1
|
Pelletier AN, Sanchez GP, Izmirly A, Watson M, Di Pucchio T, Carvalho KI, Filali-Mouhim A, Paramithiotis E, Timenetsky MDCST, Precioso AR, Kalil J, Diamond MS, Haddad EK, Kallas EG, Sekaly RP. A pre-vaccination immune metabolic interplay determines the protective antibody response to a dengue virus vaccine. Cell Rep 2024; 43:114370. [PMID: 38900640 DOI: 10.1016/j.celrep.2024.114370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 02/05/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Protective immunity to dengue virus (DENV) requires antibody response to all four serotypes. Systems vaccinology identifies a multi-OMICs pre-vaccination signature and mechanisms predictive of broad antibody responses after immunization with a tetravalent live attenuated DENV vaccine candidate (Butantan-DV/TV003). Anti-inflammatory pathways, including TGF-β signaling expressed by CD68low monocytes, and the metabolites phosphatidylcholine (PC) and phosphatidylethanolamine (PE) positively correlate with broadly neutralizing antibody responses against DENV. In contrast, expression of pro-inflammatory pathways and cytokines (IFN and IL-1) in CD68hi monocytes and primary and secondary bile acids negatively correlates with broad DENV-specific antibody responses. Induction of TGF-β and IFNs is done respectively by PC/PE and bile acids in CD68low and CD68hi monocytes. The inhibition of viral sensing by PC/PE-induced TGF-β is confirmed in vitro. Our studies show that the balance between metabolites and the pro- or anti-inflammatory state of innate immune cells drives broad and protective B cell response to a live attenuated dengue vaccine.
Collapse
Affiliation(s)
- Adam-Nicolas Pelletier
- RPM Bioinfo Solutions, Sainte-Thérèse, QC, Canada; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Gabriela Pacheco Sanchez
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Abdullah Izmirly
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Tiziana Di Pucchio
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Karina Inacio Carvalho
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Abdelali Filali-Mouhim
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | | | | | | | - Jorge Kalil
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, SP, Brazil; Institute for Investigation in Immunology-Instituto Nacional de Ciência e Tecnologia-iii-INCT, São Paulo, SP, Brazil
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elias K Haddad
- Department of Medicine and Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Esper G Kallas
- Instituto Butantan, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, Hospital das Clínicas, School of Medicine, University of Sao Paulo, São Paulo 01246-903, Brazil
| | - Rafick Pierre Sekaly
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
2
|
Pasin C, Nuñez DG, Kusejko K, Hachfeld A, Buvelot H, Cavassini M, Damonti L, Fux C, de Tejada BM, Notter J, Trkola A, Günthard HF, Aebi-Popp K, Kouyos RD, Abela IA. Impact of hormonal therapy on HIV-1 immune markers in cis women and gender minorities. HIV Med 2024. [PMID: 38830635 DOI: 10.1111/hiv.13677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/17/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Although sex hormones are recognized to induce immune variations, the effect of hormonal therapy use on immunity is only poorly understood. Here, we quantified how hormonal therapy use affects HIV-1 immune markers in cis women (CW) and trans women and non-binary people (TNBP) with HIV. METHODS We considered CD4, CD8 and lymphocyte measurements from cis men (CM), CW and TNBP in the Swiss HIV Cohort Study. We modelled HIV-1 markers using linear mixed-effects models with an interaction between 'gender' (CW, TNBP) and 'hormonal therapy use' (yes/no). Models were adjusted on age, ethnicity, education level, time since start of antiretroviral therapy and use of intravenous drugs. We assessed the inflammatory effect of hormonal therapy use in 31 TNBP using serum proteomics measurements of 92 inflammation markers. RESULTS We included 54 083 measurements from 3092 CW and 83 TNBP, and 147 230 measurements from 8611 CM. Hormonal therapy use increased CD4 count and CD4:CD8 ratio in TNBP more than in CW (pinteraction = 0.02 and 0.007, respectively). TNBP with hormonal therapy use had significantly higher CD4 counts [median = 772 cells/μL, interquartile range (IQR): 520-1006] than without (617 cells/μL, 426-892). This was similar to the effect of CW versus CM on CD4 T cells. Hormonal therapy use did not affect serum protein concentrations in TNBP. CONCLUSION This study highlights the potential role of hormonal therapy use in modulating the immune system among other biological and social factors, especially in TNBP with HIV.
Collapse
Affiliation(s)
- Chloé Pasin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Collegium Helveticum, Zurich, Switzerland
| | - David Garcia Nuñez
- Center for Gender Variance, Department of Plastic, Reconstructive, Aesthetic and Hand Surgery, University Hospital Basel, Basel, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Anna Hachfeld
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Hélène Buvelot
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Lauro Damonti
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
- Ente Ospedaliero Cantonale, Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Christoph Fux
- Department of Infectious Diseases and Hospital Hygiene, Kantonsspital Aarau, Aarau, Switzerland
| | - Begoña Martinez de Tejada
- Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva and Faculty of Medicine, Geneva, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karoline Aebi-Popp
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Irene A Abela
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
3
|
Hill BD, Zak AJ, Raja S, Bugada LF, Rizvi SM, Roslan SB, Nguyen HN, Chen J, Jiang H, Ono A, Goldstein DR, Wen F. iGATE analysis improves the interpretability of single-cell immune landscape of influenza infection. JCI Insight 2024; 9:e172140. [PMID: 38814732 DOI: 10.1172/jci.insight.172140] [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] [Indexed: 06/01/2024] Open
Abstract
Influenza poses a persistent health burden worldwide. To design equitable vaccines effective across all demographics, it is essential to better understand how host factors such as genetic background and aging affect the single-cell immune landscape of influenza infection. Cytometry by time-of-flight (CyTOF) represents a promising technique in this pursuit, but interpreting its large, high-dimensional data remains difficult. We have developed a new analytical approach, in silico gating annotating training elucidating (iGATE), based on probabilistic support vector machine classification. By rapidly and accurately "gating" tens of millions of cells in silico into user-defined types, iGATE enabled us to track 25 canonical immune cell types in mouse lung over the course of influenza infection. Applying iGATE to study effects of host genetic background, we show that the lower survival of C57BL/6 mice compared with BALB/c was associated with a more rapid accumulation of inflammatory cell types and decreased IL-10 expression. Furthermore, we demonstrate that the most prominent effect of aging is a defective T cell response, reducing survival of aged mice. Finally, iGATE reveals that the 25 canonical immune cell types exhibited differential influenza infection susceptibility and replication permissiveness in vivo, but neither property varied with host genotype or aging. The software is available at https://github.com/UmichWenLab/iGATE.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Judy Chen
- Program in Immunology
- Department of Internal Medicine
| | | | - Akira Ono
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Fei Wen
- Department of Chemical Engineering
| |
Collapse
|
4
|
Ye L, Li P, Wang M, Wu F, Han S, Ma L. Profiling of Early Immune Responses to Vaccination Using THP-1-Derived Dendritic Cells. Int J Mol Sci 2024; 25:5509. [PMID: 38791547 PMCID: PMC11121899 DOI: 10.3390/ijms25105509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
The COVID-19 pandemic has made assessing vaccine efficacy more challenging. Besides neutralizing antibody assays, systems vaccinology studies use omics technology to reveal immune response mechanisms and identify gene signatures in human peripheral blood mononuclear cells (PBMCs). However, due to their low proportion in PBMCs, profiling the immune response signatures of dendritic cells (DCs) is difficult. Here, we develop a predictive model for evaluating early immune responses in dendritic cells. We establish a THP-1-derived dendritic cell (TDDC) model and stimulate their maturation in vitro with an optimal dose of attenuated yellow fever 17D (YF-17D). Transcriptomic analysis reveals that type I interferon (IFN-I)-induced immunity plays a key role in dendritic cells. IFN-I regulatory biomarkers (IRF7, SIGLEC1) and IFN-I-inducible biomarkers (IFI27, IFI44, IFIT1, IFIT3, ISG15, MX1, OAS2, OAS3) are identified and validated in vitro and in vivo. Furthermore, we apply this TDDC approach to various types of vaccines, providing novel insights into their early immune response signatures and their heterogeneity in vaccine recipients. Our findings suggest that a standardizable TDDC model is a promising predictive approach to assessing early immunity in DCs. Further research into vaccine efficacy assessment approaches on various types of immune cells could lead to a systemic regimen for vaccine development in the future.
Collapse
Affiliation(s)
- Lei Ye
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518052, China
| | - Ping Li
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
| | - Mingzhe Wang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
| | - Feng Wu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
| | - Sanyang Han
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
| | - Lan Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518052, China
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| |
Collapse
|
5
|
Braverman G, Barbhaiya M, Nong M, Bykerk VP, Hupert N, Lewis V C, Mandl LA. Association of COVID-19 Vaccinations With Flares of Systemic Rheumatic Disease: A Case-Crossover Study. Arthritis Care Res (Hoboken) 2024; 76:733-742. [PMID: 38163750 PMCID: PMC11039379 DOI: 10.1002/acr.25288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/04/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE We aimed to determine the association of COVID-19 vaccination with flares of systemic rheumatic disease (SRD). METHODS Adults with systemic rheumatic disease (SRD) in a single-center COVID-19 Rheumatology Registry were invited to enroll in a study of flares. COVID-19 vaccine information from March 5, 2021, to September 6, 2022, was obtained from chart review and self-report. Participants self-reported periods of SRD flare and periods without SRD flare. "Hazard periods" were defined as the time before a self-report of flare and "control periods" as the time before a self-report of no flare. The association between flare and COVID-19 vaccination was evaluated during hazard and control periods through univariate conditional logistic regression stratified by participant, using lookback windows of 2, 7, and 14 days. RESULTS A total of 434 participants (mean ± SD age 59 ± 13 years, 84.1% female, 81.8% White, 64.5% with inflammatory arthritis, and 27.0% with connective tissue diseases) contributed to both the hazard and control periods and were included in analysis. A total of 1,316 COVID-19 vaccinations were identified (58.5% Pfizer-BioNTech, 39.5% Moderna, and 1.4% Johnson & Johnson); 96.1% of participants received at least one dose and 93.1% at least two doses. There was no association between COVID-19 vaccination and flares in the subsequent 2, 7, or 14 days (odds ratio [OR] 1.46, 95% confidence interval [CI] 0.86-2.46; OR 1.09, 95% CI 0.76-1.55; and OR 0.85, 95% CI 0.64-1.13, respectively). Analyses stratified on sex, age, SRD subtype, and vaccine manufacturer similarly showed no association between vaccination and flare. CONCLUSION COVID-19 vaccination was not associated with flares in this cohort of participants with SRD. These data are reassuring and can inform shared decision-making on COVID-19 immunization.
