosis infection, modulates multiple immune cell subsets, in particular conventional Th1 and Th22 cells, which should be investigated in discovery studies of correlates of protection.
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Affiliation(s)
- Virginie Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Hennie Geldenhuys
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Asma Toefy
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Frances Rantangee
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Lebohang Makhethe
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mzwandile Erasmus
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Simbarashe Mabwe
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Greg Finak
- Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA
| | - William Fulp
- Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA
| | | | | | - Muki Shey
- Aeras South Africa Endpoint Assay Laboratory, Cape Town, South Africa
| | | | | | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
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30
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Abstract
Although the development of effective vaccines has saved countless lives from infectious diseases, the basic workings of the human immune system are complex and have required the development of animal models, such as inbred mice, to define mechanisms of immunity. More recently, new strategies and technologies have been developed to directly explore the human immune system with unprecedented precision. We discuss how these approaches are advancing our mechanistic understanding of human immunology and are facilitating the development of vaccines and therapeutics for infection, autoimmune diseases, and cancer.
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Affiliation(s)
- Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA.
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H: Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA 94305, USA
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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31
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Duffy D. Understanding immune variation for improved translational medicine. Curr Opin Immunol 2020; 65:83-88. [PMID: 32745736 DOI: 10.1016/j.coi.2020.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022]
Abstract
The goal of translational medicine is to use an improved understanding of human biology to develop new clinical approaches. Immune responses are highly variable from one person to another, with this variability strongly impacting clinical outcome. Variable immunity can determine differential risks for infection, for development of autoimmunity, and for response to therapeutic interventions. Therefore, a better understanding of the causes of such differences has huge potential to improve patient management through precision medicine strategies. Variability in immunity is determined by intrinsic (e.g. age, sex), extrinsic (e.g. environment, diet), and genetic factors. There is a growing consensus that genetics factors account for 20-40% of immune variability between individuals. The remaining unexplained variability is likely due to direct environmental influences, as well as specific gene-environmental interactions, which are more challenging to quantify and study. However, population based cohort studies with systems immunology approaches are now providing new understanding into these associations.
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Affiliation(s)
- Darragh Duffy
- Translational Immunology Lab, Department of Immunology, Institut Pasteur, Paris, France; INSERM U1223, Paris, France
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32
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Russo G, Reche P, Pennisi M, Pappalardo F. The combination of artificial intelligence and systems biology for intelligent vaccine design. Expert Opin Drug Discov 2020; 15:1267-1281. [PMID: 32662677 DOI: 10.1080/17460441.2020.1791076] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION A new body of evidence depicts the applications of artificial intelligence and systems biology in vaccine design and development. The combination of both approaches shall revolutionize healthcare, accelerating clinical trial processes and reducing the costs and time involved in drug research and development. AREAS COVERED This review explores the basics of artificial intelligence and systems biology approaches in the vaccine development pipeline. The topics include a detailed description of epitope prediction tools for designing epitope-based vaccines and agent-based models for immune system response prediction, along with a focus on their potentiality to facilitate clinical trial phases. EXPERT OPINION Artificial intelligence and systems biology offer the opportunity to avoid the inefficiencies and failures that arise in the classical vaccine development pipeline. One promising solution is the combination of both methodologies in a multiscale perspective through an accurate pipeline. We are entering an 'in silico era' in which scientific partnerships, including a more and more increasing creation of an 'ecosystem' of collaboration and multidisciplinary approach, are relevant for addressing the long and risky road of vaccine discovery and development. In this context, regulatory guidance should be developed to qualify the in silico trials as evidence for intelligent vaccine development.
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Affiliation(s)
- Giulia Russo
- Department of Drug Sciences, University of Catania , Catania, Italy
| | - Pedro Reche
- Department of Immunology, Universidad Complutense De Madrid, Ciudad Universitaria , Madrid, Spain
| | - Marzio Pennisi
- Computer Science Institute, DiSIT, University of Eastern Piedmont , Italy
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Pasetti MF, Ackerman ME, Hoen AG, Alter G, Tsang JS, Marchant A. Maternal determinants of infant immunity: Implications for effective immunization and maternal-child health. Vaccine 2020; 38:4491-4494. [PMID: 32111530 PMCID: PMC9946685 DOI: 10.1016/j.vaccine.2020.01.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 12/09/2019] [Accepted: 01/16/2020] [Indexed: 10/24/2022]
Affiliation(s)
- Marcela F. Pasetti
- Center for Vaccine Development and Global Health, University of Maryland, Baltimore, MD, USA
| | | | - Annie G. Hoen
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA
| | | | - John S. Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Immune System Biology and Center for Human Immunology, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, NIH, Bethesda, MD, USA
| | - Arnaud Marchant
- Institute for Medical Immunology, Université libre de Bruxelles, Charleroi, Belgium.
