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del Giudice G, Migliaccio G, D’Alessandro N, Saarimäki LA, Torres Maia M, Annala ME, Leppänen J, Mӧbus L, Pavel A, Vaani M, Vallius A, Ylä‐Outinen L, Greco D, Serra A. Advancing chemical safety assessment through an omics-based characterization of the test system-chemical interaction. Front Toxicol 2023; 5:1294780. [PMID: 38026842 PMCID: PMC10673692 DOI: 10.3389/ftox.2023.1294780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Assessing chemical safety is essential to evaluate the potential risks of chemical exposure to human health and the environment. Traditional methods relying on animal testing are being replaced by 3R (reduction, refinement, and replacement) principle-based alternatives, mainly depending on in vitro test methods and the Adverse Outcome Pathway framework. However, these approaches often focus on the properties of the compound, missing the broader chemical-biological interaction perspective. Currently, the lack of comprehensive molecular characterization of the in vitro test system results in limited real-world representation and contextualization of the toxicological effect under study. Leveraging omics data strengthens the understanding of the responses of different biological systems, emphasizing holistic chemical-biological interactions when developing in vitro methods. Here, we discuss the relevance of meticulous test system characterization on two safety assessment relevant scenarios and how omics-based, data-driven approaches can improve the future generation of alternative methods.
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Affiliation(s)
- Giusy del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Giorgia Migliaccio
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Nicoletta D’Alessandro
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Laura Aliisa Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Marcella Torres Maia
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Maria Emilia Annala
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Jenni Leppänen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Lena Mӧbus
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Alisa Pavel
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Maaret Vaani
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Anna Vallius
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Laura Ylä‐Outinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- BioMediTech Unit, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
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Saarimäki LA, del Giudice G, Greco D. Expanding adverse outcome pathways towards one health models for nanosafety. Front Toxicol 2023; 5:1176745. [PMID: 37692900 PMCID: PMC10485555 DOI: 10.3389/ftox.2023.1176745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/15/2023] [Indexed: 09/12/2023] Open
Abstract
The ever-growing production of nano-enabled products has generated the need for dedicated risk assessment strategies that ensure safety for humans and the environment. Transdisciplinary approaches are needed to support the development of new technologies while respecting environmental limits, as also highlighted by the EU Green Deal Chemicals Strategy for Sustainability and its safe and sustainable by design (SSbD) framework. The One Health concept offers a holistic multiscale approach for the assessment of nanosafety. However, toxicology is not yet capable of explaining the interaction between chemicals and biological systems at the multiscale level and in the context of the One Health framework. Furthermore, there is a disconnect between chemical safety assessment, epidemiology, and other fields of biology that, if unified, would enable the adoption of the One Health model. The development of mechanistic toxicology and the generation of omics data has provided important biological knowledge of the response of individual biological systems to nanomaterials (NMs). On the other hand, epigenetic data have the potential to inform on interspecies mechanisms of adaptation. These data types, however, need to be linked to concepts that support their intuitive interpretation. Adverse Outcome Pathways (AOPs) represent an evolving framework to anchor existing knowledge to chemical risk assessment. In this perspective, we discuss the possibility of integrating multi-level toxicogenomics data, including toxicoepigenetic insights, into the AOP framework. We anticipate that this new direction of toxicogenomics can support the development of One Health models applicable to groups of chemicals and to multiple species in the tree of life.
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Affiliation(s)
- Laura Aliisa Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Giusy del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Di Lieto E, Serra A, Inkala SI, Saarimäki LA, del Giudice G, Fratello M, Hautanen V, Annala M, Federico A, Greco D. ESPERANTO: a GLP-field sEmi-SuPERvised toxicogenomics metadAta curatioN TOol. Bioinformatics 2023; 39:btad405. [PMID: 37354497 PMCID: PMC10313344 DOI: 10.1093/bioinformatics/btad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 06/26/2023] Open
Abstract
SUMMARY Biological data repositories are an invaluable source of publicly available research evidence. Unfortunately, the lack of convergence of the scientific community on a common metadata annotation strategy has resulted in large amounts of data with low FAIRness (Findable, Accessible, Interoperable and Reusable). The possibility of generating high-quality insights from their integration relies on data curation, which is typically an error-prone process while also being expensive in terms of time and human labour. Here, we present ESPERANTO, an innovative framework that enables a standardized semi-supervised harmonization and integration of toxicogenomics metadata and increases their FAIRness in a Good Laboratory Practice-compliant fashion. The harmonization across metadata is guaranteed with the definition of an ad hoc vocabulary. The tool interface is designed to support the user in metadata harmonization in a user-friendly manner, regardless of the background and the type of expertise. AVAILABILITY AND IMPLEMENTATION ESPERANTO and its user manual are freely available for academic purposes at https://github.com/fhaive/esperanto. The input and the results showcased in Supplementary File S1 are available at the same link.