Collapse
Affiliation(s)
- Genna Braverman
- Division of Rheumatology, Hospital for Special Surgery, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Medha Barbhaiya
- Division of Rheumatology, Hospital for Special Surgery, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | | | - Vivian P. Bykerk
- Division of Rheumatology, Hospital for Special Surgery, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nathaniel Hupert
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Colby Lewis V
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Lisa A. Mandl
- Division of Rheumatology, Hospital for Special Surgery, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
6
|
Karuppannan M, Ming LC, Abdul Wahab MS, Mohd Noordin Z, Yee S, Hermansyah A. Self-reported side effects of COVID-19 vaccines among the public. J Pharm Policy Pract 2024; 17:2308617. [PMID: 38420042 PMCID: PMC10901186 DOI: 10.1080/20523211.2024.2308617] [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] [Indexed: 03/02/2024] Open
Abstract
Background The safety, side effects and efficacy profile of COVID-19 vaccines remain subjects of ongoing concern among the public in Malaysia. The aim of this study was to determine the types of adverse effects following immunisation with COVID-19 vaccines and the differences based on various types of COVID-19 vaccines to raise public awareness and reduce vaccine hesitancy among the public. Methods A total of 901 Malaysian adults (≥18 years) who received various COVID-19 vaccines were selected to participate in our cross-sectional study through an online survey between December 2021 and January 2022. Results A total of 814 (90.3%) of the participants reported ≥1 side effect following COVID-19 immunisation. Of these, the predominant symptoms were swelling at the injection site (n = 752, 83.5%), headache (n = 638, 70.8%), pain or soreness at the injection site (n = 628, 69.7%), fatigue or tiredness (n = 544, 60.4%), muscle weakness (n = 529, 58.7%) and diarrhea (n = 451, 50.1%). Recipients of the Pfizer-BioNTech (Comirnaty ®) vaccine reported the highest number of adverse effects (n = 355, 43.6%), followed by mixed COVID-19 vaccines (n = 254, 31.2%), the Oxford-AstraZeneca (ChAdOx1-®[recombinant]) vaccine (n = 113, 13.9%) and the Sinovac (CoronaVac®) vaccine (n = 90, 11.1%). The study showed that individuals who reported significantly more side effects were of elderly age, female gender and high educational level [P value < 0.05]. Mixed COVID-19 vaccine recipients also reported significantly more local and systemic symptoms after the first dose and third dose when compared with other single vaccine recipients. Conclusion This study demonstrated the types of self-reported adverse effects following immunisation with single and mixed COVID-19 vaccines. These findings may provide the side effects of different COVID-19 vaccines with the hope of educating the public on the safety profiles of these vaccines and reducing vaccine hesitancy among the public.
Collapse
Affiliation(s)
- Mahmathi Karuppannan
- Department of Clinical Pharmacy, Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Bandar Puncak Alam, Malaysia
- Cardiology Therapeutics Research Group, Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, Bandar Puncak Alam, Malaysia
| | - Long Chiau Ming
- Department of Pharmacy Practice, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
- School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
- PAPRSB Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei
| | - Mohd Shahezwan Abdul Wahab
- Department of Clinical Pharmacy, Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Bandar Puncak Alam, Malaysia
- Cardiology Therapeutics Research Group, Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, Bandar Puncak Alam, Malaysia
| | - Zakiah Mohd Noordin
- Department of Clinical Pharmacy, Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Bandar Puncak Alam, Malaysia
- Cardiology Therapeutics Research Group, Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, Bandar Puncak Alam, Malaysia
| | - Shermaine Yee
- Faculty of Medicine, Quest International University, Ipoh, Malaysia
| | - Andi Hermansyah
- Department of Pharmacy Practice, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
| |
Collapse
|
7
|
Zhang Y, Zhao L, Zhang J, Zhang X, Han S, Sun Q, Yao M, Pang B, Duan Q, Jiang X. Antibody and transcription landscape in peripheral blood mononuclear cells of elderly adults over 70 years of age with third dose of COVID-19 BBIBP-CorV and ZF2001 booster vaccine. Immun Ageing 2024; 21:11. [PMID: 38280989 PMCID: PMC10821575 DOI: 10.1186/s12979-023-00408-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/20/2023] [Indexed: 01/29/2024]
Abstract
BACKGROUND In the context of the COVID-19 pandemic and extensive vaccination, it is important to explore the immune response of elderly adults to homologous and heterologous booster vaccines of COVID-19. At this point, we detected serum IgG antibodies and PBMC sample transcriptome profiles in 46 participants under 70 years old and 25 participants over 70 years old who received the third dose of the BBIBP-CorV and ZF2001 vaccines. RESULTS On day 7, the antibody levels of people over 70 years old after the third dose of booster vaccine were lower than those of young people, and the transcriptional responses of innate and adaptive immunity were also weak. The age of the participants showed a significant negative correlation with functions related to T-cell differentiation and costimulation. Nevertheless, 28 days after the third dose, the IgG antibodies of elderly adults reached equivalence to those of younger adults, and immune-related transcriptional regulation was significantly improved. The age showed a significant positive correlation with functions related to "chemokine receptor binding", "chemokine activity", and "chemokine-mediated signaling pathway". CONCLUSIONS Our results document that the response of elderly adults to the third dose of the vaccine was delayed, but still able to achieve comparable immune effects compared to younger adults, in regard to antibody responses as well as at the transcript level.
Collapse
Affiliation(s)
- Yuwei Zhang
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Lianxiang Zhao
- School of Public Health and Management, Binzhou Medical University, Yantai , Shandong Province, China
| | - Jinzhong Zhang
- Liaocheng Center for Disease Control and Prevention, Liaocheng, Shandong Province, China
| | - Xiaomei Zhang
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Shanshan Han
- School of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Qingshuai Sun
- School of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Mingxiao Yao
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Bo Pang
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Qing Duan
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Xiaolin Jiang
- School of Public Health and Management, Binzhou Medical University, Yantai , Shandong Province, China.
- School of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong Province, China.
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road , Jinan, 250014, Shandong Province, China.
| |
Collapse
|
8
|
Guo M, Xiong M, Peng J, Guan T, Su H, Huang Y, Yang CG, Li Y, Boraschi D, Pillaiyar T, Wang G, Yi C, Xu Y, Chen C. Multi-omics for COVID-19: driving development of therapeutics and vaccines. Natl Sci Rev 2023; 10:nwad161. [PMID: 37936830 PMCID: PMC10627145 DOI: 10.1093/nsr/nwad161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 11/09/2023] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and economy. The development of therapeutics and vaccines to combat this virus is continuously progressing. Multi-omics approaches, including genomics, transcriptomics, proteomics, metabolomics, epigenomics and metallomics, have helped understand the structural and molecular features of the virus, thereby assisting in the design of potential therapeutics and accelerating vaccine development for COVID-19. Here, we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19, in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines.
Collapse
Affiliation(s)
- Mengyu Guo
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Tong Guan
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Diana Boraschi
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Institute of Biochemistry and Cell Biology, National Research Council, Napoli 80131, Italy
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Guanbo Wang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Chen
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
| |
Collapse
|
9
|
Affaticati F, Bartholomeus E, Mullan K, Damme PV, Beutels P, Ogunjimi B, Laukens K, Meysman P. Multi-View Learning to Unravel the Different Levels Underlying Hepatitis B Vaccine Response. Vaccines (Basel) 2023; 11:1236. [PMID: 37515051 PMCID: PMC10384938 DOI: 10.3390/vaccines11071236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The immune system acts as an intricate apparatus that is dedicated to mounting a defense and ensures host survival from microbial threats. To engage this faceted immune response and provide protection against infectious diseases, vaccinations are a critical tool to be developed. However, vaccine responses are governed by levels that, when interrogated, separately only explain a fraction of the immune reaction. To address this knowledge gap, we conducted a feasibility study to determine if multi-view modeling could aid in gaining actionable insights on response markers shared across populations, capture the immune system's diversity, and disentangle confounders. We thus sought to assess this multi-view modeling capacity on the responsiveness to the Hepatitis B virus (HBV) vaccination. Seroconversion to vaccine-induced antibodies against the HBV surface antigen (anti-HBs) in early converters (n = 21; <2 months) and late converters (n = 9; <6 months) and was defined based on the anti-HBs titers (>10IU/L). The multi-view data encompassed bulk RNA-seq, CD4+ T-cell parameters (including T-cell receptor data), flow cytometry data, and clinical metadata (including age and gender). The modeling included testing single-view and multi-view joint dimensionality reductions. Multi-view joint dimensionality reduction outperformed single-view methods in terms of the area under the curve and balanced accuracy, confirming the increase in predictive power to be gained. The interpretation of these findings showed that age, gender, inflammation-related gene sets, and pre-existing vaccine-specific T-cells could be associated with vaccination responsiveness. This multi-view dimensionality reduction approach complements clinical seroconversion and all single modalities. Importantly, this modeling could identify what features could predict HBV vaccine response. This methodology could be extended to other vaccination trials to identify the key features regulating responsiveness.
Collapse
Affiliation(s)
- Fabio Affaticati
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
| | - Esther Bartholomeus
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp (VAXINFECTIO), 2610 Antwerp, Belgium
| | - Kerry Mullan
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
| | - Pierre Van Damme
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
| | - Philippe Beutels
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp (VAXINFECTIO), 2610 Antwerp, Belgium
- Department of Paediatrics, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
| |
Collapse
|
10
|
Tan CW, Valkenburg SA, Poon LLM, Wang LF. Broad-spectrum pan-genus and pan-family virus vaccines. Cell Host Microbe 2023; 31:902-916. [PMID: 37321173 PMCID: PMC10265776 DOI: 10.1016/j.chom.2023.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
Although the development and clinical application of SARS-CoV-2 vaccines during the COVID-19 pandemic demonstrated unprecedented vaccine success in a short time frame, it also revealed a limitation of current vaccines in their inability to provide broad-spectrum or universal protection against emerging variants. Broad-spectrum vaccines, therefore, remain a dream and challenge for vaccinology. This review will focus on current and future efforts in developing universal vaccines targeting different viruses at the genus and/or family levels, with a special focus on henipaviruses, influenza viruses, and coronaviruses. It is evident that strategies for developing broad-spectrum vaccines will be virus-genus or family specific, and it is almost impossible to adopt a universal approach for different viruses. On the other hand, efforts in developing broad-spectrum neutralizing monoclonal antibodies have been more successful and it is worth considering broad-spectrum antibody-mediated immunization, or "universal antibody vaccine," as an alternative approach for early intervention for future disease X outbreaks.
Collapse
Affiliation(s)
- Chee Wah Tan
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Sophie A Valkenburg
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo L M Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong SAR, China.
| | - Lin-Fa Wang
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore; Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Singhealth Duke-NUS Global Health Institute, Singapore, Singapore.
| |
Collapse
|
11
|
Hirota M, Tamai M, Yukawa S, Taira N, Matthews MM, Toma T, Seto Y, Yoshida M, Toguchi S, Miyagi M, Mori T, Tomori H, Tamai O, Kina M, Sakihara E, Yamashiro C, Miyagi M, Tamaki K, Wolf M, Collins MK, Kitano H, Ishikawa H. Human immune and gut microbial parameters associated with inter-individual variations in COVID-19 mRNA vaccine-induced immunity. Commun Biol 2023; 6:368. [PMID: 37081096 PMCID: PMC10119155 DOI: 10.1038/s42003-023-04755-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/24/2023] [Indexed: 04/22/2023] Open
Abstract
COVID-19 mRNA vaccines induce protective adaptive immunity against SARS-CoV-2 in most individuals, but there is wide variation in levels of vaccine-induced antibody and T-cell responses. However, the mechanisms underlying this inter-individual variation remain unclear. Here, using a systems biology approach based on multi-omics analyses of human blood and stool samples, we identified several factors that are associated with COVID-19 vaccine-induced adaptive immune responses. BNT162b2-induced T cell response is positively associated with late monocyte responses and inversely associated with baseline mRNA expression of activation protein 1 (AP-1) transcription factors. Interestingly, the gut microbial fucose/rhamnose degradation pathway is positively correlated with mRNA expression of AP-1, as well as a gene encoding an enzyme producing prostaglandin E2 (PGE2), which promotes AP-1 expression, and inversely correlated with BNT162b2-induced T-cell responses. These results suggest that baseline AP-1 expression, which is affected by commensal microbial activity, is a negative correlate of BNT162b2-induced T-cell responses.