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34
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Tsang JS, Dobaño C, VanDamme P, Moncunill G, Marchant A, Othman RB, Sadarangani M, Koff WC, Kollmann TR. Improving Vaccine-Induced Immunity: Can Baseline Predict Outcome? Trends Immunol 2020; 41:457-465. [PMID: 32340868 PMCID: PMC7142696 DOI: 10.1016/j.it.2020.04.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 12/21/2022]
Abstract
Immune signatures measured at baseline and immediately prior to vaccination may predict the immune response to vaccination. Such pre-vaccine assessment might allow not only population-based, but also more personalized vaccination strategies (‘precision vaccination’). If baseline immune signatures are predictive, the underlying mechanism they reflect may also determine vaccination outcome. Thus, baseline signatures might contribute to identifying interventional targets to be modulated prior to vaccination in order to improve vaccination responses. This concept has the potential to transform vaccination strategies and usher in a new approach to improve global health. Extensive baseline variability in immune responses (e.g., antibody titers) among individuals in given populations is increasingly being appreciated as a major contributor to vaccine response heterogeneity. The concept of ‘baseline may predict outcome’ has recently been reported for human influenza virus, yellow fever virus, and hepatitis B virus, as well as malaria vaccination. This concept might also apply to other vaccines. The ability to predict who might respond to immunization (and to what extent) might offer avenues for optimization of current vaccination strategies. We posit that this simple concept might be useful and significant for vaccine design: if ‘baseline determines outcome, then altering baseline prior to vaccination could alter outcome’. This approach could potentially lead to tailored (precision) vaccines ensuring that the majority, or all individuals vaccinated, respond by eliciting a protective immune response (i.e., devoid of non-responder individuals). Presumably, this approach might also allow the administration of fewer vaccine doses, potentially arriving at one vaccine dose only.
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Affiliation(s)
- John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID and Center for Human Immunology (CHI), NIH, Bethesda, MD, USA
| | - Carlota Dobaño
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Pierre VanDamme
- Centre for the Evaluation of Vaccination and Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Gemma Moncunill
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Arnaud Marchant
- Institute for Medical Immunology, Université libre de Bruxelles, Charleroi, Belgium
| | - Rym Ben Othman
- Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute and Division of Infectious Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | | | - Tobias R Kollmann
- Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia.
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35
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Lim WW, Leung NHL, Sullivan SG, Tchetgen Tchetgen EJ, Cowling BJ. Distinguishing Causation From Correlation in the Use of Correlates of Protection to Evaluate and Develop Influenza Vaccines. Am J Epidemiol 2020; 189:185-192. [PMID: 31598648 PMCID: PMC7217279 DOI: 10.1093/aje/kwz227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/23/2019] [Accepted: 09/23/2019] [Indexed: 11/13/2022] Open
Abstract
There is increasing attention to the need to identify new immune markers for the evaluation of existing and new influenza vaccines. Immune markers that could predict individual protection against infection and disease, commonly called correlates of protection (CoPs), play an important role in vaccine development and licensing. Here, we discuss the epidemiologic considerations when evaluating immune markers as potential CoPs for influenza vaccines and emphasize the distinction between correlation and causation. While an immune marker that correlates well with protection from infection can be used as a predictor of vaccine efficacy, it should be distinguished from an immune marker that plays a mechanistic role in conferring protection against a clinical endpoint-the latter might be a more reliable predictor of vaccine efficacy and a more appropriate target for rational vaccine design. To clearly distinguish mechanistic and nonmechanistic CoPs, we suggest using the term "correlates of protection" for nonmechanistic CoPs, and ''mediators of protection'' for mechanistic CoPs. Furthermore, because the interactions among and relative importance of correlates or mediators of protection can vary according to age or prior vaccine experience, the effect sizes and thresholds for protective effects for CoPs could also vary in different segments of the population.
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Affiliation(s)
- Wey Wen Lim
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, the University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Nancy H L Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, the University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Sheena G Sullivan
- World Health Organization Collaborating Centre for Reference and Research on Influenza at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Eric J Tchetgen Tchetgen
- Statistics Department, the Wharton School, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Benjamin J Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, the University of Hong Kong, Hong Kong SAR, People’s Republic of China
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36
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Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nat Med 2020; 26:618-629. [PMID: 32094927 PMCID: PMC8392163 DOI: 10.1038/s41591-020-0769-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/14/2020] [Indexed: 01/04/2023]
Abstract
Responses to vaccination and to diseases vary widely across individuals, which may be partly due to baseline immune variations. Identifying such baseline predictors of immune responses and their biological basis are of broad interest given their potential importance for cancer immunotherapy, disease outcomes, vaccination and infection responses. Here we uncover baseline blood transcriptional signatures predictive of antibody responses to both influenza and yellow fever vaccinations in healthy subjects. These same signatures evaluated at clinical quiescence are correlated with disease activity in systemic lupus erythematosus patients with plasmablast-associated flares. CITE-seq profiling of 82 surface proteins and transcriptomes of 53,201 single cells from healthy high and low influenza-vaccination responders revealed that our signatures reflect the extent of activation in a plasmacytoid dendritic cell—Type I IFN—T/B lymphocyte network. Our findings raise the prospect that modulating such immune baseline states may improve vaccine responsiveness and mitigate undesirable autoimmune disease activities.
