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Xie J, Mothe B, Alcalde Herraiz M, Li C, Xu Y, Jödicke AM, Gao Y, Wang Y, Feng S, Wei J, Chen Z, Hong S, Wu Y, Su B, Zheng X, Cohet C, Ali R, Wareham N, Alhambra DP. Relationship between HLA genetic variations, COVID-19 vaccine antibody response, and risk of breakthrough outcomes. Nat Commun 2024; 15:4031. [PMID: 38740772 DOI: 10.1038/s41467-024-48339-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
The rapid global distribution of COVID-19 vaccines, with over a billion doses administered, has been unprecedented. However, in comparison to most identified clinical determinants, the implications of individual genetic factors on antibody responses post-COVID-19 vaccination for breakthrough outcomes remain elusive. Here, we conducted a population-based study including 357,806 vaccinated participants with high-resolution HLA genotyping data, and a subset of 175,000 with antibody serology test results. We confirmed prior findings that single nucleotide polymorphisms associated with antibody response are predominantly located in the Major Histocompatibility Complex region, with the expansive HLA-DQB1*06 gene alleles linked to improved antibody responses. However, our results did not support the claim that this mutation alone can significantly reduce COVID-19 risk in the general population. In addition, we discovered and validated six HLA alleles (A*03:01, C*16:01, DQA1*01:02, DQA1*01:01, DRB3*01:01, and DPB1*10:01) that independently influence antibody responses and demonstrated a combined effect across HLA genes on the risk of breakthrough COVID-19 outcomes. Lastly, we estimated that COVID-19 vaccine-induced antibody positivity provides approximately 20% protection against infection and 50% protection against severity. These findings have immediate implications for functional studies on HLA molecules and can inform future personalised vaccination strategies.
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Affiliation(s)
- Junqing Xie
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Beatriz Mothe
- Infectious Diseases Department, IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Marta Alcalde Herraiz
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Chunxiao Li
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Annika M Jödicke
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Yaqing Gao
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Yunhe Wang
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Shuo Feng
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Jia Wei
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Zhuoyao Chen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Shenda Hong
- National Institute of Health Data Science, Peking University, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Yeda Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Binbin Su
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Xiaoying Zheng
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Catherine Cohet
- Real-World Evidence Workstream, Data Analytics and Methods Task Force, European Medicines Agency, Amsterdam, Noord-Holland, The Netherlands
| | - Raghib Ali
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
- Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nick Wareham
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Daniel Prieto Alhambra
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK.
- Department of Medical Informatics, Erasmus University Medical Centre, Rotterdam, The Netherlands.
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Féray C, Allain V, Desterke C, Roche B, Coilly A, Caillat-Zucman S. HLA-DQ Diversity Is Associated With Humoral Response to Vaccines in Patients Awaiting or After Liver Transplantation. Gastroenterology 2024; 166:915-917.e3. [PMID: 38215998 DOI: 10.1053/j.gastro.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/22/2023] [Accepted: 01/07/2024] [Indexed: 01/14/2024]
Affiliation(s)
- Cyrille Féray
- Centre Hépato-Biliaire, Assistance Publique-Hôpitaux de Paris, Hôpital Paul-Brousse, Villejuif, France; Université Paris-Saclay, UMR-S 1193 INSERM, FHU Hepatinov, Villejuif, France.
| | - Vincent Allain
- Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université de Paris, Laboratoire d'Immunologie et Histocompatibilité, Paris, France; INSERM UMR976, Université de Paris, Paris, France
| | - Christophe Desterke
- Centre Hépato-Biliaire, Assistance Publique-Hôpitaux de Paris, Hôpital Paul-Brousse, Villejuif, France; Université Paris-Saclay, UMR-S 1193 INSERM, FHU Hepatinov, Villejuif, France
| | - Bruno Roche
- Centre Hépato-Biliaire, Assistance Publique-Hôpitaux de Paris, Hôpital Paul-Brousse, Villejuif, France; Université Paris-Saclay, UMR-S 1193 INSERM, FHU Hepatinov, Villejuif, France
| | - Audrey Coilly
- Centre Hépato-Biliaire, Assistance Publique-Hôpitaux de Paris, Hôpital Paul-Brousse, Villejuif, France; Université Paris-Saclay, UMR-S 1193 INSERM, FHU Hepatinov, Villejuif, France
| | - Sophie Caillat-Zucman
- Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université de Paris, Laboratoire d'Immunologie et Histocompatibilité, Paris, France; INSERM UMR976, Université de Paris, Paris, France
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Mentzer AJ, Dilthey AT, Pollard M, Gurdasani D, Karakoc E, Carstensen T, Muhwezi A, Cutland C, Diarra A, da Silva Antunes R, Paul S, Smits G, Wareing S, Kim H, Pomilla C, Chong AY, Brandt DYC, Nielsen R, Neaves S, Timpson N, Crinklaw A, Lindestam Arlehamn CS, Rautanen A, Kizito D, Parks T, Auckland K, Elliott KE, Mills T, Ewer K, Edwards N, Fatumo S, Webb E, Peacock S, Jeffery K, van der Klis FRM, Kaleebu P, Vijayanand P, Peters B, Sette A, Cereb N, Sirima S, Madhi SA, Elliott AM, McVean G, Hill AVS, Sandhu MS. High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response. Nat Med 2024; 30:1384-1394. [PMID: 38740997 PMCID: PMC11108778 DOI: 10.1038/s41591-024-02944-5] [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: 02/08/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
How human genetic variation contributes to vaccine effectiveness in infants is unclear, and data are limited on these relationships in populations with African ancestries. We undertook genetic analyses of vaccine antibody responses in infants from Uganda (n = 1391), Burkina Faso (n = 353) and South Africa (n = 755), identifying associations between human leukocyte antigen (HLA) and antibody response for five of eight tested antigens spanning pertussis, diphtheria and hepatitis B vaccines. In addition, through HLA typing 1,702 individuals from 11 populations of African ancestry derived predominantly from the 1000 Genomes Project, we constructed an imputation resource, fine-mapping class II HLA-DR and DQ associations explaining up to 10% of antibody response variance in our infant cohorts. We observed differences in the genetic architecture of pertussis antibody response between the cohorts with African ancestries and an independent cohort with European ancestry, but found no in silico evidence of differences in HLA peptide binding affinity or breadth. Using immune cell expression quantitative trait loci datasets derived from African-ancestry samples from the 1000 Genomes Project, we found evidence of differential HLA-DRB1 expression correlating with inferred protection from pertussis following vaccination. This work suggests that HLA-DRB1 expression may play a role in vaccine response and should be considered alongside peptide selection to improve vaccine design.
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Affiliation(s)
- Alexander J Mentzer
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Alexander T Dilthey
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital of Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | | | | | | | - Allan Muhwezi
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Clare Cutland
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Amidou Diarra
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | | | - Sinu Paul
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Gaby Smits
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Susan Wareing
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | | | | | - Amanda Y Chong
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Debora Y C Brandt
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Samuel Neaves
- Avon Longitudinal Study of Parents and Children at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicolas Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Austin Crinklaw
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Anna Rautanen
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dennison Kizito
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Tom Parks
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Kate E Elliott
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tara Mills
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Katie Ewer
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Nick Edwards
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Segun Fatumo
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- The Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine London, London, UK
| | - Emily Webb
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Sarah Peacock
- Tissue Typing Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Katie Jeffery
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | | | - Bjorn Peters
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Sodiomon Sirima
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alison M Elliott
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Adrian V S Hill
- Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
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4
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Zheng K, Chong AY, Mentzer AJ. How could our genetics impact COVID-19 vaccine response? Expert Rev Clin Immunol 2024:1-13. [PMID: 38676712 DOI: 10.1080/1744666x.2024.2346584] [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: 12/22/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024]
Abstract
INTRODUCTION The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has posed unprecedented global health challenges since its emergence in December 2019. The rapid availability of vaccines has been estimated to save millions of lives, but there is variation in how individuals respond to vaccines, influencing their effectiveness at an individual, and population level. AREAS COVERED This review focuses on human genetic factors influencing the immune response and effectiveness of vaccines, highlighting the importance of associations across the HLA locus. Genome-Wide Association Studies (GWAS) and other genetic association analyses have identified statistically significant associations between specific HLA alleles including HLA-DRB1*13, DBQ1*06, and A*03 impacting antibody responses and the risk of breakthrough infections post-vaccination. Relationships between these associations and potential mechanisms and links with risks of natural infection or disease are explored, and this review concludes by emphasizing how understanding the mechanisms of these genetic determinants may inform the development of tailored vaccination strategies. EXPERT OPINION Although complex, we believe these findings from the SARS-CoV2 pandemic offer a unique opportunity to understand the relationships between HLA and infection and vaccine response, with a goal of optimizing individual protection against COVID-19 in the ongoing pandemic, and possibly influencing wider vaccine development in the future.
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Affiliation(s)
- Keyi Zheng
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Amanda Y Chong
- Centre for Human Genetics, University of Oxford, Oxford, UK
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5
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Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A. Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection. HGG ADVANCES 2024; 5:100300. [PMID: 38678364 DOI: 10.1016/j.xhgg.2024.100300] [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: 12/04/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024] Open
Abstract
Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B∗15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B∗15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the United States (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B∗15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections studied, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified.