Collapse
Affiliation(s)
- Masato Hirota
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Miho Tamai
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Sachie Yukawa
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
- Integrated Open Systems Unit, OIST, Onna-son, Okinawa, Japan
| | - Naoyuki Taira
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | | | - Takeshi Toma
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Yu Seto
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Makiko Yoshida
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Sakura Toguchi
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Mio Miyagi
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Tomoari Mori
- Research Support Division, Occupational Health and Safety, OIST, Onna-son, Okinawa, Japan
| | | | | | | | - Eishin Sakihara
- Health Care Center of the Naha Medical Association, Naha-city, Okinawa, Japan
| | - Chiaki Yamashiro
- Yamashiro Orthopedic Surgery Ophthalmology Clinic, Naha-city, Okinawa, Japan
| | | | - Kentaro Tamaki
- Naha-Nishi Clinic, Department of Breast Surgery, Naha-city, Okinawa, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, OIST, Onna-son, Okinawa, Japan
| | - Mary K Collins
- Research Support Division, Office of the Provost, OIST, Onna-son, Okinawa, Japan
| | - Hiroaki Kitano
- Integrated Open Systems Unit, OIST, Onna-son, Okinawa, Japan
| | - Hiroki Ishikawa
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan.
| |
Collapse
|
12
|
Naidu A, Nayak SS, Lulu S S, Sundararajan V. Advances in computational frameworks in the fight against TB: The way forward. Front Pharmacol 2023; 14:1152915. [PMID: 37077815 PMCID: PMC10106641 DOI: 10.3389/fphar.2023.1152915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Around 1.6 million people lost their life to Tuberculosis in 2021 according to WHO estimates. Although an intensive treatment plan exists against the causal agent, Mycobacterium Tuberculosis, evolution of multi-drug resistant strains of the pathogen puts a large number of global populations at risk. Vaccine which can induce long-term protection is still in the making with many candidates currently in different phases of clinical trials. The COVID-19 pandemic has further aggravated the adversities by affecting early TB diagnosis and treatment. Yet, WHO remains adamant on its "End TB" strategy and aims to substantially reduce TB incidence and deaths by the year 2035. Such an ambitious goal would require a multi-sectoral approach which would greatly benefit from the latest computational advancements. To highlight the progress of these tools against TB, through this review, we summarize recent studies which have used advanced computational tools and algorithms for-early TB diagnosis, anti-mycobacterium drug discovery and in the designing of the next-generation of TB vaccines. At the end, we give an insight on other computational tools and Machine Learning approaches which have successfully been applied in biomedical research and discuss their prospects and applications against TB.
Collapse
Affiliation(s)
| | | | | | - Vino Sundararajan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| |
Collapse
|
13
|
Akram N, Saeed F, Afzaal M, Shah YA, Qamar A, Faisal Z, Ghani S, Ateeq H, Akhtar MN, Tufail T, Hussain M, Asghar A, Rasheed A, Jbawi EA. Gut microbiota and synbiotic foods: Unveiling the relationship in COVID-19 perspective. Food Sci Nutr 2023; 11:1166-1177. [PMID: 36911846 PMCID: PMC10002946 DOI: 10.1002/fsn3.3162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 01/13/2023] Open
Abstract
The Coronavirus disease 2019 (COVID-19) has spread across the globe and is causing widespread disaster. The impact of gut microbiota on lung disease has been widely documented. Diet, environment, and genetics all play a role in shaping the gut microbiota, which can influence the immune system. Improving the gut microbiota profile through customized diet, nutrition, and supplementation has been shown to boost immunity, which could be one of the preventative methods for reducing the impact of various diseases. Poor nutritional status is frequently linked to inflammation and oxidative stress, both of which can affect the immune system. This review emphasizes the necessity of maintaining an adequate level of important nutrients to effectively minimize inflammation and oxidative stress, moreover to strengthen the immune system during the COVID-19 severity. Furthermore, the purpose of this review is to present information and viewpoints on the use of probiotics, prebiotics, and synbiotics as adjuvants for microbiota modification and its effects on COVID-19 prevention and treatment.
Collapse
Affiliation(s)
- Noor Akram
- Department of Food and NutritionGovernment College UniversityFaisalabadPakistan
| | - Farhan Saeed
- Department of Food ScienceGovernment College UniversityFaisalabadPakistan
| | - Muhammad Afzaal
- Department of Food ScienceGovernment College UniversityFaisalabadPakistan
| | - Yasir Abbas Shah
- Department of Food ScienceGovernment College UniversityFaisalabadPakistan
| | - Aiza Qamar
- Department of Nutrition and Health PromotionUniversity of Home Economics LahoreLahorePakistan
| | - Zargham Faisal
- Institute of Food Science and NutritionBahauddin Zakariya University MultanMultanPakistan
| | - Samia Ghani
- Faculty of Pharmaceutical SciencesGovernment College University FaisalabadPunjabPakistan
| | - Huda Ateeq
- Department of Food ScienceGovernment College UniversityFaisalabadPakistan
| | - Muhammad Nadeem Akhtar
- University Institute of Diet and Nutritional SciencesThe University of LahoreLahorePakistan
| | - Tabassum Tufail
- University Institute of Diet and Nutritional SciencesThe University of LahoreLahorePakistan
| | - Muzzamal Hussain
- Department of Food ScienceGovernment College UniversityFaisalabadPakistan
| | - Aasma Asghar
- Department of Food ScienceGovernment College UniversityFaisalabadPakistan
| | - Ammara Rasheed
- Department of Food and NutritionGovernment College UniversityFaisalabadPakistan
| | | |
Collapse
|
14
|
Sparks R, Lau WW, Liu C, Han KL, Vrindten KL, Sun G, Cox M, Andrews SF, Bansal N, Failla LE, Manischewitz J, Grubbs G, King LR, Koroleva G, Leimenstoll S, Snow L, Chen J, Tang J, Mukherjee A, Sellers BA, Apps R, McDermott AB, Martins AJ, Bloch EM, Golding H, Khurana S, Tsang JS. Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19. Nature 2023; 614:752-761. [PMID: 36599369 PMCID: PMC10481789 DOI: 10.1038/s41586-022-05670-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023]
Abstract
Acute viral infections can have durable functional impacts on the immune system long after recovery, but how they affect homeostatic immune states and responses to future perturbations remain poorly understood1-4. Here we use systems immunology approaches, including longitudinal multimodal single-cell analysis (surface proteins, transcriptome and V(D)J sequences) to comparatively assess baseline immune statuses and responses to influenza vaccination in 33 healthy individuals after recovery from mild, non-hospitalized COVID-19 (mean, 151 days after diagnosis) and 40 age- and sex-matched control individuals who had never had COVID-19. At the baseline and independent of time after COVID-19, recoverees had elevated T cell activation signatures and lower expression of innate immune genes including Toll-like receptors in monocytes. Male individuals who had recovered from COVID-19 had coordinately higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared with healthy male individuals and female individuals who had recovered from COVID-19, in part because male recoverees had monocytes with higher IL-15 responses early after vaccination coupled with elevated prevaccination frequencies of 'virtual memory'-like CD8+ T cells poised to produce more IFNγ after IL-15 stimulation. Moreover, the expression of the repressed innate immune genes in monocytes increased by day 1 to day 28 after vaccination in recoverees, therefore moving towards the prevaccination baseline of the healthy control individuals. By contrast, these genes decreased on day 1 and returned to the baseline by day 28 in the control individuals. Our study reveals sex-dimorphic effects of previous mild COVID-19 and suggests that viral infections in humans can establish new immunological set-points that affect future immune responses in an antigen-agnostic manner.
Collapse
Affiliation(s)
- Rachel Sparks
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - William W Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- Graduate Program in Biological Sciences, University of Maryland, College Park, MD, USA
| | - Kyu Lee Han
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Kiera L Vrindten
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Guangping Sun
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Milann Cox
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | | | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Laura E Failla
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jody Manischewitz
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Gabrielle Grubbs
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Lisa R King
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Galina Koroleva
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | | | - LaQuita Snow
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juanjie Tang
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | | | - Brian A Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Richard Apps
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | | | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA.
- Yale Center for Systems and Engineering Immunology and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
| |
Collapse
|
15
|
Stefanetti G, Kasper DL. Impact of the Host Microbiome on Vaccine Responsiveness: Lessons Learned and Future Perspective. Biochemistry 2022; 61:2849-2855. [PMID: 35993915 PMCID: PMC9782311 DOI: 10.1021/acs.biochem.2c00309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vaccination shows high variability in the elicited immune responses among individuals and populations for reasons still poorly understood. An increasing number of studies is supporting the evidence that gut microbiota, along with other interplaying variables, is able to modulate both humoral and cellular responses to infection and vaccination. Importantly, vaccine immunogenicity is often suboptimal at the extremes of age and also in low- and middle-income countries (LMICs), where the microbiota is believed to have an important role on immune responses. Still, contrasting findings and lack of causal evidence are calling for sophisticated methodologies to be able to overcome scientific and technical challenges to better decipher the immunomodulatory role of microbiota. In this perspective, we briefly review the status of the vaccine field in relation to the microbiome and offer possible scientific approaches to better understand the impact of the host microbiome on vaccine responsiveness.
Collapse
Affiliation(s)
- Giuseppe Stefanetti
- Department
of Biomolecular Sciences, University of
Urbino Carlo Bo, 61029 Urbino, Italy,
| | - Dennis L. Kasper
- Department
of Immunology, Blavatnik Institute, Harvard
Medical School, Boston, Massachusetts 02115, United States,
| |
Collapse
|
16
|
Haralambieva IH, Quach HQ, Ovsyannikova IG, Goergen KM, Grill DE, Poland GA, Kennedy RB. T Cell Transcriptional Signatures of Influenza A/H3N2 Antibody Response to High Dose Influenza and Adjuvanted Influenza Vaccine in Older Adults. Viruses 2022; 14:v14122763. [PMID: 36560767 PMCID: PMC9786771 DOI: 10.3390/v14122763] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Older adults experience declining influenza vaccine-induced immunity and are at higher risk of influenza and its complications. For this reason, high dose (e.g., Fluzone) and adjuvanted (e.g., Fluad) vaccines are preferentially recommended for people age 65 years and older. However, T cell transcriptional activity shaping the humoral immune responses to Fluzone and Fluad vaccines in older adults is still poorly understood. We designed a study of 234 older adults (≥65 years old) who were randomly allocated to receive Fluzone or Fluad vaccine and provided blood samples at baseline and at Day 28 after immunization. We measured the humoral immune responses (hemagglutination inhibition/HAI antibody titer) to influenza A/H3N2 and performed mRNA-Seq transcriptional profiling in purified CD4+ T cells, in order to identify T cell signatures that might explain differences in humoral immune response by vaccine type. Given the large differences in formulation (higher antigen dose vs adjuvant), our hypothesis was that each vaccine elicited a distinct transcriptomic response after vaccination. Thus, the main focus of our study was to identify the differential gene expression influencing the antibody titer in the two vaccine groups. Our analyses identified three differentially expressed, functionally linked genes/proteins in CD4+ T cells: the calcium/calmodulin dependent serine/threonine kinase IV (CaMKIV); its regulator the TMEM38B/transmembrane protein 38B, involved in maintenance of intracellular Ca2+ release; and the transcriptional coactivator CBP/CREB binding protein, as regulators of transcriptional activity/function in CD4+ T cells that impact differences in immune response by vaccine type. Significantly enriched T cell-specific pathways/biological processes were also identified that point to the importance of genes/proteins involved in Th1/Th2 cell differentiation, IL-17 signaling, calcium signaling, Notch signaling, MAPK signaling, and regulation of TRP cation Ca2+ channels in humoral immunity after influenza vaccination. In summary, we identified the genes/proteins and pathways essential for cell activation and function in CD4+ T cells that are associated with differences in influenza vaccine-induced humoral immunity by vaccine type. These findings provide an additional mechanistic perspective for achieving protective immunity in older adults.
