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Dudley MZ, Gerber JE, Budigan Ni H, Blunt M, Holroyd TA, Carleton BC, Poland GA, Salmon DA. Vaccinomics: A scoping review. Vaccine 2023; 41:2357-2367. [PMID: 36803903 PMCID: PMC10065969 DOI: 10.1016/j.vaccine.2023.02.009] [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: 04/05/2022] [Revised: 12/24/2022] [Accepted: 02/03/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND This scoping review summarizes a key aspect of vaccinomics by collating known associations between heterogeneity in human genetics and vaccine immunogenicity and safety. METHODS We searched PubMed for articles in English using terms covering vaccines routinely recommended to the general US population, their effects, and genetics/genomics. Included studies were controlled and demonstrated statistically significant associations with vaccine immunogenicity or safety. Studies of Pandemrix®, an influenza vaccine previously used in Europe, were also included, due to its widely publicized genetically mediated association with narcolepsy. FINDINGS Of the 2,300 articles manually screened, 214 were included for data extraction. Six included articles examined genetic influences on vaccine safety; the rest examined vaccine immunogenicity. Hepatitis B vaccine immunogenicity was reported in 92 articles and associated with 277 genetic determinants across 117 genes. Thirty-three articles identified 291 genetic determinants across 118 genes associated with measles vaccine immunogenicity, 22 articles identified 311 genetic determinants across 110 genes associated with rubella vaccine immunogenicity, and 25 articles identified 48 genetic determinants across 34 genes associated with influenza vaccine immunogenicity. Other vaccines had fewer than 10 studies each identifying genetic determinants of their immunogenicity. Genetic associations were reported with 4 adverse events following influenza vaccination (narcolepsy, GBS, GCA/PMR, high temperature) and 2 adverse events following measles vaccination (fever, febrile seizure). CONCLUSION This scoping review identified numerous genetic associations with vaccine immunogenicity and several genetic associations with vaccine safety. Most associations were only reported in one study. This illustrates both the potential of and need for investment in vaccinomics. Current research in this field is focused on systems and genetic-based studies designed to identify risk signatures for serious vaccine reactions or diminished vaccine immunogenicity. Such research could bolster our ability to develop safer and more effective vaccines.
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Affiliation(s)
- Matthew Z Dudley
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Institute for Vaccine Safety, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Jennifer E Gerber
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Survey Research Division, RTI International, Washington, DC, USA
| | - Haley Budigan Ni
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Office of Health Equity, California Department of Public Health, Richmond, CA, USA
| | - Madeleine Blunt
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Taylor A Holroyd
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; International Vaccine Access Center, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Bruce C Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada; Pharmaceutical Outcomes Programme, BC Children's Hospital, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Gregory A Poland
- Division of General Internal Medicine, Mayo Clinic, Rochester, MN, USA; Mayo Vaccine Research Group, Mayo Clinic, Rochester, MN, USA
| | - Daniel A Salmon
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Institute for Vaccine Safety, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Department of Health, Behavior & Society, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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2
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Ruggiero A, Pascucci GR, Cotugno N, Domínguez-Rodríguez S, Rinaldi S, Tagarro A, Rojo P, Foster C, Bamford A, De Rossi A, Nastouli E, Klein N, Morrocchi E, Fatou B, Smolen KK, Ozonoff A, Di Pastena M, Luzuriaga K, Steen H, Giaquinto C, Goulder P, Rossi P, Levy O, Pahwa S, Palma P. Determinants of B-Cell Compartment Hyperactivation in European Adolescents Living With Perinatally Acquired HIV-1 After Over 10 Years of Suppressive Therapy. Front Immunol 2022; 13:860418. [PMID: 35432380 PMCID: PMC9009387 DOI: 10.3389/fimmu.2022.860418] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/03/2022] [Indexed: 01/07/2023] Open
Abstract
Background Despite a successful antiretroviral therapy (ART), adolescents living with perinatally acquired HIV (PHIV) experience signs of B-cell hyperactivation with expansion of 'namely' atypical B-cell phenotypes, including double negative (CD27-IgD-) and termed age associated (ABCs) B-cells (T-bet+CD11c+), which may result in reduced cell functionality, including loss of vaccine-induced immunological memory and higher risk of developing B-cells associated tumors. In this context, perinatally HIV infected children (PHIV) deserve particular attention, given their life-long exposure to chronic immune activation. Methods We studied 40 PHIV who started treatment by the 2nd year of life and maintained virological suppression for 13.5 years, with 5/40 patients experiencing transient elevation of the HIV-1 load in the plasma (Spike). We applied a multi-disciplinary approach including immunological B and T cell phenotype, plasma proteomics analysis, and serum level of anti-measles antibodies as functional correlates