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Chung E, Wen X, Jia X, Ciallella HL, Aleksunes LM, Zhu H. Hybrid non-animal modeling: A mechanistic approach to predict chemical hepatotoxicity. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134297. [PMID: 38677119 DOI: 10.1016/j.jhazmat.2024.134297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024]
Abstract
Developing mechanistic non-animal testing methods based on the adverse outcome pathway (AOP) framework must incorporate molecular and cellular key events associated with target toxicity. Using data from an in vitro assay and chemical structures, we aimed to create a hybrid model to predict hepatotoxicants. We first curated a reference dataset of 869 compounds for hepatotoxicity modeling. Then, we profiled them against PubChem for existing in vitro toxicity data. Of the 2560 resulting assays, we selected the mitochondrial membrane potential (MMP) assay, a high-throughput screening (HTS) tool that can test chemical disruptors for mitochondrial function. Machine learning was applied to develop quantitative structure-activity relationship (QSAR) models with 2536 compounds tested in the MMP assay for screening new compounds. The MMP assay results, including QSAR model outputs, yielded hepatotoxicity predictions for reference set compounds with a Correct Classification Ratio (CCR) of 0.59. The predictivity improved by including 37 structural alerts (CCR = 0.8). We validated our model by testing 37 reference set compounds in human HepG2 hepatoma cells, and reliably predicting them for hepatotoxicity (CCR = 0.79). This study introduces a novel AOP modeling strategy that combines public HTS data, computational modeling, and experimental testing to predict chemical hepatotoxicity.
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Affiliation(s)
- Elena Chung
- Department of Chemistry and Biochemistry, Rowan University, NJ, USA; Center for Biomedical Informatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Xia Wen
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NJ, USA
| | - Xuelian Jia
- Department of Chemistry and Biochemistry, Rowan University, NJ, USA; Center for Biomedical Informatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Heather L Ciallella
- Department of Toxicology, Cuyahoga County Medical Examiner's Office, Cleveland, OH, USA
| | - Lauren M Aleksunes
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NJ, USA
| | - Hao Zhu
- Department of Chemistry and Biochemistry, Rowan University, NJ, USA; Center for Biomedical Informatics and Genomics, Tulane University, New Orleans, LA, USA.
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Mihajlovic M, De Boever S, Tabernilla A, Callewaert E, Sanz-Serrano J, Verhoeven A, Maerten A, Rosseel Z, De Waele E, Vinken M. Investigation of parenteral nutrition-induced hepatotoxicity using human liver spheroid co-cultures. Arch Toxicol 2024:10.1007/s00204-024-03773-8. [PMID: 38740588 DOI: 10.1007/s00204-024-03773-8] [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: 03/16/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Parenteral nutrition (PN) is typically administered to individuals with gastrointestinal dysfunction, a contraindication for enteral feeding, and a need for nutritional therapy. When PN is the only energy source in patients, it is defined as total parenteral nutrition (TPN). TPN is a life-saving approach for different patient populations, both in infants and adults. However, despite numerous benefits, TPN can cause adverse effects, including metabolic disorders and liver injury. TPN-associated liver injury, known as intestinal failure-associated liver disease (IFALD), represents a significant problem affecting up to 90% of individuals receiving TPN. IFALD pathogenesis is complex, depending on the TPN components as well as on the patient's medical conditions. Despite numerous animal studies and clinical observations, the molecular mechanisms driving IFALD remain largely unknown. The present study was set up to elucidate the mechanisms underlying IFALD. For this purpose, human liver spheroid co-cultures were treated with a TPN mixture, followed by RNA sequencing analysis. Subsequently, following exposure to TPN and its single nutritional components, several key events of liver injury, including mitochondrial dysfunction, endoplasmic reticulum stress, oxidative stress, apoptosis, and lipid accumulation (steatosis), were studied using various techniques. It was found that prolonged exposure to TPN substantially changes the transcriptome profile of liver spheroids and affects multiple metabolic and signaling pathways contributing to liver injury. Moreover, TPN and its main components, especially lipid emulsion, induce changes in all key events measured and trigger steatosis.
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Affiliation(s)
- Milos Mihajlovic
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Sybren De Boever
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Andrés Tabernilla
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Ellen Callewaert
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Julen Sanz-Serrano
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Anouk Verhoeven
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Amy Maerten
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Zenzi Rosseel
- Department of Pharmacy, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
- Department of Clinical Nutrition, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Elisabeth De Waele
- Department of Clinical Nutrition, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
- Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mathieu Vinken
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium.
