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Papadatou I, Geropeppa M, Piperi C, Spoulou V, Adamopoulos C, Papavassiliou AG. Deciphering Immune Responses to Immunization via Transcriptional Analysis: A Narrative Review of the Current Evidence towards Personalized Vaccination Strategies. Int J Mol Sci 2024; 25:7095. [PMID: 39000206 PMCID: PMC11240890 DOI: 10.3390/ijms25137095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
The development of vaccines has drastically reduced the mortality and morbidity of several diseases. Despite the great success of vaccines, the immunological processes involved in protective immunity are not fully understood and several issues remain to be elucidated. Recently, the advent of high-throughput technologies has enabled a more in-depth investigation of the immune system as a whole and the characterization of the interactions of numerous components of immunity. In the field of vaccinology, these tools allow for the exploration of the molecular mechanisms by which vaccines can induce protective immune responses. In this review, we aim to describe current data on transcriptional responses to vaccination, focusing on similarities and differences of vaccine-induced transcriptional responses among vaccines mostly in healthy adults, but also in high-risk populations, such as the elderly and children. Moreover, the identification of potential predictive biomarkers of vaccine immunogenicity, the effect of age on transcriptional response and future perspectives for the utilization of transcriptomics in the field of vaccinology will be discussed.
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Affiliation(s)
- Ioanna Papadatou
- Immunobiology and Vaccinology Research Laboratory, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (I.P.); (M.G.); (V.S.)
- First Department of Pediatrics, “Aghia Sophia” Children’s Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Geropeppa
- Immunobiology and Vaccinology Research Laboratory, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (I.P.); (M.G.); (V.S.)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.P.); (A.G.P.)
| | - Vana Spoulou
- Immunobiology and Vaccinology Research Laboratory, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (I.P.); (M.G.); (V.S.)
- First Department of Pediatrics, “Aghia Sophia” Children’s Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christos Adamopoulos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.P.); (A.G.P.)
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Athanasios G. Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.P.); (A.G.P.)
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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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3
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Haralambieva IH, Chen J, Quach HQ, Ratishvili T, Warner ND, Ovsyannikova IG, Poland GA, Kennedy RB. Early B cell transcriptomic markers of measles-specific humoral immunity following a 3 rd dose of MMR vaccine. Front Immunol 2024; 15:1358477. [PMID: 38633249 PMCID: PMC11021587 DOI: 10.3389/fimmu.2024.1358477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
B cell transcriptomic signatures hold promise for the early prediction of vaccine-induced humoral immunity and vaccine protective efficacy. We performed a longitudinal study in 232 healthy adult participants before/after a 3rd dose of MMR (MMR3) vaccine. We assessed baseline and early transcriptional patterns in purified B cells and their association with measles-specific humoral immunity after MMR vaccination using two analytical methods ("per gene" linear models and joint analysis). Our study identified distinct early transcriptional signatures/genes following MMR3 that were associated with measles-specific neutralizing antibody titer and/or binding antibody titer. The most significant genes included: the interleukin 20 receptor subunit beta/IL20RB gene (a subunit receptor for IL-24, a cytokine involved in the germinal center B cell maturation/response); the phorbol-12-myristate-13-acetate-induced protein 1/PMAIP1, the brain expressed X-linked 2/BEX2 gene and the B cell Fas apoptotic inhibitory molecule/FAIM, involved in the selection of high-affinity B cell clones and apoptosis/regulation of apoptosis; as well as IL16 (encoding the B lymphocyte-derived IL-16 ligand of CD4), involved in the crosstalk between B cells, dendritic cells and helper T cells. Significantly enriched pathways included B cell signaling, apoptosis/regulation of apoptosis, metabolic pathways, cell cycle-related pathways, and pathways associated with viral infections, among others. In conclusion, our study identified genes/pathways linked to antigen-induced B cell proliferation, differentiation, apoptosis, and clonal selection, that are associated with, and impact measles virus-specific humoral immunity after MMR vaccination.
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Affiliation(s)
- Iana H. Haralambieva
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Jun Chen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Huy Quang Quach
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Tamar Ratishvili
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Nathaniel D. Warner
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
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4
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Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum JA, Overton JA, Guzman-Orozco H, Nili S, Orfield S, Gygi JP, da Silva Antunes R, Sette A, Grant B, Olsen LR, Konstorum A, Guan L, Ay F, Kleinstein SH, Peters B. A multi-omics systems vaccinology resource to develop and test computational models of immunity. CELL REPORTS METHODS 2024; 4:100731. [PMID: 38490204 PMCID: PMC10985234 DOI: 10.1016/j.crmeth.2024.100731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/04/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Systems vaccinology studies have identified factors affecting individual vaccine responses, but comparing these findings is challenging due to varying study designs. To address this lack of reproducibility, we established a community resource for comparing Bordetella pertussis booster responses and to host annual contests for predicting patients' vaccination outcomes. We report here on our experiences with the "dry-run" prediction contest. We found that, among 20+ models adopted from the literature, the most successful model predicting vaccination outcome was based on age alone. This confirms our concerns about the reproducibility of conclusions between different vaccinology studies. Further, we found that, for newly trained models, handling of baseline information on the target variables was crucial. Overall, multiple co-inertia analysis gave the best results of the tested modeling approaches. Our goal is to engage community in these prediction challenges by making data and models available and opening a public contest in August 2024.
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Affiliation(s)
- Pramod Shinde
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ferran Soldevila
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Joaquin Reyna
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA
| | - Minori Aoki
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mikkel Rasmussen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lisa Willemsen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mari Kojima
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Brendan Ha
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jason A Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - James A Overton
- Knocean Inc., 107 Quebec Avenue, Toronto, Ontario M6P 2T3, Canada
| | - Hector Guzman-Orozco
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Somayeh Nili
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Shelby Orfield
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jeremy P Gygi
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Barry Grant
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lars Rønn Olsen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Konstorum
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Leying Guan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Ferhat Ay
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Steven H Kleinstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, San Diego, CA, USA.
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5
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Cevirgel A, Shetty SA, Vos M, Nanlohy NM, Beckers L, Bijvank E, Rots N, van Beek J, Buisman A, van Baarle D. Pre-vaccination immunotypes reveal weak and robust antibody responders to influenza vaccination. Aging Cell 2024; 23:e14048. [PMID: 38146131 PMCID: PMC10861208 DOI: 10.1111/acel.14048] [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: 08/24/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 12/27/2023] Open
Abstract
Effective vaccine-induced immune responses are particularly essential in older adults who face an increased risk of immunosenescence. However, the complexity and variability of the human immune system make predicting vaccine responsiveness challenging. To address this knowledge gap, our study aimed to characterize immune profiles that are predictive of vaccine responsiveness using "immunotypes" as an innovative approach. We analyzed an extensive set of innate and adaptive immune cell subsets in the whole blood of 307 individuals (aged 25-92) pre- and post-influenza vaccination which we associated with day 28 hemagglutination inhibition (HI) antibody titers. Building on our previous work that stratified individuals into nine immunotypes based on immune cell subsets, we identified two pre-vaccination immunotypes associated with weak and one showing robust day 28 antibody response. Notably, the weak responders demonstrated HLA-DR+ T-cell signatures, while the robust responders displayed a high naïve-to-memory T-cell ratio and percentage of nonclassical monocytes. These specific signatures deepen our understanding of the relationship between the baseline of the immune system and its functional potential. This approach could enhance our ability to identify individuals at risk of immunosenescence. Our findings highlight the potential of pre-vaccination immunotypes as an innovative tool for informing personalized vaccination strategies and improving health outcomes, particularly for aging populations.
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Affiliation(s)
- Alper Cevirgel
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology research groupUniversity Medical Center GroningenGroningenThe Netherlands
| | - Sudarshan A. Shetty
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology research groupUniversity Medical Center GroningenGroningenThe Netherlands
| | - Martijn Vos
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Nening M. Nanlohy
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Lisa Beckers
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Elske Bijvank
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Nynke Rots
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Josine van Beek
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Anne‐Marie Buisman
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology research groupUniversity Medical Center GroningenGroningenThe Netherlands
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6
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Connors J, Cusimano G, Mege N, Woloszczuk K, Konopka E, Bell M, Joyner D, Marcy J, Tardif V, Kutzler MA, Muir R, Haddad EK. Using the power of innate immunoprofiling to understand vaccine design, infection, and immunity. Hum Vaccin Immunother 2023; 19:2267295. [PMID: 37885158 PMCID: PMC10760375 DOI: 10.1080/21645515.2023.2267295] [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: 07/13/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
In the field of immunology, a systems biology approach is crucial to understanding the immune response to infection and vaccination considering the complex interplay between genetic, epigenetic, and environmental factors. Significant progress has been made in understanding the innate immune response, including cell players and critical signaling pathways, but many questions remain unanswered, including how the innate immune response dictates host/pathogen responses and responses to vaccines. To complicate things further, it is becoming increasingly clear that the innate immune response is not a linear pathway but is formed from complex networks and interactions. To further our understanding of the crosstalk and complexities, systems-level analyses and expanded experimental technologies are now needed. In this review, we discuss the most recent immunoprofiling techniques and discuss systems approaches to studying the global innate immune landscape which will inform on the development of personalized medicine and innovative vaccine strategies.
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Affiliation(s)
- Jennifer Connors
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Gina Cusimano
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Nathan Mege
- Tower Health, Reading Hospital, West Reading, PA, USA
| | - Kyra Woloszczuk
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Emily Konopka
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Matthew Bell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - David Joyner
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Molecular and Cellular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jennifer Marcy
- Department of Molecular and Cellular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Virginie Tardif
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Michele A. Kutzler
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Roshell Muir
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Family, Community, and Preventative Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Elias K. Haddad
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
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7
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Kazmin D, Clutterbuck EA, Napolitani G, Wilkins AL, Tarlton A, Thompson AJ, Montomoli E, Lapini G, Bihari S, White R, Jones C, Snape MD, Galal U, Yu LM, Rappuoli R, Del Giudice G, Pollard AJ, Pulendran B. Memory-like innate response to booster vaccination with MF-59 adjuvanted influenza vaccine in children. NPJ Vaccines 2023; 8:100. [PMID: 37443176 DOI: 10.1038/s41541-023-00702-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The pediatric population receives the majority of vaccines globally, yet there is a paucity of studies on the transcriptional response induced by immunization in this special population. In this study, we performed a systems-level analysis of immune responses to the trivalent inactivated influenza vaccine adjuvanted with MF-59 in children (15-24 months old) and in young, healthy adults. We analyzed transcriptional responses elicited by vaccination in peripheral blood, as well as cellular and antibody responses following primary and booster vaccinations. Our analysis revealed that primary vaccination induced a persistent transcriptional signature of innate immunity; booster vaccination induced a transcriptional signature of an enhanced memory-like innate response, which was consistent with enhanced activation of myeloid cells assessed by flow cytometry. Furthermore, we identified a transcriptional signature of type 1 interferon response post-booster vaccination and at baseline that was correlated with the local reactogenicity to vaccination and defined an early signature that correlated with the hemagglutinin antibody titers. These results highlight an adaptive behavior of the innate immune system in evoking a memory-like response to secondary vaccination and define molecular correlates of reactogenicity and immunogenicity in infants.
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Affiliation(s)
- Dmitri Kazmin
- Institute for Immunology, Transplantation and Infection, Stanford University, Stanford, CA, USA.
| | - Elizabeth A Clutterbuck
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Giorgio Napolitani
- Medical Research Council (MRC), Human Immunology Unit, University of Oxford, Oxford, UK
| | - Amanda L Wilkins
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
- The Royal Children's Hospital Melbourne, Parkville, VIC, Australia
| | - Andrea Tarlton
- Medical Research Council (MRC), Human Immunology Unit, University of Oxford, Oxford, UK
| | - Amber J Thompson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Emmanuele Montomoli
- VisMederi Srl, Via Fiorentina, Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | | | - Smiti Bihari
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Rachel White
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Claire Jones
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Ushma Galal
- Nuffield Department of Primary Care Health Sciences, Clinical Trials Unit, University of Oxford, Oxford, UK
| | - Ly-Mee Yu
- Nuffield Department of Primary Care Health Sciences, Clinical Trials Unit, University of Oxford, Oxford, UK
| | - Rino Rappuoli
- GlaxoSmithKline, Siena, Italy
- Fondazione Biotecnopolo, Siena, Italy
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Bali Pulendran
- Institute for Immunology, Transplantation and Infection, Stanford University, Stanford, CA, USA.