Collapse
Affiliation(s)
| | - Huy Quang Quach
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Krista M. Goergen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Diane E. Grill
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-(507)-284-4968; Fax: +1-(507)-266-4716
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Naidu A, Lulu S S. Mucosal and systemic immune responses to Vibrio cholerae infection and oral cholera vaccines (OCVs) in humans: a systematic review. Expert Rev Clin Immunol 2022; 18:1307-1318. [PMID: 36255170 DOI: 10.1080/1744666x.2022.2136650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Cholera is an enteric disease caused by Vibrio cholerae, a water-borne pathogen, and characterized by severe diarrhea. Vaccines have been recommended for use by the WHO in resource-limited settings. Efficacies of the currently licensed cholera vaccines are not optimal in endemic settings and low in children below the age of five, a section of the population most susceptible to the disease. Development of next generation of cholera vaccines would require a detailed understanding of the required protective immune responses. AREA COVERED In this review, we revisit clinical trials which are focused on the early transcriptional mucosal responses elicited during Vibrio cholerae infection and upon vaccination along with summarizing various components of the effector immune response against Vibrio cholerae. EXPERT OPINION The inability of currently licensed killed/inactivated vaccines to elicit key inflammatory pathways locally may explain their restricted efficacy in endemic settings. More studies are required to understand the immunogenicity of the live attenuated cholera vaccine in these regions. Various extrinsic and intrinsic factors influence anti-cholera immunity and need to be considered to develop region-specific next generation vaccines.
Collapse
Affiliation(s)
- Akshayata Naidu
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sajitha Lulu S
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| |
Collapse
|
19
|
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.
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Poland GA. The human immune response to vaccines is symphonic, polyphonic, homophonic, and megaphonic. Vaccine 2022; 40:6189-6191. [PMID: 36163091 DOI: 10.1016/j.vaccine.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Gregory A Poland
- Mayo Vaccine Research Group, 200 First Street, SW, Guggenheim 611B, Mayo Clinic, Rochester, MN 55905, United States.
| |
Collapse
|
22
|
Sparks R, Lau WW, Liu C, Han KL, Vrindten KL, Sun G, Cox M, Andrews SF, Bansal N, Failla LE, Manischewitz J, Grubbs G, King LR, Koroleva G, Leimenstoll S, Snow L, Chen J, Tang J, Mukherjee A, Sellers BA, Apps R, McDermott AB, Martins AJ, Bloch EM, Golding H, Khurana S, Tsang JS. Influenza vaccination and single cell multiomics reveal sex dimorphic immune imprints of prior mild COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.17.22271138. [PMID: 35233581 PMCID: PMC8887138 DOI: 10.1101/2022.02.17.22271138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Viral infections can have profound and durable functional impacts on the immune system. There is an urgent need to characterize the long-term immune effects of SARS-CoV-2 infection given the persistence of symptoms in some individuals and the continued threat of novel variants. Here we use systems immunology, including longitudinal multimodal single cell analysis (surface proteins, transcriptome, and V(D)J sequences) from 33 previously healthy individuals after recovery from mild, non-hospitalized COVID-19 and 40 age- and sex-matched healthy controls with no history of COVID-19 to comparatively assess the post-infection immune status (mean: 151 days after diagnosis) and subsequent innate and adaptive responses to seasonal influenza vaccination. Identification of both sex-specific and -independent temporally stable changes, including signatures of T-cell activation and repression of innate defense/immune receptor genes (e.g., Toll-like receptors) in monocytes, suggest that mild COVID-19 can establish new post-recovery immunological set-points. COVID-19-recovered males had higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared to healthy males and COVID-19-recovered females, partly attributable to elevated pre-vaccination frequencies of a GPR56 expressing CD8+ T-cell subset in male recoverees that are "poised" to produce higher levels of IFNγ upon inflammatory stimulation. Intriguingly, by day 1 post-vaccination in COVID-19-recovered subjects, the expression of the repressed genes in monocytes increased and moved towards the pre-vaccination baseline of healthy controls, suggesting that the acute inflammation induced by vaccination could partly reset the immune states established by mild COVID-19. Our study reveals sex-dimorphic immune imprints and in vivo functional impacts of mild COVID-19 in humans, suggesting that prior COVID-19, and possibly respiratory viral infections in general, could change future responses to vaccination and in turn, vaccines could help reset the immune system after COVID-19, both in an antigen-agnostic manner.
Collapse
Affiliation(s)
- Rachel Sparks
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA,These authors contributed equally
| | - William W. Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA,These authors contributed equally
| | - Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA,Graduate Program in Biological Sciences, University of Maryland, College Park, MD, USA,These authors contributed equally
| | - Kyu Lee Han
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Kiera L. Vrindten
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Guangping Sun
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA,Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Milann Cox
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | | | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Laura E. Failla
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jody Manischewitz
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Gabrielle Grubbs
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Lisa R. King
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Galina Koroleva
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | | | - LaQuita Snow
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | | | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juanjie Tang
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | | | | | - Richard Apps
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | | | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Evan M. Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA
| | - John S. Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA,NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA,Correspondence:
| |
Collapse
|
23
|
Kumar M, James MM, Kumawat M, Nabi B, Sharma P, Pal N, Shubham S, Tiwari RR, Sarma DK, Nagpal R. Aging and Microbiome in the Modulation of Vaccine Efficacy. Biomedicines 2022; 10:biomedicines10071545. [PMID: 35884849 PMCID: PMC9313064 DOI: 10.3390/biomedicines10071545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/29/2022] Open
Abstract
From infancy through to old age, the microbiome plays an important role in modulating the host-immune system. As we age, our immune system and our gut microbiota change significantly in composition and function, which is linked to an increased vulnerability to infectious diseases and a decrease in vaccine responses. Our microbiome remains largely stable throughout adulthood; however, aging causes a major shift in the composition and function of the gut microbiome, as well as a decrease in diversity. Considering the critical role of the gut microbiome in the host-immune system, it is important to address, prevent, and ameliorate age-related dysbiosis, which could be an effective strategy for preventing/restoring functional deficits in immune responses as we grow older. Several factors, such as the host’s genetics and nutritional state, along with the gut microbiome, can influence vaccine efficacy or reaction. Emerging evidence suggests that the microbiome could be a significant determinant of vaccine immunity. Physiological mechanisms such as senescence, or the steady loss of cellular functions, which affect the aging process and vaccination responses, have yet to be comprehended. Recent studies on several COVID-19 vaccines worldwide have provided a considerable amount of data to support the hypothesis that aging plays a crucial role in modulating COVID-19 vaccination efficacy across different populations.
Collapse
Affiliation(s)
- Manoj Kumar
- National Institute for Research in Environmental Health, Bhopal 462030, India; (M.K.); (M.M.J.); (M.K.); (P.S.); (N.P.); (S.S.); (R.R.T.)
| | - Meenu Mariya James
- National Institute for Research in Environmental Health, Bhopal 462030, India; (M.K.); (M.M.J.); (M.K.); (P.S.); (N.P.); (S.S.); (R.R.T.)
| | - Manoj Kumawat
- National Institute for Research in Environmental Health, Bhopal 462030, India; (M.K.); (M.M.J.); (M.K.); (P.S.); (N.P.); (S.S.); (R.R.T.)
| | - Bilkees Nabi
- Department of Biochemistry and Biochemical Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, India;
| | - Poonam Sharma
- National Institute for Research in Environmental Health, Bhopal 462030, India; (M.K.); (M.M.J.); (M.K.); (P.S.); (N.P.); (S.S.); (R.R.T.)
| | - Namrata Pal
- National Institute for Research in Environmental Health, Bhopal 462030, India; (M.K.); (M.M.J.); (M.K.); (P.S.); (N.P.); (S.S.); (R.R.T.)
| | - Swasti Shubham
- National Institute for Research in Environmental Health, Bhopal 462030, India; (M.K.); (M.M.J.); (M.K.); (P.S.); (N.P.); (S.S.); (R.R.T.)
| | - Rajnarayan R. Tiwari
- National Institute for Research in Environmental Health, Bhopal 462030, India; (M.K.); (M.M.J.); (M.K.); (P.S.); (N.P.); (S.S.); (R.R.T.)
| | - Devojit Kumar Sarma
- National Institute for Research in Environmental Health, Bhopal 462030, India; (M.K.); (M.M.J.); (M.K.); (P.S.); (N.P.); (S.S.); (R.R.T.)
- Correspondence: (D.K.S.); (R.N.)
| | - Ravinder Nagpal
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, FL 32302, USA
- Correspondence: (D.K.S.); (R.N.)
| |
Collapse
|
24
|
Abstract
"The Primate Malarias" book has been a uniquely important resource for multiple generations of scientists, since its debut in 1971, and remains pertinent to the present day. Indeed, nonhuman primates (NHPs) have been instrumental for major breakthroughs in basic and pre-clinical research on malaria for over 50 years. Research involving NHPs have provided critical insights and data that have been essential for malaria research on many parasite species, drugs, vaccines, pathogenesis, and transmission, leading to improved clinical care and advancing research goals for malaria control, elimination, and eradication. Whilst most malaria scientists over the decades have been studying Plasmodium falciparum, with NHP infections, in clinical studies with humans, or using in vitro culture or rodent model systems, others have been dedicated to advancing research on Plasmodium vivax, as well as on phylogenetically related simian species, including Plasmodium cynomolgi, Plasmodium coatneyi, and Plasmodium knowlesi. In-depth study of these four phylogenetically related species over the years has spawned the design of NHP longitudinal infection strategies for gathering information about ongoing infections, which can be related to human infections. These Plasmodium-NHP infection model systems are reviewed here, with emphasis on modern systems biological approaches to studying longitudinal infections, pathogenesis, immunity, and vaccines. Recent discoveries capitalizing on NHP longitudinal infections include an advanced understanding of chronic infections, relapses, anaemia, and immune memory. With quickly emerging new technological advances, more in-depth research and mechanistic discoveries can be anticipated on these and additional critical topics, including hypnozoite biology, antigenic variation, gametocyte transmission, bone marrow dysfunction, and loss of uninfected RBCs. New strategies and insights published by the Malaria Host-Pathogen Interaction Center (MaHPIC) are recapped here along with a vision that stresses the importance of educating future experts well trained in utilizing NHP infection model systems for the pursuit of innovative, effective interventions against malaria.
Collapse
Affiliation(s)
- Mary R Galinski
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Vaccine Center, Emory University, Atlanta, GA, USA.