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Mihajlovic M, Rosseel Z, De Waele E, Vinken M. Parenteral nutrition-associated liver injury: clinical relevance and mechanistic insights. Toxicol Sci 2024; 199:1-11. [PMID: 38383052 DOI: 10.1093/toxsci/kfae020] [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] [Indexed: 02/23/2024] Open
Abstract
Intestinal failure-associated liver disease (IFALD) is a relatively common complication in individuals receiving parenteral nutrition (PN). IFALD can be manifested as different types of liver injury, including steatosis, cholestasis, and fibrosis, and could result in liver failure in some cases. The onset and progression of IFALD are highly dependent on various patient and PN-related risk factors. Despite still being under investigation, several mechanisms have been proposed. Liver injury can originate due to caloric overload, nutrient deficiency, and toxicity, as well as phytosterol content, and omega-6 to omega-3 fatty acids ratio contained in lipid emulsions. Additional mechanisms include immature or defective bile acid metabolism, acute heart failure, infections, and sepsis exerting negative effects via Toll-like receptor 4 and nuclear factor κB inflammatory signaling. Furthermore, lack of enteral feeding, gut dysbiosis, and altered enterohepatic circulation that affect the farnesoid x receptor-fibroblast growth factor 19 axis can also contribute to IFALD. Various best practices can be adopted to minimize the risk of developing IFALD, such as prevention and management of central line infections and sepsis, preservation of intestine's length, a switch to oral and enteral feeding, cyclic PN, avoidance of overfeeding and soybean oil-based lipid formulations, and avoiding hepatotoxic substances. The present review thus provides a comprehensive overview of all relevant aspects inherent to IFALD. Further research focused on clinical observations, translational models, and advanced toxicological knowledge frameworks is needed to gain more insight into the molecular pathogenesis of hepatotoxicity, reduce IFALD incidence, and encourage the safe use of PN.
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Affiliation(s)
- Milos Mihajlovic
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Zenzi Rosseel
- Department of Pharmacy, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
- Department of Clinical Nutrition, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Elisabeth De Waele
- Department of Clinical Nutrition, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
- Department of Intensive Care, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
- Faculty of Medicine and Pharmacy, Department of Clinical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mathieu Vinken
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium
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Sahoo AK, Chivukula N, Ramesh K, Singha J, Marigoudar SR, Sharma KV, Samal A. An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170968. [PMID: 38367714 DOI: 10.1016/j.scitotenv.2024.170968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/19/2024]
Abstract
Cadmium is a prominent toxic heavy metal that contaminates both terrestrial and aquatic environments. Owing to its high biological half-life and low excretion rates, cadmium causes a variety of adverse biological outcomes. Adverse outcome pathway (AOP) networks were envisioned to systematically capture toxicological information to enable risk assessment and chemical regulation. Here, we leveraged AOP-Wiki and integrated heterogeneous data from four other exposome-relevant resources to build the first AOP network relevant for inorganic cadmium-induced toxicity. From AOP-Wiki, we filtered 309 high confidence AOPs, identified 312 key events (KEs) associated with inorganic cadmium from five exposome-relevant databases using a data-centric approach, and thereafter, curated 30 cadmium relevant AOPs (cadmium-AOPs). By constructing the undirected AOP network, we identified a large connected component of 18 cadmium-AOPs. Further, we analyzed the directed network of 59 KEs and 82 key event relationships (KERs) in the largest component using graph-theoretic approaches. Subsequently, we mined published literature using artificial intelligence-based tools to provide auxiliary evidence of cadmium association for all KEs in the largest component. Finally, we performed case studies to verify the rationality of cadmium-induced toxicity in humans and aquatic species. Overall, cadmium-AOP network constructed in this study will aid ongoing research in systems toxicology and chemical exposome.
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Affiliation(s)
- Ajaya Kumar Sahoo
- The Institute of Mathematical Sciences (IMSc), Chennai, India; Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Nikhil Chivukula
- The Institute of Mathematical Sciences (IMSc), Chennai, India; Homi Bhabha National Institute (HBNI), Mumbai, India
| | | | - Jasmine Singha
- National Centre for Coastal Research, Ministry of Earth Sciences, Government of India, Pallikaranai, Chennai, India
| | | | - Krishna Venkatarama Sharma
- National Centre for Coastal Research, Ministry of Earth Sciences, Government of India, Pallikaranai, Chennai, India
| | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, India; Homi Bhabha National Institute (HBNI), Mumbai, India.
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5
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Sanz-Serrano J, Callewaert E, De Boever S, Drees A, Verhoeven A, Vinken M. Chemical-induced liver cancer: an adverse outcome pathway perspective. Expert Opin Drug Saf 2024; 23:425-438. [PMID: 38430529 DOI: 10.1080/14740338.2024.2326479] [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: 11/15/2023] [Accepted: 02/29/2024] [Indexed: 03/04/2024]
Abstract
INTRODUCTION The evaluation of the potential carcinogenicity is a key consideration in the risk assessment of chemicals. Predictive toxicology is currently switching toward non-animal approaches that rely on the mechanistic understanding of toxicity. AREAS COVERED Adverse outcome pathways (AOPs) present toxicological processes, including chemical-induced carcinogenicity, in a visual and comprehensive manner, which serve as the conceptual backbone for the development of non-animal approaches eligible for hazard identification. The current review provides an overview of the available AOPs leading to liver cancer and discusses their use in advanced testing of liver carcinogenic chemicals. Moreover, the challenges related to their use in risk assessment are outlined, including the exploitation of available data, the need for semantic ontologies, and the development of quantitative AOPs. EXPERT OPINION To exploit the potential of liver cancer AOPs in the field of risk assessment, 3 immediate prerequisites need to be fulfilled. These include developing human relevant AOPs for chemical-induced liver cancer, increasing the number of AOPs integrating quantitative toxicodynamic and toxicokinetic data, and developing a liver cancer AOP network. As AOPs and other areas in the field continue to evolve, liver cancer AOPs will progress into a reliable and robust tool serving future risk assessment and management.