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Affiliation(s)
- Emanuele Di Lieto
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Angela Serra
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
- Tampere Institute for Advanced Study, Tampere, 33520, Finland
| | - Simo Iisakki Inkala
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Laura Aliisa Saarimäki
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Giusy del Giudice
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Michele Fratello
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Veera Hautanen
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Maria Annala
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Antonio Federico
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
- Tampere Institute for Advanced Study, Tampere, 33520, Finland
| | - Dario Greco
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki 00790, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00790, Finland
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Saarimäki LA, Morikka J, Pavel A, Korpilähde S, del Giudice G, Federico A, Fratello M, Serra A, Greco D. Toxicogenomics Data for Chemical Safety Assessment and Development of New Approach Methodologies: An Adverse Outcome Pathway-Based Approach. Adv Sci (Weinh) 2023; 10:e2203984. [PMID: 36479815 PMCID: PMC9839874 DOI: 10.1002/advs.202203984] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/09/2022] [Indexed: 05/25/2023]
Abstract
Mechanistic toxicology provides a powerful approach to inform on the safety of chemicals and the development of safe-by-design compounds. Although toxicogenomics supports mechanistic evaluation of chemical exposures, its implementation into the regulatory framework is hindered by uncertainties in the analysis and interpretation of such data. The use of mechanistic evidence through the adverse outcome pathway (AOP) concept is promoted for the development of new approach methodologies (NAMs) that can reduce animal experimentation. However, to unleash the full potential of AOPs and build confidence into toxicogenomics, robust associations between AOPs and patterns of molecular alteration need to be established. Systematic curation of molecular events to AOPs will create the much-needed link between toxicogenomics and systemic mechanisms depicted by the AOPs. This, in turn, will introduce novel ways of benefitting from the AOPs, including predictive models and targeted assays, while also reducing the need for multiple testing strategies. Hence, a multi-step strategy to annotate AOPs is developed, and the resulting associations are applied to successfully highlight relevant adverse outcomes for chemical exposures with strong in vitro and in vivo convergence, supporting chemical grouping and other data-driven approaches. Finally, a panel of AOP-derived in vitro biomarkers for pulmonary fibrosis (PF) is identified and experimentally validated.
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Affiliation(s)
- Laura Aliisa Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Jack Morikka
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Alisa Pavel
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Seela Korpilähde
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Giusy del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Antonio Federico
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Michele Fratello
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Angela Serra
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
- Tampere Institute for Advanced StudyTampere UniversityKalevantie 4Tampere33100Finland
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
- Institute of BiotechnologyUniversity of HelsinkiP.O.Box 56HelsinkiUusimaa00014Finland
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5
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Federico A, Pavel A, Möbus L, McKean D, del Giudice G, Fortino V, Niehues H, Rastrick J, Eyerich K, Eyerich S, van den Bogaard E, Smith C, Weidinger S, de Rinaldis E, Greco D. The integration of large-scale public data and network analysis uncovers molecular characteristics of psoriasis. Hum Genomics 2022; 16:62. [PMID: 36437479 PMCID: PMC9703794 DOI: 10.1186/s40246-022-00431-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
In recent years, a growing interest in the characterization of the molecular basis of psoriasis has been observed. However, despite the availability of a large amount of molecular data, many pathogenic mechanisms of psoriasis are still poorly understood. In this study, we performed an integrated analysis of 23 public transcriptomic datasets encompassing both lesional and uninvolved skin samples from psoriasis patients. We defined comprehensive gene co-expression network models of psoriatic lesions and uninvolved skin. Moreover, we curated and exploited a wide range of functional information from multiple public sources in order to systematically annotate the inferred networks. The integrated analysis of transcriptomics data and co-expression networks highlighted genes that are frequently dysregulated and show aberrant patterns of connectivity in the psoriatic lesion compared with the unaffected skin. Our approach allowed us to also identify plausible, previously unknown, actors in the expression of the psoriasis phenotype. Finally, we characterized communities of co-expressed genes associated with relevant molecular functions and expression signatures of specific immune cell types associated with the psoriasis lesion. Overall, integrating experimental driven results with curated functional information from public repositories represents an efficient approach to empower knowledge generation about psoriasis and may be applicable to other complex diseases.