- Emory National Primate Research Center (Yerkes National Primate Research Center), Emory University, Atlanta, GA, USA.
| |
Collapse
|
25
|
2021 White Paper on Recent Issues in Bioanalysis: TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness ( Part 3 - Recommendations on Gene Therapy, Cell Therapy, Vaccine Assays; Immunogenicity of Biotherapeutics and Novel Modalities; Integrated Summary of Immunogenicity Harmonization). Bioanalysis 2022; 14:737-793. [PMID: 35578991 DOI: 10.4155/bio-2022-0081] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The 15th edition of the Workshop on Recent Issues in Bioanalysis (15th WRIB) was held on 27 September to 1 October 2021. Even with a last-minute move from in-person to virtual, an overwhelmingly high number of nearly 900 professionals representing pharma and biotech companies, contract research organizations (CROs), and multiple regulatory agencies still eagerly convened to actively discuss the most current topics of interest in bioanalysis. The 15th WRIB included 3 Main Workshops and 7 Specialized Workshops that together spanned 1 week in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on biomarker assay development and validation (BAV) (focused on clarifying the confusion created by the increased use of the term "Context of Use - COU"); mass spectrometry of proteins (therapeutic, biomarker and transgene); state-of-the-art cytometry innovation and validation; and, critical reagent and positive control generation were the special features of the 15th edition. This 2021 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2021 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations on TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness. Part 1A (Endogenous Compounds, Small Molecules, Complex Methods, Regulated Mass Spec of Large Molecules, Small Molecule, PoC), Part 1B (Regulatory Agencies' Inputs on Bioanalysis, Biomarkers, Immunogenicity, Gene & Cell Therapy and Vaccine) and Part 2 (ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry) are published in volume 14 of Bioanalysis, issues 9 and 10 (2022), respectively.
Collapse
|
26
|
Sherrill-Mix S, Yang M, Aldrovandi GM, Brenchley JM, Bushman FD, Collman RG, Dandekar S, Klatt NR, Lagenaur LA, Landay AL, Paredes R, Tachedjian G, Turpin JA, Serrano-Villar S, Lozupone CA, Ghosh M. A Summary of the Sixth International Workshop on Microbiome in HIV Pathogenesis, Prevention, and Treatment. AIDS Res Hum Retroviruses 2022; 38:173-180. [PMID: 34969255 PMCID: PMC9009592 DOI: 10.1089/aid.2021.0173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In October of 2020, researchers from around the world met online for the sixth annual International Workshop on Microbiome in HIV Pathogenesis, Prevention, and Treatment. New research was presented on the roles of the microbiome on immune response and HIV transmission and pathogenesis and the potential for alterations in the microbiome to decrease transmission and affect comorbidities. This article presents a summary of the findings reported.
Collapse
Affiliation(s)
- Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Address correspondence to: Scott Sherrill-Mix, Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 424 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Michelle Yang
- Department of Epidemiology, The George Washington University, Washington, District of Columbia, USA
| | - Grace M. Aldrovandi
- Department of Pediatrics, University of California, Los Angeles, California, USA
| | | | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Satya Dandekar
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Nichole R. Klatt
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Alan L. Landay
- Division of Gerontology, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Roger Paredes
- Institut de Recerca de la SIDA IrsiCaixa i Unitat VIH, Universitat Autònoma de Barcelona, Universitat de Vic, Catalonia, Spain
| | | | - Jim A. Turpin
- Divison of AIDS, NIAID, NIH, Bethesda, Maryland, USA
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | | | - Mimi Ghosh
- Department of Epidemiology, The George Washington University, Washington, District of Columbia, USA
| |
Collapse
|
27
|
Vijayan KKV, Cross KA, Curtis AD, Van Rompay KKA, Pollara J, Fox CB, Tomai M, Hanke T, Fouda G, Hudgens MG, Permar SR, De Paris K. Early Post-Vaccination Gene Signatures Correlate With the Magnitude and Function of Vaccine-Induced HIV Envelope-Specific Plasma Antibodies in Infant Rhesus Macaques. Front Immunol 2022; 13:840976. [PMID: 35572573 PMCID: PMC9094446 DOI: 10.3389/fimmu.2022.840976] [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: 12/21/2021] [Accepted: 03/28/2022] [Indexed: 01/21/2023] Open
Abstract
A better understanding of the impact of early innate immune responses after vaccine priming on vaccine-elicited adaptive immune responses could inform rational design for effective HIV vaccines. The current study compared the whole blood molecular immune signatures of a 3M-052-SE adjuvanted HIV Env protein vaccine to a regimen combining the adjuvanted Env protein with simultaneous administration of a modified Vaccinia Ankara vector expressing HIV Env in infant rhesus macaques at days 0, 1, and 3 post vaccine prime. Both vaccines induced a rapid innate response, evident by elevated inflammatory plasma cytokines and altered gene expression. We identified 25 differentially-expressed genes (DEG) on day 1 compared to day 0 in the HIV protein vaccine group. In contrast, in the group that received both the Env protein and the MVA-Env vaccine only two DEG were identified, implying that the MVA-Env modified the innate response to the adjuvanted protein vaccine. By day 3, only three DEG maintained altered expression, indicative of the transient nature of the innate response. The DEG represented immune pathways associated with complement activation, type I interferon and interleukin signaling, pathogen sensing, and induction of adaptive immunity. DEG expression on day 1 was correlated to Env-specific antibody responses, in particular antibody-dependent cytotoxicity responses at week 34, and Env-specific follicular T helper cells. Results from network analysis supported the interaction of DEG and their proteins in B cell activation. These results emphasize that vaccine-induced HIV-specific antibody responses can be optimized through the modulation of the innate response to the vaccine prime.
Collapse
Affiliation(s)
- K K Vidya Vijayan
- Department of Microbiology and Immunology, Center for AIDS Research, and Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kaitlyn A Cross
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alan D Curtis
- Department of Microbiology and Immunology, Center for AIDS Research, and Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Justin Pollara
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States.,Departent of Surgery, Duke University School of Medicine, Durham, NC, United States.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, United States
| | | | - Mark Tomai
- 3M Corporate Research Materials Laboratory, Saint Paul, MN, United States
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford, United Kingdom.,Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Genevieve Fouda
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States
| | - Michael G Hudgens
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medical College, New York, NY, United States
| | - Kristina De Paris
- Department of Microbiology and Immunology, Center for AIDS Research, and Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
28
|
Ma J, Boudewijns R, Sanchez-Felipe L, Mishra N, Vercruysse T, Buh Kum D, Thibaut HJ, Neyts J, Dallmeier K. Comparing immunogenicity and protective efficacy of the yellow fever 17D vaccine in mice. Emerg Microbes Infect 2021; 10:2279-2290. [PMID: 34792431 PMCID: PMC8648041 DOI: 10.1080/22221751.2021.2008772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The live-attenuated yellow fever 17D (YF17D) vaccine is one of the most efficacious human vaccines and also employed as a vector for novel vaccines. However, in the lack of appropriate immunocompetent small animal models, mechanistic insight in YF17D-induced protective immunity remains limited. To better understand YF17D vaccination and to identify a suitable mouse model, we evaluated the immunogenicity and protective efficacy of YF17D in five complementary mouse models, i.e. wild-type (WT) BALB/c, C57BL/6, IFN-α/β receptor (IFNAR-/-) deficient mice, and in WT mice in which type I IFN signalling was temporally ablated by an IFNAR blocking (MAR-1) antibody. Alike in IFNAR-/- mice, YF17D induced in either WT mice strong humoral immune responses dominated by IgG2a/c isotype (Th1 type) antibodies, yet only when IFNAR was blocked. Vigorous cellular immunity characterized by CD4+ T-cells producing IFN-γ and TNF-α were mounted in MAR-1 treated C57BL/6 and in IFNAR-/- mice. Surprisingly, vaccine-induced protection was largely mouse model dependent. Full protection against lethal intracranial challenge and a massive reduction of virus loads was conferred already by a minimal dose of 2 PFU YF17D in BALB/c and IFNAR-/- mice, but not in C57BL/6 mice. Correlation analysis of infection outcome with pre-challenge immunological markers indicates that YFV-specific IgG might suffice for protection, even in the absence of detectable levels of neutralizing antibodies. Finally, we propose that, in addition to IFNAR-/- mice, C57BL/6 mice with temporally blocked IFN-α/β receptors represent a promising immunocompetent mouse model for the study of YF17D-induced immunity and evaluation of YF17D-derived vaccines.
Collapse
Affiliation(s)
- Ji Ma
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Rega Institute, Leuven, Belgium
| | - Robbert Boudewijns
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Rega Institute, Leuven, Belgium
| | - Lorena Sanchez-Felipe
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Rega Institute, Leuven, Belgium
| | - Niraj Mishra
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Rega Institute, Leuven, Belgium
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Rega Institute, Leuven, Belgium.,KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Dieudonné Buh Kum
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Rega Institute, Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Rega Institute, Leuven, Belgium.,KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Rega Institute, Leuven, Belgium.,Global Virus Network (GVN), Baltimore, MD, USA
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Rega Institute, Leuven, Belgium.,Global Virus Network (GVN), Baltimore, MD, USA
| |
Collapse
|
29
|
Swaminathan G, Citron M, Xiao J, Norton JE, Reens AL, Topçuoğlu BD, Maritz JM, Lee KJ, Freed DC, Weber TM, White CH, Kadam M, Spofford E, Bryant-Hall E, Salituro G, Kommineni S, Liang X, Danilchanka O, Fontenot JA, Woelk CH, Gutierrez DA, Hazuda DJ, Hannigan GD. Vaccine Hyporesponse Induced by Individual Antibiotic Treatment in Mice and Non-Human Primates Is Diminished upon Recovery of the Gut Microbiome. Vaccines (Basel) 2021; 9:vaccines9111340. [PMID: 34835271 PMCID: PMC8619314 DOI: 10.3390/vaccines9111340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/19/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
Emerging evidence demonstrates a connection between microbiome composition and suboptimal response to vaccines (vaccine hyporesponse). Harnessing the interaction between microbes and the immune system could provide novel therapeutic strategies for improving vaccine response. Currently we do not fully understand the mechanisms and dynamics by which the microbiome influences vaccine response. Using both mouse and non-human primate models, we report that short-term oral treatment with a single antibiotic (vancomycin) results in the disruption of the gut microbiome and this correlates with a decrease in systemic levels of antigen-specific IgG upon subsequent parenteral vaccination. We further show that recovery of microbial diversity before vaccination prevents antibiotic-induced vaccine hyporesponse, and that the antigen specific IgG response correlates with the recovery of microbiome diversity. RNA sequencing analysis of small intestine, spleen, whole blood, and secondary lymphoid organs from antibiotic treated mice revealed a dramatic impact on the immune system, and a muted inflammatory signature is correlated with loss of bacteria from Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. These results suggest that microbially modulated immune pathways may be leveraged to promote vaccine response and will inform future vaccine design and development strategies.