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Affiliation(s)
- Julen Sanz-Serrano
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ellen Callewaert
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sybren De Boever
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Annika Drees
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Anouk Verhoeven
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mathieu Vinken
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
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6
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Barnes DA, Firman JW, Belfield SJ, Cronin MTD, Vinken M, Janssen MJ, Masereeuw R. Development of an adverse outcome pathway network for nephrotoxicity. Arch Toxicol 2024; 98:929-942. [PMID: 38197913 PMCID: PMC10861692 DOI: 10.1007/s00204-023-03637-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
Adverse outcome pathways (AOPs) were introduced in modern toxicology to provide evidence-based representations of the events and processes involved in the progression of toxicological effects across varying levels of the biological organisation to better facilitate the safety assessment of chemicals. AOPs offer an opportunity to address knowledge gaps and help to identify novel therapeutic targets. They also aid in the selection and development of existing and new in vitro and in silico test methods for hazard identification and risk assessment of chemical compounds. However, many toxicological processes are too intricate to be captured in a single, linear AOP. As a result, AOP networks have been developed to aid in the comprehension and placement of associated events underlying the emergence of related forms of toxicity-where complex exposure scenarios and interactions may influence the ultimate adverse outcome. This study utilised established criteria to develop an AOP network that connects thirteen individual AOPs associated with nephrotoxicity (as sourced from the AOP-Wiki) to identify several key events (KEs) linked to various adverse outcomes, including kidney failure and chronic kidney disease. Analysis of the modelled AOP network and its topological features determined mitochondrial dysfunction, oxidative stress, and tubular necrosis to be the most connected and central KEs. These KEs can provide a logical foundation for guiding the selection and creation of in vitro assays and in silico tools to substitute for animal-based in vivo experiments in the prediction and assessment of chemical-induced nephrotoxicity in human health.
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Affiliation(s)
- D A Barnes
- Division of Pharmacology, Utrecht University, Utrecht Institute for Pharmaceutical Sciences, Utrecht, The Netherlands
| | - J W Firman
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - S J Belfield
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - M T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - M Vinken
- Department of Pharmaceutical and Pharmacological Sciences, Entity of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Brussels, Belgium
| | - M J Janssen
- Division of Pharmacology, Utrecht University, Utrecht Institute for Pharmaceutical Sciences, Utrecht, The Netherlands
| | - R Masereeuw
- Division of Pharmacology, Utrecht University, Utrecht Institute for Pharmaceutical Sciences, Utrecht, The Netherlands.
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7
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Lucena MI, Villanueva-Paz M, Alvarez-Alvarez I, Aithal GP, Björnsson ES, Cakan-Akdogan G, Cubero FJ, Esteves F, Falcon-Perez JM, Fromenty B, Garcia-Ruiz C, Grove JI, Konu O, Kranendonk M, Kullak-Ublick GA, Miranda JP, Remesal-Doblado A, Sancho-Bru P, Nelson L, Andrade RJ, Daly AK, Fernandez-Checa JC. Roadmap to DILI research in Europe. A proposal from COST action ProEuroDILINet. Pharmacol Res 2024; 200:107046. [PMID: 38159783 DOI: 10.1016/j.phrs.2023.107046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
In the current article the aims for a constructive way forward in Drug-Induced Liver Injury (DILI) are to highlight the most important priorities in research and clinical science, therefore supporting a more informed, focused, and better funded future for European DILI research. This Roadmap aims to identify key challenges, define a shared vision across all stakeholders for the opportunities to overcome these challenges and propose a high-quality research program to achieve progress on the prediction, prevention, diagnosis and management of this condition and impact on healthcare practice in the field of DILI. This will involve 1. Creation of a database encompassing optimised case report form for prospectively identified DILI cases with well-characterised controls with competing diagnoses, biological samples, and imaging data; 2. Establishing of preclinical models to improve the assessment and prediction of hepatotoxicity in humans to guide future drug safety testing; 3. Emphasis on implementation science and 4. Enhanced collaboration between drug-developers, clinicians and regulatory scientists. This proposed operational framework will advance DILI research and may bring together basic, applied, translational and clinical research in DILI.
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Affiliation(s)
- M I Lucena
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Plataforma de Investigación Clínica y Ensayos Clínicos UICEC-IBIMA, Plataforma ISCIII de Investigación Clínica, Madrid, Spain.