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Affiliation(s)
- Antonio Federico
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Tampere Institute for Advanced Studies, Tampere University, Tampere, Finland
| | - Alisa Pavel
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland
| | - Lena Möbus
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland
| | - David McKean
- Sanofi Immunology and Inflammation Research Therapeutic Area, Precision Immunology Cluster, Cambridge, Massachusetts USA
| | - Giusy del Giudice
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland
| | - Vittorio Fortino
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Hanna Niehues
- grid.461760.20000 0004 0580 1253Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Joe Rastrick
- grid.418727.f0000 0004 5903 3819Immunology Therapeutic Area, UCB Pharma, Slough, UK
| | - Kilian Eyerich
- grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany ,grid.24381.3c0000 0000 9241 5705Unit of Dermatology and Venerology, Department of Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Stefanie Eyerich
- grid.6936.a0000000123222966ZAUM-Center of Allergy and Environment, Technical University and Helmholtz Center Munich, Munich, Germany
| | - Ellen van den Bogaard
- grid.461760.20000 0004 0580 1253Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Catherine Smith
- grid.13097.3c0000 0001 2322 6764St. John’s Institute of Dermatology, King’s College London, London, UK
| | - Stephan Weidinger
- grid.9764.c0000 0001 2153 9986Department of Dermatology, Kiel University, 24105 Kiel, Germany
| | - Emanuele de Rinaldis
- Sanofi Immunology and Inflammation Research Therapeutic Area, Precision Immunology Cluster, Cambridge, Massachusetts USA
| | - Dario Greco
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland ,grid.7737.40000 0004 0410 2071Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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6
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Toscano E, Sepe L, del Giudice G, Tufano R, Paolella G. A three component model for superdiffusive motion effectively describes migration of eukaryotic cells moving freely or under a directional stimulus. PLoS One 2022; 17:e0272259. [PMID: 35917375 PMCID: PMC9345344 DOI: 10.1371/journal.pone.0272259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Although the simple diffusion model can effectively describe the movement of eukaryotic cells on a culture surface observed at relatively low sampling frequency, at higher sampling rates more complex models are often necessary to better fit the experimental data. Currently available models can describe motion paths by involving additional parameters, such as linearity or directional persistence in time. However sometimes difficulties arise as it is not easy to effectively evaluate persistence in presence of a directional bias. Here we present a procedure which helps solve this problem, based on a model which describes displacement as the vectorial sum of three components: diffusion, persistence and directional bias. The described model has been tested by analysing the migratory behaviour of simulated cell populations and used to analyse a collection of experimental datasets, obtained by observing cell cultures in time lapse microscopy. Overall, the method produces a good description of migration behaviour as it appears to capture the expected increase in the directional bias in presence of wound without a large concomitant increase in the persistence module, allowing it to remain as a physically meaningful quantity in the presence of a directional stimulus.
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Affiliation(s)
- Elvira Toscano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
- Ceinge Biotecnologie Avanzate, Napoli, Italy
| | - Leandra Sepe
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
- Ceinge Biotecnologie Avanzate, Napoli, Italy
| | - Giusy del Giudice
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
| | | | - Giovanni Paolella
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
- Ceinge Biotecnologie Avanzate, Napoli, Italy
- * E-mail:
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7
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Clerbaux LA, Albertini MC, Amigó N, Beronius A, Bezemer GFG, Coecke S, Daskalopoulos EP, del Giudice G, Greco D, Grenga L, Mantovani A, Muñoz A, Omeragic E, Parissis N, Petrillo M, Saarimäki LA, Soares H, Sullivan K, Landesmann B. Factors Modulating COVID-19: A Mechanistic Understanding Based on the Adverse Outcome Pathway Framework. J Clin Med 2022; 11:4464. [PMID: 35956081 PMCID: PMC9369763 DOI: 10.3390/jcm11154464] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 12/10/2022] Open
Abstract
Addressing factors modulating COVID-19 is crucial since abundant clinical evidence shows that outcomes are markedly heterogeneous between patients. This requires identifying the factors and understanding how they mechanistically influence COVID-19. Here, we describe how eleven selected factors (age, sex, genetic factors, lipid disorders, heart failure, gut dysbiosis, diet, vitamin D deficiency, air pollution and exposure to chemicals) influence COVID-19 by applying the Adverse Outcome Pathway (AOP), which is well-established in regulatory toxicology. This framework aims to model the sequence of events leading to an adverse health outcome. Several linear AOPs depicting pathways from the binding of the virus to ACE2 up to clinical outcomes observed in COVID-19 have been developed and integrated into a network offering a unique overview of the mechanisms underlying the disease. As SARS-CoV-2 infectibility and ACE2 activity are the major starting points and inflammatory response is central in the development of COVID-19, we evaluated how those eleven intrinsic and extrinsic factors modulate those processes impacting clinical outcomes. Applying this AOP-aligned approach enables the identification of current knowledge gaps orientating for further research and allows to propose biomarkers to identify of high-risk patients. This approach also facilitates expertise synergy from different disciplines to address public health issues.