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Pathology, and Microbiology & Immunology, Stanford University, Stanford, CA, USA.
- Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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8
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Abd Alhadi M, Friedman LM, Karlsson EA, Cohen-Lavi L, Burkovitz A, Schultz-Cherry S, Noah TL, Weir SS, Shulman LM, Beck MA, Hertz T. Obesity Is Associated with an Impaired Baseline Repertoire of Anti-Influenza Virus Antibodies. Microbiol Spectr 2023; 11:e0001023. [PMID: 37098954 PMCID: PMC10269616 DOI: 10.1128/spectrum.00010-23] [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: 01/02/2023] [Accepted: 03/27/2023] [Indexed: 04/27/2023] Open
Abstract
Obesity is a risk factor for severe disease and mortality for both influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. While previous studies show that individuals with obesity generate antibody responses following influenza vaccination, infection rates within the obese group were twice as high as those in the healthy-weight group. The repertoire of antibodies raised against influenza viruses following previous vaccinations and/or natural exposures is referred to here as baseline immune history (BIH). To investigate the hypothesis that obesity impacts immune memory to infections and vaccines, we profiled the BIH of obese and healthy-weight adults vaccinated with the 2010-2011 seasonal influenza vaccine in response to conformational and linear antigens. Despite the extensive heterogeneity of the BIH profiles in both groups, there were striking differences between obese and healthy subjects, especially with regard to A/H1N1 strains and the 2009 pandemic virus (Cal09). Individuals with obesity had lower IgG and IgA magnitude and breadth for a panel of A/H1N1 whole viruses and hemagglutinin proteins from 1933 to 2009 but increased IgG magnitude and breadth for linear peptides from the Cal09 H1 and N1 proteins. Age was also associated with A/H1N1 BIH, with young individuals with obesity being more likely to have reduced A/H1N1 BIH. We found that individuals with low IgG BIH had significantly lower neutralizing antibody titers than individuals with high IgG BIH. Taken together, our findings suggest that increased susceptibility of obese participants to influenza infection may be mediated in part by obesity-associated differences in the memory B-cell repertoire, which cannot be ameliorated by current seasonal vaccination regimens. Overall, these data have vital implications for the next generation of influenza virus and SARS-CoV-2 vaccines. IMPORTANCE Obesity is associated with increased morbidity and mortality from influenza and SARS-CoV-2 infection. While vaccination is the most effective strategy for preventing influenza virus infection, our previous studies showed that influenza vaccines fail to provide optimal protection in obese individuals despite reaching canonical correlates of protection. Here, we show that obesity may impair immune history in humans and cannot be overcome by seasonal vaccination, especially in younger individuals with decreased lifetime exposure to infections and seasonal vaccines. Low baseline immune history is associated with decreased protective antibody responses. Obesity potentially handicaps overall responses to vaccination, biasing it toward responses to linear epitopes, which may reduce protective capacity. Taken together, our data suggest that young obese individuals are at an increased risk of reduced protection by vaccination, likely due to altered immune history biased toward nonprotective antibody responses. Given the worldwide obesity epidemic coupled with seasonal respiratory virus infections and the inevitable next pandemic, it is imperative that we understand and improve vaccine efficacy in this high-risk population. The design, development, and usage of vaccines for and in obese individuals may need critical evaluation, and immune history should be considered an alternate correlate of protection in future vaccine clinical trials.
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Affiliation(s)
- Marwa Abd Alhadi
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lilach M. Friedman
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Erik A. Karlsson
- Virology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Liel Cohen-Lavi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anat Burkovitz
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Terry L. Noah
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samuel S. Weir
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lester M. Shulman
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Melinda A. Beck
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Tomer Hertz
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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9
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Davis MM. Systems Immunology: Origins. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:845-847. [PMID: 36947821 PMCID: PMC10325628 DOI: 10.4049/jimmunol.2200631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Affiliation(s)
- Mark M Davis
- Department of Microbiology and Immunology Stanford Institute for Immunity, Transplantation and Infection
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10
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Currenti J, Simmons J, Oakes J, Gaudieri S, Warren CM, Gangula R, Alves E, Ram R, Leary S, Armitage JD, Smith RM, Chopra A, Halasa NB, Pilkinton MA, Kalams SA. Tracking of activated cTfh cells following sequential influenza vaccinations reveals transcriptional profile of clonotypes driving a vaccine-induced immune response. Front Immunol 2023; 14:1133781. [PMID: 37063867 PMCID: PMC10095155 DOI: 10.3389/fimmu.2023.1133781] [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: 12/29/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Introduction A vaccine against influenza is available seasonally but is not 100% effective. A predictor of successful seroconversion in adults is an increase in activated circulating T follicular helper (cTfh) cells after vaccination. However, the impact of repeated annual vaccinations on long-term protection and seasonal vaccine efficacy remains unclear. Methods In this study, we examined the T cell receptor (TCR) repertoire and transcriptional profile of vaccine-induced expanded cTfh cells in individuals who received sequential seasonal influenza vaccines. We measured the magnitude of cTfh and plasmablast cell activation from day 0 (d0) to d7 post-vaccination as an indicator of a vaccine response. To assess TCR diversity and T cell expansion we sorted activated and resting cTfh cells at d0 and d7 post-vaccination and performed TCR sequencing. We also single cell sorted activated and resting cTfh cells for TCR analysis and transcriptome sequencing. Results and discussion The percent of activated cTfh cells significantly increased from d0 to d7 in each of the 2016-17 (p < 0.0001) and 2017-18 (p = 0.015) vaccine seasons with the magnitude of cTfh activation increase positively correlated with the frequency of circulating plasmablast cells in the 2016-17 (p = 0.0001) and 2017-18 (p = 0.003) seasons. At d7 post-vaccination, higher magnitudes of cTfh activation were associated with increased clonality of cTfh TCR repertoire. The TCRs from vaccine-expanded clonotypes were identified and tracked longitudinally with several TCRs found to be present in both years. The transcriptomic profile of these expanded cTfh cells at the single cell level demonstrated overrepresentation of transcripts of genes involved in the type-I interferon pathway, pathways involved in gene expression, and antigen presentation and recognition. These results identify the expansion and transcriptomic profile of vaccine-induced cTfh cells important for B cell help.
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Affiliation(s)
- Jennifer Currenti
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Joshua Simmons
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jared Oakes
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Christian M. Warren
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rama Gangula
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Eric Alves
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Jesse D. Armitage
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Rita M. Smith
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Natasha B. Halasa
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mark A. Pilkinton
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Spyros A. Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
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11
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Roberts NJ. The Enigma of Lymphocyte Apoptosis in the Response to Influenza Virus Infection. Viruses 2023; 15:v15030759. [PMID: 36992468 PMCID: PMC10052818 DOI: 10.3390/v15030759] [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: 02/05/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
In the pathogenesis of influenza virus infection, lymphocyte apoptosis as a part of the infection and/or the immune response to the virus can be somewhat puzzling. The percentage of human T lymphocytes within the peripheral blood mononuclear cell population that becomes apoptotic greatly exceeds the percentage that are infected after exposure to the virus, consistent with substantial apoptosis of bystander T lymphocytes. Studies reveal an important role of viral neuraminidase expression by co-cultured monocyte/macrophages in induction of apoptosis, including that of uninfected bystander lymphocytes. Despite these observations, it is a reasonable perspective to recognize that the development of lymphocyte apoptosis during the response to infection does not preclude a successful immune response and recovery of the infected host in the great majority of cases. Further investigation is clearly warranted to understand its role in the pathogenesis of influenza virus infection for human subjects.
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Affiliation(s)
- Norbert J. Roberts
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA;
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Gaveston, TX 77555, USA
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12
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Feng A, Yang EY, Moore AR, Dhingra S, Chang SE, Yin X, Pi R, Mack EK, Völkel S, Geßner R, Gündisch M, Neubauer A, Renz H, Tsiodras S, Fragkou PC, Asuni AA, Levitt JE, Wilson JG, Leong M, Lumb JH, Mao R, Pinedo K, Roque J, Richards CM, Stabile M, Swaminathan G, Salagianni ML, Triantafyllia V, Bertrams W, Blish CA, Carette JE, Frankovich J, Meffre E, Nadeau KC, Singh U, Wang TT, Luning Prak ET, Herold S, Andreakos E, Schmeck B, Skevaki C, Rogers AJ, Utz PJ. Autoantibodies are highly prevalent in non-SARS-CoV-2 respiratory infections and critical illness. JCI Insight 2023; 8:e163150. [PMID: 36752204 PMCID: PMC9977421 DOI: 10.1172/jci.insight.163150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/14/2022] [Indexed: 02/09/2023] Open
Abstract
The widespread presence of autoantibodies in acute infection with SARS-CoV-2 is increasingly recognized, but the prevalence of autoantibodies in non-SARS-CoV-2 infections and critical illness has not yet been reported. We profiled IgG autoantibodies in 267 patients from 5 independent cohorts with non-SARS-CoV-2 viral, bacterial, and noninfectious critical illness. Serum samples were screened using Luminex arrays that included 58 cytokines and 55 autoantigens, many of which are associated with connective tissue diseases (CTDs). Samples positive for anti-cytokine antibodies were tested for receptor blocking activity using cell-based functional assays. Anti-cytokine antibodies were identified in > 50% of patients across all 5 acutely ill cohorts. In critically ill patients, anti-cytokine antibodies were far more common in infected versus uninfected patients. In cell-based functional assays, 11 of 39 samples positive for select anti-cytokine antibodies displayed receptor blocking activity against surface receptors for Type I IFN, GM-CSF, and IL-6. Autoantibodies against CTD-associated autoantigens were also commonly observed, including newly detected antibodies that emerged in longitudinal samples. These findings demonstrate that anti-cytokine and autoantibodies are common across different viral and nonviral infections and range in severity of illness.
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Affiliation(s)
- Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Emily Y. Yang
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Andrew Reese Moore
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Shaurya Dhingra
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Sarah Esther Chang
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Xihui Yin
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Ruoxi Pi
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Elisabeth K.M. Mack
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Sara Völkel
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Reinhard Geßner
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Margrit Gündisch
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Andreas Neubauer
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - Paraskevi C. Fragkou
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Respiratory Viruses (ESGREV), Basel, Switzerland
| | - Adijat A. Asuni
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Joseph E. Levitt
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | | | - Michelle Leong
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer H. Lumb
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Rong Mao
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Kassandra Pinedo
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Jonasel Roque
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Christopher M. Richards
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Mikayla Stabile
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Gayathri Swaminathan
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Maria L. Salagianni
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Vasiliki Triantafyllia
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Wilhelm Bertrams
- Institute for Lung Research, UGMLC, Philipps University Marburg, Marburg, Germany
| | - Catherine A. Blish
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jan E. Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer Frankovich
- Department of Pediatrics, Division of Allergy, Immunology, Rheumatology, Stanford University School of Medicine, Stanford, California, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
| | - Kari Christine Nadeau
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
| | - Upinder Singh
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Taia T. Wang
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine and
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susanne Herold
- Department of Internal Medicine V, Infectious Diseases and Infection Control, UKGM, Justus Liebig University, and Institute for Lung Health (ILH), Giessen, Germany
- DZL and UGMLC, Giessen, Germany
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Bernd Schmeck
- Institute for Lung Research, UGMLC, Philipps University Marburg, Marburg, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Marburg, Germany
- DZL, German Center for Infection Research (DZIF), Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Angela J. Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Paul J. Utz
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
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13
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Wimmers F, Burrell AR, Feng Y, Zheng H, Arunachalam PS, Hu M, Spranger S, Nyhoff L, Joshi D, Trisal M, Awasthi M, Bellusci L, Ashraf U, Kowli S, Konvinse KC, Yang E, Blanco M, Pellegrini K, Tharp G, Hagan T, Chinthrajah RS, Grifoni A, Sette A, Nadeau KC, Haslam DB, Bosinger SE, Wrammert J, Maecker HT, Utz PJ, Wang TT, Khurana S, Khatri P, Staat MA, Pulendran B. Systems biological assessment of the temporal dynamics of immunity to a viral infection in the first weeks and months of life. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.28.23285133. [PMID: 36778389 PMCID: PMC9915811 DOI: 10.1101/2023.01.28.23285133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The dynamics of innate and adaptive immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to SARS-CoV-2 infection in infants and young children in the first weeks and months of life by analyzing blood samples collected before, during, and after infection with Omicron and Non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, were stably maintained for >300 days. Antigen-specific memory B cell (MCB) responses were durable for 150 days but waned thereafter. Somatic hypermutation of V-genes in MCB accumulated progressively over 9 months. The innate response was characterized by upregulation of activation markers on blood innate cells, and a plasma cytokine profile distinct from that seen in adults, with no inflammatory cytokines, but an early and transient accumulation of chemokines (CXCL10, IL8, IL-18R1, CSF-1, CX3CL1), and type I IFN. The latter was strongly correlated with viral load, and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell transcriptomics. Consistent with this, single-cell ATAC-seq revealed enhanced accessibility of chromatic loci targeted by interferon regulatory factors (IRFs) and reduced accessibility of AP-1 targeted loci, as well as traces of epigenetic imprinting in monocytes, during convalescence. Together, these data provide the first snapshot of immunity to infection during the initial weeks and months of life.