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Affiliation(s)
- Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France
| | | | - Iva Neveux
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Evangelos Bellos
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Ivana Nemes-Bokun
- Department of Infectious Disease, Imperial College London, London, UK
| | | | | | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, New South Wales, Australia
| | - András N Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Justin B Lack
- NIAID Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD, USA
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University Paris Cité, Paris, France; AP-HP, Bichat-Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France
| | - Charles Burdet
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University Paris Cité, Paris, France; AP-HP, Hôpital Bichat, Centre d'Investigation Clinique, INSERM CIC 1425, Paris, France; Département Epidémiologie, Biostatistiques et Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, 75018 Paris, France
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d'immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Département de Santé Publique, Unitéde Recherche Clinique PSL-CFX, CIC-1901, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France; GRC-14 BIOSFAST Sorbonne Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Joseph J Grzymski
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA; Renown Health, Reno, NV, USA
| | - Vanessa Sancho-Shimizu
- Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Pediatrics, Necker Hospital for Sick Children, Paris, France; Howard Hughes Medical Institute, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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6
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Santos-Rebouças CB, Ferreira CDS, Nogueira JDS, Brustolini OJ, de Almeida LGP, Gerber AL, Guimarães APDC, Piergiorge RM, Struchiner CJ, Porto LC, de Vasconcelos ATR. Immune response stability to the SARS-CoV-2 mRNA vaccine booster is influenced by differential splicing of HLA genes. Sci Rep 2024; 14:8982. [PMID: 38637586 PMCID: PMC11026523 DOI: 10.1038/s41598-024-59259-1] [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: 09/12/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Many molecular mechanisms that lead to the host antibody response to COVID-19 vaccines remain largely unknown. In this study, we used serum antibody detection combined with whole blood RNA-based transcriptome analysis to investigate variability in vaccine response in healthy recipients of a booster (third) dose schedule of the mRNA BNT162b2 vaccine against COVID-19. The cohort was divided into two groups: (1) low-stable individuals, with antibody concentration anti-SARS-CoV IgG S1 below 0.4 percentile at 180 days after boosting vaccination; and (2) high-stable individuals, with antibody values greater than 0.6 percentile of the range in the same period (median 9525 [185-80,000] AU/mL). Differential gene expression, expressed single nucleotide variants and insertions/deletions, differential splicing events, and allelic imbalance were explored to broaden our understanding of the immune response sustenance. Our analysis revealed a differential expression of genes with immunological functions in individuals with low antibody titers, compared to those with higher antibody titers, underscoring the fundamental importance of the innate immune response for boosting immunity. Our findings also provide new insights into the determinants of the immune response variability to the SARS-CoV-2 mRNA vaccine booster, highlighting the significance of differential splicing regulatory mechanisms, mainly concerning HLA alleles, in delineating vaccine immunogenicity.
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Affiliation(s)
- Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Cristina Dos Santos Ferreira
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Jeane de Souza Nogueira
- Histocompatibility and Cryopreservation Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Otávio José Brustolini
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Luiz Gonzaga Paula de Almeida
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Alexandra Lehmkuhl Gerber
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Ana Paula de Campos Guimarães
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Cláudio José Struchiner
- School of Applied Mathematics, Getúlio Vargas Foundation, Rio de Janeiro, Brazil
- Social Medicine Institute Hesio Cordeiro, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Ana Tereza Ribeiro de Vasconcelos
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil.
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7
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Esposito M, Minnai F, Copetti M, Miscio G, Perna R, Piepoli A, De Vincentis G, Benvenuto M, D'Addetta P, Croci S, Baldassarri M, Bruttini M, Fallerini C, Brugnoni R, Cavalcante P, Baggi F, Corsini EMG, Ciusani E, Andreetta F, Dragani TA, Fratelli M, Carella M, Mantegazza RE, Renieri A, Colombo F. Human leukocyte antigen variants associate with BNT162b2 mRNA vaccine response. COMMUNICATIONS MEDICINE 2024; 4:63. [PMID: 38575714 PMCID: PMC10995155 DOI: 10.1038/s43856-024-00490-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Since the beginning of the anti-COVID-19 vaccination campaign, it has become evident that vaccinated subjects exhibit considerable inter-individual variability in the response to the vaccine that could be partly explained by host genetic factors. A recent study reported that the immune response elicited by the Oxford-AstraZeneca vaccine in individuals from the United Kingdom was influenced by a specific allele of the human leukocyte antigen gene HLA-DQB1. METHODS We carried out a genome-wide association study to investigate the genetic determinants of the antibody response to the Pfizer-BioNTech vaccine in an Italian cohort of 1351 subjects recruited in three centers. Linear regressions between normalized antibody levels and genotypes of more than 7 million variants was performed, using sex, age, centers, days between vaccination boost and serological test, and five principal components as covariates. We also analyzed the association between normalized antibody levels and 204 HLA alleles, with the same covariates as above. RESULTS Our study confirms the involvement of the HLA locus and shows significant associations with variants in HLA-A, HLA-DQA1, and HLA-DQB1 genes. In particular, the HLA-A*03:01 allele is the most significantly associated with serum levels of anti-SARS-CoV-2 antibodies. Other alleles, from both major histocompatibility complex class I and II are significantly associated with antibody levels. CONCLUSIONS These results support the hypothesis that HLA genes modulate the response to Pfizer-BioNTech vaccine and highlight the need for genetic studies in diverse populations and for functional studies aimed to elucidate the relationship between HLA-A*03:01 and CD8+ cell response upon Pfizer-BioNTech vaccination.
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Affiliation(s)
- Martina Esposito
- National Research Council, Institute for Biomedical Technologies, Segrate, MI, Italy
| | - Francesca Minnai
- National Research Council, Institute for Biomedical Technologies, Segrate, MI, Italy
- Department of Medical Biotechnology and Translational Medicine (BioMeTra), Università degli Studi di Milano, Milan, Italy
| | - Massimiliano Copetti
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Giuseppe Miscio
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Rita Perna
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Ada Piepoli
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | | | - Mario Benvenuto
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Paola D'Addetta
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Susanna Croci
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Margherita Baldassarri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Mirella Bruttini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | | | | | - Fulvio Baggi
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | | | - Emilio Ciusani
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | | | | | | | - Massimo Carella
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | | | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Francesca Colombo
- National Research Council, Institute for Biomedical Technologies, Segrate, MI, Italy.
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8
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Aharon A, Benedek G, Barhoum B, Parnasa E, Magadle N, Perzon O, Mevorach D. HLA binding-groove motifs are associated with myocarditis induction after Pfizer-BioNTech BNT162b2 vaccination. Eur J Clin Invest 2024; 54:e14142. [PMID: 38071404 DOI: 10.1111/eci.14142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/16/2023] [Accepted: 11/25/2023] [Indexed: 03/13/2024]
Abstract
BACKGROUND AND AIMS We found a higher incidence of myocarditis in young males who had received at least two Pfizer-BioNTech BNT162b2 vaccinations. The human leukocyte antigens (HLA) are known to play an important role in infectious and autoinflammatory diseases. We hypothesized that certain HLA alleles might be associated with vaccination-induced myocarditis. METHODS HLA typing was performed using next-generation sequencing technology with the Illumina Iseq100 platform. HLA class I and II loci were genotyped in 29 patients with post-vaccination myocarditis and compared with HLA data from 300 healthy controls. RESULTS We demonstrate that the DRB1*14:01, DRB1*15:03 alleles and the motifs in HLA-A - Leu62 and Gln63, which are part of binding pocket B and HLA-DR Tyr47, His60, Arg70 and Glu74, which are part of binding pockets P4, P7 and P9, were significantly associated with disease susceptibility. CONCLUSIONS Our findings suggest that immunogenetic fingerprints in HLA peptide-binding grooves may affect the presentation of peptides derived from the Pfizer-BioNTech BNT162b2 vaccination to T cells and induce an inflammatory process that results in myocarditis.
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Affiliation(s)
- Aviran Aharon
- Hebrew University-Hadassah Faculty of Medicine, Jerusalem, Israel
| | - Gil Benedek
- Hebrew University-Hadassah Faculty of Medicine, Jerusalem, Israel
- Tissue Typing and Immunogenetics Unit, Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Barhoum Barhoum
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Elchanan Parnasa
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Nur Magadle
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ofer Perzon
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dror Mevorach
- Hebrew University-Hadassah Faculty of Medicine, Jerusalem, Israel
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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9
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Monteiro MES, Lechuga GC, Napoleão-Pêgo P, Carvalho JPRS, Gomes LR, Morel CM, Provance DW, De-Simone SG. Humoral Immune Response to SARS-CoV-2 Spike Protein Receptor-Binding Motif Linear Epitopes. Vaccines (Basel) 2024; 12:342. [PMID: 38675725 PMCID: PMC11055068 DOI: 10.3390/vaccines12040342] [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] [Revised: 03/05/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
The worldwide spread of SARS-CoV-2 has led to a significant economic and social burden on a global scale. Even though the pandemic has concluded, apprehension remains regarding the emergence of highly transmissible variants capable of evading immunity induced by either vaccination or prior infection. The success of viral penetration is due to the specific amino acid residues of the receptor-binding motif (RBM) involved in viral attachment. This region interacts with the cellular receptor ACE2, triggering a neutralizing antibody (nAb) response. In this study, we evaluated serum immunogenicity from individuals who received either a single dose or a combination of different vaccines against the original SARS-CoV-2 strain and a mutated linear RBM. Despite a modest antibody response to wild-type SARS-CoV-2 RBM, the Omicron variants exhibit four mutations in the RBM (S477N, T478K, E484A, and F486V) that result in even lower antibody titers. The primary immune responses observed were directed toward IgA and IgG. While nAbs typically target the RBD, our investigation has unveiled reduced seroreactivity within the RBD's crucial subregion, the RBM. This deficiency may have implications for the generation of protective nAbs. An evaluation of S1WT and S2WT RBM peptides binding to nAbs using microscale thermophoresis revealed a higher affinity (35 nM) for the S2WT sequence (GSTPCNGVEGFNCYF), which includes the FNCY patch. Our findings suggest that the linear RBM of SARS-CoV-2 is not an immunodominant region in vaccinated individuals. Comprehending the intricate dynamics of the humoral response, its interplay with viral evolution, and host genetics is crucial for formulating effective vaccination strategies, targeting not only SARS-CoV-2 but also anticipating potential future coronaviruses.