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Affiliation(s)
- Laure-Alix Clerbaux
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | | | - Núria Amigó
- Biosfer Teslab SL., 43204 Reus, Spain;
- Department of Basic Medical Sciences, Universitat Rovira i Virgili (URV), 23204 Reus, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Anna Beronius
- Institute of Environmental Medicine, Karolinska Institutet, 17177 Stockholm, Sweden;
| | - Gillina F. G. Bezemer
- Impact Station, 1223 JR Hilversum, The Netherlands;
- Department of Pharmaceutical Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Sandra Coecke
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Evangelos P. Daskalopoulos
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Giusy del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Ceze, France;
| | - Alberto Mantovani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Amalia Muñoz
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium;
| | - Elma Omeragic
- Faculty of Pharmacy, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Nikolaos Parissis
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Mauro Petrillo
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Laura A. Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Helena Soares
- Laboratory of Immunobiology and Pathogenesis, Chronic Diseases Research Centre, Faculdade de Ciências Médicas Medical School, University of Lisbon, 1649-004 Lisbon, Portugal;
| | - Kristie Sullivan
- Physicians Committee for Responsible Medicine, Washington, DC 20016, USA;
| | - Brigitte Landesmann
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
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8
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Serra A, del Giudice G, Kinaret PAS, Saarimäki LA, Poulsen SS, Fortino V, Halappanavar S, Vogel U, Greco D. Characterization of ENM Dynamic Dose-Dependent MOA in Lung with Respect to Immune Cells Infiltration. Nanomaterials (Basel) 2022; 12:nano12122031. [PMID: 35745370 PMCID: PMC9228743 DOI: 10.3390/nano12122031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023]
Abstract
The molecular effects of exposures to engineered nanomaterials (ENMs) are still largely unknown. In classical inhalation toxicology, cell composition of bronchoalveolar lavage (BAL) is a toxicity indicator at the lung tissue level that can aid in interpreting pulmonary histological changes. Toxicogenomic approaches help characterize the mechanism of action (MOA) of ENMs by investigating the differentially expressed genes (DEG). However, dissecting which molecular mechanisms and events are directly induced by the exposure is not straightforward. It is now generally accepted that direct effects follow a monotonic dose-dependent pattern. Here, we applied an integrated modeling approach to study the MOA of four ENMs by retrieving the DEGs that also show a dynamic dose-dependent profile (dddtMOA). We further combined the information of the dddtMOA with the dose dependency of four immune cell populations derived from BAL counts. The dddtMOA analysis highlighted the specific adaptation pattern to each ENM. Furthermore, it revealed the distinct effect of the ENM physicochemical properties on the induced immune response. Finally, we report three genes dose-dependent in all the exposures and correlated with immune deregulation in the lung. The characterization of dddtMOA for ENM exposures, both for apical endpoints and molecular responses, can further promote toxicogenomic approaches in a regulatory context.
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Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (G.d.G.); (L.A.S.)
- BioMediTech Institute, Tampere University, 33520 Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), 33520 Tampere, Finland
| | - Giusy del Giudice
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (G.d.G.); (L.A.S.)
- BioMediTech Institute, Tampere University, 33520 Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), 33520 Tampere, Finland
| | | | - Laura Aliisa Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (G.d.G.); (L.A.S.)