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37
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Gonçalves E, Combadière B. Prédire la réponse à la vaccination contre la grippe. Med Sci (Paris) 2020; 36:31-37. [DOI: 10.1051/medsci/2019266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
La vaccination est l’un des progrès majeurs de la médecine moderne. Mais afin d’améliorer l’efficacité des vaccins existants et d’en élaborer de nouveaux, nous devons mieux connaître les mécanismes d’action à l’origine de l’immunité protectrice et les stratégies vaccinales permettant d’induire une défense durable. La voie cutanée est une stratégie de vaccination importante, en raison de la richesse qu’elle présente en cellules de l’immunité innée qui ont un rôle clé dans la qualité, l’intensité et la persistance des réponses adaptatives qu’elles induisent. L’intégration des données biologiques obtenues au cours d’un essai clinique de vaccination antigrippale nous donne un aperçu de l’impact de la voie d’immunisation et de la signature innée sur la qualité des réponses immunitaires.
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38
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Idoko OT, Smolen KK, Wariri O, Imam A, Shannon CP, Dibassey T, Diray-Arce J, Darboe A, Strandmark J, Ben-Othman R, Odumade OA, McEnaney K, Amenyogbe N, Pomat WS, van Haren S, Sanchez-Schmitz G, Brinkman RR, Steen H, Hancock REW, Tebbutt SJ, Richmond PC, van den Biggelaar AHJ, Kollmann TR, Levy O, Ozonoff A, Kampmann B. Clinical Protocol for a Longitudinal Cohort Study Employing Systems Biology to Identify Markers of Vaccine Immunogenicity in Newborn Infants in The Gambia and Papua New Guinea. Front Pediatr 2020; 8:197. [PMID: 32426309 PMCID: PMC7205022 DOI: 10.3389/fped.2020.00197] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/01/2020] [Indexed: 01/30/2023] Open
Abstract
Background: Infection contributes to significant morbidity and mortality particularly in the very young and in low- and middle-income countries. While vaccines are a highly cost-effective tool against infectious disease little is known regarding the cellular and molecular pathways by which vaccines induce protection at an early age. Immunity is distinct in early life and greater precision is required in our understanding of mechanisms of early life protection to inform development of new pediatric vaccines. Methods and Analysis: We will apply transcriptomic, proteomic, metabolomic, multiplex cytokine/chemokine, adenosine deaminase, and flow cytometry immune cell phenotyping to delineate early cellular and molecular signatures that correspond to vaccine immunogenicity. This approach will be applied to a neonatal cohort in The Gambia (N ~ 720) receiving at birth: (1) Hepatitis B (HepB) vaccine alone, (2) Bacille Calmette Guerin (BCG) vaccine alone, or (3) HepB and BCG vaccines, (4) HepB and BCG vaccines delayed till day 10 at the latest. Each study participant will have a baseline peripheral blood sample drawn at DOL0 and a second blood sample at DOL1,-3, or-7 as well as late timepoints to assess HepB vaccine immunogenicity. Blood will be fractionated via a "small sample big data" standard operating procedure that enables multiple downstream systems biology assays. We will apply both univariate and multivariate frameworks and multi-OMIC data integration to identify features associated with anti-Hepatitis B (anti-HB) titer, an established correlate of protection. Cord blood sample collection from a subset of participants will enable human in vitro modeling to test mechanistic hypotheses identified in silico regarding vaccine action. Maternal anti-HB titer and the infant microbiome will also be correlated with our findings which will be validated in a smaller cohort in Papua New Guinea (N ~ 80). Ethics and Dissemination: The study has been approved by The Gambia Government/MRCG Joint Ethics Committee and The Boston Children's Hospital Institutional Review Board. Ethics review is ongoing with the Papua New Guinea Medical Research Advisory Committee. All de-identified data will be uploaded to public repositories following submission of study output for publication. Feedback meetings will be organized to disseminate output to the study communities. Clinical Trial Registration: Clinicaltrials.gov Registration Number: NCT03246230.