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Affiliation(s)
- Maria E. S. Monteiro
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Program of Post-Graduation on Parasitic Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Guilherme C. Lechuga
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Paloma Napoleão-Pêgo
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - João P. R. S. Carvalho
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, RJ, Brazil
| | - Larissa R. Gomes
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
| | - Carlos M. Morel
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
| | - David W. Provance
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Salvatore G. De-Simone
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Program of Post-Graduation on Parasitic Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, RJ, Brazil
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10
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Sugrue JA, Duffy D. Systems vaccinology studies - achievements and future potential. Microbes Infect 2024:105318. [PMID: 38460935 DOI: 10.1016/j.micinf.2024.105318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Human immune responses to vaccination are variable both within and between populations. Systems vaccinology, which is the application of multi-omics technologies to vaccine studies, seeks to understand such variation and predict responses to optimise vaccine strategies. Here, we outline new approaches to systems vaccinology, focusing on the incorporation of additional cohorts, endpoints and technologies.
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Affiliation(s)
- Jamie A Sugrue
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France.
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11
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Kurtz SL, Baker RE, Boehm FJ, Lehman CC, Mittereder LR, Khan H, Rossi AP, Gatti DM, Beamer G, Sassetti CM, Elkins KL. Multiple genetic loci influence vaccine-induced protection against Mycobacterium tuberculosis in genetically diverse mice. PLoS Pathog 2024; 20:e1012069. [PMID: 38452145 PMCID: PMC10950258 DOI: 10.1371/journal.ppat.1012069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/19/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Mycobacterium tuberculosis (M.tb.) infection leads to over 1.5 million deaths annually, despite widespread vaccination with BCG at birth. Causes for the ongoing tuberculosis endemic are complex and include the failure of BCG to protect many against progressive pulmonary disease. Host genetics is one of the known factors implicated in susceptibility to primary tuberculosis, but less is known about the role that host genetics plays in controlling host responses to vaccination against M.tb. Here, we addressed this gap by utilizing Diversity Outbred (DO) mice as a small animal model to query genetic drivers of vaccine-induced protection against M.tb. DO mice are a highly genetically and phenotypically diverse outbred population that is well suited for fine genetic mapping. Similar to outcomes in people, our previous studies demonstrated that DO mice have a wide range of disease outcomes following BCG vaccination and M.tb. challenge. In the current study, we used a large population of BCG-vaccinated/M.tb.-challenged mice to perform quantitative trait loci mapping of complex infection traits; these included lung and spleen M.tb. burdens, as well as lung cytokines measured at necropsy. We found sixteen chromosomal loci associated with complex infection traits and cytokine production. QTL associated with bacterial burdens included a region encoding major histocompatibility antigens that are known to affect susceptibility to tuberculosis, supporting validity of the approach. Most of the other QTL represent novel associations with immune responses to M.tb. and novel pathways of cytokine regulation. Most importantly, we discovered that protection induced by BCG is a multigenic trait, in which genetic loci harboring functionally-distinct candidate genes influence different aspects of immune responses that are crucial collectively for successful protection. These data provide exciting new avenues to explore and exploit in developing new vaccines against M.tb.
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Affiliation(s)
- Sherry L. Kurtz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Richard E. Baker
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Frederick J. Boehm
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Chelsea C. Lehman
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Lara R. Mittereder
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Hamda Khan
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Amy P. Rossi
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- College of Medicine, University of Cincinatti, Cincinatti, Ohio, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Gillian Beamer
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Karen L. Elkins
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
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12
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Alamad B, Elliott K, Knight JC. Cross-population applications of genomics to understand the risk of multifactorial traits involving inflammation and immunity. CAMBRIDGE PRISMS. PRECISION MEDICINE 2024; 2:e3. [PMID: 38549844 PMCID: PMC10953767 DOI: 10.1017/pcm.2023.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/15/2023] [Accepted: 12/18/2023] [Indexed: 04/26/2024]
Abstract
The interplay between genetic and environmental factors plays a significant role in interindividual variation in immune and inflammatory responses. The availability of high-throughput low-cost genotyping and next-generation sequencing has revolutionized our ability to identify human genetic variation and understand how this varies within and between populations, and the relationship with disease. In this review, we explore the potential of genomics for patient benefit, specifically in the diagnosis, prognosis and treatment of inflammatory and immune-related diseases. We summarize the knowledge arising from genetic and functional genomic approaches, and the opportunity for personalized medicine. The review covers applications in infectious diseases, rare immunodeficiencies and autoimmune diseases, illustrating advances in diagnosis and understanding risk including use of polygenic risk scores. We further explore the application for patient stratification and drug target prioritization. The review highlights a key challenge to the field arising from the lack of sufficient representation of genetically diverse populations in genomic studies. This currently limits the clinical utility of genetic-based diagnostic and risk-based applications in non-Caucasian populations. We highlight current genome projects, initiatives and biobanks from diverse populations and how this is being used to improve healthcare globally by improving our understanding of genetic susceptibility to diseases and regional pathogens such as malaria and tuberculosis. Future directions and opportunities for personalized medicine and wider application of genomics in health care are described, for the benefit of individual patients and populations worldwide.
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Affiliation(s)
- Bana Alamad
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kate Elliott
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C. Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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13
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Cruz Cisneros MC, Anderson EJ, Hampton BK, Parotti B, Sarkar S, Taft-Benz S, Bell TA, Blanchard M, Dillard JA, Dinnon KH, Hock P, Leist SR, Madden EA, Shaw GD, West A, Baric RS, Baxter VK, Pardo-Manuel de Villena F, Heise MT, Ferris MT. Host Genetic Variation Impacts SARS-CoV-2 Vaccination Response in the Diversity Outbred Mouse Population. Vaccines (Basel) 2024; 12:103. [PMID: 38276675 PMCID: PMC10821422 DOI: 10.3390/vaccines12010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic led to the rapid and worldwide development of highly effective vaccines against SARS-CoV-2. However, there is significant individual-to-individual variation in vaccine efficacy due to factors including viral variants, host age, immune status, environmental and host genetic factors. Understanding those determinants driving this variation may inform the development of more broadly protective vaccine strategies. While host genetic factors are known to impact vaccine efficacy for respiratory pathogens such as influenza and tuberculosis, the impact of host genetic variation on vaccine efficacy against COVID-19 is not well understood. To model the impact of host genetic variation on SARS-CoV-2 vaccine efficacy, while controlling for the impact of non-genetic factors, we used the Diversity Outbred (DO) mouse model. We found that DO mice immunized against SARS-CoV-2 exhibited high levels of variation in vaccine-induced neutralizing antibody responses. While the majority of the vaccinated mice were protected from virus-induced disease, similar to human populations, we observed vaccine breakthrough in a subset of mice. Importantly, we found that this variation in neutralizing antibody, virus-induced disease, and viral titer is heritable, indicating that the DO serves as a useful model system for studying the contribution of genetic variation of both vaccines and disease outcomes.
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Affiliation(s)
- Marta C. Cruz Cisneros
- Genetics and Molecular Biology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; (M.C.C.C.); (B.K.H.)
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Elizabeth J. Anderson
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (E.J.A.); (V.K.B.)
| | - Brea K. Hampton
- Genetics and Molecular Biology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; (M.C.C.C.); (B.K.H.)
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Breantié Parotti
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sharon Taft-Benz
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Timothy A. Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Matthew Blanchard
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Jacob A. Dillard
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Kenneth H. Dinnon
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Emily A. Madden
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Ralph S. Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Victoria K. Baxter
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (E.J.A.); (V.K.B.)
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mark T. Heise
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
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14
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Bian S, Guo X, Yang X, Wei Y, Yang Z, Cheng S, Yan J, Chen Y, Chen GB, Du X, Francis SS, Shu Y, Liu S. Genetic determinants of IgG antibody response to COVID-19 vaccination. Am J Hum Genet 2024; 111:181-199. [PMID: 38181733 PMCID: PMC10806743 DOI: 10.1016/j.ajhg.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024] Open
Abstract
Human humoral immune responses to SARS-CoV-2 vaccines exhibit substantial inter-individual variability and have been linked to vaccine efficacy. To elucidate the underlying mechanism behind this variability, we conducted a genome-wide association study (GWAS) on the anti-spike IgG serostatus of UK Biobank participants who were previously uninfected by SARS-CoV-2 and had received either the first dose (n = 54,066) or the second dose (n = 46,232) of COVID-19 vaccines. Our analysis revealed significant genome-wide associations between the IgG antibody serostatus following the initial vaccine and human leukocyte antigen (HLA) class II alleles. Specifically, the HLA-DRB1∗13:02 allele (MAF = 4.0%, OR = 0.75, p = 2.34e-16) demonstrated the most statistically significant protective effect against IgG seronegativity. This protective effect was driven by an alteration from arginine (Arg) to glutamic acid (Glu) at position 71 on HLA-DRβ1 (p = 1.88e-25), leading to a change in the electrostatic potential of pocket 4 of the peptide binding groove. Notably, the impact of HLA alleles on IgG responses was cell type specific, and we observed a shared genetic predisposition between IgG status and susceptibility/severity of COVID-19. These results were replicated within independent cohorts where IgG serostatus was assayed by two different antibody serology tests. Our findings provide insights into the biological mechanism underlying individual variation in responses to COVID-19 vaccines and highlight the need to consider the influence of constitutive genetics when designing vaccination strategies for optimizing protection and control of infectious disease across diverse populations.
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Affiliation(s)
- Shengzhe Bian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Xinxin Guo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Xilai Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Yuandan Wei
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Zijing Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Shiyao Cheng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Jiaqi Yan
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Yongkun Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Guo-Bo Chen
- Center for General Practice Medicine, Department of General Practice Medicine, Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310059, Zhejiang, P.R. China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou 310063, Zhejiang, P.R. China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Stephen S Francis
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China; Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, P.R. China.
| | - Siyang Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China.