| | - M Villanueva-Paz
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - I Alvarez-Alvarez
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - G P Aithal
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
| | - E S Björnsson
- Faculty of Medicine, University of Iceland, Department of Gastroenterology and Hepatology, Landspitali University Hospital, Reykjavik, Iceland
| | - G Cakan-Akdogan
- Izmir Biomedicine and Genome Center, Izmir, Turkey. Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - F J Cubero
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Department of Immunology, Ophthalmology and ORL, Complutense University School of Medicine, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - F Esteves
- Center for Toxicogenomics and Human Health (ToxOmics), NMS | FCM, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - J M Falcon-Perez
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, 48160, Spain. IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia 48009, Spain
| | - B Fromenty
- INSERM, Univ Rennes, INRAE, Institut NUMECAN (Nutrition Metabolisms and Cancer) UMR_A 1341, UMR_S 1317, F-35000 Rennes, France
| | - C Garcia-Ruiz
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. University of Barcelona, Barcelona, Spain; Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, Barcelona, Spain
| | - J I Grove
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
| | - O Konu
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey; Interdisciplinary Neuroscience Program, Bilkent University, Ankara, Turkey; UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey
| | - M Kranendonk
- Center for Toxicogenomics and Human Health (ToxOmics), NMS | FCM, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - G A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; CMO & Patient Safety, Global Drug Development, Novartis Pharma, Basel, Switzerland
| | - J P Miranda
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - A Remesal-Doblado
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain
| | - P Sancho-Bru
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. University of Barcelona, Barcelona, Spain
| | - L Nelson
- Institute for Bioengineering, School of Engineering, Faraday Building, The University of Edinburgh, Scotland, UK
| | - R J Andrade
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - A K Daly
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - J C Fernandez-Checa
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. University of Barcelona, Barcelona, Spain; Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, Barcelona, Spain; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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8
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van Ertvelde J, Verhoeven A, Maerten A, Cooreman A, Santos Rodrigues BD, Sanz-Serrano J, Mihajlovic M, Tripodi I, Teunis M, Jover R, Luechtefeld T, Vanhaecke T, Jiang J, Vinken M. Optimization of an adverse outcome pathway network on chemical-induced cholestasis using an artificial intelligence-assisted data collection and confidence level quantification approach. J Biomed Inform 2023; 145:104465. [PMID: 37541407 DOI: 10.1016/j.jbi.2023.104465] [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: 06/07/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Adverse outcome pathway (AOP) networks are versatile tools in toxicology and risk assessment that capture and visualize mechanisms driving toxicity originating from various data sources. They share a common structure consisting of a set of molecular initiating events and key events, connected by key event relationships, leading to the actual adverse outcome. AOP networks are to be considered living documents that should be frequently updated by feeding in new data. Such iterative optimization exercises are typically done manually, which not only is a time-consuming effort, but also bears the risk of overlooking critical data. The present study introduces a novel approach for AOP network optimization of a previously published AOP network on chemical-induced cholestasis using artificial intelligence to facilitate automated data collection followed by subsequent quantitative confidence assessment of molecular initiating events, key events, and key event relationships. METHODS Artificial intelligence-assisted data collection was performed by means of the free web platform Sysrev. Confidence levels of the tailored Bradford-Hill criteria were quantified for the purpose of weight-of-evidence assessment of the optimized AOP network. Scores were calculated for biological plausibility, empirical evidence, and essentiality, and were integrated into a total key event relationship confidence value. The optimized AOP network was visualized using Cytoscape with the node size representing the incidence of the key event and the edge size indicating the total confidence in the key event relationship. RESULTS This resulted in the identification of 38 and 135 unique key events and key event relationships, respectively. Transporter changes was the key event with the highest incidence, and formed the most confident key event relationship with the adverse outcome, cholestasis. Other important key events present in the AOP network include: nuclear receptor changes, intracellular bile acid accumulation, bile acid synthesis changes, oxidative stress, inflammation and apoptosis. CONCLUSIONS This process led to the creation of an extensively informative AOP network focused on chemical-induced cholestasis. This optimized AOP network may serve as a mechanistic compass for the development of a battery of in vitro assays to reliably predict chemical-induced cholestatic injury.
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Affiliation(s)
- Jonas van Ertvelde
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Anouk Verhoeven
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Amy Maerten
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Axelle Cooreman
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bruna Dos Santos Rodrigues
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Julen Sanz-Serrano
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Milos Mihajlovic
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Marc Teunis
- Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht, Utrecht, The Netherlands
| | - Ramiro Jover
- Joint Research Unit in Experimental Hepatology, University of Valencia, Health Research Institute Hospital La Fe & CIBER of Hepatic and Digestive Diseases, Spain
| | | | - Tamara Vanhaecke
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jian Jiang
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mathieu Vinken
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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9
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Suciu I, Pamies D, Peruzzo R, Wirtz PH, Smirnova L, Pallocca G, Hauck C, Cronin MTD, Hengstler JG, Brunner T, Hartung T, Amelio I, Leist M. G × E interactions as a basis for toxicological uncertainty. Arch Toxicol 2023; 97:2035-2049. [PMID: 37258688 PMCID: PMC10256652 DOI: 10.1007/s00204-023-03500-9] [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: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 06/02/2023]
Abstract
To transfer toxicological findings from model systems, e.g. animals, to humans, standardized safety factors are applied to account for intra-species and inter-species variabilities. An alternative approach would be to measure and model the actual compound-specific uncertainties. This biological concept assumes that all observed toxicities depend not only on the exposure situation (environment = E), but also on the genetic (G) background of the model (G × E). As a quantitative discipline, toxicology needs to move beyond merely qualitative G × E concepts. Research programs are required that determine the major biological variabilities affecting toxicity and categorize their relative weights and contributions. In a complementary approach, detailed case studies need to explore the role of genetic backgrounds in the adverse effects of defined chemicals. In addition, current understanding of the selection and propagation of adverse outcome pathways (AOP) in different biological environments is very limited. To improve understanding, a particular focus is required on modulatory and counter-regulatory steps. For quantitative approaches to address uncertainties, the concept of "genetic" influence needs a more precise definition. What is usually meant by this term in the context of G × E are the protein functions encoded by the genes. Besides the gene sequence, the regulation of the gene expression and function should also be accounted for. The widened concept of past and present "gene expression" influences is summarized here as Ge. Also, the concept of "environment" needs some re-consideration in situations where exposure timing (Et) is pivotal: prolonged or repeated exposure to the insult (chemical, physical, life style) affects Ge. This implies that it changes the model system. The interaction of Ge with Et might be denoted as Ge × Et. We provide here general explanations and specific examples for this concept and show how it could be applied in the context of New Approach Methodologies (NAM).