- BioMediTech Institute, Tampere University, 33520 Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), 33520 Tampere, Finland
| | - Sarah Søs Poulsen
- National Research Centre for the Working Environment, 2100 Copenhagen, Denmark; (S.S.P.); (U.V.)
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, 70211 Kuopio, Finland;
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada;
| | - Ulla Vogel
- National Research Centre for the Working Environment, 2100 Copenhagen, Denmark; (S.S.P.); (U.V.)
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (G.d.G.); (L.A.S.)
- BioMediTech Institute, Tampere University, 33520 Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), 33520 Tampere, Finland
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland;
- Correspondence:
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9
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Serra A, Saarimäki LA, Pavel A, del Giudice G, Fratello M, Cattelani L, Federico A, Laurino O, Marwah VS, Fortino V, Scala G, Sofia Kinaret PA, Greco D. Nextcast: a software suite to analyse and model toxicogenomics data. Comput Struct Biotechnol J 2022; 20:1413-1426. [PMID: 35386103 PMCID: PMC8956870 DOI: 10.1016/j.csbj.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 11/28/2022] Open
Abstract
Toxicogenomics is emerging as a valid approach to characterise the mechanism of action of chemicals. Structured pipelines for toxicogenomics increase standardisation and regulatory acceptance. We developed the Nextcast software suite for robust analysis and modelling of toxicogenomic data. Nextcast offers customisable modular pipelines to tackle multiple biological questions.
The recent advancements in toxicogenomics have led to the availability of large omics data sets, representing the starting point for studying the exposure mechanism of action and identifying candidate biomarkers for toxicity prediction. The current lack of standard methods in data generation and analysis hampers the full exploitation of toxicogenomics-based evidence in regulatory risk assessment. Moreover, the pipelines for the preprocessing and downstream analyses of toxicogenomic data sets can be quite challenging to implement. During the years, we have developed a number of software packages to address specific questions related to multiple steps of toxicogenomics data analysis and modelling. In this review we present the Nextcast software collection and discuss how its individual tools can be combined into efficient pipelines to answer specific biological questions. Nextcast components are of great support to the scientific community for analysing and interpreting large data sets for the toxicity evaluation of compounds in an unbiased, straightforward, and reliable manner. The Nextcast software suite is available at: ( https://github.com/fhaive/nextcast).
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Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Laura Aliisa Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Alisa Pavel
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Giusy del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Luca Cattelani
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | | | - Veer Singh Marwah
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Giovanni Scala
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Pia Anneli Sofia Kinaret
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Corresponding author.
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10
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Pavel A, del Giudice G, Federico A, Di Lieto A, Kinaret PAS, Serra A, Greco D. Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment. Brief Bioinform 2021; 22:1430-1441. [PMID: 33569598 PMCID: PMC7929418 DOI: 10.1093/bib/bbaa417] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/13/2020] [Accepted: 12/19/2020] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 disease led to an unprecedented health emergency, still ongoing worldwide. Given the lack of a vaccine or a clear therapeutic strategy to counteract the infection as well as its secondary effects, there is currently a pressing need to generate new insights into the SARS-CoV-2 induced host response. Biomedical data can help to investigate new aspects of the COVID-19 pathogenesis, but source heterogeneity represents a major drawback and limitation. In this work, we applied data integration methods to develop a Unified Knowledge Space (UKS) and used it to identify a new set of genes associated with SARS-CoV-2 host response, both in vitro and in vivo. Functional analysis of these genes reveals possible long-term systemic effects of the infection, such as vascular remodelling and fibrosis. Finally, we identified a set of potentially relevant drugs targeting proteins involved in multiple steps of the host response to the virus.