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Affiliation(s)
- Olubukola T Idoko
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia.,Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,CIH LMU Center for International Health, Medical Center of the University of Munich (LMU), Munich, Germany.,The Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kinga K Smolen
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Oghenebrume Wariri
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Abdulazeez Imam
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | | | - Tida Dibassey
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Alansana Darboe
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Julia Strandmark
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Rym Ben-Othman
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Oludare A Odumade
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,The Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Division of Medicine Critical Care, Harvard Medical School, Boston Children's Hospital, Boston, MA, United States
| | - Kerry McEnaney
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Department of Cardiology, Boston Children's Hospital, Boston, MA, United States
| | - Nelly Amenyogbe
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - William S Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Simon van Haren
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Guzmán Sanchez-Schmitz
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Ryan R Brinkman
- BC Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Hanno Steen
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States.,Department of Pathology, Boston Children's Hospital, Boston, MA, United States
| | - Robert E W Hancock
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Scott J Tebbutt
- PROOF Centre of Excellence, Vancouver, BC, Canada.,Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada.,Division of Respiratory Medicine, Department of Medicine, UBC, Vancouver, BC, Canada
| | - Peter C Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia.,Division of Pediatrics, School of Medicine, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Anita H J van den Biggelaar
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Tobias R Kollmann
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT & Harvard, Cambridge, MA, United States
| | - Al Ozonoff
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia.,The Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
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39
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Immunobiological aspects of vaccines in pregnancy: Maternal perspective. MATERNAL IMMUNIZATION 2020. [PMCID: PMC7149477 DOI: 10.1016/b978-0-12-814582-1.00003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Immunization during pregnancy is an efficient strategy to protect both the mother and the newborn infant against infectious pathogens. Pregnant women have an increased susceptibility to severe infections caused by some pathogens, but the mechanisms involved remain poorly understood. Pregnancy is associated with dynamic changes in maternal immune system that are critical for tolerance of the fetus. These changes could also play an important role in shaping maternal immune components that are transferred to the newborn infant following natural infection or vaccination to prevent infectious diseases in early life. As the momentum for maternal immunization is growing, there is a need to increase our understanding of the immunobiology of maternal immunization in order to better prevent infectious diseases in the pregnant women and the young infant.
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40
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Novel Bead-Based Epitope Assay is a sensitive and reliable tool for profiling epitope-specific antibody repertoire in food allergy. Sci Rep 2019; 9:18425. [PMID: 31804555 PMCID: PMC6895130 DOI: 10.1038/s41598-019-54868-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/09/2019] [Indexed: 12/16/2022] Open
Abstract
Identification of allergenic IgE epitopes is instrumental for the development of novel diagnostic and prognostic methods in food allergy. In this work, we present the quantification and validation of a Bead-Based Epitope Assay (BBEA) that through multiplexing of epitopes and multiple sample processing enables completion of large experiments in a short period of time, using minimal quantities of patients’ blood. Peptides that are uniquely coupled to beads are incubated with serum or plasma samples, and after a secondary fluorophore-labeled antibody is added, the level of fluorescence is quantified with a Luminex reader. The signal is then normalized and converted to epitope-specific antibody binding values. We show that the effect of technical artifacts, i.e. well position or reading order, is minimal; and batch effects - different individual microplate runs - can be easily estimated and eliminated from the data. Epitope-specific antibody binding quantified with BBEA is highly reliable, reproducible and has greater sensitivity of epitope detection compared to peptide microarrays. IgE directed at allergenic epitopes is a sensitive biomarker of food allergy and can be used to predict allergy severity and phenotypes; and quantification of the relationship between epitope-specific IgE and IgG4 can further improve our understanding of the immune mechanisms behind allergic sensitization.
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41
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Mosley YYC, Radder JE, HogenEsch H. Genetic Variation in the Magnitude and Longevity of the IgG Subclass Response to a Diphtheria-Tetanus-Acellular Pertussis (DTaP) Vaccine in Mice. Vaccines (Basel) 2019; 7:E124. [PMID: 31547158 PMCID: PMC6963843 DOI: 10.3390/vaccines7040124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 11/17/2022] Open
Abstract
The type of IgG subclasses induced by vaccination is an important determinant of vaccine efficacy because the IgG subclasses vary in their biological function. The goal of this study was to determine the influence of the genetic background on the production and duration of vaccine-induced IgG subclasses. IgG1, IgG2b, and IgG3 titers against diphtheria toxoid (DT), pertussis toxin (PT), filamentous hemagglutinin (FHA), and pertactin (Prn) were measured in mice from 28 different inbred and wild-derived strains vaccinated with an aluminum hydroxide-adjuvanted DTaP vaccine. The titers and duration of vaccine-specific IgG subclass responses were different among mouse strains, indicating that genetic factors contribute to this variation. Statistical associations were used to identify potential mechanisms that contribute to antibody production and longevity. This analysis showed that the mechanisms guiding the magnitude of antibody production were antigen-dependent for IgG1 but antigen-independent for IgG2b and IgG3. However, the mechanisms driving the longevity of antibody titers were antigen-independent for IgG1, IgG2b, and IgG3. The ratio of IgG1 and IgG3 titers identified Th1 and Th2-prone mouse strains. TLR4-deficient C3H/HeJ mice had an enhanced IgG1 response compared with C3H/HeOuJ mice with intact TLR4. This work demonstrates that the genetic background contributes significantly to the magnitude and longevity of vaccine-induced IgG1, IgG2b, and IgG3 titers in mice.
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Affiliation(s)
- Yung-Yi C Mosley
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907 USA.
| | - Josiah E Radder
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
| | - Harm HogenEsch
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907 USA.
- Purdue Institute of Inflammation, Immunology, and Infectious Diseases, Purdue University, Indiana Purdue University, West Lafayette, IN 47907, USA.