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Affiliation(s)
- Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tuebingen, Tuebingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functional Instructed Tumor Therapy’ (iFIT), University of Tuebingen, Tuebingen, Germany
- German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Allison R. Burrell
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Environmental and Public Health Sciences, Division of Epidemiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Hong Zheng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Prabhu S. Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Sara Spranger
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Lindsay Nyhoff
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine
| | - Devyani Joshi
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Mayanka Awasthi
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Usama Ashraf
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Katherine C. Konvinse
- Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Emily Yang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Blanco
- Stanford Genomics Service Center, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Gregory Tharp
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Thomas Hagan
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - R. Sharon Chinthrajah
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kari C. Nadeau
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - David B. Haslam
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Steven E. Bosinger
- Yerkes National Primate Research Center, Atlanta, GA, USA
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine
| | - Holden T. Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul J. Utz
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taia T. Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Mary A. Staat
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
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14
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Fourati S, Tomalin LE, Mulè MP, Chawla DG, Gerritsen B, Rychkov D, Henrich E, Miller HER, Hagan T, Diray-Arce J, Dunn P, Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Pulendran B, Kleinstein SH, Sékaly RP. Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination. Nat Immunol 2022; 23:1777-1787. [PMID: 36316476 PMCID: PMC9747610 DOI: 10.1038/s41590-022-01329-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022]
Abstract
Several studies have shown that the pre-vaccination immune state is associated with the antibody response to vaccination. However, the generalizability and mechanisms that underlie this association remain poorly defined. Here, we sought to identify a common pre-vaccination signature and mechanisms that could predict the immune response across 13 different vaccines. Analysis of blood transcriptional profiles across studies revealed three distinct pre-vaccination endotypes, characterized by the differential expression of genes associated with a pro-inflammatory response, cell proliferation, and metabolism alterations. Importantly, individuals whose pre-vaccination endotype was enriched in pro-inflammatory response genes known to be downstream of nuclear factor-kappa B showed significantly higher serum antibody responses 1 month after vaccination. This pro-inflammatory pre-vaccination endotype showed gene expression characteristic of the innate activation state triggered by Toll-like receptor ligands or adjuvants. These results demonstrate that wide variations in the transcriptional state of the immune system in humans can be a key determinant of responsiveness to vaccination.
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Affiliation(s)
- Slim Fourati
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Lewis E Tomalin
- Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID and Center for Human Immunology (CHI), NIH, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program, Cambridge University, Cambridge, UK
| | | | | | - Dmitry Rychkov
- Division of Transplant Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Evan Henrich
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Thomas Hagan
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Patrick Dunn
- ImmPort Curation Team, NG Health Solutions, Rockville, MD, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Raphael Gottardo
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Biomedical Data Science Center, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Minnie M Sarwal
- Division of Transplant Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID and Center for Human Immunology (CHI), NIH, Bethesda, MD, USA
| | - Mayte Suárez-Fariñas
- Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bali Pulendran
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Rafick-Pierre Sékaly
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.
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15
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Hagan T, Gerritsen B, Tomalin LE, Fourati S, Mulè MP, Chawla DG, Rychkov D, Henrich E, Miller HER, Diray-Arce J, Dunn P, Lee A, Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Sékaly RP, Kleinstein SH, Pulendran B. Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses. Nat Immunol 2022; 23:1788-1798. [PMID: 36316475 PMCID: PMC9869360 DOI: 10.1038/s41590-022-01328-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/12/2022] [Indexed: 11/27/2022]
Abstract
Systems vaccinology has defined molecular signatures and mechanisms of immunity to vaccination. However, comparative analysis of immunity to different vaccines is lacking. We integrated transcriptional data of over 3,000 samples, from 820 adults across 28 studies of 13 vaccines and analyzed vaccination-induced signatures of antibody responses. Most vaccines induced signatures of innate immunity and plasmablasts at days 1 and 7, respectively, after vaccination. However, the yellow fever vaccine induced an early transient signature of T and B cell activation at day 1, followed by delayed antiviral/interferon and plasmablast signatures that peaked at days 7 and 14-21, respectively. Thus, there was no evidence for a 'universal signature' that predicted antibody response to all vaccines. However, accounting for the asynchronous nature of responses, we defined a time-adjusted signature that predicted antibody responses across vaccines. These results provide a transcriptional atlas of immunity to vaccination and define a common, time-adjusted signature of antibody responses.
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Affiliation(s)
- Thomas Hagan
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bram Gerritsen
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lewis E Tomalin
- Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Slim Fourati
- Emory University School of Medicine, Atlanta, GA, USA
| | - Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID and Center for Human Immunology (CHI), NIH, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program, Cambridge University, Cambridge, UK
| | - Daniel G Chawla
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Dmitri Rychkov
- Division of Transplant Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Evan Henrich
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Joann Diray-Arce
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Patrick Dunn
- ImmPort Curation Team, NG Health Solutions, Rockville, MD, USA
| | - Audrey Lee
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Raphael Gottardo
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Minne M Sarwal
- Division of Transplant Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID and Center for Human Immunology (CHI), NIH, Bethesda, MD, USA
| | - Mayte Suárez-Fariñas
- Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Bali Pulendran
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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16
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Distinct immunological and molecular signatures underpinning influenza vaccine responsiveness in the elderly. Nat Commun 2022; 13:6894. [PMID: 36371426 PMCID: PMC9653450 DOI: 10.1038/s41467-022-34487-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Seasonal influenza outbreaks, especially in high-risk groups such as the elderly, represent an important public health problem. Prevailing inadequate efficacy of seasonal vaccines is a crucial bottleneck. Understanding the immunological and molecular mechanisms underpinning differential influenza vaccine responsiveness is essential to improve vaccination strategies. Here we show comprehensive characterization of the immune response of randomly selected elderly participants (≥ 65 years), immunized with the adjuvanted influenza vaccine Fluad. In-depth analyses by serology, multi-parametric flow cytometry, multiplex and transcriptome analysis, coupled to bioinformatics and mathematical modelling, reveal distinguishing immunological and molecular features between responders and non-responders defined by vaccine-induced seroconversion. Non-responders are specifically characterized by multiple suppressive immune mechanisms. The generated comprehensive high dimensional dataset enables the identification of putative mechanisms and nodes responsible for vaccine non-responsiveness independently of confounding age-related effects, with the potential to facilitate development of tailored vaccination strategies for the elderly.
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17
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Diray-Arce J, Miller HER, Henrich E, Gerritsen B, Mulè MP, Fourati S, Gygi J, Hagan T, Tomalin L, Rychkov D, Kazmin D, Chawla DG, Meng H, Dunn P, Campbell J, Sarwal M, Tsang JS, Levy O, Pulendran B, Sekaly R, Floratos A, Gottardo R, Kleinstein SH, Suárez-Fariñas M. The Immune Signatures data resource, a compendium of systems vaccinology datasets. Sci Data 2022; 9:635. [PMID: 36266291 PMCID: PMC9584267 DOI: 10.1038/s41597-022-01714-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/22/2022] [Indexed: 01/04/2023] Open
Abstract
Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern 'omic profiling techniques and computational modeling to promote rapid and transformative advances in vaccinology and vaccine discovery. The NIH/NIAID Human Immunology Project Consortium (HIPC) has leveraged systems immunology approaches to identify molecular signatures associated with the immunogenicity of many vaccines. However, comparative analyses have been limited by the distributed nature of some data, potential batch effects across studies, and the absence of multiple relevant studies from non-HIPC groups in ImmPort. To support comparative analyses across different vaccines, we have created the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets. This data resource is available through ImmuneSpace, along with code to reproduce the processing and batch normalization starting from the underlying study data in ImmPort and the Gene Expression Omnibus (GEO). The current release comprises 1405 participants from 53 cohorts profiling the response to 24 different vaccines. This novel systems vaccinology data release represents a valuable resource for comparative and meta-analyses that will accelerate our understanding of mechanisms underlying vaccine responses.
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Affiliation(s)
- Joann Diray-Arce
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Helen E R Miller
- Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Evan Henrich
- Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID NIH Center for Human Immunology, NIH, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program, Department of Medicine, Cambridge University, Atlanta, GA, USA
| | - Slim Fourati
- Emory University School of Medicine, Atlanta, GA, USA
| | - Jeremy Gygi
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Thomas Hagan
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lewis Tomalin
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dmitry Rychkov
- University of California, San Francisco, San Francisco, CA, USA
| | - Dmitri Kazmin
- The Jackson Laboratory for Genomic Medicine, Farmington CT, Rockville, MD, USA
| | - Daniel G Chawla
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | | | - Patrick Dunn
- ImmPort Curation Team, NG Health Solutions, Rockville, MD, USA
| | - John Campbell
- ImmPort Curation Team, NG Health Solutions, Rockville, MD, USA
| | - Minnie Sarwal
- University of California, San Francisco, San Francisco, CA, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID NIH Center for Human Immunology, NIH, Bethesda, MD, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Bali Pulendran
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Rafick Sekaly
- Emory University School of Medicine, Atlanta, GA, USA
| | - Aris Floratos
- Columbia University Medical Center, New York, NY, USA
| | - Raphael Gottardo
- Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland
| | | | - Mayte Suárez-Fariñas
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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18
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Chou C, Mohanty S, Kang HA, Kong L, Avila‐Pacheco J, Joshi SR, Ueda I, Devine L, Raddassi K, Pierce K, Jeanfavre S, Bullock K, Meng H, Clish C, Santori FR, Shaw AC, Xavier RJ. Metabolomic and transcriptomic signatures of influenza vaccine response in healthy young and older adults. Aging Cell 2022; 21:e13682. [PMID: 35996998 PMCID: PMC9470889 DOI: 10.1111/acel.13682] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 01/25/2023] Open
Abstract
Seasonal influenza causes mild to severe respiratory infections and significant morbidity, especially in older adults. Transcriptomic analysis in populations across multiple flu seasons has provided insights into the molecular determinants of vaccine response. Still, the metabolic changes that underlie the immune response to influenza vaccination remain poorly characterized. We performed untargeted metabolomics to analyze plasma metabolites in a cohort of younger and older subjects before and after influenza vaccination to identify vaccine-induced molecular signatures. Metabolomic and transcriptomic data were combined to define networks of gene and metabolic signatures indicative of high and low antibody response in these individuals. We observed age-related differences in metabolic baselines and signatures of antibody response to influenza vaccination and the abundance of α-linolenic and linoleic acids, sterol esters, fatty-acylcarnitines, and triacylglycerol metabolism. We identified a metabolomic signature associated with age-dependent vaccine response, finding increased tryptophan and decreased polyunsaturated fatty acids (PUFAs) in young high responders (HRs), while fatty acid synthesis and cholesteryl esters accumulated in older HRs. Integrated metabolomic and transcriptomic analysis shows that depletion of PUFAs, which are building blocks for prostaglandins and other lipid immunomodulators, in young HR subjects at Day 28 is related to a robust immune response to influenza vaccination. Increased glycerophospholipid levels were associated with an inflammatory response in older HRs to flu vaccination. This multi-omics approach uncovered age-related molecular markers associated with influenza vaccine response and provides insight into vaccine-induced metabolic responses that may help guide development of more effective influenza vaccines.