of vaccine-induced immunity. Results Phenotypic signs of B cell hyperactivation were elevated in subjects starting ART later (%DN T-bet+CD11c+ p=0.03; %AM T-bet+CD11c+ p=0.02) and were associated with detectable cell-associated HIV-1 RNA (%AM T-bet+CD11c+ p=0.0003) and transient elevation of the plasma viral load (spike). Furthermore, B-cell hyperactivation appeared to be present in individuals with higher frequency of exhausted T-cells, in particular: %CD4 TIGIT+ were associated with %DN (p=0.008), %DN T-bet+CD11c+ (p=0.0002) and %AM T-bet+CD11c+ (p=0.002) and %CD4 PD-1 were associated with %DN (p=0.048), %DN T-bet+CD11c+ (p=0.039) and %AM T-bet+CD11c+ (p=0.006). The proteomic analysis revealed that subjects with expansion of these atypical B-cells and exhausted T-cells had enrichment of proteins involved in immune inflammation and complement activation pathways. Furthermore, we observed that higher levels of ABCs were associated a reduced capacity to maintain vaccine-induced antibody immunity against measles (%B-cells CD19+CD10- T-bet+, p=0.035). Conclusion We identified that the levels of hyperactivated B cell subsets were strongly affected by time of ART start and associated with clinical, viral, cellular and plasma soluble markers. Furthermore, the expansion of ABCs also had a direct impact on the capacity to develop antibodies response following routine vaccination.
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Affiliation(s)
- Alessandra Ruggiero
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Giuseppe Rubens Pascucci
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Chair of Pediatrics Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
| | - Nicola Cotugno
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Chair of Pediatrics Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
| | - Sara Domínguez-Rodríguez
- Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, RITIP (Traslational Research Network in Pediatric Infectious Diseases), Madrid, Spain
| | - Stefano Rinaldi
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Alfredo Tagarro
- Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, RITIP (Traslational Research Network in Pediatric Infectious Diseases), Madrid, Spain
- Department of Pediatrics, Infanta Sofía University Hospital. Infanta Sofia University Hospital and Henares University Hospital Foundation for Biomedical Research and Innovation (FIIB HUIS HHEN), San Sebastián de los Reyes, Madrid, Spain
- Universidad Europea, Madrid, Spain
| | - Pablo Rojo
- Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, RITIP (Traslational Research Network in Pediatric Infectious Diseases), Madrid, Spain
| | - Caroline Foster
- Department of Pediatric Infectious Diseases, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Alasdair Bamford
- MRC Clinical Trials Unit at UCL, London, United Kingdom
- Great Ormond Street Hospital for Children NHS Trust, London, United Kingdom
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Anita De Rossi
- Department of Oncology, Surgery and Gastroenterology, University of Padova, Padova, Italy
- Istituto Oncologico Veneto (IOV)- IRCCS, Padova, Italy
| | - Eleni Nastouli
- Great Ormond Street Hospital for Children NHS Trust, London, United Kingdom
| | - Nigel Klein
- Infection, Immunity & Inflammation Department, UCL GOS Institute of Child Health, London, United Kingdom
| | - Elena Morrocchi
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Benoit Fatou
- Precision Vaccines Program, Boston Children Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Department of Pathology, Boston Children’s Hospital, Boston, MA, United States
| | - Kinga K. Smolen
- Precision Vaccines Program, Boston Children Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Al Ozonoff
- Precision Vaccines Program, Boston Children Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Michela Di Pastena
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- UOSD Unit of Clinical Psychology – Dept. of Neuroscience and Neurorehabilitation, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Katherine Luzuriaga
- Program in Molecular Medicine, Umass Chan Medical School, Worcester, MA, United States
| | - Hanno Steen
- Precision Vaccines Program, Boston Children Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Department of Pathology, Boston Children’s Hospital, Boston, MA, United States
| | - Carlo Giaquinto
- Department of Mother and Child Health, University of Padova, Padova, Italy
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Paolo Rossi
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Chair of Pediatrics Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
| | - Ofer Levy
- Precision Vaccines Program, Boston Children Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Savita Pahwa
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Paolo Palma
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Chair of Pediatrics Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
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3