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15
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Odak I, Riemann L, Sandrock I, Cossmann A, Ramos GM, Hammerschmidt SI, Ritter C, Friedrichsen M, Hassan A, Dopfer-Jablonka A, Stankov MV, Weskamm LM, Addo MM, Ravens I, Willenzon S, Schimrock A, Ristenpart J, Janssen A, Barros-Martins J, Hansen G, Falk C, Behrens GMN, Förster R. Systems biology analysis reveals distinct molecular signatures associated with immune responsiveness to the BNT162b COVID-19 vaccine. EBioMedicine 2024; 99:104947. [PMID: 38160529 PMCID: PMC10792461 DOI: 10.1016/j.ebiom.2023.104947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/11/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Human immune responses to COVID-19 vaccines display a large heterogeneity of induced immunity and the underlying immune mechanisms for this remain largely unknown. METHODS Using a systems biology approach, we longitudinally profiled a unique cohort of female high and low responders to the BNT162b vaccine, who were known from previous COVID-19 vaccinations to develop maximum and minimum immune responses to the vaccine. We utilized high dimensional flow cytometry, bulk and single cell mRNA sequencing and 48-plex serum cytokine analyses. FINDINGS We revealed early, transient immunological and molecular signatures that distinguished high from low responders and correlated with B and T cell responses measured 14 days later. High responders featured a distinct transcriptional activity of interferon-driven genes and genes connected to enhanced antigen presentation. This was accompanied by a robust cytokine response related to Th1 differentiation. Both transcriptome and serum cytokine signatures were confirmed in two independent confirmatory cohorts. INTERPRETATION Collectively, our data contribute to a better understanding of the immunogenicity of mRNA-based COVID-19 vaccines, which might lead to the optimization of vaccine designs for individuals with poor vaccine responses. FUNDING German Center for Infection Research, German Center for Lung Research, German Research Foundation, Excellence Strategy EXC 2155 "RESIST" and European Regional Development Fund.
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Affiliation(s)
- Ivan Odak
- Institute of Immunology, Hannover Medical School, Germany
| | - Lennart Riemann
- Institute of Immunology, Hannover Medical School, Germany; Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Germany; Clinician Scientist Program TITUS, Else-Kröner-Fresenius Foundation, Hannover Medical School, Germany
| | - Inga Sandrock
- Institute of Immunology, Hannover Medical School, Germany
| | - Anne Cossmann
- Department for Rheumatology and Immunology, Hannover Medical School, Germany
| | - Gema Morillas Ramos
- Department for Rheumatology and Immunology, Hannover Medical School, Germany
| | | | | | | | - Ahmed Hassan
- Institute of Immunology, Hannover Medical School, Germany
| | - Alexandra Dopfer-Jablonka
- Department for Rheumatology and Immunology, Hannover Medical School, Germany; German Center for Infection Research (DZIF), Partner Sites Hannover-Braunschweig, Germany
| | - Metodi V Stankov
- Department for Rheumatology and Immunology, Hannover Medical School, Germany
| | - Leonie M Weskamm
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marylyn M Addo
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany; First Department of Medicine, Division of Infectious Diseases, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Inga Ravens
- Institute of Immunology, Hannover Medical School, Germany
| | | | - Anja Schimrock
- Institute of Immunology, Hannover Medical School, Germany
| | | | - Anika Janssen
- Institute of Immunology, Hannover Medical School, Germany
| | | | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Germany; Clinician Scientist Program TITUS, Else-Kröner-Fresenius Foundation, Hannover Medical School, Germany; German Center of Lung Research (DZL), BREATH, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Germany
| | - Christine Falk
- Institute for Transplantation Immunology, Hannover Medical School, Hannover, Germany
| | - Georg M N Behrens
- Department for Rheumatology and Immunology, Hannover Medical School, Germany; German Center for Infection Research (DZIF), Partner Sites Hannover-Braunschweig, Germany; Centre for Individualized Infection Medicine (CiiM), Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, Germany; Clinician Scientist Program TITUS, Else-Kröner-Fresenius Foundation, Hannover Medical School, Germany; German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany; German Center of Lung Research (DZL), BREATH, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Germany.
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16
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Liblau RS, Latorre D, Kornum BR, Dauvilliers Y, Mignot EJ. The immunopathogenesis of narcolepsy type 1. Nat Rev Immunol 2024; 24:33-48. [PMID: 37400646 DOI: 10.1038/s41577-023-00902-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
Narcolepsy type 1 (NT1) is a chronic sleep disorder resulting from the loss of a small population of hypothalamic neurons that produce wake-promoting hypocretin (HCRT; also known as orexin) peptides. An immune-mediated pathology for NT1 has long been suspected given its exceptionally tight association with the MHC class II allele HLA-DQB1*06:02, as well as recent genetic evidence showing associations with polymorphisms of T cell receptor genes and other immune-relevant loci and the increased incidence of NT1 that has been observed after vaccination with the influenza vaccine Pandemrix. The search for both self-antigens and foreign antigens recognized by the pathogenic T cell response in NT1 is ongoing. Increased T cell reactivity against HCRT has been consistently reported in patients with NT1, but data demonstrating a primary role for T cells in neuronal destruction are currently lacking. Animal models are providing clues regarding the roles of autoreactive CD4+ and CD8+ T cells in the disease. Elucidation of the pathogenesis of NT1 will allow for the development of targeted immunotherapies at disease onset and could serve as a model for other immune-mediated neurological diseases.
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Affiliation(s)
- Roland S Liblau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, Toulouse, France.
- Department of Immunology, Toulouse University Hospitals, Toulouse, France.
| | | | - Birgitte R Kornum
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yves Dauvilliers
- National Reference Center for Orphan Diseases, Narcolepsy, Idiopathic Hypersomnia and Kleine-Levin Syndrome, Department of Neurology, Gui-de-Chauliac Hospital, CHU de Montpellier, Montpellier, France
- INSERM Institute for Neurosciences of Montpellier, Montpellier, France
| | - Emmanuel J Mignot
- Stanford University, Center for Narcolepsy, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, USA.
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17
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Ferri C, Raimondo V, Giuggioli D, Gragnani L, Lorini S, Dagna L, Bosello SL, Foti R, Riccieri V, Guiducci S, Cuomo G, Tavoni A, De Angelis R, Cacciapaglia F, Zanatta E, Cozzi F, Murdaca G, Cavazzana I, Romeo N, Codullo V, Pellegrini R, Varcasia G, De Santis M, Selmi C, Abignano G, Caminiti M, L'Andolina M, Olivo D, Lubrano E, Spinella A, Lumetti F, De Luca G, Ruscitti P, Urraro T, Visentini M, Bellando-Randone S, Visalli E, Testa D, Sciascia G, Masini F, Pellegrino G, Saccon F, Balestri E, Elia G, Ferrari SM, Tonutti A, Dall’Ara F, Pagano Mariano G, Pettiti G, Zanframundo G, Brittelli R, Aiello V, Dal Bosco Y, Foti R, Di Cola I, Scorpiniti D, Fusaro E, Ferrari T, Gigliotti P, Campochiaro C, Francioso F, Iandoli C, Caira V, Zignego AL, D'Angelo S, Franceschini F, Matucci-Cerinic M, Giacomelli R, Doria A, Santini SA, Fallahi P, Iannone F, Antonelli A. Impact of COVID-19 and vaccination campaign on 1,755 systemic sclerosis patients during first three years of pandemic. Possible risks for individuals with impaired immunoreactivity to vaccine, ongoing immunomodulating treatments, and disease-related lung involvement during the next pandemic phase. J Transl Autoimmun 2023; 7:100212. [PMID: 37854035 PMCID: PMC10580042 DOI: 10.1016/j.jtauto.2023.100212] [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: 08/18/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Introduction The impact of COVID-19 pandemic represents a serious challenge for 'frail' patients' populations with inflammatory autoimmune systemic diseases such as systemic sclerosis (SSc). We investigated the prevalence and severity of COVID-19, as well the effects of COVID-19 vaccination campaign in a large series of SSc patients followed for the entire period (first 38 months) of pandemic. Patients and method This prospective survey study included 1755 unselected SSc patients (186 M, 1,569F; mean age 58.7 ± 13.4SD years, mean disease duration 8.8 ± 7.3SD years) recruited in part by telephone survey at 37 referral centers from February 2020 to April 2023. The following parameters were carefully evaluated: i. demographic, clinical, serological, and therapeutical features; ii. prevalence and severity of COVID-19; and iii. safety, immunogenicity, and efficacy of COVID-19 vaccines. Results The prevalence of COVID-19 recorded during the whole pandemic was significantly higher compared to Italian general population (47.3 % vs 43.3 %, p < 0.000), as well the COVID-19-related mortality (1.91 % vs 0.72 %, p < 0.001). As regards the putative prognostic factors of worse outcome, COVID-19 positive patients with SSc-related interstitial lung involvement showed significantly higher percentage of COVID-19-related hospitalization compared to those without (5.85 % vs 1.73 %; p < 0.0001), as well as of mortality rate (2.01 % vs 0.4 %; p = 0.002). Over half of patients (56.3 %) received the first two plus one booster dose of vaccine; while a fourth dose was administered to 35.6 %, and only few of them (1.99 %) had five or more doses of vaccine. Of note, an impaired seroconversion was recorded in 25.6 % of individuals after the first 2 doses of vaccine, and in 8.4 % of patients also after the booster dose. Furthermore, the absence of T-cell immunoreactivity was observed in 3/7 patients tested by QuantiFERON® SARSCoV-2 Starter Set (Qiagen). The efficacy of vaccines, evaluated by comparing the COVID-19-related death rate recorded during pre- and post-vaccination pandemic periods, revealed a quite stable outcome in SSc patients (death rate from 2.54 % to 1.76 %; p = ns), despite the significant drop of mortality observed in the Italian general population (from 2.95 % to 0.29 %; p < 0.0001). Conclusions An increased COVID-19 prevalence and mortality rate was recorded in SSc patients; moreover, the efficacy of vaccines in term of improved outcomes was less evident in SSc compared to Italian general population. This discrepancy might be explained by concomitant adverse prognostic factors: increased rate of non-responders to vaccine in SSc series, low percentage of individuals with four or more doses of vaccine, ongoing immunomodulating treatments, disease-related interstitial lung disease, and/or reduced preventive measures in the second half of pandemic. A careful monitoring of response to COVID-19 vaccines together with adequate preventive/therapeutical strategies are highly recommendable in the near course of pandemic in this frail patients' population.