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Affiliation(s)
- Chih‐Hung Chou
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | | | - Lingjia Kong
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | | | - Samit R. Joshi
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Ikuyo Ueda
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Lesley Devine
- Department of Laboratory MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Khadir Raddassi
- Department of NeurologyYale School of MedicineNew HavenConnecticutUSA
| | - Kerry Pierce
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | | | - Kevin Bullock
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Hailong Meng
- Department of PathologyYale School of MedicineNew HavenConnecticutUSA
| | - Clary Clish
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Fabio R. Santori
- Center for Molecular MedicineUniversity of GeorgiaAthensGeorgiaUSA
| | - Albert C. Shaw
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Ramnik J. Xavier
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Klarman Cell ObservatoryBroad Institute of Harvard and MITCambridgeMassachusettsUSA
- Center for Computational and Integrative Biology and Department of Molecular BiologyMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusettsUSA
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19
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Inci N, Akyildiz EO, Bulbul AA, Turanli ET, Akgun E, Baykal AT, Colak F, Bozaykut P. Transcriptomics and Proteomics Analyses Reveal JAK Signaling and Inflammatory Phenotypes during Cellular Senescence in Blind Mole Rats: The Reflections of Superior Biology. BIOLOGY 2022; 11:biology11091253. [PMID: 36138732 PMCID: PMC9495822 DOI: 10.3390/biology11091253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/04/2022] [Accepted: 08/15/2022] [Indexed: 11/28/2022]
Abstract
Simple Summary Blind mole rats (BMR) (Spalax, Nannospalax sp.) are extraordinary organisms with cancer resistance and a long lifespan for their size. Cellular senescence is a condition in which cells cease dividing irreversibly and secrete proinflammatory cytokines. To understand the mechanisms behind their superior traits, we utilized transcriptomics and proteomics tools in senescent BMR cells to compare them to similarly sized mice. The results revealed the alterations in Janus kinase (JAK) signaling and the cytokine-mediated pathway during the cellular senescence process in BMRs. These findings might reveal the novel mechanisms behind the unique biology of BMRs through cytokine-mediated adaptations. Abstract The blind mole rat (BMR), a long-living subterranean rodent, is an exceptional model for both aging and cancer research since they do not display age-related phenotypes or tumor formation. The Janus kinase–signal transducer and activator of transcription (JAK–STAT) signaling is a cytokine-stimulated pathway that has a crucial role in immune regulation, proliferation, and cytokine production. Therefore, the pathway has recently attracted interest in cellular senescence studies. Here, by using publicly available data, we report that JAK–STAT signaling was suppressed in the BMR in comparison to the mouse. Interestingly, our experimental results showed upregulated Jak1/2 expressions in BMR fibroblasts during the replicative senescence process. The transcriptomic analysis using publicly available data also demonstrated that various cytokines related to JAK–STAT signaling were upregulated in the late passage cells, while some other cytokines such as MMPs and SERPINs were downregulated, representing a possible balance of senescence-associated secretory phenotypes (SASPs) in the BMR. Finally, our proteomics data also confirmed cytokine-mediated signaling activation in senescent BMR fibroblasts. Together, our findings suggest the critical role of JAK–STAT and cytokine-mediated signaling pathways during cellular senescence, pointing to the possible contribution of divergent inflammatory factors to the superior resistance of aging and cancer in BMRs.
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Affiliation(s)
- Nurcan Inci
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Erdogan Oguzhan Akyildiz
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Abdullah Alper Bulbul
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Eda Tahir Turanli
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Emel Akgun
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - Faruk Colak
- Department of Biology, Faculty of Arts and Science, Zonguldak Bulent Ecevit University, Zonguldak 67100, Turkey
| | - Perinur Bozaykut
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
- Correspondence:
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20
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Lipsit S, Facciuolo A, Scruten E, Wilkinson J, Plastow G, Kusalik A, Napper S. Signaling differences in peripheral blood mononuclear cells of high and low vaccine responders prior to, and following, vaccination in piglets. Vaccine X 2022; 11:100167. [PMID: 35692279 PMCID: PMC9175112 DOI: 10.1016/j.jvacx.2022.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/29/2022] [Accepted: 04/25/2022] [Indexed: 10/28/2022] Open
Abstract
Individual variability in responses to vaccination can result in vaccinated subjects failing to develop a protective immune response. Vaccine non-responders can remain susceptible to infection and may compromise efforts to achieve herd immunity. Biomarkers of vaccine unresponsiveness could aid vaccine research and development as well as strategically improve vaccine administration programs. We previously vaccinated piglets (n = 117) against a commercial Mycoplasma hyopneumoniae vaccine (RespiSure-One) and observed in low vaccine responder piglets, as defined by serum IgG antibody titers, differential phosphorylation of peptides involved in pro-inflammatory cytokine signaling within peripheral blood mononuclear cells (PBMCs) prior to vaccination, elevated plasma interferon-gamma concentrations, and lower birth weight compared to high vaccine responder piglets. In the current study, we use kinome analysis to investigate signaling events within PBMCs collected from the same high and low vaccine responders at 2 and 6 days post-vaccination. Furthermore, we evaluate the use of inflammatory plasma cytokines, birthweight, and signaling events as biomarkers of vaccine unresponsiveness in a validation cohort of high and low vaccine responders. Differential phosphorylation events (FDR < 0.05) within PBMCs are established between high and low responders at the time of vaccination and at six days post-vaccination. A subset of these phosphorylation events were determined to be consistently differentially phosphorylated (p < 0.05) in the validation cohort of high and low vaccine responders. In contrast, there were no differences in birth weight (p > 0.5) and plasma IFNγ concentrations at the time of vaccination (p > 0.6) between high and low responders within the validation cohort. The results in this study suggest, at least within this study population, phosphorylation biomarkers are more robust predictors of vaccine responsiveness than other physiological markers.
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Affiliation(s)
- Sean Lipsit
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Antonio Facciuolo
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Erin Scruten
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - James Wilkinson
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Scott Napper
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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21
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Yu Y, Zhu MJ, Wei CF, Yang J, Song JY, Dong L, Xiang S, Zhang L, Qiu Y, Lian F. Age-related differential gene expression in granulosa cells and its effects on fertility using high-throughput transcriptomics. Syst Biol Reprod Med 2022; 68:190-202. [PMID: 35331074 DOI: 10.1080/19396368.2022.2028320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
More couples worldwide, delay their childbearing years. The increase in age causes a gradual decrease in female ovarian function and fertility, leading to an exponential decrease in women over 35 years of age having children. Although promising for some, assisted reproductive technology (ART) is not promising for older women. Decreased fertility in advanced age has become a growing concern in the field of reproduction. In this study, high-throughput transcriptome sequencing was used to identify the differentially expressed genes (DEGs) in the ovarian granulosa cells (GCs) of older women (aged 35-44) with infertility and younger women (aged 25-34). The enriched functions and signaling pathways of DEGs were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The function of DEGs were analyzed and predicted combined with clinical ART data. Sequencing results were verified by quantitative reverse transcription-polymerase chain reaction. Retrospective clinical data and bioinformatics analyses revealed marked reductions in the retrieved oocyte, metaphase II oocyte, 2PN fertilization, and effective embryo numbers in older women. Although the clinical pregnancy and live birth rates did not differ notably between the groups, the miscarriage rate increased significantly in older women. In total, 620 DEGs were identified, of which 246 were upregulated, and 374 were downregulated in the older group. GO, and KEGG analyses indicated that the mechanism of fertility decline in older women was probably related to chronic inflammation, cytokine receptor interaction, and oxidative stress. In conclusion, combined with basic clinical ART data and pregnancy outcomes, we tried to provide a more intuitive and in-depth understanding of age-related reduction in ovarian function and pathogenesis of infertility with regard to chronic inflammation and oxidative stress.
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Affiliation(s)
- Yi Yu
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China.,Reproductive and Genetic Center of Integrated Traditional and Western Medicine, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ming-Jie Zhu
- School of Medicine, Department of Orthopedics, University of Colorado, Colorado, CO, USA
| | - Chao-Feng Wei
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jie Yang
- The personnel department, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jing-Yan Song
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Li Dong
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shan Xiang
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Liang Zhang
- Reproductive and Genetic Center of Integrated Traditional and Western Medicine, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yue Qiu
- Reproductive and Genetic Center of Integrated Traditional and Western Medicine, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Fang Lian
- Reproductive and Genetic Center of Integrated Traditional and Western Medicine, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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22
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Moritzky SA, Richards KA, Glover MA, Krammer F, Chaves FA, Topham DJ, Branche A, Nayak JL, Sant AJ. The Negative Effect of Preexisting Immunity on Influenza Vaccine Responses Transcends the Impact of Vaccine Formulation Type and Vaccination History. J Infect Dis 2022; 227:381-390. [PMID: 35199825 PMCID: PMC9891420 DOI: 10.1093/infdis/jiac068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/22/2022] [Indexed: 02/05/2023] Open
Abstract
The most effective measure to induce protection from influenza is vaccination. Thus, yearly vaccination is recommended, which, together with infections, establishes diverse repertoires of B cells, antibodies, and T cells. We examined the impact of this accumulated immunity on human responses in adults to split, subunit, and recombinant protein-based influenza vaccines. Enzyme-linked immunosorbent assay (ELISA) assays, to quantify serum antibodies, and peptide-stimulated CD4 T-cell cytokine ELISpots revealed that preexisting levels of hemagglutinin (HA)-specific antibodies were negatively associated with gains in antibody postvaccination, while preexisting levels of CD4 T cells were negatively correlated with vaccine-induced expansion of CD4 T cells. These patterns were seen independently of the vaccine formulation administered and the subjects' influenza vaccine history. Thus, although memory CD4 T cells and serum antibodies consist of components that can enhance vaccine responses, on balance, the accumulated immunity specific for influenza A H1 and H3 proteins is associated with diminished future responses.
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Affiliation(s)
- Savannah A Moritzky
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Katherine A Richards
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Maryah A Glover
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA,Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Francisco A Chaves
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Angela Branche
- Department of Medicine, Division of Infectious Diseases, University of Rochester Medical Center, Rochester, New York, USA
| | - Jennifer L Nayak
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Rochester Medical Center, Rochester, New York, USA
| | - Andrea J Sant
- Correspondence: Andrea J. Sant, PhD, University of Rochester Medical Center, David H. Smith Center for Vaccine Biology and Immunology, 601 Elmwood Avenue, Box 609, Rochester, NY 14642 ()
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23
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Brahadeeswaran S, Sivagurunathan N, Calivarathan L. Inflammasome Signaling in the Aging Brain and Age-Related Neurodegenerative Diseases. Mol Neurobiol 2022; 59:2288-2304. [PMID: 35066762 DOI: 10.1007/s12035-021-02683-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/06/2021] [Indexed: 12/28/2022]
Abstract
Inflammasomes are intracellular protein complexes, members of the innate immune system, and their activation and regulation play an essential role in maintaining homeostatic conditions against exogenous and endogenous stimuli. Inflammasomes occur as cytosolic proteins and assemble into a complex during the recognition of pathogen-associated or danger-associated molecular patterns by pattern-recognition receptors in host cells. The formation of the inflammasome complex elicits signaling molecules of proinflammatory cytokines such as interleukin-1β and interleukin 18 via activation of caspase-1 in the canonical inflammasome pathway whereas caspase-11 in the case of a mouse and caspase-4 and caspase-5 in the case of humans in the non-canonical inflammasome pathway, resulting in pyroptotic or inflammatory cell death which ultimately leads to neuroinflammation and neurodegenerative diseases. Inflammasome activation, particularly in microglial cells and macrophages, has been linked to aging as well as age-related neurodegenerative diseases. The accumulation of abnormal/ misfolded proteins acts as a ligand for inflammasome activation in neurodegenerative diseases. Although recent studies have revealed the inflammasomes' functionality in both in vitro and in vivo models, many inflammasome signaling cascade activations during biological aging, neuroinflammation, and neurodegeneration are still ambiguous. In this review, we comprehensively unveil the cellular and molecular mechanisms of inflammasome activation during neuronal aging and age-related neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis, prion disease, and amyotrophic lateral sclerosis.