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Affiliation(s)
- Ilinca Suciu
- In Vitro Toxicology and Biomedicine, Department Inaugurated By the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany
| | - David Pamies
- Department of Biological Sciences, University of Lausanne, 1005, Lausanne, Switzerland
| | - Roberta Peruzzo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Petra H Wirtz
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78457, Constance, Germany
- Biological Work and Health Psychology, Department of Psychology, University of Konstanz, 78457, Constance, Germany
| | - Lena Smirnova
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | | | - Christof Hauck
- Department of Cell Biology, University of Konstanz, 78457, Constance, Germany
| | - Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, 44139, Dortmund, Germany
| | - Thomas Brunner
- Biochemical Pharmacology, Department of Biology, University of Konstanz, 78457, Constance, Germany
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- CAAT Europe, University of Konstanz, 78457, Constance, Germany
| | - Ivano Amelio
- Division for Systems Toxicology, Department of Biology, University of Konstanz, 78457, Constance, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated By the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany.
- CAAT Europe, University of Konstanz, 78457, Constance, Germany.
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10
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Saarimäki LA, Fratello M, Pavel A, Korpilähde S, Leppänen J, Serra A, Greco D. A curated gene and biological system annotation of adverse outcome pathways related to human health. Sci Data 2023; 10:409. [PMID: 37355733 PMCID: PMC10290716 DOI: 10.1038/s41597-023-02321-w] [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: 11/01/2022] [Accepted: 06/20/2023] [Indexed: 06/26/2023] Open
Abstract
Adverse outcome pathways (AOPs) are emerging as a central framework in modern toxicology and other fields in biomedicine. They serve as an extension of pathway-based concepts by depicting biological mechanisms as causally linked sequences of key events (KEs) from a molecular initiating event (MIE) to an adverse outcome. AOPs guide the use and development of new approach methodologies (NAMs) aimed at reducing animal experimentation. While AOPs model the systemic mechanisms at various levels of biological organisation, toxicogenomics provides the means to study the molecular mechanisms of chemical exposures. Systematic integration of these two concepts would improve the application of AOP-based knowledge while also supporting the interpretation of complex omics data. Hence, we established this link through rigorous curation of molecular annotations for the KEs of human relevant AOPs. We further expanded and consolidated the annotations of the biological context of KEs. These curated annotations pave the way to embed AOPs in molecular data interpretation, facilitating the emergence of new knowledge in biomedicine.
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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
| | - Michele Fratello
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alisa Pavel
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Seela Korpilähde
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jenni Leppänen
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Angela Serra
- 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 for Advanced Study, Tampere University, Tampere, 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.
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11
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Ramhøj L, Axelstad M, Baert Y, Cañas-Portilla AI, Chalmel F, Dahmen L, De La Vieja A, Evrard B, Haigis AC, Hamers T, Heikamp K, Holbech H, Iglesias-Hernandez P, Knapen D, Marchandise L, Morthorst JE, Nikolov NG, Nissen ACVE, Oelgeschlaeger M, Renko K, Rogiers V, Schüürmann G, Stinckens E, Stub MH, Torres-Ruiz M, Van Duursen M, Vanhaecke T, Vergauwen L, Wedebye EB, Svingen T. New approach methods to improve human health risk assessment of thyroid hormone system disruption-a PARC project. FRONTIERS IN TOXICOLOGY 2023; 5:1189303. [PMID: 37265663 PMCID: PMC10229837 DOI: 10.3389/ftox.2023.1189303] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
Current test strategies to identify thyroid hormone (TH) system disruptors are inadequate for conducting robust chemical risk assessment required for regulation. The tests rely heavily on histopathological changes in rodent thyroid glands or measuring changes in systemic TH levels, but they lack specific new approach methodologies (NAMs) that can adequately detect TH-mediated effects. Such alternative test methods are needed to infer a causal relationship between molecular initiating events and adverse outcomes such as perturbed brain development. Although some NAMs that are relevant for TH system disruption are available-and are currently in the process of regulatory validation-there is still a need to develop more extensive alternative test batteries to cover the range of potential key events along the causal pathway between initial chemical disruption and adverse outcomes in humans. This project, funded under the Partnership for the Assessment of Risk from Chemicals (PARC) initiative, aims to facilitate the development of NAMs that are specific for TH system disruption by characterizing in vivo mechanisms of action that can be targeted by in embryo/in vitro/in silico/in chemico testing strategies. We will develop and improve human-relevant in vitro test systems to capture effects on important areas of the TH system. Furthermore, we will elaborate on important species differences in TH system disruption by incorporating non-mammalian vertebrate test species alongside classical laboratory rat species and human-derived in vitro assays.