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42
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Erbelding EJ, Post DJ, Stemmy EJ, Roberts PC, Augustine AD, Ferguson S, Paules CI, Graham BS, Fauci AS. A Universal Influenza Vaccine: The Strategic Plan for the National Institute of Allergy and Infectious Diseases. J Infect Dis 2019; 218:347-354. [PMID: 29506129 DOI: 10.1093/infdis/jiy103] [Citation(s) in RCA: 310] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/21/2018] [Indexed: 11/13/2022] Open
Abstract
A priority for the National Institute of Allergy and Infectious Diseases is development of a universal influenza vaccine providing durable protection against multiple influenza strains. NIAID will use this strategic plan as a foundation for future investments in influenza research.
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Affiliation(s)
- Emily J Erbelding
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Division of Microbiology and Infectious Diseases
| | - Diane J Post
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Division of Microbiology and Infectious Diseases
| | - Erik J Stemmy
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Division of Microbiology and Infectious Diseases
| | - Paul C Roberts
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Division of Microbiology and Infectious Diseases
| | - Alison Deckhut Augustine
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Division of Allergy, Immunology, and Transplantation
| | - Stacy Ferguson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Division of Allergy, Immunology, and Transplantation
| | - Catharine I Paules
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Barney S Graham
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Vaccine Research Center
| | - Anthony S Fauci
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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43
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Holbrook AK, Peterson HD, Bianchi SA, Macdonald BW, Bredahl EC, Belshan M, Siedlik JA. CD4 + T cell activation and associated susceptibility to HIV-1 infection in vitro increased following acute resistance exercise in human subjects. Physiol Rep 2019; 7:e14234. [PMID: 31552706 PMCID: PMC6759488 DOI: 10.14814/phy2.14234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/22/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
Early studies in exercise immunology suggested acute bouts of exercise had an immunosuppressive effect in human subjects. However, recent data, show acute bouts of combined aerobic and resistance training increase both lymphocyte activation and proliferation. We quantified resistance exercise-induced changes in the activation state of CD4+ T lymphocytes via surface protein expression and using a medically relevant model of infection (HIV-1). Using a randomized cross-over design, 10 untrained subjects completed a control and exercise session. The control session consisted of 30-min seated rest while the exercise session entailed 3 sets × 10 repetitions of back squat, leg press, and leg extensions at 70% 1-RM with 2-min rest between each set. Venous blood samples were obtained pre/post each session. CD4+ T lymphocytes were isolated from whole blood by negative selection. Expression of activation markers (CD69 & CD25) in both nonstimulated and stimulated (costimulation through CD3+ CD28) cells were assessed by flow cytometry. Resistance exercised-induced effects on intracellular activation was further evaluated via in vitro infection with HIV-1. Nonstimulated CD4+ T lymphocytes obtained postexercise exhibited elevated CD25 expression following 24 h in culture. Enhanced HIV-1 replication was observed in cells obtained postexercise. Our results demonstrate that an acute bout of resistance exercise increases the activation state of CD4+ T lymphocytes and results in a greater susceptibility to HIV-1 infection in vitro. These findings offer further evidence that exercise induces activation of T lymphocytes and provides a foundation for the use of medically relevant pathogens as indirect measures of intracellular activation.
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Affiliation(s)
| | - Hunter D. Peterson
- Department of Exercise Science and Pre‐Health ProfessionsCreighton UniversityOmahaNebraska
| | - Samantha A. Bianchi
- Department of Exercise Science and Pre‐Health ProfessionsCreighton UniversityOmahaNebraska
| | - Brad W. Macdonald
- Department of Exercise Science and Pre‐Health ProfessionsCreighton UniversityOmahaNebraska
| | - Eric C. Bredahl
- Department of Exercise Science and Pre‐Health ProfessionsCreighton UniversityOmahaNebraska
| | - Michael Belshan
- Department of Medical Microbiology and ImmunologyCreighton UniversityOmahaNebraska
| | - Jacob A. Siedlik
- Department of Exercise Science and Pre‐Health ProfessionsCreighton UniversityOmahaNebraska
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44
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Shim BS, Kwon YC, Ricciardi MJ, Stone M, Otsuka Y, Berri F, Kwal JM, Magnani DM, Jackson CB, Richard AS, Norris P, Busch M, Curry CL, Farzan M, Watkins D, Choe H. Zika Virus-Immune Plasmas from Symptomatic and Asymptomatic Individuals Enhance Zika Pathogenesis in Adult and Pregnant Mice. mBio 2019; 10:e00758-19. [PMID: 31266863 PMCID: PMC6606798 DOI: 10.1128/mbio.00758-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/30/2019] [Indexed: 01/02/2023] Open
Abstract
Preexisting immunity against dengue virus or West Nile virus was previously reported to mediate antibody-dependent enhancement (ADE) of Zika virus (ZIKV) infection in a mouse model. We show here that ZIKV-immune plasma samples from both symptomatic and asymptomatic individuals mediated ZIKV ADE of infection in vitro and in mice. In a lethal infection model with a viral inoculum 10 times higher, both ADE and protection were observed, depending on the amount of infused immune plasma. In a vertical-transmission model, ZIKV-immune plasma infused to timed pregnant mice increased fetal demise and decreased the body weight of surviving fetuses. Depletion of IgG from an immune plasma abolished ADE of infection, and the presence of purified IgG alone mediated ADE of infection. Higher viral loads and proinflammatory cytokines were detected in mice treated with ZIKV-immune plasma samples compared to those receiving control plasma. Together, these data show that passive immunization with homotypic ZIKV antibodies, depending on the concentration, could either worsen or limit a subsequent ZIKV infection.IMPORTANCE Antibody-dependent enhancement (ADE) of virus infection is common to many viruses and is problematic when plasma antibody levels decline to subneutralizing concentrations. ADE of infection is especially important among flaviviruses, many of which are the cause of global health problems. Recently, human plasma samples immune to heterologous flaviviruses were shown to promote Zika virus (ZIKV) infection. Here we showed in immunocompromised mouse models that homologous immune plasma samples protect mice from subsequent infection at high antibody concentrations but that they mediate ADE of infection and increase ZIKV pathogenesis in adult mice and fetal demise during pregnancy at low concentrations.