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Cotugno N, Ruggiero A, Pascucci GR, Bonfante F, Petrara MR, Pighi C, Cifaldi L, Zangari P, Bernardi S, Cursi L, Santilli V, Manno EC, Amodio D, Linardos G, Piccioni L, Barbieri MA, Perrotta D, Campana A, Donà D, Giaquinto C, Concato C, Brodin P, Rossi P, De Rossi A, Palma P. Virological and immunological features of SARS-COV-2 infected children with distinct symptomatology. Pediatr Allergy Immunol 2021; 32:1833-1842. [PMID: 34174102 PMCID: PMC8420243 DOI: 10.1111/pai.13585] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/21/2021] [Accepted: 05/28/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Although SARS-CoV-2 immunizations have started in most countries, children are not currently included in the vaccination programs; thus, it remains crucial to define their anti-SARS-CoV-2 immune response in order to minimize the risk for other epidemic waves. This study sought to provide a description of the virology ad anti-SARS-CoV-2 immunity in children with distinct symptomatology. METHODS Between March and July 2020, we recruited 15 SARS-CoV-2 asymptomatic (AS) and 51 symptomatic (SY) children, stratified according to WHO clinical classification. We measured SARS-CoV-2 viral load using ddPCR and qPCR in longitudinally collected nasopharyngeal swab samples. To define anti-SARS-CoV-2 antibodies, we measured neutralization activity and total IgG load (DiaSorin). We also evaluated antigen-specific B and CD8+T cells, using a labeled S1+S2 protein and ICAM expression, respectively. Plasma protein profiling was performed with Olink. RESULTS Virological profiling showed that AS patients had lower viral load at diagnosis (p = .004) and faster virus clearance (p = .0002) compared with SY patients. Anti-SARS-CoV-2 humoral and cellular response did not appear to be associated with the presence of symptoms. AS and SY patients showed similar titers of SARS-CoV-2 IgG, levels of neutralizing activity, and frequency of Ag-specific B and CD8+ T cells, whereas pro-inflammatory plasma protein profile was found to be associated with symptomatology. CONCLUSION We demonstrated the development of anti-SARS-CoV-2 humoral and cellular response with any regard to symptomatology, suggesting the ability of both SY and AS patients to contribute toward herd immunity. The virological profiling of AS patients suggested that they have lower virus load associated with faster virus clearance.
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Affiliation(s)
- Nicola Cotugno
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Alessandra Ruggiero
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Giuseppe Rubens Pascucci
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Francesco Bonfante
- Laboratory of Experimental Animal Models, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Maria Raffaella Petrara
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, Unit of Viral Oncology and AIDS Reference Center, University of Padova, Padova, Italy
| | - Chiara Pighi
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Loredana Cifaldi
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Paola Zangari
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefania Bernardi
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Laura Cursi
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Veronica Santilli
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Emma Concetta Manno
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Donato Amodio
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Giulia Linardos
- Division of Virology, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Livia Piccioni
- Division of Virology, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Daniela Perrotta
- Department of Pediatric Emergency, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Campana
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniele Donà
- Department of Mother and Child Health, University of Padova, Padova, Italy
| | - Carlo Giaquinto
- Department of Mother and Child Health, University of Padova, Padova, Italy
| | | | - Carlo Concato
- Division of Virology, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Petter Brodin
- Department of Woman's and Children Health, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Rossi
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Anita De Rossi
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, Unit of Viral Oncology and AIDS Reference Center, University of Padova, Padova, Italy.,Istituto Oncologico Veneto (IOV)-IRCCS, Padova, Italy
| | - Paolo Palma
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
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4
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Cotugno N, Ruggiero A, Bonfante F, Petrara MR, Zicari S, Pascucci GR, Zangari P, De Ioris MA, Santilli V, Manno EC, Amodio D, Bortolami A, Pagliari M, Concato C, Linardos G, Campana A, Donà D, Giaquinto C, Brodin P, Rossi P, De Rossi A, Palma P. Virological and immunological features of SARS-CoV-2-infected children who develop neutralizing antibodies. Cell Rep 2021; 34:108852. [PMID: 33730580 PMCID: PMC7962998 DOI: 10.1016/j.celrep.2021.108852] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/28/2020] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
As the global COVID-19 pandemic progresses, it is paramount to gain knowledge on adaptive immunity to SARS-CoV-2 in children to define immune correlates of protection upon immunization or infection. We analyzed anti-SARS-CoV-2 antibodies and their neutralizing activity (PRNT) in 66 COVID-19-infected children at 7 (±2) days after symptom onset. Individuals with specific humoral responses presented faster virus clearance and lower viral load associated with a reduced in vitro infectivity. We demonstrated that the frequencies of SARS-CoV-2-specific CD4+CD40L+ T cells and Spike-specific B cells were associated with the anti-SARS-CoV-2 antibodies and the magnitude of neutralizing activity. The plasma proteome confirmed the association between cellular and humoral SARS-CoV-2 immunity, and PRNT+ patients show higher viral signal transduction molecules (SLAMF1, CD244, CLEC4G). This work sheds lights on cellular and humoral anti-SARS-CoV-2 responses in children, which may drive future vaccination trial endpoints and quarantine measures policies.