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Affiliation(s)
- Louise Ramhøj
- Research Group for Molecular and Reproductive Toxicology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marta Axelstad
- Research Group for Molecular and Reproductive Toxicology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Yoni Baert
- Department In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel, Jette, Belgium
| | - Ana I. Cañas-Portilla
- Environmental Toxicology Unit from National Center for Environmental Health (CNSA), Endocrine Tumor Unit from UFIEC, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), Rennes, France
| | - Lars Dahmen
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Antonio De La Vieja
- Environmental Toxicology Unit from National Center for Environmental Health (CNSA), Endocrine Tumor Unit from UFIEC, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), Rennes, France
| | - Ann-Cathrin Haigis
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Timo Hamers
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Kim Heikamp
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Centre for Health Protection (GZB), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Henrik Holbech
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Patricia Iglesias-Hernandez
- Environmental Toxicology Unit from National Center for Environmental Health (CNSA), Endocrine Tumor Unit from UFIEC, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Dries Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Lorna Marchandise
- Department In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel, Jette, Belgium
| | - Jane E. Morthorst
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Nikolai Georgiev Nikolov
- Group for Chemical Risk Assessment and GMO, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ana C. V. E. Nissen
- Group for Chemical Risk Assessment and GMO, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael Oelgeschlaeger
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Kostja Renko
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Vera Rogiers
- Department In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel, Jette, Belgium
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Evelyn Stinckens
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Mette H. Stub
- Research Group for Molecular and Reproductive Toxicology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Monica Torres-Ruiz
- Environmental Toxicology Unit from National Center for Environmental Health (CNSA), Endocrine Tumor Unit from UFIEC, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Majorie Van Duursen
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Tamara Vanhaecke
- Department In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel, Jette, Belgium
| | - Lucia Vergauwen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Eva Bay Wedebye
- Group for Chemical Risk Assessment and GMO, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Terje Svingen
- Research Group for Molecular and Reproductive Toxicology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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12
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Brescia S, Alexander-White C, Li H, Cayley A. Risk assessment in the 21st century: where are we heading? Toxicol Res (Camb) 2023; 12:1-11. [PMID: 36866215 PMCID: PMC9972812 DOI: 10.1093/toxres/tfac087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023] Open
Abstract
Reliance on animal tests for chemical safety assessment is increasingly being challenged, not only because of ethical reasons, but also because they procrastinate regulatory decisions and because of concerns over the transferability of results to humans. New approach methodologies (NAMs) need to be fit for purpose and new thinking is required to reconsider chemical legislation, validation of NAMs and opportunities to move away from animal tests. This article summarizes the presentations from a symposium at the 2022 Annual Congress of the British Toxicology Society on the topic of the future of chemical risk assessment in the 21st century. The symposium included three case-studies where NAMs have been used in safety assessments. The first case illustrated how read-across augmented with some in vitro tests could be used reliably to perform the risk assessment of analogues lacking data. The second case showed how specific bioactivity assays could identify an NAM point of departure (PoD) and how this could be translated through physiologically based kinetic modelling in an in vivo PoD for the risk assessment. The third case showed how adverse-outcome pathway (AOP) information, including molecular-initiating event and key events with their underlying data, established for certain chemicals could be used to produce an in silico model that is able to associate chemical features of an unstudied substance with specific AOPs or AOP networks. The manuscript presents the discussions that took place regarding the limitations and benefits of these new approaches, and what are the barriers and the opportunities for their increased use in regulatory decision making.
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Affiliation(s)
- Susy Brescia
- Health & Safety Executive, Chemicals Regulation Division, Redgrave Court, Merton Road, Bootle, Merseyside L20 7HS, UK
| | | | - Hequn Li
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Alex Cayley
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11, 5PS, UK
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13
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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. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 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] [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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14
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Zhang Q, Taniguchi S, So K, Tsuda M, Higuchi Y, Hashida M, Yamashita F. CREB is a potential marker associated with drug-induced liver injury: Identification and validation through transcriptome database analysis. J Toxicol Sci 2022; 47:337-348. [PMID: 35922923 DOI: 10.2131/jts.47.337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Drug-induced liver injury (DILI) is the main cause of failure in drug development and postapproval withdrawal. Although toxicogenomic techniques provide an unprecedented opportunity for mechanistic assessment and biomarker discovery, they are not suitable for the screening of large numbers of exploratory compounds in early drug discovery. Using a comprehensive analysis of toxicogenomics (TGx) data, we aimed to find DILI-relevant transcription factors (TFs) that could be incorporated into a reporter gene assay system. Gene set enrichment analysis (GSEA) of the Open TG-GATEs dataset highlighted 4 DILI-relevant TFs, including CREB, NRF2, ELK-1, and E2F. Using ten drugs with already assigned idiosyncratic toxicity (IDT) risks, reporter gene assays were conducted in HepG2 cells in the presence of the S9 mix. There were weak correlations between NRF2 activity and IDT risk, whereas strong correlations were observed between CREB activity and IDT risk. In addition, CREB activation associated with 3 Withdrawn/Black box Warning drugs was reversed by pretreatment with a PKA inhibitor. Collectively, we suggest that CREB might be a sensitive biomarker for DILI prediction, and its response to stress induced by high-risk drugs might be primarily regulated by the PKA/CREB signaling pathway.