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Affiliation(s)
- Byoung-Shik Shim
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Young-Chan Kwon
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Michael J Ricciardi
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Mars Stone
- Viral Reference Laboratory and Repository Core, Blood Systems Research Institute, San Francisco, California, USA
| | - Yuka Otsuka
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Fatma Berri
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Jaclyn M Kwal
- Department of Obstetrics and Gynecology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Diogo M Magnani
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Cody B Jackson
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Audrey S Richard
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Philip Norris
- Viral Reference Laboratory and Repository Core, Blood Systems Research Institute, San Francisco, California, USA
- Laboratory Medicine and Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Michael Busch
- Viral Reference Laboratory and Repository Core, Blood Systems Research Institute, San Francisco, California, USA
- Laboratory Medicine and Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Christine L Curry
- Department of Obstetrics and Gynecology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - David Watkins
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Hyeryun Choe
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
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45
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Stereotypic Immune System Development in Newborn Children. Cell 2019; 174:1277-1292.e14. [PMID: 30142345 PMCID: PMC6108833 DOI: 10.1016/j.cell.2018.06.045] [Citation(s) in RCA: 415] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/18/2018] [Accepted: 06/22/2018] [Indexed: 02/07/2023]
Abstract
Epidemiological data suggest that early life exposures are key determinants of immune-mediated disease later in life. Young children are also particularly susceptible to infections, warranting more analyses of immune system development early in life. Such analyses mostly have been performed in mouse models or human cord blood samples, but these cannot account for the complex environmental exposures influencing human newborns after birth. Here, we performed longitudinal analyses in 100 newborn children, sampled up to 4 times during their first 3 months of life. From 100 μL of blood, we analyze the development of 58 immune cell populations by mass cytometry and 267 plasma proteins by immunoassays, uncovering drastic changes not predictable from cord blood measurements but following a stereotypic pattern. Preterm and term children differ at birth but converge onto a shared trajectory, seemingly driven by microbial interactions and hampered by early gut bacterial dysbiosis. Cord blood is not representative of postnatal immunity Preterm and term children differ at birth but rapidly converge thereafter Immune system development follows a stereotypic pattern early in life Dynamic parameters imply microbial interactions during early immune development
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46
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Dovrolis N, Filidou E, Kolios G. Systems biology in inflammatory bowel diseases: on the way to precision medicine. Ann Gastroenterol 2019; 32:233-246. [PMID: 31040620 PMCID: PMC6479645 DOI: 10.20524/aog.2019.0373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eirini Filidou
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Correspondence to: Prof. George Kolios, MD PhD, Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Dragana, Alexandroupolis, 68100, Greece, e-mail:
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47
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Dynamic molecular changes during the first week of human life follow a robust developmental trajectory. Nat Commun 2019; 10:1092. [PMID: 30862783 PMCID: PMC6414553 DOI: 10.1038/s41467-019-08794-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 01/24/2019] [Indexed: 02/06/2023] Open
Abstract
Systems biology can unravel complex biology but has not been extensively applied to human newborns, a group highly vulnerable to a wide range of diseases. We optimized methods to extract transcriptomic, proteomic, metabolomic, cytokine/chemokine, and single cell immune phenotyping data from <1 ml of blood, a volume readily obtained from newborns. Indexing to baseline and applying innovative integrative computational methods reveals dramatic changes along a remarkably stable developmental trajectory over the first week of life. This is most evident in changes of interferon and complement pathways, as well as neutrophil-associated signaling. Validated across two independent cohorts of newborns from West Africa and Australasia, a robust and common trajectory emerges, suggesting a purposeful rather than random developmental path. Systems biology and innovative data integration can provide fresh insights into the molecular ontogeny of the first week of life, a dynamic developmental phase that is key for health and disease. The first week of life impacts health for all of life, but the mechanisms are little-understood. Here the authors extract multi-omic data from small volumes of blood to study the dynamic molecular changes during the first week of life, revealing a robust developmental trajectory common to different populations.