Collapse
Affiliation(s)
- Gokul Swaminathan
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
- Correspondence: (G.S.); (G.D.H.)
| | - Michael Citron
- Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, PA 19486, USA; (M.C.); (J.X.); (D.C.F.); (T.M.W.)
| | - Jianying Xiao
- Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, PA 19486, USA; (M.C.); (J.X.); (D.C.F.); (T.M.W.)
| | - James E. Norton
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Abigail L. Reens
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Begüm D. Topçuoğlu
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Julia M. Maritz
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Keun-Joong Lee
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism, MRL, Merck & Co. Inc., Rahway, NJ 07065, USA; (K.-J.L.); (G.S.)
| | - Daniel C. Freed
- Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, PA 19486, USA; (M.C.); (J.X.); (D.C.F.); (T.M.W.)
| | - Teresa M. Weber
- Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, PA 19486, USA; (M.C.); (J.X.); (D.C.F.); (T.M.W.)
| | - Cory H. White
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Mahika Kadam
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Erin Spofford
- Safety Assessment and Laboratory Animal Research, MRL, Merck & Co. Inc., Boston, MA 02115, USA; (E.S.); (E.B.-H.)
| | - Erin Bryant-Hall
- Safety Assessment and Laboratory Animal Research, MRL, Merck & Co. Inc., Boston, MA 02115, USA; (E.S.); (E.B.-H.)
| | - Gino Salituro
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism, MRL, Merck & Co. Inc., Rahway, NJ 07065, USA; (K.-J.L.); (G.S.)
| | - Sushma Kommineni
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Xue Liang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Olga Danilchanka
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Jane A. Fontenot
- New Iberia Research Center, University of Louisiana at Lafayette, Lafayette, LA 70503, USA;
| | - Christopher H. Woelk
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Dario A. Gutierrez
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
| | - Daria J. Hazuda
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
- Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, PA 19486, USA; (M.C.); (J.X.); (D.C.F.); (T.M.W.)
| | - Geoffrey D. Hannigan
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA; (J.E.N.J.); (A.L.R.); (B.D.T.); (J.M.M.); (C.H.W.); (M.K.); (S.K.); (X.L.); (O.D.); (C.H.W.); (D.A.G.); (D.J.H.)
- Correspondence: (G.S.); (G.D.H.)
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
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.
Collapse
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.)
| |
Collapse
|
32
|
The metabolic hormone leptin promotes the function of T FH cells and supports vaccine responses. Nat Commun 2021; 12:3073. [PMID: 34031386 PMCID: PMC8144586 DOI: 10.1038/s41467-021-23220-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/16/2021] [Indexed: 12/17/2022] Open
Abstract
Follicular helper T (TFH) cells control antibody responses by supporting antibody affinity maturation and memory formation. Inadequate TFH function has been found in individuals with ineffective responses to vaccines, but the mechanism underlying TFH regulation in vaccination is not understood. Here, we report that lower serum levels of the metabolic hormone leptin associate with reduced vaccine responses to influenza or hepatitis B virus vaccines in healthy populations. Leptin promotes mouse and human TFH differentiation and IL-21 production via STAT3 and mTOR pathways. Leptin receptor deficiency impairs TFH generation and antibody responses in immunisation and infection. Similarly, leptin deficiency induced by fasting reduces influenza vaccination-mediated protection for the subsequent infection challenge, which is mostly rescued by leptin replacement. Our results identify leptin as a regulator of TFH cell differentiation and function and indicate low levels of leptin as a risk factor for vaccine failure. T follicular helper (TFH) cell numbers are increased after vaccination and fewer of these cells might result in reduced vaccine responses. Here the authors show in mice and humans that leptin promotes TFH differentiation and that low leptin levels can impair TFH response to vaccines and virus protection in mice.
Collapse
|
33
|
Reens AL, Cabral DJ, Liang X, Norton JE, Therien AG, Hazuda DJ, Swaminathan G. Immunomodulation by the Commensal Microbiome During Immune-Targeted Interventions: Focus on Cancer Immune Checkpoint Inhibitor Therapy and Vaccination. Front Immunol 2021; 12:643255. [PMID: 34054810 PMCID: PMC8155485 DOI: 10.3389/fimmu.2021.643255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/22/2021] [Indexed: 12/11/2022] Open
Abstract
Emerging evidence in clinical and preclinical studies indicates that success of immunotherapies can be impacted by the state of the microbiome. Understanding the role of the microbiome during immune-targeted interventions could help us understand heterogeneity of treatment success, predict outcomes, and develop additional strategies to improve efficacy. In this review, we discuss key studies that reveal reciprocal interactions between the microbiome, the immune system, and the outcome of immune interventions. We focus on cancer immune checkpoint inhibitor treatment and vaccination as two crucial therapeutic areas with strong potential for immunomodulation by the microbiota. By juxtaposing studies across both therapeutic areas, we highlight three factors prominently involved in microbial immunomodulation: short-chain fatty acids, microbe-associate molecular patterns (MAMPs), and inflammatory cytokines. Continued interrogation of these models and pathways may reveal critical mechanistic synergies between the microbiome and the immune system, resulting in novel approaches designed to influence the efficacy of immune-targeted interventions.
Collapse
Affiliation(s)
- Abigail L. Reens
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - Damien J. Cabral
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - Xue Liang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - James E. Norton
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - Alex G. Therien
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - Daria J. Hazuda
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
- Infectious Disease and Vaccine Research, Merck & Co., Inc., West Point, PA, United States
| | - Gokul Swaminathan
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| |
Collapse
|
34
|
Abstract
Vaccines are the most effective means available for preventing infectious diseases. However, vaccine-induced immune responses are highly variable between individuals and between populations in different regions of the world. Understanding the basis of this variation is, thus, of fundamental importance to human health. Although the factors that are associated with intra- and inter-population variation in vaccine responses are manifold, emerging evidence points to a key role for the gut microbiome in controlling immune responses to vaccination. Much of this evidence comes from studies in mice, and causal evidence for the impact of the microbiome on human immunity is sparse. However, recent studies on vaccination in subjects treated with broad-spectrum antibiotics have provided causal evidence and mechanistic insights into how the microbiota controls immune responses in humans.
Collapse
|
35
|
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.
Collapse
|
36
|
The vaccinologist's "dirty little secret": a better understanding of structure-function relationships of viral immunogens might advance rational HIV vaccine design. Arch Virol 2021; 166:1297-1303. [PMID: 33606111 PMCID: PMC7892722 DOI: 10.1007/s00705-021-04982-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022]
Abstract
I will offer a conceptual analysis of different notions of structure and function of viral immunogens and of different structure-function relationships. My focus will then be on the mechanisms by which the desired immune response is induced and why strategies based on three-dimensional molecular antigen structures and their rational design are limited in their ability to induce the desired immunogenicity. I will look at the mechanisms of action of adjuvants (thus the wordplay with Janeway’s “immunologist’s dirty little secret”). Strategies involving adjuvants and other (more successful) vaccination strategies rely on taking into account activities and functions (“what is going on”), and not just the structures involved (“who is there”), in binding in a “lock and key” fashion. Functional patterns as well as other organizational and temporal patterns, I will argue, are crucial for inducing the desired immune response and immunogenicity. The 3D structural approach by itself has its benefits – and its limits, which I want to highlight by this philosophical analysis, pointing out the importance of structure-function relationships. Different functional aspects such as antigenicity, immunogenicity, and immunity need to be kept separate and cannot be reduced to three-dimensional structures of vaccines. Taking into account different notions of structure and function and their relationships might thus advance our understanding of the immune system and rational HIV vaccine design, to which end philosophy can provide useful tools.
Collapse
|
37
|
Fathi A, Addo MM, Dahlke C. Sex Differences in Immunity: Implications for the Development of Novel Vaccines Against Emerging Pathogens. Front Immunol 2021; 11:601170. [PMID: 33488596 PMCID: PMC7820860 DOI: 10.3389/fimmu.2020.601170] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022] Open
Abstract
Vaccines are one of the greatest public health achievements and have saved millions of lives. They represent a key countermeasure to limit epidemics caused by emerging infectious diseases. The Ebola virus disease crisis in West Africa dramatically revealed the need for a rapid and strategic development of vaccines to effectively control outbreaks. Seven years later, in light of the SARS-CoV-2 pandemic, this need has never been as urgent as it is today. Vaccine development and implementation of clinical trials have been greatly accelerated, but still lack strategic design and evaluation. Responses to vaccination can vary widely across individuals based on factors like age, microbiome, co-morbidities and sex. The latter aspect has received more and more attention in recent years and a growing body of data provide evidence that sex-specific effects may lead to different outcomes of vaccine safety and efficacy. As these differences might have a significant impact on the resulting optimal vaccine regimen, sex-based differences should already be considered and investigated in pre-clinical and clinical trials. In this Review, we will highlight the clinical observations of sex-specific differences in response to vaccination, delineate sex differences in immune mechanisms, and will discuss the possible resulting implications for development of vaccine candidates against emerging infections. As multiple vaccine candidates against COVID-19 that target the same antigen are tested, vaccine development may undergo a decisive change, since we now have the opportunity to better understand mechanisms that influence vaccine-induced reactogenicity and effectiveness of different vaccines.
Collapse
Affiliation(s)
- Anahita Fathi
- University Medical Center Hamburg-Eppendorf, 1st Department of Medicine, Division of Infectious Diseases, Hamburg, Germany.,Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marylyn M Addo
- University Medical Center Hamburg-Eppendorf, 1st Department of Medicine, Division of Infectious Diseases, Hamburg, Germany.,Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Christine Dahlke
- University Medical Center Hamburg-Eppendorf, 1st Department of Medicine, Division of Infectious Diseases, Hamburg, Germany.,Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| |
Collapse
|
38
|
van Regenmortel MHV. What does it mean to develop an HIV vaccine by rational design? Arch Virol 2020; 166:27-33. [PMID: 33251565 DOI: 10.1007/s00705-020-04884-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/03/2020] [Indexed: 12/29/2022]
Abstract
This review argues that the three popular concepts of design, rationality and reductionism, which guided vaccine research for many years, actually contributed to the inability of vaccinologists to develop an effective HIV vaccine. The strong goal-directed intentionality inherent in the concept of design together with excessive confidence in the power of rational thinking convinced investigators that the accumulated structural knowledge on HIV epitopes, derived from crystallographic studies of complexes of neutralizing antibodies bound to HIV Env epitopes, would allow them to rationally design complementary immunogens capable of inducing anti-HIV protective antibodies. This strategy failed because it was not appreciated that the structures observed in epitope-paratope crystallographic complexes result from mutually induced fit between the two partners and do not represent structures present in the free disordered molecules before they had interacted. In addition, reductionist thinking led investigators to accept that biology could be reduced to chemistry, and this made them neglect the fundamental difference between chemical antigenicity and biological immunogenicity. As a result, they did not investigate which inherent constituents of immune systems controlled the induction of protective antibodies and focused instead only on the steric complementarity that exists between bound epitopes and paratopes.
Collapse
|
39
|
Scanlon N, Saklawi Y, Rouphael N. The Role of Systems Vaccinology in Understanding the Immune Defects to Vaccination in Solid Organ Transplant Recipients. Front Immunol 2020; 11:582201. [PMID: 33324400 PMCID: PMC7723964 DOI: 10.3389/fimmu.2020.582201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/19/2020] [Indexed: 12/26/2022] Open
Abstract
Solid organ transplant recipients (SOTRs) are at increased risk for many infections, whether viral, bacterial, or fungal, due to immunosuppressive therapy to prevent organ rejection. The same immune defects that render transplanted patients susceptible to infection dampen their immune response to vaccination. Therefore, it is vital to identify immune defects to vaccination in transplant recipients and methods to obviate them. These methods can include alternative vaccine composition, dosage, adjuvants, route of administration, timing, and re-vaccination strategies. Systems biology is a relatively new field of study, which utilizes high throughput means to better understand biological systems and predict outcomes. Systems biology approaches have been used to help obtain a global picture of immune responses to infections and vaccination (i.e. systems vaccinology), but little work has been done to use systems biology to improve vaccine efficacy in immunocompromised patients, particularly SOTRs, thus far. Systems vaccinology approaches may hold key insights to vaccination in this vulnerable population.