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Affiliation(s)
- Qiyue Zhang
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Shiori Taniguchi
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Kanako So
- Department of Applied Pharmaceutics and Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Masahiro Tsuda
- Department of Applied Pharmaceutics and Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Yuriko Higuchi
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Mitsuru Hashida
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Fumiyoshi Yamashita
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University.,Department of Applied Pharmaceutics and Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyoto University
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15
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de Bruijn VMP, Rietjens IMCM, Bouwmeester H. Population pharmacokinetic model to generate mechanistic insights in bile acid homeostasis and drug-induced cholestasis. Arch Toxicol 2022; 96:2717-2730. [PMID: 35876888 PMCID: PMC9352636 DOI: 10.1007/s00204-022-03345-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/14/2022] [Indexed: 12/05/2022]
Abstract
Bile acids (BA) fulfill a wide range of physiological functions, but are also involved in pathologies, such as cholestasis. Cholestasis is characterized by an intrahepatic accumulation of BAs and subsequent spillage to the systemic circulation. The aim of the present study was to develop physiologically based kinetic (PBK) models that would provide a tool to predict dose-dependent BA accumulation in humans upon treatment with a Bile Salt Export Pump (BSEP) inhibitor. We developed a PBK model describing the BA homeostasis using glycochenodeoxycholic acid as an exemplary BA. Population wide distributions of BSEP abundances were incorporated in the PBK model using Markov Chain Monte Carlo simulations, and alternatively the total amount of BAs was scaled empirically to describe interindividual differences in plasma BA levels. Next, the effects of the BSEP inhibitor bosentan on the BA levels were simulated. The PBK model developed adequately predicted the in vivo BA dynamics. Both the Markov Chain Monte Carlo simulations based on a distribution of BSEP abundances and empirical scaling of the total BA pool readily described the variations within and between data in human volunteers. Bosentan treatment disproportionally increased the maximum BA concentration in individuals with a large total BA pool or low BSEP abundance. Especially individuals having a large total BA pool size and a low BSEP abundance were predicted to be at risk for rapid saturation of BSEP and subsequent intrahepatic BA accumulation. This model provides a first estimate of personalized safe therapeutic external dose levels of compounds with BSEP-inhibitory properties.
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Affiliation(s)
- Véronique M P de Bruijn
- Division of Toxicology, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands.
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands
| | - Hans Bouwmeester
- Division of Toxicology, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands
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16
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Pogrmic-Majkic K, Samardzija Nenadov D, Tesic B, Fa Nedeljkovic S, Kokai D, Stanic B, Andric N. Mapping DEHP to the adverse outcome pathway network for human female reproductive toxicity. Arch Toxicol 2022; 96:2799-2813. [PMID: 35790550 PMCID: PMC9352620 DOI: 10.1007/s00204-022-03333-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/15/2022] [Indexed: 01/09/2023]
Abstract
Adverse outcome pathways (AOPs) and AOP networks are tools for mechanistic presentation of toxicological effects across different levels of biological organization. These tools are used to better understand how chemicals impact human health. In this study, a four-step workflow was used to derive the AOP network of human female reproductive toxicity (HFRT-AOP) from five AOPs available in the AOP-Wiki and ten AOPs obtained from the literature. Standard network analysis identified key events (KEs) that are point of convergence and divergence, upstream and downstream KEs, and bottlenecks across the network. To map di-(2-ethylhexyl) phthalate (DEHP) to the HFRT-AOP network, we extracted DEHP target genes and proteins from the Comparative Toxicogenomic and the CompTox Chemicals Dashboard databases. Enriched GO terms analysis was used to identify relevant biological processes in the ovary that are DEHP targets, whereas screening of scientific literature was performed manually and automatically using AOP-helpFinder. We combined this information to map DEHP to HFRT-AOP network to provide insight on the KEs and system-level perturbations caused by this endocrine disruptor and the emergent paths. This approach can enable better understanding of the toxic mechanism of DEHP-induced human female reproductive toxicity and reveal potential novel DEHP female reproductive targets for experimental studies.