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Affiliation(s)
- Subhashini Brahadeeswaran
- Molecular Pharmacology and Toxicology Laboratory, Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Neelakudi Campus, Thiruvarur, Tamil Nadu, 610005, India
| | - Narmadhaa Sivagurunathan
- Molecular Pharmacology and Toxicology Laboratory, Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Neelakudi Campus, Thiruvarur, Tamil Nadu, 610005, India
| | - Latchoumycandane Calivarathan
- Molecular Pharmacology and Toxicology Laboratory, Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Neelakudi Campus, Thiruvarur, Tamil Nadu, 610005, India.
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Human immune diversity: from evolution to modernity. Nat Immunol 2021; 22:1479-1489. [PMID: 34795445 DOI: 10.1038/s41590-021-01058-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/17/2021] [Indexed: 02/08/2023]
Abstract
The extreme diversity of the human immune system, forged and maintained throughout evolutionary history, provides a potent defense against opportunistic pathogens. At the same time, this immune variation is the substrate upon which a plethora of immune-associated diseases develop. Genetic analysis suggests that thousands of individually weak loci together drive up to half of the observed immune variation. Intense selection maintains this genetic diversity, even selecting for the introgressed Neanderthal or Denisovan alleles that have reintroduced variation lost during the out-of-Africa migration. Variations in age, sex, diet, environmental exposure, and microbiome each potentially explain the residual variation, with proof-of-concept studies demonstrating both plausible mechanisms and correlative associations. The confounding interaction of many of these variables currently makes it difficult to assign definitive contributions. Here, we review the current state of play in the field, identify the key unknowns in the causality of immune variation, and identify the multidisciplinary pathways toward an improved understanding.
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Sheerin D, Dold C, O'Connor D, Pollard AJ, Rollier CS. Distinct patterns of whole blood transcriptional responses are induced in mice following immunisation with adenoviral and poxviral vector vaccines encoding the same antigen. BMC Genomics 2021; 22:777. [PMID: 34717548 PMCID: PMC8556829 DOI: 10.1186/s12864-021-08061-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Viral vectors, including adenovirus (Ad) and modified vaccinia Ankara (MVA), have gained increasing attention as vaccine platforms in recent years due to their capacity to express antigens from a wide array of pathogens, their rapid induction of humoral and cellular protective immune responses, and their relatively low production costs. In particular, the chimpanzee Ad vector, ChAdOx1, has taken centre stage as a leading COVID-19 vaccine candidate. However, despite mounting data, both clinical and pre-clinical, demonstrating effective induction of adaptive immune responses, the innate immune signals that precede the protective responses that make these vectors attractive vaccine platforms remain poorly understood. RESULTS In this study, a mouse immunisation model was used to evaluate whole blood gene expression changes 24 h after either a single dose or heterologous prime-boost regimen of an Ad and/or MVA vaccine. We demonstrate through comparative analysis of Ad vectors encoding different antigens that a transgene product-specific gene signature can be discerned from the vector-induced transcriptional response. Expression of genes involved in TLR2 stimulation and γδ T cell and natural killer cell activation were induced after a single dose of Ad, while MVA led to greater expression of type I interferon genes. The order of prime-boost combinations was found to influence the magnitude of the gene expression changes, with MVA/Ad eliciting greater transcriptional perturbation than Ad/MVA. Contrasting the two regimens revealed significant enrichment of epigenetic regulation pathways and augmented expression of MHC class I and II molecules associated with MVA/Ad. CONCLUSION These data demonstrate that the order in which vaccines from heterologous prime-boost regimens are administered leads to distinct transcriptional responses and may shape the immune response induced by such combinations. The characterisation of early vaccine-induce responses strengthens our understanding of viral vector vaccine mechanisms of action ahead of their characterisation in human clinical trials and are a valuable resource to inform the pre-clinical design of appropriate vaccine constructs for emerging infectious diseases.
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Affiliation(s)
- Dylan Sheerin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford, UK.
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research (WEHI), Melbourne, Victoria, 3052, Australia.
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford, UK
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford, UK
| | - Christine S Rollier
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford, UK
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Curran SP, Lithgow GJ, Verdin E, P C. University of Southern California and buck institute nathan shock center: multidimensional models of aging. GeroScience 2021; 43:2119-2127. [PMID: 34269983 PMCID: PMC8599784 DOI: 10.1007/s11357-021-00416-z] [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: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022] Open
Abstract
The USC-Buck Nathan Shock Center of Excellence in the Biology of Aging is a new and fully integrated multi-institutional center focused on training the next generation of geroscientists and providing access to cutting-edge geroscience technologies to investigators across the nation. The USC-Buck NSC is devoted to forging a deeper understanding of how and why aging processes cause disease in order to advance the translation of basic research on aging into effective preventions and therapies. Including more than 61 NIA-supported investigators, six NIA-funded research centers, four NIA T32s, and several additional aging research centers of excellence, the USC-Buck NSC constitutes one of the largest collections of leaders in geroscience research within the USA; the unique nature of the USC-Buck NSC research infrastructure ensures an integrated organization that is representative of the wide breadth of topics encompassed by the biology of aging field. By leveraging the 25-year-long relationship, current collaborations and joint administrational activities of the University of Southern California and the Buck Institute for Aging Research, the USC-Buck NSC aims to enhance and expand promising research in the biology of aging at both at the and to make a positive impact across California, the nation and throughout the world. Specialized cores provide services to all Shock Center members, as well as provide support for services to the community at large.
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Affiliation(s)
- Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, USA.
| | | | - Eric Verdin
- Buck Institute for Research On Aging, Novato, CA, USA
- UCSF Department of Medicine, San Francisco, CA, USA
| | - Cohen P
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, USA
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27
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Chang SE, Feng A, Meng W, Apostolidis SA, Mack E, Artandi M, Barman L, Bennett K, Chakraborty S, Chang I, Cheung P, Chinthrajah S, Dhingra S, Do E, Finck A, Gaano A, Geßner R, Giannini HM, Gonzalez J, Greib S, Gündisch M, Hsu AR, Kuo A, Manohar M, Mao R, Neeli I, Neubauer A, Oniyide O, Powell AE, Puri R, Renz H, Schapiro J, Weidenbacher PA, Wittman R, Ahuja N, Chung HR, Jagannathan P, James JA, Kim PS, Meyer NJ, Nadeau KC, Radic M, Robinson WH, Singh U, Wang TT, Wherry EJ, Skevaki C, Luning Prak ET, Utz PJ. New-onset IgG autoantibodies in hospitalized patients with COVID-19. Nat Commun 2021; 12:5417. [PMID: 34521836 PMCID: PMC8440763 DOI: 10.1038/s41467-021-25509-3] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
COVID-19 is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. Here we develop three protein arrays to measure IgG autoantibodies associated with connective tissue diseases, anti-cytokine antibodies, and anti-viral antibody responses in serum from 147 hospitalized COVID-19 patients. Autoantibodies are identified in approximately 50% of patients but in less than 15% of healthy controls. When present, autoantibodies largely target autoantigens associated with rare disorders such as myositis, systemic sclerosis and overlap syndromes. A subset of autoantibodies targeting traditional autoantigens or cytokines develop de novo following SARS-CoV-2 infection. Autoantibodies track with longitudinal development of IgG antibodies recognizing SARS-CoV-2 structural proteins and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
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Affiliation(s)
- Sarah Esther Chang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elisabeth Mack
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Maja Artandi
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford CROWN Clinic, Stanford University School of Medicine, Stanford, CA, USA
| | - Linda Barman
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Kate Bennett
- Molecular Pathology and Imaging Core, Department of Medicine, Gastroenterology Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Iris Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Peggie Cheung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon Chinthrajah
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaurya Dhingra
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Evan Do
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Amanda Finck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Gaano
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Reinhard Geßner
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Heather M Giannini
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Joyce Gonzalez
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Greib
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Margrit Gündisch
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Alex Ren Hsu
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Kuo
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Monali Manohar
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rong Mao
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Indira Neeli
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andreas Neubauer
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Oluwatosin Oniyide
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abigail E Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, USA
| | - Rajan Puri
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Harald Renz
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
- Member of the Universities of Giessen and Marburg Lung Center (UGMLC), and the German Center for Lung Research (DZL), Giessen, Germany
| | - Jeffrey Schapiro
- TPMG Regional Reference Laboratory, Kaiser Permanente Northern California, Berkeley, CA, USA
| | - Payton A Weidenbacher
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, USA
| | - Richard Wittman
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Neera Ahuja
- Department of Medicine, Division of Hospital Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ho-Ryun Chung
- Institute for Medical Bioinformatics and Biostatistics, Philipps University Marburg, Marburg, Germany
| | - Prasanna Jagannathan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Judith A James
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Peter S Kim
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nuala J Meyer
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kari C Nadeau
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - William H Robinson
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Upinder Singh
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - E John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany.
- Member of the Universities of Giessen and Marburg Lung Center (UGMLC), and the German Center for Lung Research (DZL), Giessen, Germany.
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
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Lin X, Lin F, Liang T, Ducatez MF, Zanin M, Wong SS. Antibody Responsiveness to Influenza: What Drives It? Viruses 2021; 13:v13071400. [PMID: 34372607 PMCID: PMC8310379 DOI: 10.3390/v13071400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 02/06/2023] Open
Abstract
The induction of a specific antibody response has long been accepted as a serological hallmark of recent infection or antigen exposure. Much of our understanding of the influenza antibody response has been derived from studying antibodies that target the hemagglutinin (HA) protein. However, growing evidence points to limitations associated with this approach. In this review, we aim to highlight the issue of antibody non-responsiveness after influenza virus infection and vaccination. We will then provide an overview of the major factors known to influence antibody responsiveness to influenza after infection and vaccination. We discuss the biological factors such as age, sex, influence of prior immunity, genetics, and some chronic infections that may affect the induction of influenza antibody responses. We also discuss the technical factors, such as assay choices, strain variations, and viral properties that may influence the sensitivity of the assays used to measure influenza antibodies. Understanding these factors will hopefully provide a more comprehensive picture of what influenza immunogenicity and protection means, which will be important in our effort to improve influenza vaccines.
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Affiliation(s)
- Xia Lin
- State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, 195 Dongfengxi Rd, Guangzhou 510182, China; (X.L.); (F.L.); (T.L.); (M.Z.)
| | - Fangmei Lin
- State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, 195 Dongfengxi Rd, Guangzhou 510182, China; (X.L.); (F.L.); (T.L.); (M.Z.)
| | - Tingting Liang
- State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, 195 Dongfengxi Rd, Guangzhou 510182, China; (X.L.); (F.L.); (T.L.); (M.Z.)
| | | | - Mark Zanin
- State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, 195 Dongfengxi Rd, Guangzhou 510182, China; (X.L.); (F.L.); (T.L.); (M.Z.)
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Sook-San Wong
- State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, 195 Dongfengxi Rd, Guangzhou 510182, China; (X.L.); (F.L.); (T.L.); (M.Z.)
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Correspondence: ; Tel.: +86-178-2584-6078
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29
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Sayed N, Huang Y, Nguyen K, Krejciova-Rajaniemi Z, Grawe AP, Gao T, Tibshirani R, Hastie T, Alpert A, Cui L, Kuznetsova T, Rosenberg-Hasson Y, Ostan R, Monti D, Lehallier B, Shen-Orr SS, Maecker HT, Dekker CL, Wyss-Coray T, Franceschi C, Jojic V, Haddad F, Montoya JG, Wu JC, Davis MM, Furman D. An inflammatory aging clock (iAge) based on deep learning tracks multimorbidity, immunosenescence, frailty and cardiovascular aging. ACTA ACUST UNITED AC 2021; 1:598-615. [PMID: 34888528 PMCID: PMC8654267 DOI: 10.1038/s43587-021-00082-y] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
While many diseases of aging have been linked to the immunological system, immune metrics capable of identifying the most at-risk individuals are lacking. From the blood immunome of 1,001 individuals aged 8-96 years, we developed a deep-learning method based on patterns of systemic age-related inflammation. The resulting inflammatory clock of aging (iAge) tracked with multimorbidity, immunosenescence, frailty and cardiovascular aging, and is also associated with exceptional longevity in centenarians. The strongest contributor to iAge was the chemokine CXCL9, which was involved in cardiac aging, adverse cardiac remodeling and poor vascular function. Furthermore, aging endothelial cells in human and mice show loss of function, cellular senescence and hallmark phenotypes of arterial stiffness, all of which are reversed by silencing CXCL9. In conclusion, we identify a key role of CXCL9 in age-related chronic inflammation and derive a metric for multimorbidity that can be utilized for the early detection of age-related clinical phenotypes.