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Affiliation(s)
- Clodoveo Ferri
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
- Rheumatology Clinic ‘Madonna Dello Scoglio’ Cotronei, Crotone, Italy
| | - Vincenzo Raimondo
- Rheumatology Clinic ‘Madonna Dello Scoglio’ Cotronei, Crotone, Italy
| | - Dilia Giuggioli
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
| | - Laura Gragnani
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | - Serena Lorini
- MASVE Interdepartmental Hepatology Center, Department of Experimental and Clinical Medicine, University of Florence, Center for Research and Innovation CRIA-MASVE, AOU Careggi, Florence, Italy
| | | | - Silvia Laura Bosello
- Division of Rheumatology, Catholic University of the Sacred Heart, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Rosario Foti
- AOU Policlinico Vittorio Emanuele, Catania, Italy
| | | | | | | | | | - Rossella De Angelis
- Rheumatology Clinic, Department of Clinical & Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | | | | | | | - Giuseppe Murdaca
- Ospedale Policlinico S. Martino-University of Genova, Genova, Italy
| | | | | | | | | | | | - Maria De Santis
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Carlo Selmi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | | | - Maurizio Caminiti
- UOD Reumatologia- Grande Ospedale Metropolitano, Reggio Calabria, Italy
| | - Massimo L'Andolina
- Rheumatology Outpatient Clinic, ASP- Vibo Valentia-Tropea Hospital, Italy
| | - Domenico Olivo
- Rheumatology Outpatient Clinic, San Giovanni di Dio Hospital, Crotone, Italy
| | - Ennio Lubrano
- Rheumatology, Università Del Molise, Campobasso, Italy
| | - Amelia Spinella
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
| | - Federica Lumetti
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
| | | | - Piero Ruscitti
- Rheumatology Unit, Department of Biotechnological & Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Teresa Urraro
- Rheumatology Unit, "M. Scarlato" Hospital, Scafati, Italy
| | - Marcella Visentini
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | | | | | - Davide Testa
- Clinical Immunology, University of Pisa, Pisa, Italy
| | | | | | | | | | - Eugenia Balestri
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Giusy Elia
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Silvia Martina Ferrari
- Department of Clinical and Experimental Medicine, University of Pisa, School of Medicine, Pisa, Italy
| | - Antonio Tonutti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Francesca Dall’Ara
- Child and Adolescent Neuropsychiatric Service (UONPIA) Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | | | | | - Vincenzo Aiello
- Rheumatology Clinic ‘Madonna Dello Scoglio’ Cotronei, Crotone, Italy
| | | | - Roberta Foti
- AOU Policlinico Vittorio Emanuele, Catania, Italy
| | - Ilenia Di Cola
- Rheumatology Unit, Department of Biotechnological & Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Enrico Fusaro
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città Della Salute e Della Scienza, Torino, Italy
| | | | | | | | - Francesca Francioso
- Rheumatology Clinic, Department of Clinical & Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | - Carlo Iandoli
- University of Campania, Luigi Vanvitelli, Napoli, Italy
| | - Virginia Caira
- U.O.S. Reumatologia, Ospedale Castrovillari, Cosenza, Italy
| | - Anna Linda Zignego
- MASVE Interdepartmental Hepatology Center, Department of Experimental and Clinical Medicine, University of Florence, Center for Research and Innovation CRIA-MASVE, AOU Careggi, Florence, Italy
| | | | | | | | - Roberto Giacomelli
- Clinical and Research Section of Rheumatology and Clinical Immunology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Andrea Doria
- Rheumatology, University of Padova, Padova, Italy
| | - Stefano Angelo Santini
- Department of Basic, Clinical, Intensive and Perioperative Biotechnological Sciences, Catholic University School of Medicine, Rome, Italy
- Synlab Lazio, Roma, Italy
| | - Poupak Fallahi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | | | - Alessandro Antonelli
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - for the COVID-19 & ASD Italian Study Group
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
- Rheumatology Clinic ‘Madonna Dello Scoglio’ Cotronei, Crotone, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
- MASVE Interdepartmental Hepatology Center, Department of Experimental and Clinical Medicine, University of Florence, Center for Research and Innovation CRIA-MASVE, AOU Careggi, Florence, Italy
- Department of Ospedale S. Raffaele, Milano, Italy
- Division of Rheumatology, Catholic University of the Sacred Heart, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- AOU Policlinico Vittorio Emanuele, Catania, Italy
- Rheumatology, Sapienza-University of Rome, Roma, Italy
- Rheumatology, University of Florence, Italy
- University of Campania, Luigi Vanvitelli, Napoli, Italy
- Clinical Immunology, University of Pisa, Pisa, Italy
- Rheumatology Clinic, Department of Clinical & Molecular Sciences, Marche Polytechnic University, Ancona, Italy
- UO Reumatologia - DETO, Università di Bari, Bari, Italy
- Rheumatology, University of Padova, Padova, Italy
- Ospedale "Villa Salus", Mestre, Italy
- Ospedale Policlinico S. Martino-University of Genova, Genova, Italy
- Rheumatology, Spedali Civili di Brescia, Brescia, Italy
- ASO S. Croce e Carle, Cuneo, Italy
- Rheumatology, Policlinico San Matteo, Pavia, Italy
- U.O.C. Medicina Interna 'M.Valentini" P.O, Annunziata, Cosenza, Italy
- U.O.S. Reumatologia, Ospedale Castrovillari, Cosenza, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
- AOR San Carlo di Potenza, Potenza, Italy
- UOD Reumatologia- Grande Ospedale Metropolitano, Reggio Calabria, Italy
- Rheumatology Outpatient Clinic, ASP- Vibo Valentia-Tropea Hospital, Italy
- Rheumatology Outpatient Clinic, San Giovanni di Dio Hospital, Crotone, Italy
- Rheumatology, Università Del Molise, Campobasso, Italy
- Rheumatology Unit, Department of Biotechnological & Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Rheumatology Unit, "M. Scarlato" Hospital, Scafati, Italy
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, School of Medicine, Pisa, Italy
- Child and Adolescent Neuropsychiatric Service (UONPIA) Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città Della Salute e Della Scienza, Torino, Italy
- U.O.T. Specialistica Ambulatoriale ASP 201, Cosenza, Italy
- Clinical and Research Section of Rheumatology and Clinical Immunology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Basic, Clinical, Intensive and Perioperative Biotechnological Sciences, Catholic University School of Medicine, Rome, Italy
- Synlab Lazio, Roma, Italy
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18
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Neale I, Ali M, Kronsteiner B, Longet S, Abraham P, Deeks AS, Brown A, Moore SC, Stafford L, Dobson SL, Plowright M, Newman TAH, Wu MY, Carr EJ, Beale R, Otter AD, Hopkins S, Hall V, Tomic A, Payne RP, Barnes E, Richter A, Duncan CJA, Turtle L, de Silva TI, Carroll M, Lambe T, Klenerman P, Dunachie S. CD4+ and CD8+ T cells and antibodies are associated with protection against Delta vaccine breakthrough infection: a nested case-control study within the PITCH study. mBio 2023; 14:e0121223. [PMID: 37655880 PMCID: PMC10653804 DOI: 10.1128/mbio.01212-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE Defining correlates of protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine breakthrough infection informs vaccine policy for booster doses and future vaccine designs. Existing studies demonstrate humoral correlates of protection, but the role of T cells in protection is still unclear. In this study, we explore antibody and T cell immune responses associated with protection against Delta variant vaccine breakthrough infection in a well-characterized cohort of UK Healthcare Workers (HCWs). We demonstrate evidence to support a role for CD4+ and CD8+ T cells as well as antibodies against Delta vaccine breakthrough infection. In addition, our results suggest a potential role for cross-reactive T cells in vaccine breakthrough.