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Gonçalves E, Bonduelle O, Soria A, Loulergue P, Rousseau A, Cachanado M, Bonnabau H, Thiebaut R, Tchitchek N, Behillil S, van der Werf S, Vogt A, Simon T, Launay O, Combadière B. Innate gene signature distinguishes humoral versus cytotoxic responses to influenza vaccination. J Clin Invest 2019; 129:1960-1971. [PMID: 30843873 DOI: 10.1172/jci125372] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Systems vaccinology allows cutting-edge analysis of innate biomarkers of vaccine efficacy. We have been exploring novel strategies to shape the adaptive immune response, by targeting innate immune cells through novel immunization routes. METHODS This randomized phase I/II clinical study (n=60 healthy subjects aged 18-45 years old) used transcriptomic analysis to discover early biomarkers of immune response quality after transcutaneous (t.c.), intradermal (i.d.), and intramuscular (i.m.) administration of a trivalent influenza vaccine (TIV season 2012-2013) (1:1:1 ratio). Safety and immunogenicity (hemagglutinin inhibition (HI), microneutralization (MN) antibodies and CD4, CD8 effector T cells) were measured at baseline Day (D)0 and at D21. Blood transcriptome was analyzed at D0 and D1. RESULTS TIV-specific CD8+GranzymeB+(GRZ) T cells appeared in more individuals immunized by the t.c. and i.d. routes, while immunization by the i.d. and i.m. routes prompted high levels of HI antibody titers and MN against A/H1N1 and A/H3N2 influenza viral strains. The early innate gene signature anticipated immunological outcome by discriminating two clusters of individuals with either distinct humoral or CD8 cytotoxic responses. Several pathways explained this dichotomy confirmed by nine genes and serum level of CXCL10 were correlated with either TIV-specific cytotoxic CD8+GRZ+ T-cell or antibody responses. A logistic regression analysis demonstrated that these nine genes and serum levels of CXCL10 (D1/D0) best foreseen TIV-specific CD8+GRZ+ T-cell and antibody responses at D21. CONCLUSION This study provides new insight into the impact of immunization routes and innate signature in the quality of adaptive immune responses.
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Affiliation(s)
- Eléna Gonçalves
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses - Paris (Cimi-Paris), INSERM U1135, Paris, France
| | - Olivia Bonduelle
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses - Paris (Cimi-Paris), INSERM U1135, Paris, France
| | - Angèle Soria
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses - Paris (Cimi-Paris), INSERM U1135, Paris, France.,Service de Dermatologie et Allergologie, Hôpital Tenon, Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France
| | - Pierre Loulergue
- Université Paris Descartes, Sorbonne Paris Cité, Centre d'Investigation Clinique Cochin Pasteur, INSERM CIC 1417, French Clinical Research Infrastructure Network, Innovative Clinical Research Network in Vaccinology, AP-HP, Hôpital Cochin, Paris, France
| | - Alexandra Rousseau
- Department of Clinical Pharmacology and Clinical Research Platform of East of Paris, Assistance Publique-Hôpitaux de Paris, Paris, France. Sorbonne Université, Paris, France
| | - Marine Cachanado
- Department of Clinical Pharmacology and Clinical Research Platform of East of Paris, Assistance Publique-Hôpitaux de Paris, Paris, France. Sorbonne Université, Paris, France
| | - Henri Bonnabau
- INSERM U1219, INRIA SISTM, Université de Bordeaux, Bordeaux France
| | | | - Nicolas Tchitchek
- CEA - Université Paris Sud 11 - INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, Institut de Biologie François Jacob, 92265 Fontenay-aux-Roses, France
| | - Sylvie Behillil
- Institut Pasteur, CNR des Virus des Infections Respiratoires, Département de Virologie and Centre National de Recherche Scientifique UMR CNRS 3569, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
| | - Sylvie van der Werf
- Institut Pasteur, CNR des Virus des Infections Respiratoires, Département de Virologie and Centre National de Recherche Scientifique UMR CNRS 3569, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
| | - Annika Vogt
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses - Paris (Cimi-Paris), INSERM U1135, Paris, France.,Clinical Research Center for Hair and Skin Science, Department of Dermatology and Allergy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tabassome Simon
- Department of Clinical Pharmacology and Clinical Research Platform of East of Paris, Assistance Publique-Hôpitaux de Paris, Paris, France. Sorbonne Université, Paris, France
| | - Odile Launay
- Université Paris Descartes, Sorbonne Paris Cité, Centre d'Investigation Clinique Cochin Pasteur, INSERM CIC 1417, French Clinical Research Infrastructure Network, Innovative Clinical Research Network in Vaccinology, AP-HP, Hôpital Cochin, Paris, France
| | - Behazine Combadière
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses - Paris (Cimi-Paris), INSERM U1135, Paris, France
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A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring. Nat Med 2019; 25:487-495. [PMID: 30842675 DOI: 10.1038/s41591-019-0381-y] [Citation(s) in RCA: 244] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 01/07/2019] [Indexed: 01/08/2023]
Abstract
Immune responses generally decline with age. However, the dynamics of this process at the individual level have not been characterized, hindering quantification of an individual's immune age. Here, we use multiple 'omics' technologies to capture population- and individual-level changes in the human immune system of 135 healthy adult individuals of different ages sampled longitudinally over a nine-year period. We observed high inter-individual variability in the rates of change of cellular frequencies that was dictated by their baseline values, allowing identification of steady-state levels toward which a cell subset converged and the ordered convergence of multiple cell subsets toward an older adult homeostasis. These data form a high-dimensional trajectory of immune aging (IMM-AGE) that describes a person's immune status better than chronological age. We show that the IMM-AGE score predicted all-cause mortality beyond well-established risk factors in the Framingham Heart Study, establishing its potential use in clinics for identification of patients at risk.