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Cortese M, Sherman AC, Rouphael NG, Pulendran B. Systems Biological Analysis of Immune Response to Influenza Vaccination. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038596. [PMID: 32152245 DOI: 10.1101/cshperspect.a038596] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The last decade has witnessed tremendous progress in immunology and vaccinology, owing to several scientific and technological breakthroughs. Systems vaccinology is a field that has emerged at the forefront of vaccine research and development and provides a unique way to probe immune responses to vaccination in humans. The goals of systems vaccinology are to use systems-based approaches to define signatures that can be used to predict vaccine immunogenicity and efficacy and to delineate the molecular mechanisms driving protective immunity. The application of systems biological approaches in influenza vaccination studies has enabled the discovery of early signatures that predict immunogenicity to vaccination and yielded novel mechanistic insights about vaccine-induced immunity. Here we review the contributions of systems vaccinology to influenza vaccine development and critically examine the potential of systems vaccinology toward enabling the development of a universal influenza vaccine that provides robust and durable immunity against diverse influenza viruses.
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Affiliation(s)
- Mario Cortese
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Amy C Sherman
- Hope Clinic of the Emory Vaccine Center, Decatur, Georgia 30030, USA
| | - Nadine G Rouphael
- Hope Clinic of the Emory Vaccine Center, Decatur, Georgia 30030, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California 94305, USA.,Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA.,Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA
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31
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Van Tilbeurgh M, Lemdani K, Beignon AS, Chapon C, Tchitchek N, Cheraitia L, Marcos Lopez E, Pascal Q, Le Grand R, Maisonnasse P, Manet C. Predictive Markers of Immunogenicity and Efficacy for Human Vaccines. Vaccines (Basel) 2021; 9:579. [PMID: 34205932 PMCID: PMC8226531 DOI: 10.3390/vaccines9060579] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
Vaccines represent one of the major advances of modern medicine. Despite the many successes of vaccination, continuous efforts to design new vaccines are needed to fight "old" pandemics, such as tuberculosis and malaria, as well as emerging pathogens, such as Zika virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Vaccination aims at reaching sterilizing immunity, however assessing vaccine efficacy is still challenging and underscores the need for a better understanding of immune protective responses. Identifying reliable predictive markers of immunogenicity can help to select and develop promising vaccine candidates during early preclinical studies and can lead to improved, personalized, vaccination strategies. A systems biology approach is increasingly being adopted to address these major challenges using multiple high-dimensional technologies combined with in silico models. Although the goal is to develop predictive models of vaccine efficacy in humans, applying this approach to animal models empowers basic and translational vaccine research. In this review, we provide an overview of vaccine immune signatures in preclinical models, as well as in target human populations. We also discuss high-throughput technologies used to probe vaccine-induced responses, along with data analysis and computational methodologies applied to the predictive modeling of vaccine efficacy.
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Affiliation(s)
- Matthieu Van Tilbeurgh
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Katia Lemdani
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Anne-Sophie Beignon
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Catherine Chapon
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Nicolas Tchitchek
- Unité de Recherche i3, Inserm UMR-S 959, Bâtiment CERVI, Hôpital de la Pitié-Salpêtrière, 75013 Paris, France;
| | - Lina Cheraitia
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Ernesto Marcos Lopez
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Quentin Pascal
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Roger Le Grand
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Pauline Maisonnasse
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Caroline Manet
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
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Tomic A, Pollard AJ, Davis MM. Systems Immunology: Revealing Influenza Immunological Imprint. Viruses 2021; 13:v13050948. [PMID: 34065617 PMCID: PMC8160800 DOI: 10.3390/v13050948] [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] [Received: 04/14/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding protective influenza immunity and identifying immune correlates of protection poses a major challenge and requires an appreciation of the immune system in all of its complexity. While adaptive immune responses such as neutralizing antibodies and influenza-specific T lymphocytes are contributing to the control of influenza virus, key factors of long-term protection are not well defined. Using systems immunology, an approach that combines experimental and computational methods, we can capture the systems-level state of protective immunity and reveal the essential pathways that are involved. New approaches and technological developments in systems immunology offer an opportunity to examine roles and interrelationships of clinical, biological, and genetic factors in the control of influenza infection and have the potential to lead to novel discoveries about influenza immunity that are essential for the development of more effective vaccines to prevent future pandemics. Here, we review recent developments in systems immunology that help to reveal key factors mediating protective immunity.
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Affiliation(s)
- Adriana Tomic
- Oxford Vaccine Group, University of Oxford, Oxford OX3 7LJ, UK;
- Correspondence: (A.T.); (M.M.D.)
| | - Andrew J. Pollard
- Oxford Vaccine Group, University of Oxford, Oxford OX3 7LJ, UK;
- NIHR Oxford Biomedical Research Center, Oxford OX3 7LJ, UK
| | - Mark M. Davis
- Institute of Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94304, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94304, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94304, USA
- Correspondence: (A.T.); (M.M.D.)
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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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Abstract
Adjuvants are vaccine components that enhance the magnitude, breadth and durability of the immune response. Following its introduction in the 1920s, alum remained the only adjuvant licensed for human use for the next 70 years. Since the 1990s, a further five adjuvants have been included in licensed vaccines, but the molecular mechanisms by which these adjuvants work remain only partially understood. However, a revolution in our understanding of the activation of the innate immune system through pattern recognition receptors (PRRs) is improving the mechanistic understanding of adjuvants, and recent conceptual advances highlight the notion that tissue damage, different forms of cell death, and metabolic and nutrient sensors can all modulate the innate immune system to activate adaptive immunity. Furthermore, recent advances in the use of systems biology to probe the molecular networks driving immune response to vaccines ('systems vaccinology') are revealing mechanistic insights and providing a new paradigm for the vaccine discovery and development process. Here, we review the 'known knowns' and 'known unknowns' of adjuvants, discuss these emerging concepts and highlight how our expanding knowledge about innate immunity and systems vaccinology are revitalizing the science and development of novel adjuvants for use in vaccines against COVID-19 and future pandemics.
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Signatures of immune dysfunction in HIV and HCV infection share features with chronic inflammation in aging and persist after viral reduction or elimination. Proc Natl Acad Sci U S A 2021; 118:2022928118. [PMID: 33811141 PMCID: PMC8040665 DOI: 10.1073/pnas.2022928118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Chronic inflammation is thought to be a major cause of morbidity and mortality in aging, but whether similar mechanisms underlie dysfunction in infection-associated chronic inflammation is unclear. Here, we profiled the immune proteome, and cellular composition and signaling states in a cohort of aging individuals versus a set of HIV patients on long-term antiretroviral therapy therapy or hepatitis C virus (HCV) patients before and after sofosbuvir treatment. We found shared alterations in aging-associated and infection-associated chronic inflammation including T cell memory inflation, up-regulation of intracellular signaling pathways of inflammation, and diminished sensitivity to cytokines in lymphocytes and myeloid cells. In the HIV cohort, these dysregulations were evident despite viral suppression for over 10 y. Viral clearance in the HCV cohort partially restored cellular sensitivity to interferon-α, but many immune system alterations persisted for at least 1 y posttreatment. Our findings indicate that in the HIV and HCV cohorts, a broad remodeling and degradation of the immune system can persist for a year or more, even after the removal or drastic reduction of the pathogen load and that this shares some features of chronic inflammation in aging.
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Chang SE, Feng A, Meng W, Apostolidis SA, Mack E, Artandi M, Barman L, Bennett K, Chakraborty S, Chang I, Cheung P, Chinthrajah S, Dhingra S, Do E, Finck A, Gaano A, Geßner R, Giannini HM, Gonzalez J, Greib S, Gündisch M, Hsu AR, Kuo A, Manohar M, Mao R, Neeli I, Neubauer A, Oniyide O, Powell AE, Puri R, Renz H, Schapiro JM, Weidenbacher PA, Wittman R, Ahuja N, Chung HR, Jagannathan P, James J, Kim PS, Meyer NJ, Nadeau K, Radic M, Robinson WH, Singh U, Wang TT, Wherry EJ, Skevaki C, Prak ETL, Utz PJ. New-Onset IgG Autoantibodies in Hospitalized Patients with COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33532787 DOI: 10.1101/2021.01.27.21250559] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. We developed three different protein arrays to measure hallmark IgG autoantibodies associated with Connective Tissue Diseases (CTDs), Anti-Cytokine Antibodies (ACA), and anti-viral antibody responses in 147 hospitalized COVID-19 patients in three different centers. Autoantibodies were identified in approximately 50% of patients, but in <15% of healthy controls. When present, autoantibodies largely targeted autoantigens associated with rare disorders such as myositis, systemic sclerosis and CTD overlap syndromes. Anti-nuclear antibodies (ANA) were observed in ∼25% of patients. Patients with autoantibodies tended to demonstrate one or a few specificities whereas ACA were even more prevalent, and patients often had antibodies to multiple cytokines. Rare patients were identified with IgG antibodies against angiotensin converting enzyme-2 (ACE-2). A subset of autoantibodies and ACA developed de novo following SARS-CoV-2 infection while others were transient. Autoantibodies tracked with longitudinal development of IgG antibodies that recognized SARS-CoV-2 structural proteins such as S1, S2, M, N and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. COVID-19 patients with one or more autoantibodies tended to have higher levels of antibodies against SARS-CoV-2 Nonstructural Protein 1 (NSP1) and Methyltransferase (ME). We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
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Frasca D, Blomberg BB. Aging induces B cell defects and decreased antibody responses to influenza infection and vaccination. IMMUNITY & AGEING 2020; 17:37. [PMID: 33292323 PMCID: PMC7674578 DOI: 10.1186/s12979-020-00210-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
Background Aging is characterized by a progressive decline in the capacity of the immune system to fight influenza virus infection and to respond to vaccination. Among the several factors involved, in addition to increased frailty and high-risk conditions, the age-associated decrease in cellular and humoral immune responses plays a relevant role. This is in large part due to inflammaging, the chronic low-grade inflammatory status of the elderly, associated with intrinsic inflammation of the immune cells and decreased immune function. Results Aging is usually associated with reduced influenza virus-specific and influenza vaccine-specific antibody responses but some elderly individuals with higher pre-exposure antibody titers, due to a previous infection or vaccination, have less probability to get infected. Examples of this exception are the elderly individuals infected during the 2009 pandemic season who made antibodies with broader epitope recognition and higher avidity than those made by younger individuals. Several studies have allowed the identification of B cell intrinsic defects accounting for sub-optimal antibody responses of elderly individuals. These defects include 1) reduced class switch recombination, responsible for the generation of a secondary response of class switched antibodies, 2) reduced de novo somatic hypermutation of the antibody variable region, 3) reduced binding and neutralization capacity, as well as binding specificity, of the secreted antibodies, 4) increased epigenetic modifications that are associated with lower antibody responses, 5) increased frequencies of inflammatory B cell subsets, and 6) shorter telomeres. Conclusions Although influenza vaccination represents the most effective way to prevent influenza infection, vaccines with greater immunogenicity are needed to improve the response of elderly individuals. Recent advances in technology have made possible a broad approach to better understand the age-associated changes in immune cells, needed to design tailored vaccines and effective therapeutic strategies that will be able to improve the immune response of vulnerable individuals.