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Affiliation(s)
- Isabel Neale
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephanie Longet
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Priyanka Abraham
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Alexandra S. Deeks
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Shona C. Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Lizzie Stafford
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Susan L. Dobson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Megan Plowright
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Thomas A. H. Newman
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Mary Y. Wu
- Covid Surveillance Unit, The Francis Crick Institute, London, United Kingdom
| | - Crick COVID Immunity Pipeline
- Covid Surveillance Unit, The Francis Crick Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- UCL Department of Renal Medicine, Royal Free Hospital, London, United Kingdom
| | | | | | | | - Adriana Tomic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Rebecca P. Payne
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Christopher J. A. Duncan
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle, United Kingdom
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Thushan I. de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Miles Carroll
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Teresa Lambe
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - On behalf of the PITCH Consortium
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
- Covid Surveillance Unit, The Francis Crick Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- UCL Department of Renal Medicine, Royal Free Hospital, London, United Kingdom
- UK Health Security Agency, Porton Down, United Kingdom
- UK Health Security Agency, London, United Kingdom
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle, United Kingdom
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
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19
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Ovsyannikova IG, Haralambieva IH, Schaid DJ, Warner ND, Poland GA, Kennedy RB. Genome-wide determinants of cellular immune responses to mumps vaccine. Vaccine 2023; 41:6579-6588. [PMID: 37778899 DOI: 10.1016/j.vaccine.2023.09.001] [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: 04/21/2023] [Revised: 08/03/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND We have previously described genetic polymorphisms in candidate genes that are associated with inter-individual variations in antibody responses to mumps vaccination. To expand upon our previous work, we performed a genome-wide association study (GWAS) to discover host genetic variants associated with mumps vaccine-induced cellular immune responses. METHODS We performed a GWAS of mumps-specific immune response outcomes (11 secreted cytokines/chemokines) in a cohort of 1,406 subjects. RESULTS Among the 11 cytokine/chemokines we studied, four (IFN-γ, IL-2, IL-1β, and TNFα) demonstrated GWAS signals reaching genome-wide significance (p < 5 × 10-8). A genomic region (encoding Sialic acid-binding immunoglobulin-type lectins/SIGLEC) located on chromosome 19q13 (p < 5 × 10-8) was associated with both IL-1β and TNFα responses. The SIGLEC5/SIGLEC14 region contained 11 statistically significant single nucleotide polymorphisms (SNPs), including the intronic SIGLEC5 rs872629 (p = 1.3E-11) and rs1106476 (p = 1.32E-11) whose alternate alleles were significantly associated with decreased levels of mumps-specific IL-1β (rs872629, p = 1.77E-09; rs1106476, p = 1.78E-09) and TNFα (rs872629, p = 1.3E-11; rs1106476, p = 1.32E-11) production. CONCLUSIONS Our results suggest that SNPs in the SIGLEC5/SIGLEC14 genes play a role in cellular and inflammatory immune responses to mumps vaccination. These findings motivate further research into the functional roles of SIGLEC genes in the regulation of mumps vaccine-induced immunity.
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Affiliation(s)
| | | | - Daniel J Schaid
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Nathaniel D Warner
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
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20
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Li Y, Han L, Li P, Ge J, Xue Y, Chen L. Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks. BMC Genomics 2023; 24:619. [PMID: 37853311 PMCID: PMC10583333 DOI: 10.1186/s12864-023-09719-1] [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: 02/27/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
To explore the potential network markers and related signaling pathways of human B cells infected by COVID-19, we performed standardized integration and analysis of single-cell sequencing data to construct conditional cell-specific networks (CCSN) for each cell. Then the peripheral blood cells were clustered and annotated based on the conditional network degree matrix (CNDM) and gene expression matrix (GEM), respectively, and B cells were selected for further analysis. Besides, based on the CNDM of B cells, the hub genes and 'dark' genes (a gene has a significant difference between case and control samples not in a gene expression level but in a conditional network degree level) closely related to COVID-19 were revealed. Interestingly, some of the 'dark' genes and differential degree genes (DDGs) encoded key proteins in the JAK-STAT pathway, which had antiviral effects. The protein p21 encoded by the 'dark' gene CDKN1A was a key regulator for the COVID-19 infection-related signaling pathway. Elevated levels of proteins encoded by some DDGs were directly related to disease severity of patients with COVID-19. In short, the proteins encoded by 'dark' genes complement some missing links in COVID-19 and these signaling pathways played an important role in the growth and activation of B cells.
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Affiliation(s)
- Ying Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China
- Longmen Laboratory, Luoyang, 471003, Henan, China
| | - Liqin Han
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China
- Longmen Laboratory, Luoyang, 471003, Henan, China
| | - Peiluan Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China.
- Longmen Laboratory, Luoyang, 471003, Henan, China.
| | - Jing Ge
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 201100, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310000, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201100, China.
- West China Biomedical Big Data Center, Med-X Center for Informatics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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21
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Castro-Santos P, Carracedo Á, Díaz-Peña R. HLA alleles: important pieces to the COVID-19 puzzle. Trends Immunol 2023; 44:754-756. [PMID: 37690961 DOI: 10.1016/j.it.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
Research on human leukocyte antigen (HLA) molecules in coronavirus disease 2019 (COVID-19) raised high expectations but has yielded limited results. Augusto et al.'s recent study in Nature unveils a strong association of HLA-B*15:01 with asymptomatic COVID-19, representing an important contribution to genetics in COVID-19.
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Affiliation(s)
- Patricia Castro-Santos
- Fundación Pública Galega de Medicina Xenómica (SERGAS). Centro Nacional de Genotipado. Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Faculty of Health Sciences, Universidad Autónoma de Chile, Talca, Chile
| | - Ángel Carracedo
- Fundación Pública Galega de Medicina Xenómica (SERGAS). Centro Nacional de Genotipado. Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica- CIMUS- Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Roberto Díaz-Peña
- Fundación Pública Galega de Medicina Xenómica (SERGAS). Centro Nacional de Genotipado. Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Faculty of Health Sciences, Universidad Autónoma de Chile, Talca, Chile.
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22
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Peng Y, Zhang L, Mok CKP, Ching JYL, Zhao S, Wong MKL, Zhu J, Chen C, Wang S, Yan S, Qin B, Liu Y, Zhang X, Cheung CP, Cheong PK, Ip KL, Fung ACH, Wong KKY, Hui DSC, Chan FKL, Ng SC, Tun HM. Baseline gut microbiota and metabolome predict durable immunogenicity to SARS-CoV-2 vaccines. Signal Transduct Target Ther 2023; 8:373. [PMID: 37743379 PMCID: PMC10518331 DOI: 10.1038/s41392-023-01629-8] [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: 05/22/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
The role of gut microbiota in modulating the durability of COVID-19 vaccine immunity is yet to be characterised. In this cohort study, we collected blood and stool samples of 121 BNT162b2 and 40 CoronaVac vaccinees at baseline, 1 month, and 6 months post vaccination (p.v.). Neutralisation antibody, plasma cytokine and chemokines were measured and associated with the gut microbiota and metabolome composition. A significantly higher level of neutralising antibody (at 6 months p.v.) was found in BNT162b2 vaccinees who had higher relative abundances of Bifidobacterium adolescentis, Bifidobacterium bifidum, and Roseburia faecis as well as higher concentrations of nicotinic acid (Vitamin B) and γ-Aminobutyric acid (P < 0.05) at baseline. CoronaVac vaccinees with high neutralising antibodies at 6 months p.v. had an increased relative abundance of Phocaeicola dorei, a lower relative abundance of Faecalibacterium prausnitzii, and a higher concentration of L-tryptophan (P < 0.05) at baseline. A higher antibody level at 6 months p.v. was also associated with a higher relative abundance of Dorea formicigenerans at 1 month p.v. among CoronaVac vaccinees (Rho = 0.62, p = 0.001, FDR = 0.123). Of the species altered following vaccination, 79.4% and 42.0% in the CoronaVac and BNT162b2 groups, respectively, recovered at 6 months. Specific to CoronaVac vaccinees, both bacteriome and virome diversity depleted following vaccination and did not recover to baseline at 6 months p.v. (FDR < 0.1). In conclusion, this study identified potential microbiota-based adjuvants that may extend the durability of immune responses to SARS-CoV-2 vaccines.
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Affiliation(s)
- Ye Peng
- Microbiota I-Center (MagIC), Hong Kong, China
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Chris K P Mok
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jessica Y L Ching
- Microbiota I-Center (MagIC), Hong Kong, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Shilin Zhao
- Microbiota I-Center (MagIC), Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew K L Wong
- Microbiota I-Center (MagIC), Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Zhu
- Microbiota I-Center (MagIC), Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Chunke Chen
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Shilan Wang
- Microbiota I-Center (MagIC), Hong Kong, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Shuai Yan
- Microbiota I-Center (MagIC), Hong Kong, China
| | - Biyan Qin
- Microbiota I-Center (MagIC), Hong Kong, China
| | - Yingzhi Liu
- Microbiota I-Center (MagIC), Hong Kong, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Zhang
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pun Cheung
- Microbiota I-Center (MagIC), Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Pui Kuan Cheong
- Microbiota I-Center (MagIC), Hong Kong, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Long Ip
- Microbiota I-Center (MagIC), Hong Kong, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Adrian C H Fung
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kenneth K Y Wong
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - David S C Hui
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong, China
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hein M Tun
- Microbiota I-Center (MagIC), Hong Kong, China.
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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23
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Li D, Pavlovitch-Bedzyk AJ, Ebinger JE, Khan A, Hamideh M, Merchant A, Figueiredo JC, Cheng S, Davis MM, McGovern DPB, Melmed GY, Xu AM, Braun J. A Paratope-Enhanced Method to Determine Breadth and Depth TCR Clonal Metrics of the Private Human T-Cell Vaccine Response after SARS-CoV-2 Vaccination. Int J Mol Sci 2023; 24:14223. [PMID: 37762524 PMCID: PMC10531868 DOI: 10.3390/ijms241814223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Quantitative metrics for vaccine-induced T-cell responses are an important need for developing correlates of protection and their use in vaccine-based medical management and population health. Molecular TCR analysis is an appealing strategy but currently requires a targeted methodology involving complex integration of ex vivo data (antigen-specific functional T-cell cytokine responses and TCR molecular responses) that uncover only public antigen-specific metrics. Here, we describe an untargeted private TCR method that measures breadth and depth metrics of the T-cell response to vaccine challenge using a simple pre- and post-vaccine subject sampling, TCR immunoseq analysis, and a bioinformatic approach using self-organizing maps and GLIPH2. Among 515 subjects undergoing SARS-CoV-2 mRNA vaccination, we found that breadth and depth metrics were moderately correlated between the targeted public TCR response and untargeted private TCR response methods. The untargeted private TCR method was sufficiently sensitive to distinguish subgroups of potential clinical significance also observed using public TCR methods (the reduced T-cell vaccine response with age and the paradoxically elevated T-cell vaccine response of patients on anti-TNF immunotherapy). These observations suggest the promise of this untargeted private TCR method to produce T-cell vaccine-response metrics in an antigen-agnostic and individual-autonomous context.