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Affiliation(s)
- Alisa Pavel
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Giusy del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Antonio Di Lieto
- Department of Forensic Psychiatry, Aarhus University, Aarhus, Denmark
| | - Pia A S Kinaret
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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11
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Hannesdottir SG, Olafsdottir TA, Giudice GD, Jonsdottir I. Adjuvants LT-K63 and CpG enhance the activation of dendritic cells in neonatal mice. Scand J Immunol 2008; 68:469-75. [PMID: 18946928 DOI: 10.1111/j.1365-3083.2008.02165.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dendritic cells (DC) play a major role in the priming of T cells and initiating specific immune responses. We assessed the effects of the adjuvants LT-K63 and CpG on neonatal DC in vivo and in vitro. Cytokine levels (IL-10, IL-12p70 and IL-12p40/IL-23p40) were measured and the expression of the activation markers CD86, CD40 and MHCII on CD11c+ DC was analysed by using FACS. The proportion of MHCII high CD11c+ DC was higher in neonatal mice immunized with a pneumococcal conjugate (PncTT) and LT-K63 or CpG compared with that when PncTT was alone. In vitro stimulation with LT-K63 enhanced the expression of CD86 more on CD11c+ DC from spleens of mice immunized as neonates than those immunized as adults, whereas in vitro stimulation with CpG enhanced the expression of CD86 and CD40 on CD11c+ DC similarly in both age groups. CpG stimulation in vitro enhanced IL-10 and IL-12(p70) production in mice immunized as neonates with PncTT and either adjuvant, but not PncTT alone. The adjuvants LT-K63 and CpG enhance the activation of CD11c+ DC in mice immunized as neonates and can thereby overcome one of the limiting factors in the initiation of the immune response to conjugate vaccines in early life. The fact that neonatal DC are more susceptible to stimulation with either adjuvant, LT-K63 or CpG, could imply that neonatal CD11c+ DC are more easily activated than adult CD11c+ DC, and /or be a consequence of the predominance of different DC subsets in neonatal and adult mice.
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12
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Olafsdottir TA, Hannesdottir SG, Giudice GD, Trannoy E, Jonsdottir I. Effects of LT-K63 and CpG2006 on phenotype and function of murine neonatal lymphoid cells. Scand J Immunol 2007; 66:426-34. [PMID: 17850587 DOI: 10.1111/j.1365-3083.2007.01970.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The immature state of the immune system of neonates makes them vulnerable to infectious agents, including Streptococcus pneumoniae. The aim of our study was to analyse and compare the effects of Escherichia coli heat-labile enterototoxin (LT)-K63 and CpG2006 on cells and key molecules of the neonatal immune system, using a previously established immunization model with pneumococcal polysaccharide of serotype 1 conjugated to tetanus toxoid (TT) (Pnc1-TT). The cellular response was evaluated by measuring cytokine secretion and proliferation upon in vitro stimulation with TT, the protein moiety of Pnc1-TT, and antibody (Ab) to both the polysaccharide (PS) and protein parts of the vaccine were measured by enzyme-linked immunosorbent assay (ELISA). Antigen (Ag)-presenting and co-stimulatory capacity of neonatal B-cells was evaluated by staining for major histocompatibility complex (MHC)II, CD80, CD86 and CD40. The results showed that both LT-K63 and CpG2006 significantly enhanced the neonatal Ab response to Pnc1-TT. Spleen cells from mice receiving LT-K63 showed enhanced proliferation and interferon (IFN)-gamma, interleukin (IL)-4, IL-5 and IL-10 secretion upon TT stimulation, whereas cells from mice receiving CpG2006 could only enhance IL-10 secretion. LT-K63 and to a lesser extent CpG2006 enhanced the capacity of B-cells to up-regulate the expression of co-stimulatory and activation markers compared with those of mice receiving Pnc1-TT alone. Thus, we conclude that LT-K63 markedly improves T-cell activation whereas the direct adjuvant effect of CpG2006 on neonatal B-cells may partly compensate for lower T-cell help resulting in enhanced neonatal Ab responses to both the TT and PS parts of the vaccine by both adjuvants.
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Affiliation(s)
- T A Olafsdottir
- Department of Immunology, Landspitali-University Hospital, and Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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13
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Giudice GD. Helivax Antex Biologics. Curr Opin Investig Drugs 2001; 2:896-9. [PMID: 11757787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
Antex Biologics is developing an oral vaccine against Helicobacter pylori infection as a potential treatment and prophylaxis for gastric ulcers. The vaccine incorporates a mucosal adjuvant and is in phase II trials [376332]. Enrollment for the trial was completed in September 2000 and results are expected in 2001 [382128]. In July 2000, Antex started a two-part phase Ib/II clinical trial of the vaccine. The first part was an open-label study to assess the general safety of the vaccine in uninfected and asymptomatic Helicobacter pylori-infected individuals. The second part was an expanded placebo-controlled study to evaluate safety and immunogenicity of the vaccine. The vaccine was generally well-tolerated and it generated an immune response in both infected and non-infected individuals [312681].
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Affiliation(s)
- G D Giudice
- IRIS Research Center, Chiron SpA, Siena, Italy.
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