Collapse
Affiliation(s)
- Nicholas Scanlon
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States.,The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Emory University, Decatur, GA, United States
| | - Youssef Saklawi
- The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Emory University, Decatur, GA, United States
| | - Nadine Rouphael
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States.,The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Emory University, Decatur, GA, United States
| |
Collapse
|
40
|
Mo AXY, Pesce J, Augustine AD, Bodmer JL, Breen J, Leitner W, Hall BF. Understanding vaccine-elicited protective immunity against pre-erythrocytic stage malaria in endemic regions. Vaccine 2020; 38:7569-7577. [PMID: 33071001 DOI: 10.1016/j.vaccine.2020.09.071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/26/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022]
Abstract
Recent malaria vaccine trials in endemic areas have yielded disparate results compared to studies conducted in non-endemic areas. A workshop was organized to discuss the differential pre-erythrocytic stage malaria vaccine (Pre-E-Vac) efficacies and underlying protective immunity under various conditions. It was concluded that many factors, including vaccine technology platforms, host genetics or physiologic conditions, and parasite and mosquito vector variations, may all contribute to Pre-E-Vac efficacy. Cross-disciplinary approaches are needed to decipher the multi-dimensional variables that contribute to the observed vaccine hypo-responsiveness. The malaria vaccine community has an opportunity to leverage recent advances in immunology, systems vaccinology, and high dimensionality data science methodologies to generate new clinical datasets with unprecedented levels of functional resolution as well as capitalize on existing datasets for comprehensive and aggregate analyses. These approaches would help to unlock our understanding of Pre-E-Vac immunology and to translate new candidates from the laboratory to the field more predictably.
Collapse
Affiliation(s)
- Annie X Y Mo
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA.
| | - John Pesce
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
| | - Alison Deckhut Augustine
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
| | | | - Joseph Breen
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
| | - Wolfgang Leitner
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
| | - B Fenton Hall
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Department of Health and Human Service, Rockville, MD 20892, MSC 9825, USA
| |
Collapse
|
41
|
Soni D, Van Haren SD, Idoko OT, Evans JT, Diray-Arce J, Dowling DJ, Levy O. Towards Precision Vaccines: Lessons From the Second International Precision Vaccines Conference. Front Immunol 2020; 11:590373. [PMID: 33178222 PMCID: PMC7593811 DOI: 10.3389/fimmu.2020.590373] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/23/2020] [Indexed: 12/16/2022] Open
Abstract
Other than clean drinking water, vaccines have been the most effective public health intervention in human history, yet their full potential is still untapped. To date, vaccine development has been largely limited to empirical approaches focused on infectious diseases and has targeted entire populations, potentially disregarding distinct immunity in vulnerable populations such as infants, elders, and the immunocompromised. Over the past few decades innovations in genetic engineering, adjuvant discovery, formulation science, and systems biology have fueled rapid advances in vaccine research poised to consider demographic factors (e.g., age, sex, genetics, and epigenetics) in vaccine discovery and development. Current efforts are focused on leveraging novel approaches to vaccine discovery and development to optimize vaccinal antigen and, as needed, adjuvant systems to enhance vaccine immunogenicity while maintaining safety. These approaches are ushering in an era of precision vaccinology aimed at tailoring immunization for vulnerable populations with distinct immunity. To foster collaboration among leading vaccinologists, government, policy makers, industry partners, and funders from around the world, the Precision Vaccines Program at Boston Children's Hospital hosted the 2nd International Precision Vaccines Conference (IPVC) at Harvard Medical School on the 17th-18th October 2019. The conference convened experts in vaccinology, including vaccine formulation and adjuvantation, immunology, cell signaling, systems biology, biostatistics, bioinformatics, as well as vaccines for non-infectious indications such as cancer and opioid use disorder. Herein we review highlights from the 2nd IPVC and discuss key concepts in the field of precision vaccines.
Collapse
Affiliation(s)
- Dheeraj Soni
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Simon D. Van Haren
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Olubukola T. Idoko
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jay T. Evans
- Center for Translational Medicine, University of Montana, Missoula, MT, United States
| | - Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT & Harvard, Cambridge, MA, United States
| | - David J. Dowling
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT & Harvard, Cambridge, MA, United States
| |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Abstract
SARS-CoV-2, the virus that causes COVID-19, emerged in late 2019, and was declared a global pandemic on March 11th 2020. With over 50 million cases and 1.2 million deaths around the world, to date, this pandemic represents the gravest global health crisis of our times. Thus, the race to develop a COVID-19 vaccine is an urgent global imperative. At the time of writing, there are over 165 vaccine candidates being developed, with 33 in various stages of clinical testing. In this review, we discuss emerging insights about the human immune response to SARS-CoV-2, and their implications for vaccine design. We then review emerging knowledge of the immunogenicity of the numerous vaccine candidates that are currently being tested in the clinic and discuss the range of immune defense mechanisms that can be harnessed to develop novel vaccines that confer durable protection against SARS-CoV-2. Finally, we conclude with a discussion of the potential role of a systems vaccinology approach in accelerating the clinical testing of vaccines, to meet the urgent needs posed by the pandemic.
Collapse
Affiliation(s)
- Lilit Grigoryan
- Institute for Immunology, Transplantation and Infectious Diseases, Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, United States
| | - Bali Pulendran
- Institute for Immunology, Transplantation and Infectious Diseases, Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, United States.
| |
Collapse
|
44
|
Olagoke O, Quigley BL, Hemmatzadeh F, Tzipori G, Timms P. Therapeutic vaccination of koalas harbouring endogenous koala retrovirus (KoRV) improves antibody responses and reduces circulating viral load. NPJ Vaccines 2020; 5:60. [PMID: 32699650 PMCID: PMC7367292 DOI: 10.1038/s41541-020-0210-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023] Open
Abstract
The long-term survival of the koala is under serious threat from multiple factors, including infectious disease agents such as Chlamydia and koala retrovirus (KoRV). KoRV is present in both exogenous and endogenous forms, depending on the geographical location of the population. In the northern half of Australia, it is present as an endogenous infection in all koalas, making a case for an urgent need to develop a therapeutic vaccine that might prevent KoRV-associated pathologies in these koalas. To this end, we determined the therapeutic effects of vaccinating koalas harbouring endogenous KoRV with a recombinant KoRV Env protein combined with a Tri-adjuvant. We found that vaccination led to a significant increase in circulating anti-KoRV IgG levels, as well as increase in neutralising antibodies. Our study also showed that post-vaccination antibodies were able to recognize epitopes on the Env protein that were unrecognised pre-vaccination, as well as resulting in an increase in the recognition of the previously recognised epitopes. The vaccine also induced antibodies that were cross-reactive against multiple KoRV-subtypes. Finally, we found a complete clearance of KoRV-A in plasma from koalas that had detectable levels of KoRV-A pre-vaccination. Similarly, there was a significant reduction in the expression of KoRV-B viral RNA levels post-vaccination. Collectively, this study showed that koalas harbouring endogenous KoRV can benefit from prophylactic vaccination against KoRV using a recombinant KoRV-A Env protein and that the mechanism of this protection might be through the boosting of natural anti-KoRV antibodies and expanding the breadth of the recognised epitopes.
Collapse
Affiliation(s)
- Olusola Olagoke
- Genecology Research Center, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556 Australia
| | - Bonnie L Quigley
- Genecology Research Center, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556 Australia
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA 5371 Australia
| | - Galit Tzipori
- Lone Pine Koala Sanctuary, Fig Tree Pocket, Queensland, Australia
| | - Peter Timms
- Genecology Research Center, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556 Australia
| |
Collapse
|
45
|
Russo G, Reche P, Pennisi M, Pappalardo F. The combination of artificial intelligence and systems biology for intelligent vaccine design. Expert Opin Drug Discov 2020; 15:1267-1281. [PMID: 32662677 DOI: 10.1080/17460441.2020.1791076] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION A new body of evidence depicts the applications of artificial intelligence and systems biology in vaccine design and development. The combination of both approaches shall revolutionize healthcare, accelerating clinical trial processes and reducing the costs and time involved in drug research and development. AREAS COVERED This review explores the basics of artificial intelligence and systems biology approaches in the vaccine development pipeline. The topics include a detailed description of epitope prediction tools for designing epitope-based vaccines and agent-based models for immune system response prediction, along with a focus on their potentiality to facilitate clinical trial phases. EXPERT OPINION Artificial intelligence and systems biology offer the opportunity to avoid the inefficiencies and failures that arise in the classical vaccine development pipeline. One promising solution is the combination of both methodologies in a multiscale perspective through an accurate pipeline. We are entering an 'in silico era' in which scientific partnerships, including a more and more increasing creation of an 'ecosystem' of collaboration and multidisciplinary approach, are relevant for addressing the long and risky road of vaccine discovery and development. In this context, regulatory guidance should be developed to qualify the in silico trials as evidence for intelligent vaccine development.
Collapse
Affiliation(s)
- Giulia Russo
- Department of Drug Sciences, University of Catania , Catania, Italy
| | - Pedro Reche
- Department of Immunology, Universidad Complutense De Madrid, Ciudad Universitaria , Madrid, Spain
| | - Marzio Pennisi
- Computer Science Institute, DiSIT, University of Eastern Piedmont , Italy
| | | |
Collapse
|
46
|
Boccard M, Albert-Vega C, Mouton W, Durieu I, Brengel-Pesce K, Venet F, Trouillet-Assant S, Ader F. [Functional immunoassays in the setting of infectious risk and immunosuppressive therapy of non-HIV immunocompromised patients]. Rev Med Interne 2020; 41:545-551. [PMID: 32624260 DOI: 10.1016/j.revmed.2020.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/24/2020] [Accepted: 04/09/2020] [Indexed: 11/25/2022]
Abstract
The holistic approach of the human immune system is based on the study of its components collectively driving a functional response to an immunogenic stimulus. To appreciate a specific immune dysfunction, a condition is mimicked ex vivo and the immune response induced is assessed. The application field of such assays are broad and expanding, from the diagnosis of primary and secondary immunodeficiencies, immunotherapy for cancer to the management of patients at-risk for infections and vaccination. These assays are immune monitoring tools that may contribute to a personalised and precision medicine. The purpose of this review is to describe immune functional assays available in the setting of non-HIV acquired immune deficiency. First, we will address the use of theses assays in the diagnosis of opportunistic infections such as viral reactivation. Secondly, we will report the usefulness of these assays to assess vaccine efficacy and to manage immunosuppressive therapies.