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Affiliation(s)
- Dalin Li
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Ana Jimena Pavlovitch-Bedzyk
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; (A.J.P.-B.); (M.M.D.)
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (J.E.E.); (S.C.)
| | - Abdul Khan
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Mohamed Hamideh
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Akil Merchant
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Jane C. Figueiredo
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (J.E.E.); (S.C.)
| | - Mark M. Davis
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; (A.J.P.-B.); (M.M.D.)
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dermot P. B. McGovern
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Gil Y. Melmed
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Alexander M. Xu
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Jonathan Braun
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
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24
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Tripathy AS, Wagh P, Vishwakarma S, Akolkar K, Tripathy S, Jali P, Kakrani AL, Barthwal M, Gurav Y, Kadgi N, Nakate L, Abraham P. Association of human leukocyte antigen class I and class II alleles and haplotypes in COVID-19 infection in a western Indian population. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105468. [PMID: 37331496 PMCID: PMC10273771 DOI: 10.1016/j.meegid.2023.105468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/22/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Affiliation(s)
| | - Priyanka Wagh
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | | | - Srikanth Tripathy
- Dr. D. Y. Patil Medical College, Hospital & Research Centre, Pune, India
| | - Priyanka Jali
- Dr. D. Y. Patil Medical College, Hospital & Research Centre, Pune, India
| | - Arjun Lal Kakrani
- Dr. D. Y. Patil Medical College, Hospital & Research Centre, Pune, India
| | | | - Yogesh Gurav
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nalini Kadgi
- BJMC and Sassoon General Hospital, Pune, Maharashtra, India
| | - Leena Nakate
- BJMC and Sassoon General Hospital, Pune, Maharashtra, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune, Maharashtra, India
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25
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Butler-Laporte G, Auckland K, Noor Z, Kabir M, Alam M, Carstensen T, Wojcik GL, Chong AY, Pomilla C, Noble JA, McDevitt SL, Smits G, Wareing S, van der Klis FRM, Jeffery K, Kirkpatrick BD, Sirima S, Madhi S, Elliott A, Richards JB, Hill AVS, Duggal P, Sandhu MS, Haque R, Petri WA, Mentzer AJ. Targeting hepatitis B vaccine escape using immunogenetics in Bangladeshi infants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.26.23291885. [PMID: 37425840 PMCID: PMC10327284 DOI: 10.1101/2023.06.26.23291885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Hepatitis B virus (HBV) vaccine escape mutants (VEM) are increasingly described, threatening progress in control of this virus worldwide. Here we studied the relationship between host genetic variation, vaccine immunogenicity and viral sequences implicating VEM emergence. In a cohort of 1,096 Bangladeshi children, we identified human leukocyte antigen (HLA) variants associated with response vaccine antigens. Using an HLA imputation panel with 9,448 south Asian individuals DPB1*04:01 was associated with higher HBV antibody responses (p=4.5×10-30). The underlying mechanism is a result of higher affinity binding of HBV surface antigen epitopes to DPB1*04:01 dimers. This is likely a result of evolutionary pressure at the HBV surface antigen 'a-determinant' segment incurring VEM specific to HBV. Prioritizing pre-S isoform HBV vaccines may tackle the rise of HBV vaccine evasion.
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Affiliation(s)
- Guillaume Butler-Laporte
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Division of Infectious Diseases, McGill University Health Centre, Montréal, Québec, Canada
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Zannatun Noor
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mamun Kabir
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Masud Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tommy Carstensen
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
- Queen Mary University of London, London, United Kingdom
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amanda Y Chong
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Cristina Pomilla
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
| | - Janelle A Noble
- Children’s Hospital Oakland Research Institute, Oakland, California, USA
- Department of Pediatrics, University of California, San Francisco, California, USA
| | | | - Gaby Smits
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Susan Wareing
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | - Fiona RM van der Klis
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Katie Jeffery
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | - Beth D Kirkpatrick
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, University of Vermont College of Medicine, Vermont, USA
| | - Sodiomon Sirima
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248 Ouagadougou, Burkina Faso
| | - Shabir Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alison Elliott
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
| | - Adrian VS Hill
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Manjinder S Sandhu
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, United Kingdom
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - William A Petri
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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26
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Purcell RA, Theisen RM, Arnold KB, Chung AW, Selva KJ. Polyfunctional antibodies: a path towards precision vaccines for vulnerable populations. Front Immunol 2023; 14:1183727. [PMID: 37600816 PMCID: PMC10433199 DOI: 10.3389/fimmu.2023.1183727] [Citation(s) in RCA: 2] [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: 03/10/2023] [Accepted: 05/30/2023] [Indexed: 08/22/2023] Open
Abstract
Vaccine efficacy determined within the controlled environment of a clinical trial is usually substantially greater than real-world vaccine effectiveness. Typically, this results from reduced protection of immunologically vulnerable populations, such as children, elderly individuals and people with chronic comorbidities. Consequently, these high-risk groups are frequently recommended tailored immunisation schedules to boost responses. In addition, diverse groups of healthy adults may also be variably protected by the same vaccine regimen. Current population-based vaccination strategies that consider basic clinical parameters offer a glimpse into what may be achievable if more nuanced aspects of the immune response are considered in vaccine design. To date, vaccine development has been largely empirical. However, next-generation approaches require more rational strategies. We foresee a generation of precision vaccines that consider the mechanistic basis of vaccine response variations associated with both immunogenetic and baseline health differences. Recent efforts have highlighted the importance of balanced and diverse extra-neutralising antibody functions for vaccine-induced protection. However, in immunologically vulnerable populations, significant modulation of polyfunctional antibody responses that mediate both neutralisation and effector functions has been observed. Here, we review the current understanding of key genetic and inflammatory modulators of antibody polyfunctionality that affect vaccination outcomes and consider how this knowledge may be harnessed to tailor vaccine design for improved public health.
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Affiliation(s)
- Ruth A. Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Robert M. Theisen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Kelly B. Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Amy W. Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Kevin J. Selva
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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27
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Khamjan NA, Lohani M, Khan MF, Khan S, Algaissi A. Immunoinformatics Strategy to Develop a Novel Universal Multiple Epitope-Based COVID-19 Vaccine. Vaccines (Basel) 2023; 11:1090. [PMID: 37376479 DOI: 10.3390/vaccines11061090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 06/29/2023] Open
Abstract
Currently available COVID vaccines are effective in reducing mortality and severity but do not prevent transmission of the virus or reinfection by the emerging SARS-CoV-2 variants. There is an obvious need for better and longer-lasting effective vaccines for various prevailing strains and the evolving SARS-CoV-2 virus, necessitating the development of a broad-spectrum vaccine that can be used to prevent infection by reducing both the transmission rate and re-infection. During the initial phases of SARS-CoV-2 infection, the nucleocapsid (N) protein is one of the most abundantly expressed proteins. Additionally, it has been identified as the most immunogenic protein of SARS-CoV-2. In this study, state-of-the-art bioinformatics techniques have been exploited to design novel multiple epitope vaccines using conserved regions of N proteins from prevalent strains of SARS-CoV-2 for the prediction of B- and T-cell epitopes. These epitopes were sorted based on their immunogenicity, antigenicity score, and toxicity. The most effective multi-epitope construct with possible immunogenic properties was created using epitope combinations. EAAAK, AAY, and GPGPG were used as linkers to connect epitopes. The developed vaccines have shown positive results in terms of overall population coverage and stimulation of the immune response. Potential expression of the chimeric protein construct was detected after it was cloned into the Pet28a/Cas9-cys vector for expression screening in Escherichia coli. The developed vaccine performed well in computer-based immune response simulation and covered a diverse allelic population worldwide. These computational findings are very encouraging for the further testing of our candidate vaccine, which could eventually aid in the control and prevention of SARS-CoV-2 infections globally.
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Affiliation(s)
- Nizar A Khamjan
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Mohtashim Lohani
- Department of Emergency Medical Services, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Medical Research Centre, Jazan University, Jazan 45142, Saudi Arabia
| | - Mohammad Faheem Khan
- Department of Biotechnology, K.C.M.T., M. J. P. Rohilkhand University, Bareilly 243006, India
| | - Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Hail University, Hail 2440, Saudi Arabia
| | - Abdullah Algaissi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Medical Research Centre, Jazan University, Jazan 45142, Saudi Arabia
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28
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Villemonteix J, Allain V, Verstraete E, Jorge-Cordeiro D, Socié G, Xhaard A, Feray C, Caillat-Zucman S. HLA-DP diversity is associated with improved response to SARS-Cov-2 vaccine in hematopoietic stem cell transplant recipients. iScience 2023; 26:106763. [PMID: 37168557 PMCID: PMC10132830 DOI: 10.1016/j.isci.2023.106763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/26/2023] [Accepted: 04/24/2023] [Indexed: 05/13/2023] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients show lower humoral vaccine responsiveness than immunocompetent individuals. HLA diversity, measured by the HLA evolutionary divergence (HED) metrics, reflects the diversity of the antigenic repertoire presented to T cells, and has been shown to predict response to cancer immunotherapy. We retrospectively investigated the association of HED with humoral response to SARS-CoV-2 vaccine in allo-HSCT recipients. HED was calculated as pairwise genetic distance between alleles at HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 loci in recipients and their donors. Low anti-spike IgG levels (<30 BAU/mL) were associated with short time from allo-SCT and low donor DPB1-HED, mostly related to donor DPB1 homozygosity. The diversity of donor HLA-DP molecules, assessed by heterozygosity or sequence divergence, may thus impact the efficacy of donor-derived CD4 T cells to sustain vaccine-mediated antibody response in allo-HSCT recipients.