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Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, RMSB 3146A, 1600 NW 10th Ave, Miami, FL, 33136, USA.
| | - Bonnie B Blomberg
- Department of Microbiology and Immunology and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, RMSB 3146A, 1600 NW 10th Ave, Miami, FL, 33136, USA
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Ciabattini A, Garagnani P, Santoro F, Rappuoli R, Franceschi C, Medaglini D. Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population. Semin Immunopathol 2020; 42:619-634. [PMID: 33159214 PMCID: PMC7646713 DOI: 10.1007/s00281-020-00821-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 pandemic urgently calls for the development of effective preventive tools. COVID-19 hits greatly the elder and more fragile fraction of the population boosting the evergreen issue of the vaccination of older people. The development of a vaccine against SARS-CoV-2 tailored for the elderly population faces the challenge of the poor immune responsiveness of the older population due to immunosenescence, comorbidities, and pharmacological treatments. Moreover, it is likely that the inflammaging phenotype associated with age could both influence vaccination efficacy and exacerbate the risk of COVID-19-related "cytokine storm syndrome" with an overlap between the factors which impact vaccination effectiveness and those that boost virulence and worsen the prognosis of SARS-CoV-2 infection. The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of immune responses, and the lack of clear correlates of protection, make the design of vaccination strategies for older people extremely challenging. In the ongoing effort in vaccine development, different SARS-CoV-2 vaccine candidates have been developed, tested in pre-clinical and clinical studies and are undergoing clinical testing, but only a small fraction of these are currently being tested in the older fraction of the population. Recent advances in systems biology integrating clinical, immunologic, and omics data can help to identify stable and robust markers of vaccine response and move towards a better understanding of SARS-CoV-2 vaccine responses in the elderly.
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Affiliation(s)
- Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Paolo Garagnani
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institute at Huddinge University Hospital, SE-171 77, Stockholm, Sweden
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40139, Bologna, Italy
- Interdepartmental Centre 'L. Galvan' (CIG), University of Bologna, Via G. Petroni 26, 40139, Bologna, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Rino Rappuoli
- GSK, Siena, Italy
- vAMRes Lab, Toscana Life Sciences, Siena, Italy
- Faculty of Medicine, Imperial College, London, UK
| | | | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, Siena, Italy.
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39
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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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40
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Sasaki E, Asanuma H, Momose H, Furuhata K, Mizukami T, Hamaguchi I. Immunogenicity and Toxicity of Different Adjuvants Can Be Characterized by Profiling Lung Biomarker Genes After Nasal Immunization. Front Immunol 2020; 11:2171. [PMID: 33013912 PMCID: PMC7516075 DOI: 10.3389/fimmu.2020.02171] [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] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
The efficacy of vaccine adjuvants depends on their ability to appropriately enhance the immunogenicity of vaccine antigens, which is often insufficient in non-adjuvanted vaccines. Genomic analyses of immune responses elicited by vaccine adjuvants provide information that is critical for the rational design of adjuvant vaccination strategies. In this study, biomarker genes from the genomic analyses of lungs after priming were used to predict the efficacy and toxicity of vaccine adjuvants. Based on the results, it was verified whether the efficacy and toxicity of the tested adjuvants could be predicted based on the biomarker gene profiles after priming. Various commercially available adjuvants were assessed by combining them with the split influenza vaccine and were subsequently administered in mice through nasal inoculation. The expression levels of lung biomarker genes within 24 h after priming were analyzed. Furthermore, we analyzed the antibody titer, cytotoxic T lymphocyte (CTL) induction, IgG1/IgG2a ratio, leukopenic toxicity, and cytotoxicity in mice vaccinated at similar doses. The association between the phenotypes and the changes in the expression levels of biomarker genes were analyzed. The ability of the adjuvants to induce the production of antigen-specific IgA could be assessed based on the levels of Timp1 expression. Furthermore, the expression of this gene partially correlated with the levels of other damage-associated molecular patterns in bronchoalveolar lavage fluid. Additionally, the changes in the expression of proteasome- and transporter-related genes involved in major histocompatibility complex class 1 antigen presentation could be monitored to effectively assess the expansion of CTL by adjuvants. The monitoring of certain genes is necessary for the assessment of leukopenic toxicity and cytotoxicity of the tested adjuvant. These results indicate that the efficacy and toxicity of various adjuvants can be characterized by profiling lung biomarker genes after the first instance of immunization. This approach could make a significant contribution to the development of optimal selection and exploratory screening strategies for novel adjuvants.
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Affiliation(s)
- Eita Sasaki
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Asanuma
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Haruka Momose
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keiko Furuhata
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takuo Mizukami
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, Japan
| | - Isao Hamaguchi
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, Japan
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Emerging technologies for systems vaccinology - multi-omics integration and single-cell (epi)genomic profiling. Curr Opin Immunol 2020; 65:57-64. [PMID: 32504952 DOI: 10.1016/j.coi.2020.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022]
Abstract
Systems vaccinology leverages high-throughput 'omics' technologies, such as transcriptomics, metabolomics, and mass cytometry, coupled with computational approaches to construct a global map of the complex processes that occur during an immune response to vaccination. Its goal is to define the mechanisms of protective immunity and to identify cellular and molecular correlates of vaccine efficacy. Emerging technological advances including integration of multi-omics datasets, and single-cell genomic and epigenomic profiling of immune responses, have invigorated systems vaccinology, and provide new insights into the mechanisms by which the cellular and molecular information underlying immune memory is stored in the innate and adaptive immune systems. Here, we will review these emerging directions in systems vaccinology, with a particular focus on the epigenome, and its impact on modulating vaccination induced memory in the innate and adaptive immune systems.
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Choi A, García-Sastre A, Schotsaert M. Host immune response-inspired development of the influenza vaccine. Ann Allergy Asthma Immunol 2020; 125:28-35. [PMID: 32325117 PMCID: PMC7327511 DOI: 10.1016/j.anai.2020.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 12/27/2022]
Abstract
Objective To assess the current and future development of influenza vaccines. Data Sources PubMed searches were performed cross-referencing the keywords influenza, influenza vaccine, host immune response, correlates of protection, vaccine development, vaccine efficacy. Articles were reviewed for additional citations. Study Selections Articles were reviewed and selected on the basis of relevance to subject matter. Results In this review, we first introduce the influenza virus, its nomenclature, and the concepts of antigenic drift and shift. Second, we discuss the status of currently licensed influenza virus vaccines. We briefly focus on influenza vaccine responses beyond hemagglutination inhibition that may correlate with protection against influenza viruses of different subtypes. Third, we explain how studying host responses to influenza infection and vaccination with advanced serologic methods, B-cell receptor sequencing, and transcriptomic profiling can guide the development of improved influenza virus vaccines. Fourth, we provide 2 suggestions on how current influenza vaccines can be optimized by redirecting immune responses toward conserved viral antigens and the use of adjuvants. Conclusion Influenza vaccine design can benefit from novel insights obtained from the study of host responses to influenza virus infection and vaccination. Integration of the large amount of available clinical and preclinical data requires systems approaches that can elucidate novel correlates of protection and will guide further development of influenza vaccine.
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Affiliation(s)
- Angela Choi
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adolfo García-Sastre
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York; The Tish Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael Schotsaert
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York.
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Church JA, Chasekwa B, Rukobo S, Govha M, Lee B, Carmolli MP, Ntozini R, Mutasa K, McNeal MM, Majo FD, Tavengwa NV, Kirkpatrick BD, Moulton LH, Humphrey JH, Prendergast AJ. Predictors of oral rotavirus vaccine immunogenicity in rural Zimbabwean infants. Vaccine 2020; 38:2870-2878. [PMID: 32088018 PMCID: PMC7065039 DOI: 10.1016/j.vaccine.2020.01.097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/16/2020] [Accepted: 01/26/2020] [Indexed: 01/13/2023]
Abstract
BACKGROUND Oral rotavirus vaccines (RVV) have poor immunogenicity in low-income countries, for reasons that remain unclear. This study identified the determinants of RVV immunogenicity among infants in rural Zimbabwe. METHODS Anti-rotavirus IgA titres were measured among a sub-group of infants enrolled in the Sanitation Hygiene Infant Nutrition Efficacy (SHINE) trial (NCT01824940). SHINE was a cluster-randomized trial of improved infant and young child feeding, and improved water, sanitation and hygiene (WASH) in two rural Zimbabwean districts. Infants received RVV as part of the national immunisation programme. Among HIV-unexposed infants in the non-WASH trial arms, we evaluated associations between potential risk factors (vaccine schedule and dose, maternal and infant nutritional status, infant diarrhoea, and household environment) and RVV immunogenicity (seroconversion, seropositivity and geometric mean titres) using multivariable regression. RESULTS Among 219 infants with seroconversion data, 43 (20%) successfully seroconverted and 176 (80%) failed to seroconvert to RVV. Seroconversion was positively associated with a higher length-for-age Z-score (LAZ) around the time of vaccination (adjusted RR 1.27 (95% CI 1.04, 1.55), P = 0.021), and negatively associated with concurrent OPV and RVV administration (adjusted RR 0.36 (0.19, 0.71), P = 0.003). Among 472 infants with post-vaccination titres, a higher LAZ score was associated with increased seropositivity (aRR 1.21 (95% CI 1.06, 1.38), P = 0.004), and higher birthweight was associated with increased IgA titres (0.45 (95%CI 0.18, 1.09) U/mL greater per 100 g gain in birthweight; P = 0.001). CONCLUSIONS Infant ponderal and linear growth were positively associated with RVV immunogenicity, while concurrent administration of OPV was negatively associated with RVV immunogenicity. Together, these findings suggest that improving foetal growth and separating RVV and OPV administration are plausible approaches to increasing RVV immunogenicity.
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Affiliation(s)
- James A Church
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe; Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, UK.
| | - Bernard Chasekwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Sandra Rukobo
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Margaret Govha
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Benjamin Lee
- Vaccine Testing Center, Department of Pediatrics, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Marya P Carmolli
- Vaccine Testing Center, Department of Microbiology & Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Robert Ntozini
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Kuda Mutasa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Monica M McNeal
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Florence D Majo
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Naume V Tavengwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Beth D Kirkpatrick
- Vaccine Testing Center, Department of Microbiology & Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Lawrence H Moulton
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jean H Humphrey
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe; Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew J Prendergast
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe; Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, UK; Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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44
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Avey S, Mohanty S, Chawla DG, Meng H, Bandaranayake T, Ueda I, Zapata HJ, Park K, Blevins TP, Tsang S, Belshe RB, Kaech SM, Shaw AC, Kleinstein SH. Seasonal Variability and Shared Molecular Signatures of Inactivated Influenza Vaccination in Young and Older Adults. THE JOURNAL OF IMMUNOLOGY 2020; 204:1661-1673. [PMID: 32060136 DOI: 10.4049/jimmunol.1900922] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/08/2020] [Indexed: 01/01/2023]
Abstract
The seasonal influenza vaccine is an important public health tool but is only effective in a subset of individuals. The identification of molecular signatures provides a mechanism to understand the drivers of vaccine-induced immunity. Most previously reported molecular signatures of human influenza vaccination were derived from a single age group or season, ignoring the effects of immunosenescence or vaccine composition. Thus, it remains unclear how immune signatures of vaccine response change with age across multiple seasons. In this study we profile the transcriptional landscape of young and older adults over five consecutive vaccination seasons to identify shared signatures of vaccine response as well as marked seasonal differences. Along with substantial variability in vaccine-induced signatures across seasons, we uncovered a common transcriptional signature 28 days postvaccination in both young and older adults. However, gene expression patterns associated with vaccine-induced Ab responses were distinct in young and older adults; for example, increased expression of killer cell lectin-like receptor B1 (KLRB1; CD161) 28 days postvaccination positively and negatively predicted vaccine-induced Ab responses in young and older adults, respectively. These findings contribute new insights for developing more effective influenza vaccines, particularly in older adults.