Collapse
Affiliation(s)
- M Boccard
- Centre International de Recherche en Infectiologie (CIRI), Inserm 1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France; Département de médecine interne et vasculaire, centre hospitalier Lyon Sud, Hospices civils de Lyon, 69310 Pierre-Bénite, France; Unité mixte Hospices civils de Lyon-bioMérieux, centre hospitalier Lyon Sud, Hospices civils de Lyon, Pierre-Bénite, 69495 Lyon, France.
| | - C Albert-Vega
- Unité mixte Hospices civils de Lyon-bioMérieux, centre hospitalier Lyon Sud, Hospices civils de Lyon, Pierre-Bénite, 69495 Lyon, France
| | - W Mouton
- Unité mixte Hospices civils de Lyon-bioMérieux, centre hospitalier Lyon Sud, Hospices civils de Lyon, Pierre-Bénite, 69495 Lyon, France; Laboratoire virologie et pathologies humaines (VirPath), faculté de médecine Lyon Est, université Claude-Bernard Lyon 1, 69008 Lyon, France
| | - I Durieu
- Département de médecine interne et vasculaire, centre hospitalier Lyon Sud, Hospices civils de Lyon, 69310 Pierre-Bénite, France
| | - K Brengel-Pesce
- Unité mixte Hospices civils de Lyon-bioMérieux, centre hospitalier Lyon Sud, Hospices civils de Lyon, Pierre-Bénite, 69495 Lyon, France
| | - F Venet
- Unité mixte Hospices civils de Lyon-bioMérieux, centre hospitalier Lyon Sud, Hospices civils de Lyon, Pierre-Bénite, 69495 Lyon, France; Laboratoire d'immunologie, hôpital Édouard-Herriot, Hospices civils de Lyon, 69003 Lyon, France; EA7426 Pathophysiology of injury-induced immunosuppression, université Claude-Bernard Lyon 1, 69008 Lyon, France
| | - S Trouillet-Assant
- Unité mixte Hospices civils de Lyon-bioMérieux, centre hospitalier Lyon Sud, Hospices civils de Lyon, Pierre-Bénite, 69495 Lyon, France; Laboratoire virologie et pathologies humaines (VirPath), faculté de médecine Lyon Est, université Claude-Bernard Lyon 1, 69008 Lyon, France
| | - F Ader
- Centre International de Recherche en Infectiologie (CIRI), Inserm 1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France; Département des maladies infectieuses et tropicales, hôpital de la Croix-Rousse, Hospices civils de Lyon, 69004 Lyon, France
| |
Collapse
|
47
|
Zhang W, Le L, Ahmad G, Molehin AJ, Siddiqui AJ, Torben W, Karmakar S, Rojo JU, Sennoune S, Lazarus S, Khatoon S, Freeborn J, Sudduth J, Rezk AF, Carey D, Wolf RF, Papin JF, Damian R, Gray SA, Marks F, Carter D, Siddiqui AA. Fifteen Years of Sm-p80-Based Vaccine Trials in Nonhuman Primates: Antibodies From Vaccinated Baboons Confer Protection in vivo and in vitro From Schistosoma mansoni and Identification of Putative Correlative Markers of Protection. Front Immunol 2020; 11:1246. [PMID: 32636844 PMCID: PMC7318103 DOI: 10.3389/fimmu.2020.01246] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
Recent advances in systems biology have shifted vaccine development from a largely trial-and-error approach to an approach that promote rational design through the search for immune signatures and predictive correlates of protection. These advances will doubtlessly accelerate the development of a vaccine for schistosomiasis, a neglected tropical disease that currently affects over 250 million people. For over 15 years and with contributions of over 120 people, we have endeavored to test and optimize Sm-p80-based vaccines in the non-human primate model of schistosomiasis. Using RNA-sequencing on eight different Sm-p80-based vaccine strategies, we sought to elucidate immune signatures correlated with experimental protective efficacy. Furthermore, we aimed to explore the role of antibodies through in vivo passive transfer of IgG obtained from immunized baboons and in vitro killing of schistosomula using Sm-p80-specific antibodies. We report that passive transfer of IgG from Sm-p80-immunized baboons led to significant worm burden reduction, egg reduction in liver, and reduced egg hatching percentages from tissues in mice compared to controls. In addition, we observed that sera from Sm-p80-immunized baboons were able to kill a significant percent of schistosomula and that this effect was complement-dependent. While we did not find a universal signature of immunity, the large datasets generated by this study will serve as a substantial resource for further efforts to develop vaccine or therapeutics for schistosomiasis.
Collapse
Affiliation(s)
- Weidong Zhang
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Loc Le
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Gul Ahmad
- Department of Natural Sciences, Peru State College, Peru, NE, United States
| | - Adebayo J. Molehin
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | | | - Workineh Torben
- Department of Biological Sciences, Louisiana State University of Alexandria, Alexandria, LA, United States
| | - Souvik Karmakar
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Juan U. Rojo
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Souad Sennoune
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Samara Lazarus
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Sabiha Khatoon
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Jasmin Freeborn
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Justin Sudduth
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Ashraf F. Rezk
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - David Carey
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Roman F. Wolf
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Oklahoma City VA Health Care System, Oklahoma City, OK, United States
| | - James F. Papin
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Ray Damian
- Department of Cellular Biology, University of Georgia, Athens, GA, United States
| | | | - Florian Marks
- International Vaccine Institute, SNU Research Park, Seoul, South Korea
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Darrick Carter
- PAI Life Sciences, Seattle, WA, United States
- Infectious Disease Research Institute, Seattle, WA, United States
| | - Afzal A. Siddiqui
- Center for Tropical Medicine and Infectious Diseases, Texas Tech University Health Sciences Center, Lubbock, TX, United States
- Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| |
Collapse
|
48
|
Hagan T, Cortese M, Rouphael N, Boudreau C, Linde C, Maddur MS, Das J, Wang H, Guthmiller J, Zheng NY, Huang M, Uphadhyay AA, Gardinassi L, Petitdemange C, McCullough MP, Johnson SJ, Gill K, Cervasi B, Zou J, Bretin A, Hahn M, Gewirtz AT, Bosinger SE, Wilson PC, Li S, Alter G, Khurana S, Golding H, Pulendran B. Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans. Cell 2020; 178:1313-1328.e13. [PMID: 31491384 DOI: 10.1016/j.cell.2019.08.010] [Citation(s) in RCA: 350] [Impact Index Per Article: 87.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 06/21/2019] [Accepted: 08/06/2019] [Indexed: 12/16/2022]
Abstract
Emerging evidence indicates a central role for the microbiome in immunity. However, causal evidence in humans is sparse. Here, we administered broad-spectrum antibiotics to healthy adults prior and subsequent to seasonal influenza vaccination. Despite a 10,000-fold reduction in gut bacterial load and long-lasting diminution in bacterial diversity, antibody responses were not significantly affected. However, in a second trial of subjects with low pre-existing antibody titers, there was significant impairment in H1N1-specific neutralization and binding IgG1 and IgA responses. In addition, in both studies antibiotics treatment resulted in (1) enhanced inflammatory signatures (including AP-1/NR4A expression), observed previously in the elderly, and increased dendritic cell activation; (2) divergent metabolic trajectories, with a 1,000-fold reduction in serum secondary bile acids, which was highly correlated with AP-1/NR4A signaling and inflammasome activation. Multi-omics integration revealed significant associations between bacterial species and metabolic phenotypes, highlighting a key role for the microbiome in modulating human immunity.
Collapse
Affiliation(s)
- Thomas Hagan
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mario Cortese
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Decatur, GA 30030, USA
| | - Carolyn Boudreau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Caitlin Linde
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mohan S Maddur
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Jishnu Das
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hong Wang
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Jenna Guthmiller
- Department of Medicine, Section of Rheumatology, Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Amit A Uphadhyay
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Luiz Gardinassi
- Department of Medicine, Emory University, Atlanta, GA 30303, USA
| | - Caroline Petitdemange
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | | | - Sara Jo Johnson
- Hope Clinic of the Emory Vaccine Center, Decatur, GA 30030, USA
| | - Kiran Gill
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Barbara Cervasi
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Jun Zou
- Center for Inflammation, Immunity, and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Alexis Bretin
- Center for Inflammation, Immunity, and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Megan Hahn
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity, and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Steve E Bosinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Shuzhao Li
- Department of Medicine, Emory University, Atlanta, GA 30303, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
49
|
The Role of Single-Cell Technology in the Study and Control of Infectious Diseases. Cells 2020; 9:cells9061440. [PMID: 32531928 PMCID: PMC7348906 DOI: 10.3390/cells9061440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
The advent of single-cell research in the recent decade has allowed biological studies at an unprecedented resolution and scale. In particular, single-cell analysis techniques such as Next-Generation Sequencing (NGS) and Fluorescence-Activated Cell Sorting (FACS) have helped show substantial links between cellular heterogeneity and infectious disease progression. The extensive characterization of genomic and phenotypic biomarkers, in addition to host-pathogen interactions at the single-cell level, has resulted in the discovery of previously unknown infection mechanisms as well as potential treatment options. In this article, we review the various single-cell technologies and their applications in the ongoing fight against infectious diseases, as well as discuss the potential opportunities for future development.
Collapse
|
50
|
Hernandez Puente CV, Hsu PC, Rogers LJ, Jousheghany F, Siegel E, Kadlubar SA, Beck JT, Makhoul I, Hutchins LF, Kieber-Emmons T, Monzavi-Karbassi B. Association of DNA-Methylation Profiles With Immune Responses Elicited in Breast Cancer Patients Immunized With a Carbohydrate-Mimicking Peptide: A Pilot Study. Front Oncol 2020; 10:879. [PMID: 32582547 PMCID: PMC7290046 DOI: 10.3389/fonc.2020.00879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 05/04/2020] [Indexed: 02/04/2023] Open
Abstract
Immune response to a given antigen, particularly in cancer patients, is complex and is controlled by various genetic and environmental factors. Identifying biomarkers that can predict robust response to immunization is an urgent need in clinical cancer vaccine development. Given the involvement of DNA methylation in the development of lymphocytes, tumorigenicity and tumor progression, we aimed to analyze pre-vaccination DNA methylation profiles of peripheral blood mononuclear cells (PBMCs) from breast cancer subjects vaccinated with a novel peptide-based vaccine referred to as P10s-PADRE. This pilot study was performed to evaluate whether signatures of differentially methylated (DM) loci can be developed as potential predictive biomarkers for prescreening subjects with cancer who will most likely generate an immune response to the vaccine. Genomic DNA was isolated from PBMCs of eight vaccinated subjects, and their DNA methylation profiles were determined using Infinium® MethylationEPIC BeadChip array from Illumina. A linear regression model was applied to identify loci that were differentially methylated with respect to anti-peptide antibody titers and with IFN-γ production. The data were summarized using unsupervised-learning methods: hierarchical clustering and principal-component analysis. Pathways and networks involved were predicted by Ingenuity Pathway Analysis. We observed that the profile of DM loci separated subjects in regards to the levels of immune responses. Canonical pathways and networks related to metabolic and immunological functions were found to be involved. The data suggest that it is feasible to correlate methylation signatures in pre-treatment PBMCs with immune responses post-treatment in cancer patients going through standard-of-care chemotherapy. Larger and prospective studies that focus on DM loci in PBMCs is warranted to develop pre-screening biomarkers before BC vaccination. Clinical Trial Registration:www.ClinicalTrials.gov, Identifier: NCT02229084.
Collapse
Affiliation(s)
- Cinthia Violeta Hernandez Puente
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,UnivLyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Ping-Ching Hsu
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Lora J Rogers
- Division of Medical Genetics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Fariba Jousheghany
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Eric Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Susan A Kadlubar
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Division of Medical Genetics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - Issam Makhoul
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Division of Hematology Oncology, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Laura F Hutchins
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Division of Hematology Oncology, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Thomas Kieber-Emmons
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Behjatolah Monzavi-Karbassi
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| |
Collapse
|