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Narang V, Lu Y, Tan C, Camous XFN, Nyunt SZ, Carre C, Mok EWH, Wong G, Maurer-Stroh S, Abel B, Burdin N, Poidinger M, Tambyah PA, Bosco N, Visan L, Ng TP, Larbi A. Influenza Vaccine-Induced Antibody Responses Are Not Impaired by Frailty in the Community-Dwelling Elderly With Natural Influenza Exposure. Front Immunol 2018; 9:2465. [PMID: 30405641 PMCID: PMC6207627 DOI: 10.3389/fimmu.2018.02465] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022] Open
Abstract
Background: Elderly adults over 65 years of age are recommended to receive seasonal influenza vaccination as they are at a higher risk of infection and its complications than the younger community. The elderly are often stratified according to frailty status where frail individuals are more susceptible to adverse health outcomes than their non-frail counterparts, however, it is not known whether immunity induced by influenza vaccination is impaired in the frail elderly. Study Design: Two hundred and five elderly subjects of Chinese ethnicity in Singapore (mean age 73.3 ± 5.3 years, 128 females and 77 males) were administered the recommended trivalent inactivated 2013–14 seasonal influenza vaccine (Vaxigrip™) containing A/H1N1, A/H3N2, and B strains. The elderly subjects were stratified into three groups according to Fried's frailty criteria (59 frail, 85 pre-frail, 61 robust) and were also ranked by Rockwood's frailty index (RFI). Statistical associations were evaluated between frailty status and pre- and post-vaccination antibody titres in sera measured by Hemagglutination inhibition (HAI) and microneutralization (MN) assays. Immunological responses across frailty strata were also studied in terms of leukocyte cellular distribution, cytokine levels and gene expression. Results: Post-vaccination, 83.4% of the subjects seroconverted for A/H1N1, 80.5% for A/H3N2, and 81% for the B strain. The seroconversion rates were comparable across frailty groups (A/H1N1, ANOVA, p = 0.7910; A/H3N2, ANOVA, p = 0.8356, B, ANOVA, p = 0.9741). Geometric mean titres of HAI and MN as well as seroprotection rates were also similar in all three frailty groups and uncorrelated with RFI (Spearman, r = 0.023, p = 0.738). No statistically significant differences were observed between the frailty groups in vaccine-induced modulation of leukocyte populations, cytokine responses, and gene expression profiles of peripheral blood mononuclear cells (PBMCs). Whereas, post- and pre-vaccination HAI titres were positively correlated after adjusting for age and gender (A/H1N1, R2 = 0.216, p = 9.1e−11; A/H3N2, R2 = 0.166, p = 3.4e−8; B, R2 = 0.104, p = 3.1e−5). With most subjects lacking previous history of influenza vaccination, the pre-vaccination titres were likely due to natural exposure and seen to match the pattern of influenza subtype prevalence in the time period of vaccination. Conclusion: The majority of the elderly subjects seroconverted for seasonal influenza upon vaccination, and importantly, influenza vaccination-induced humoral immune responses and seroprotection were similar across the frailty strata, indicating that frail individuals may also benefit from influenza vaccination. Pre-existing antibodies due to natural exposure appeared to positively influence vaccine-induced antibody responses.
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Affiliation(s)
- Vipin Narang
- Singapore Immunology Network, Singapore, Singapore
| | - Yanxia Lu
- Singapore Immunology Network, Singapore, Singapore
| | - Crystal Tan
- Singapore Immunology Network, Singapore, Singapore
| | | | - Shwe Zin Nyunt
- Department of Psychological Medicine, National University Hospital, Singapore, Singapore
| | | | | | - Glenn Wong
- Singapore Immunology Network, Singapore, Singapore
| | | | - Brian Abel
- Singapore Immunology Network, Singapore, Singapore
| | | | | | | | - Nabil Bosco
- Nestlé Research Singapore Hub, Singapore, Singapore
| | | | - Tze Pin Ng
- Department of Psychological Medicine, National University Hospital, Singapore, Singapore
| | - Anis Larbi
- Singapore Immunology Network, Singapore, Singapore
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