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Affiliation(s)
- Stefan Avey
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520
| | - Daniel G Chawla
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511
| | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520
| | - Thilinie Bandaranayake
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520
| | - Ikuyo Ueda
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520
| | - Heidi J Zapata
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520
| | - Koonam Park
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520; and
| | - Tamara P Blevins
- Division of Infectious Diseases, Department of Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104
| | - Sui Tsang
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520
| | - Robert B Belshe
- Division of Infectious Diseases, Department of Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104
| | - Susan M Kaech
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520; and
| | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520;
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511; .,Department of Pathology, Yale School of Medicine, New Haven, CT 06520.,Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520; and
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45
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Khoomrung S, Nookaew I, Sen P, Olafsdottir TA, Persson J, Moritz T, Andersen P, Harandi AM, Nielsen J. Metabolic Profiling and Compound-Class Identification Reveal Alterations in Serum Triglyceride Levels in Mice Immunized with Human Vaccine Adjuvant Alum. J Proteome Res 2020; 19:269-278. [PMID: 31625748 DOI: 10.1021/acs.jproteome.9b00517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Alum has been widely used as an adjuvant for human vaccines; however, the impact of Alum on host metabolism remains largely unknown. Herein, we applied mass spectrometry (MS) (liquid chromatography-MS)-based metabolic and lipid profiling to monitor the effects of the Alum adjuvant on mouse serum at 6, 24, 72, and 168 h post-vaccination. We propose a new strategy termed subclass identification and annotation for metabolomics for class-wise identification of untargeted metabolomics data generated from high-resolution MS. Using this approach, we identified and validated the levels of several lipids in mouse serum that were significantly altered following Alum administration. These lipids showed a biphasic response even 168 h after vaccination. The majority of the lipids were triglycerides (TAGs), where TAGs with long-chain unsaturated fatty acids (FAs) decreased at 24 h and TAGs with short-chain FAs decreased at 168 h. To our knowledge, this is the first report on the impact of human vaccine adjuvant Alum on the host metabolome, which may provide new insights into the mechanism of action of Alum.
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Affiliation(s)
- Sakda Khoomrung
- Systems and Synthetic Biology, Department of Biology and Biological Engineering , Chalmers University of Technology , Gothenburg SE-412 96 , Sweden.,Department of Biochemistry and Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok 10700 , Thailand.,Center for Innovation in Chemistry (PERCH-CIC), Faculty of Science , Mahidol University , Rama 6 Road , Bangkok 10400 , Thailand
| | - Intawat Nookaew
- Systems and Synthetic Biology, Department of Biology and Biological Engineering , Chalmers University of Technology , Gothenburg SE-412 96 , Sweden.,Department of Biomedical Informatics, College of Medicine , University of Arkansas for Medical Sciences , Little Rock 72205 , United States
| | - Partho Sen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering , Chalmers University of Technology , Gothenburg SE-412 96 , Sweden
| | - Thorunn A Olafsdottir
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Gothenburg SE-405 30 , Sweden
| | - Josefine Persson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Gothenburg SE-405 30 , Sweden
| | - Thomas Moritz
- Swedish Metabolomics Centre, Department of Forest Genetics and Plant Physiology , Swedish University of Agricultural Sciences , Umeå 750 07 , Sweden
| | | | - Ali M Harandi
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Gothenburg SE-405 30 , Sweden.,Vaccine Evaluation Center, BC Children's Hospital Research Institute , The University of British Columbia , 950 West 28th Avenue , Vancouver , BC V5Z 4H4 , Canada
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering , Chalmers University of Technology , Gothenburg SE-412 96 , Sweden
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46
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Bongen E, Lucian H, Khatri A, Fragiadakis GK, Bjornson ZB, Nolan GP, Utz PJ, Khatri P. Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection. Cell Rep 2019; 29:1961-1973.e4. [PMID: 31722210 PMCID: PMC6856718 DOI: 10.1016/j.celrep.2019.10.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/12/2019] [Accepted: 10/03/2019] [Indexed: 02/09/2023] Open
Abstract
Sex differences in autoimmunity and infection suggest that a better understanding of molecular sex differences will improve the diagnosis and treatment of immune-related disease. We identified 144 differentially expressed genes, referred to as immune sex expression signature (iSEXS), between human males and females using an integrated multi-cohort analysis of blood transcriptome profiles from six discovery cohorts from five continents with 458 healthy individuals. We validated iSEXS in 11 additional cohorts of 524 peripheral blood samples. When we separated iSEXS into genes located on sex chromosomes (XY-iSEXS) or autosomes (autosomal-iSEXS), both modules distinguished males and females. iSEXS reflects sex differences in immune cell proportions, with female-associated genes showing higher expression by CD4+ T cells and male-associated genes showing higher expression by myeloid cells. Autosomal-iSEXS detected an increase in monocytes with age in females, reflected sex-differential immune cell dynamics during influenza infection, and predicted antibody response in males, but not females.
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Affiliation(s)
- Erika Bongen
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Haley Lucian
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Avani Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gabriela K Fragiadakis
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zachary B Bjornson
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
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47
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Rogers LRK, de Los Campos G, Mias GI. Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination. Front Immunol 2019; 10:2616. [PMID: 31787983 PMCID: PMC6854009 DOI: 10.3389/fimmu.2019.02616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/21/2019] [Indexed: 12/18/2022] Open
Abstract
Influenza, a communicable disease, affects thousands of people worldwide. Young children, elderly, immunocompromised individuals and pregnant women are at higher risk for being infected by the influenza virus. Our study aims to highlight differentially expressed genes in influenza disease compared to influenza vaccination, including variability due to age and sex. To accomplish our goals, we conducted a meta-analysis using publicly available microarray expression data. Our inclusion criteria included subjects with influenza, subjects who received the influenza vaccine and healthy controls. We curated 18 microarray datasets for a total of 3,481 samples (1,277 controls, 297 influenza infection, 1,907 influenza vaccination). We pre-processed the raw microarray expression data in R using packages available to pre-process Affymetrix and Illumina microarray platforms. We used a Box-Cox power transformation of the data prior to our down-stream analysis to identify differentially expressed genes. Statistical analyses were based on linear mixed effects model with all study factors and successive likelihood ratio tests (LRT) to identify differentially-expressed genes. We filtered LRT results by disease (Bonferroni adjusted p < 0.05) and used a two-tailed 10% quantile cutoff to identify biologically significant genes. Furthermore, we assessed age and sex effects on the disease genes by filtering for genes with a statistically significant (Bonferroni adjusted p < 0.05) interaction between disease and age, and disease and sex. We identified 4,889 statistically significant genes when we filtered the LRT results by disease factor, and gene enrichment analysis (gene ontology and pathways) included innate immune response, viral process, defense response to virus, Hematopoietic cell lineage and NF-kappa B signaling pathway. Our quantile filtered gene lists comprised of 978 genes each associated with influenza infection and vaccination. We also identified 907 and 48 genes with statistically significant (Bonferroni adjusted p < 0.05) disease-age and disease-sex interactions, respectively. Our meta-analysis approach highlights key gene signatures and their associated pathways for both influenza infection and vaccination. We also were able to identify genes with an age and sex effect. This gives potential for improving current vaccines and exploring genes that are expressed equally across ages when considering universal vaccinations for influenza.
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Affiliation(s)
- Lavida R K Rogers
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Gustavo de Los Campos
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States.,Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States
| | - George I Mias
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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48
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Tomic A, Tomic I, Dekker CL, Maecker HT, Davis MM. The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system. Sci Data 2019; 6:214. [PMID: 31636302 PMCID: PMC6803714 DOI: 10.1038/s41597-019-0213-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 08/27/2019] [Indexed: 01/30/2023] Open
Abstract
Machine learning has the potential to identify novel biological factors underlying successful antibody responses to influenza vaccines. The first attempts have revealed a high level of complexity in establishing influenza immunity, and many different cellular and molecular components are involved. Of note is that the previously identified correlates of protection fail to account for the majority of individual responses across different age groups and influenza seasons. Challenges remain from the small sample sizes in most studies and from often limited data sets, such as transcriptomic data. Here we report the creation of a unified database, FluPRINT, to enable large-scale studies exploring the cellular and molecular underpinnings of successful antibody responses to influenza vaccines. Over 3,000 parameters were considered, including serological responses to influenza strains, serum cytokines, cell phenotypes, and cytokine stimulations. FluPRINT, facilitates the application of machine learning algorithms for data mining. The data are publicly available and represent a resource to uncover new markers and mechanisms that are important for influenza vaccine immunogenicity. Measurement(s) | immune response trait | Technology Type(s) | digital curation | Factor Type(s) | gender • race • visit_age • bmi • flu_vaccination_history • statin_use • influenza_infection_history • influenza_hospitalization • cmv_status • ebv_status | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9902447
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Affiliation(s)
- Adriana Tomic
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94304, USA. .,Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, OX3 9DU, UK.
| | | | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Holden T Maecker
- Human Immune Monitoring Center, Stanford University, Stanford, CA, 94304, USA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94304, USA. .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94304, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94304, USA.
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49
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Shah NM, Imami N, Kelleher P, Barclay WS, Johnson MR. Pregnancy-related immune suppression leads to altered influenza vaccine recall responses. Clin Immunol 2019; 208:108254. [PMID: 31470087 DOI: 10.1016/j.clim.2019.108254] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/17/2019] [Accepted: 08/26/2019] [Indexed: 01/12/2023]
Abstract
Pregnancy is a risk factor for severe influenza infection. Despite achieving seroprotective antibody titres post immunisation fewer pregnant women experience a reduction in influenza-like illness compared to non-pregnant cohorts. This may be due to the effects that immune-modulation in pregnancy has on vaccine efficacy leading to a less favourable immunologic response. To understand this, we investigated the antigen-specific cellular responses and leukocyte phenotype in pregnant and non-pregnant women who achieved seroprotection post immunisation. We show that pregnancy is associated with better antigen-specific inflammatory (IFN-γ) responses and an expansion of central memory T cells (Tcm) post immunisation, but low-level pregnancy-related immune regulation (HLA-G, PIBF) and associated reduced B-cell antibody maintenance (TGF-β) suggest poor immunologic responses compared to the non-pregnant. Thus far, studies of influenza vaccine immunogenicity have focused on the induction of antibodies but understanding additional vaccine-related cellular responses is needed to fully appreciate how pregnancy impacts on vaccine effectiveness.
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Affiliation(s)
- Nishel M Shah
- Department of Surgery and Cancer, Imperial College London, Chelsea and Westminster Hospital, London SW10 9NH, United Kingdom.
| | - Nesrina Imami
- Department of Medicine, Imperial College London, Chelsea and Westminster Hospital, London SW10 9NH, United Kingdom
| | - Peter Kelleher
- Department of Medicine, Imperial College London, Chelsea and Westminster Hospital, London SW10 9NH, United Kingdom
| | - Wendy S Barclay
- Department of Medicine, Imperial College London, Chelsea and Westminster Hospital, London SW10 9NH, United Kingdom
| | - Mark R Johnson
- Department of Surgery and Cancer, Imperial College London, Chelsea and Westminster Hospital, London SW10 9NH, United Kingdom
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50
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Hussain T, Quinn KM. Similar but different: virtual memory CD8 T cells as a memory-like cell population. Immunol Cell Biol 2019; 97:675-684. [PMID: 31140625 DOI: 10.1111/imcb.12277] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/26/2019] [Accepted: 05/26/2019] [Indexed: 01/02/2023]
Abstract
Immunological memory is a phenomenon where the immune system can respond more rapidly to pathogens and immunological challenges that it has previously encountered. It is defined by several key hallmarks. After an initial encounter, immune cells (1) expand and (2) differentiate to form memory cell populations. Memory cells are (3) long-lived and (4) facilitate more rapid immune responses to subsequent infection because of (i) an increase in cell number, (ii) a decrease in the signaling threshold required for entry into cell cycle or effector function and (iii) localization of cells to tissue sites for surveillance. Classically, immunological memory has been antigen specific but it is becoming apparent that mechanisms of immunological memory can be co-opted by innate or antigen-inexperienced immune cells to generate heterogeneity in immune responses. One such cell is the virtual memory CD8 T (TVM ) cell, which is a semi-differentiated but antigen-naïve CD8 T-cell population. This review will summarize current knowledge of how TVM cells are generated, their memory-like hallmarks, how they are maintained during steady state, infection and aging, and propose a model to integrate key signaling pathways during their generation.
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Affiliation(s)
- Tabinda Hussain
- Monash University Biomedicine Discovery Institute, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Kylie M Quinn
- Monash University Biomedicine Discovery Institute, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,RMIT University School of Biomedical and Health Sciences, Bundoora, VIC, Australia
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