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Affiliation(s)
- Nicola Cotugno
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy; Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata," 00185 Rome, Italy
| | - Alessandra Ruggiero
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Francesco Bonfante
- Laboratory of Experimental Animal Models, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Maria Raffaella Petrara
- Section of Oncology and Immunology, Department of Surgery, Oncology, and Gastroenterology, Unit of Viral Oncology and AIDS Reference Center, University of Padova, 35128 Padova, Italy
| | - Sonia Zicari
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Giuseppe Rubens Pascucci
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Paola Zangari
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | | | - Veronica Santilli
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - E C Manno
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Donato Amodio
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy; Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata," 00185 Rome, Italy
| | - Alessio Bortolami
- Laboratory of Experimental Animal Models, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Matteo Pagliari
- Laboratory of Experimental Animal Models, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Carlo Concato
- Department of Laboratories, Division of Virology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Giulia Linardos
- Department of Laboratories, Division of Virology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Andrea Campana
- Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Daniele Donà
- Department of Mother and Child Health, University of Padova, 35128 Padova, Italy
| | - Carlo Giaquinto
- Department of Mother and Child Health, University of Padova, 35128 Padova, Italy
| | - Petter Brodin
- Pediatric Rheumatology, Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Paolo Rossi
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy; Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata," 00185 Rome, Italy
| | - Anita De Rossi
- Section of Oncology and Immunology, Department of Surgery, Oncology, and Gastroenterology, Unit of Viral Oncology and AIDS Reference Center, University of Padova, 35128 Padova, Italy; Istituto Oncologico Veneto (IOV)-IRCCS, 35128 Padova, Italy
| | - Paolo Palma
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy; Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata," 00185 Rome, Italy.
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5
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Cotugno N, Santilli V, Pascucci GR, Manno EC, De Armas L, Pallikkuth S, Deodati A, Amodio D, Zangari P, Zicari S, Ruggiero A, Fortin M, Bromley C, Pahwa R, Rossi P, Pahwa S, Palma P. Artificial Intelligence Applied to in vitro Gene Expression Testing (IVIGET) to Predict Trivalent Inactivated Influenza Vaccine Immunogenicity in HIV Infected Children. Front Immunol 2020; 11:559590. [PMID: 33123133 PMCID: PMC7569088 DOI: 10.3389/fimmu.2020.559590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
The number of patients affected by chronic diseases with special vaccination needs is burgeoning. In this scenario, predictive markers of immunogenicity, as well as signatures of immune responses are typically missing even though it would especially improve the identification of personalized immunization practices in these populations. We aimed to develop a predictive score of immunogenicity to Influenza Trivalent Inactivated Vaccination (TIV) by applying deep machine learning algorithms using transcriptional data from sort-purified lymphocyte subsets after in vitro stimulation. Peripheral blood mononuclear cells (PBMCs) collected before TIV from 23 vertically HIV infected children under ART and virally controlled were stimulated in vitro with p09/H1N1 peptides (stim) or left unstimulated (med). A multiplexed-qPCR for 96 genes was made on fixed numbers of 3 B cell subsets, 3 T cell subsets and total PBMCs. The ability to respond to TIV was assessed through hemagglutination Inhibition Assay (HIV) and ELIspot and patients were classified as Responders (R) and Non Responders (NR). A predictive modeling framework was applied to the data set in order to define genes and conditions with the higher predicted probability able to inform the final score. Twelve NR and 11 R were analyzed for gene expression differences in all subsets and 3 conditions [med, stim or Δ (stim-med)]. Differentially expressed genes between R and NR were selected and tested with the Adaptive Boosting Model to build a prediction score. The score obtained from subsets revealed the best prediction score from 46 genes from 5 different subsets and conditions. Calculating a combined score based on these 5 categories, we achieved a model accuracy of 95.6% and only one misclassified patient. These data show how a predictive bioinformatic model applied to transcriptional analysis deriving from in-vitro stimulated lymphocytes subsets may predict poor or protective vaccination immune response in vulnerable populations, such as HIV-infected individuals. Future studies on larger cohorts are needed to validate such strategy in the context of vaccination trials.
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Affiliation(s)
- Nicola Cotugno
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy.,Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Veronica Santilli
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Giuseppe Rubens Pascucci
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Emma Concetta Manno
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Lesley De Armas
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Suresh Pallikkuth
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Annalisa Deodati
- Academic Department of Pediatrics (DPUO), Research Unit of Growth Disorders, Bambino Gesù Children's Hospital, Rome, Italy
| | - Donato Amodio
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy.,Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Paola Zangari
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Sonia Zicari
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Alessandra Ruggiero
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | | | | | - Rajendra Pahwa
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Paolo Rossi
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy.,Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Savita Pahwa
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Paolo Palma
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy.,Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
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