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Affiliation(s)
- Juliette Villemonteix
- Laboratoire d'Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, 75010 Paris, France
| | - Vincent Allain
- Laboratoire d'Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, 75010 Paris, France
- INSERM UMR 976, Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), 75010 Paris, France
| | - Emma Verstraete
- Service d'hématologie-greffe, Hôpital Saint-Louis, AP-HP, Université Paris Cité, 75010 Paris, France
| | - Debora Jorge-Cordeiro
- Laboratoire d'Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, 75010 Paris, France
| | - Gérard Socié
- INSERM UMR 976, Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), 75010 Paris, France
- Service d'hématologie-greffe, Hôpital Saint-Louis, AP-HP, Université Paris Cité, 75010 Paris, France
| | - Alienor Xhaard
- Service d'hématologie-greffe, Hôpital Saint-Louis, AP-HP, Université Paris Cité, 75010 Paris, France
| | - Cyrille Feray
- Centre Hépato-Biliaire, Hôpital Paul-Brousse, AP-HP, Université Paris-Saclay, FHU Hepatinov, 94800 Villejuif, France
- Institut National de la santé et de la recherche médicale (INSERM) UMR-S 1193, 94800 Villejuif, France
| | - Sophie Caillat-Zucman
- Laboratoire d'Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, 75010 Paris, France
- INSERM UMR 976, Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), 75010 Paris, France
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29
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Reynolds JA, Faustini SE, Tosounidou S, Plant T, Ubhi M, Gilman R, Richter AG, Gordon C. Anti-SARS-CoV-2 antibodies following vaccination are associated with lymphocyte count and serum immunoglobulins in SLE. Lupus 2023; 32:431-437. [PMID: 36631440 PMCID: PMC9843147 DOI: 10.1177/09612033231151603] [Citation(s) in RCA: 2] [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: 07/29/2022] [Accepted: 11/20/2022] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Patients with Systemic Lupus Erythematosus are known to have dysregulated immune responses and may have reduced response to vaccination against COVID-19 while being at risk of severe COVID-19 disease. The aim of this study was to identify whether vaccine responses were attenuated in SLE and to assess disease- and treatment-specific associations. METHODS Patients with SLE were matched by age, sex and ethnic background to healthcare worker healthy controls (HC). Anti-SARS-CoV-2 spike glycoprotein antibodies were measured at 4-8 weeks following the second COVID-19 vaccine dose (either BNT162b2 or ChAdOx1 nCoV-19) using a CE-marked combined ELISA detecting IgG, IgA and IgM (IgGAM). Antibody levels were considered as a continuous variable and in tertiles and compared between SLE patients and HC and associations with medication, disease activity and serological parameters were determined. RESULTS Antibody levels were lower in 43 SLE patients compared to 40 HC (p < 0.001). There was no association between antibody levels and medication, lupus disease activity, vaccine type or prior COVID infection. Higher serum IgA, but not IgG or IgM, was associated with being in a higher anti-SARS-CoV-2 antibody level tertile (OR [95% CI] 1.820 [1.050, 3.156] p = 0.033). Similarly, higher lymphocyte count was also associated with being in a higher tertile of anti-SARS-CoV-2 (OR 3.330 [1.505, 7.366] p = 0.003). CONCLUSION Patients with SLE have lower antibody levels following 2 doses of COVID-19 vaccines compared to HC. In SLE lower lymphocyte counts and serum IgA levels are associated with lower antibody levels post vaccination, potentially identifying a subgroup of patients who may therefore be at increased risk of infection.
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Affiliation(s)
- John A Reynolds
- Rheumatology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Rheumatology Department, Sandwell and West Birmingham NHS Trust, Birmingham UK
| | - Sian E Faustini
- Clinical Immunology Service, Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Sofia Tosounidou
- Rheumatology Department, Sandwell and West Birmingham NHS Trust, Birmingham UK
| | - Tim Plant
- Clinical Immunology Service, Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Mandeep Ubhi
- Rheumatology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Rebecca Gilman
- Rheumatology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Rheumatology Department, Sandwell and West Birmingham NHS Trust, Birmingham UK
| | - Alex G Richter
- Clinical Immunology Service, Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Caroline Gordon
- Rheumatology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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30
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Ferraresi A, Isidoro C. Will Omics Biotechnologies Save Us from Future Pandemics? Lessons from COVID-19 for Vaccinomics and Adversomics. Biomedicines 2022; 11:biomedicines11010052. [PMID: 36672560 PMCID: PMC9855897 DOI: 10.3390/biomedicines11010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
The COVID-19 pandemic had cross-cutting impacts on planetary health, quotidian life, and society. Mass vaccination with the current gene-based vaccines has helped control the pandemic but unfortunately it has not shown effectiveness in preventing the spread of the virus. In addition, not all individuals respond to these vaccines, while others develop adverse reactions that cannot be neglected. It is also a fact that some individuals are more susceptible to infection while others develop effective immunization post-infection. We note here that the person-to-person and population variations in vaccine efficacy and side effects have been studied in the field of vaccinomics long before the COVID-19 pandemic. Additionally, the field of adversomics examines the mechanisms of individual differences in the side effects of health interventions. In this review, we discuss the potential of a multi-omics approach for comprehensive profiling of the benefit/risk ratios of vaccines. Vaccinomics and adversomics stand to benefit planetary health and contribute to the prevention of future pandemics in the 21st century by offering precision guidance to clinical trials as well as promoting precision use of vaccines in ways that proactively respond to individual and population differences in their efficacy and safety. This vision of pandemic prevention based on personalized instead of mass vaccination also calls for equity in access to precision vaccines and diagnostics that support a vision and practice of vaccinomics and adversomics in planetary health.
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31
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Yang C, Zhao H, Shannon CP, Tebbutt SJ. Omicron variants of SARS-CoV-2 and long COVID. Front Immunol 2022; 13:1061686. [PMID: 36569883 PMCID: PMC9780375 DOI: 10.3389/fimmu.2022.1061686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Understanding the epidemiology of long COVID and emerging variants has significant public-health implications as physical interventions and restrictions that help limit viral spread are eased globally. Here, we provide rationales for the necessity of updating current vaccines to improve protection against omicron and emerging variants, as well as more research into understanding the epidemiology and mechanisms of long COVID.
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Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada,Centre for Heart Lung Innovation, Providence Research, St. Paul’s Hospital, Vancouver, BC, Canada,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Hedi Zhao
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Casey P. Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada,Centre for Heart Lung Innovation, Providence Research, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Scott J. Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada,Centre for Heart Lung Innovation, Providence Research, St. Paul’s Hospital, Vancouver, BC, Canada,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada,*Correspondence: Scott J. Tebbutt,
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32
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Phetsouphanh C, Khoo WH, Jackson K, Klemm V, Howe A, Aggarwal A, Akerman A, Milogiannakis V, Stella AO, Rouet R, Schofield P, Faulks ML, Law H, Danwilai T, Starr M, Munier CML, Christ D, Singh M, Croucher PI, Brilot-Turville F, Turville S, Phan TG, Dore GJ, Darley D, Cunningham P, Matthews GV, Kelleher AD, Zaunders JJ. High titre neutralizing antibodies in response to SARS-CoV-2 infection require RBD-specific CD4 T cells that include proliferative memory cells. Front Immunol 2022; 13:1032911. [PMID: 36544780 PMCID: PMC9762180 DOI: 10.3389/fimmu.2022.1032911] [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: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022] Open
Abstract
Background Long-term immunity to SARS-CoV-2 infection, including neutralizing antibodies and T cell-mediated immunity, is required in a very large majority of the population in order to reduce ongoing disease burden. Methods We have investigated the association between memory CD4 and CD8 T cells and levels of neutralizing antibodies in convalescent COVID-19 subjects. Findings Higher titres of convalescent neutralizing antibodies were associated with significantly higher levels of RBD-specific CD4 T cells, including specific memory cells that proliferated vigorously in vitro. Conversely, up to half of convalescent individuals had low neutralizing antibody titres together with a lack of receptor binding domain (RBD)-specific memory CD4 T cells. These low antibody subjects had other, non-RBD, spike-specific CD4 T cells, but with more of an inhibitory Foxp3+ and CTLA-4+ cell phenotype, in contrast to the effector T-bet+, cytotoxic granzymes+ and perforin+ cells seen in RBD-specific memory CD4 T cells from high antibody subjects. Single cell transcriptomics of antigen-specific CD4+ T cells from high antibody subjects similarly revealed heterogenous RBD-specific CD4+ T cells that comprised central memory, transitional memory and Tregs, as well as cytotoxic clusters containing diverse TCR repertoires, in individuals with high antibody levels. However, vaccination of low antibody convalescent individuals led to a slight but significant improvement in RBD-specific memory CD4 T cells and increased neutralizing antibody titres. Interpretation Our results suggest that targeting CD4 T cell epitopes proximal to and within the RBD-region should be prioritized in booster vaccines.
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Affiliation(s)
| | - Weng Hua Khoo
- Garvan Institute of Medical Research, Sydney, NSW, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | | | - Vera Klemm
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Annett Howe
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Anupriya Aggarwal
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Anouschka Akerman
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | | | | | - Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Megan L. Faulks
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Hannah Law
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Thidarat Danwilai
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Mitchell Starr
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
| | - C. Mee Ling Munier
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | | | - Fabienne Brilot-Turville
- Brain and Mind Centre, Children’s Hospital at Westmead, University of Sydney, Sydney, NSW, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
| | - Stuart Turville
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Tri Giang Phan
- Garvan Institute of Medical Research, Sydney, NSW, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | - Gregory J. Dore
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia,Department of Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - David Darley
- Department of Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - Philip Cunningham
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Gail V. Matthews
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia,Department of Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - Anthony D. Kelleher
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia,Department of Immunology, St Vincent's Hospital, Sydney, NSW, Australia
| | - John J. Zaunders
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia,*Correspondence: John J. Zaunders,
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