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Affiliation(s)
- Kristina Pogrmic-Majkic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 2, 21000, Novi Sad, Serbia.
| | - Dragana Samardzija Nenadov
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 2, 21000, Novi Sad, Serbia
| | - Biljana Tesic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 2, 21000, Novi Sad, Serbia
| | - Svetlana Fa Nedeljkovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 2, 21000, Novi Sad, Serbia
| | - Dunja Kokai
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 2, 21000, Novi Sad, Serbia
| | - Bojana Stanic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 2, 21000, Novi Sad, Serbia
| | - Nebojsa Andric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 2, 21000, Novi Sad, Serbia
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17
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Ravichandran J, Karthikeyan BS, Samal A. Investigation of a derived adverse outcome pathway (AOP) network for endocrine-mediated perturbations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154112. [PMID: 35219661 DOI: 10.1016/j.scitotenv.2022.154112] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/18/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
An adverse outcome pathway (AOP) is a compact representation of the available mechanistic information on observed adverse effects upon environmental exposure. Sharing of events across individual AOPs has led to the emergence of AOP networks. Since AOP networks are expected to be functional units of toxicity prediction, there is current interest in their development tailored to specific research question or regulatory problem. To this end, we have developed a detailed workflow to construct an endocrine-relevant AOP (ED-AOP) network based on the existing information available in AOP-Wiki. We propose a cumulative weight of evidence (WoE) score for each ED-AOP based on the WoE scores assigned to key event relationships (KERs) by AOP-Wiki, revealing gaps in AOP development. Connectivity analysis of the ED-AOP network comprising 48 AOPs reveals 7 connected components and 12 isolated AOPs. Subsequently, we apply standard network measures to perform an in-depth analysis of the two largest connected components of the ED-AOP network. Notably, the graph-theoretic analyses led to the identification of important events including points of convergence or divergence in the ED-AOP network. These findings can suggest potential adverse outcomes and facilitate the development of new endpoints or assays for chemical risk assessment. Detailed analysis of the largest component in the ED-AOP network gives insights on the systems-level perturbations caused by endocrine disruption, emergent paths, and stressor-event associations. In sum, the derived ED-AOP network can provide a broader view of the biological events disrupted by endocrine disruption, as well as facilitate better risk assessment of environmental chemicals.
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Affiliation(s)
- Janani Ravichandran
- The Institute of Mathematical Sciences (IMSc), Chennai 600113, India; Homi Bhabha National Institute (HBNI), Mumbai 400094, India
| | | | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai 600113, India; Homi Bhabha National Institute (HBNI), Mumbai 400094, India.
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18
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de Bruijn VMP, Wang Z, Bakker W, Zheng W, Spee B, Bouwmeester H. Hepatic bile acid synthesis and secretion: Comparison of in vitro methods. Toxicol Lett 2022; 365:46-60. [PMID: 35724847 DOI: 10.1016/j.toxlet.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/30/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022]
Abstract
Reliable hepatic in vitro systems are crucial for the safety assessment of xenobiotics. Certain xenobiotics decrease the hepatic bile efflux, which can ultimately result in cholestasis. Preclinical animal models and the currently available in vitro systems poorly predict a xenobiotic's cholestatic potential. Here, we compared the phenotype and capacity of three liver derived in vitro systems to emulate human functionality to synthesize and secrete bile acids (BAs). To this end, basal BA production of sandwich cultured human hepatocytes (SCHHs), HepaRG cells (HepaRGs) and hepatocyte-like intrahepatic cholangiocyte organoids (ICO-heps) were analysed, and the effect of the known BSEP (Bile Salt Export Pump)-inhibitors bosentan and lopinavir on BA disposition in SCHHs and HepaRGs was quantified. RT-qPCR of selected target genes involved in maturation status, synthesis, transport and conjugation of BAs was performed to mechanistically underpin the observed differences in BA homeostasis. ICO-heps produced a (very) low amount of BAs. SCHHs are a powerful tool in cholestasis-testing due to their high basal BA production and high transporter expression compared to the other models tested. HepaRGs were responsive to both selected BSEP-inhibitors and produced a BA profile that is most similar to the human in vivo situation, making them a suitable and practical candidate for cholestasis-testing.
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Affiliation(s)
| | - Zhenguo Wang
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands; Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Wouter Bakker
- Division of Toxicology, Wageningen University & Research, the Netherlands
| | - Weijia Zheng
- Division of Toxicology, Wageningen University & Research, the Netherlands
| | - Bart Spee
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Hans Bouwmeester
- Division of Toxicology, Wageningen University & Research, the Netherlands
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19
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Sonawane A, Vadloori B, Poosala S, Kandarova H, Kulkarni M, Olayanju A, Dey T, Saxena U, Smirnova L, Kanda Y, Reddy J, Dravida S, Biswas S, Vinken M, Gettayacamin M, Ahluwalia A, Mondini F, Bhattacharya S, Kulkarni P, Jacobsen KR, Vangala S, Millás AL. Advances in Animal Models and Cutting-Edge Research in Alternatives: Proceedings of the Second International Conference on 3Rs Research and Progress, Hyderabad, 2021. Altern Lab Anim 2022; 50:156-171. [PMID: 35410493 DOI: 10.1177/02611929221089216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The fact that animal models fail to replicate human disease faithfully is now being widely accepted by researchers across the globe. As a result, they are exploring the use of alternatives to animal models. The time has come to refine our experimental practices, reduce the numbers and eventually replace the animals used in research with human-derived and human-relevant 3-D disease models. Oncoseek Bio-Acasta Health, which is an innovative biotechnology start-up company based in Hyderabad and Vishakhapatnam, India, organises an annual International Conference on 3Rs Research and Progress. In 2021, this conference was on 'Advances in Research Animal Models and Cutting-Edge Research in Alternatives'. This annual conference is a platform that brings together eminent scientists and researchers from various parts of the world, to share recent advances from their research in the field of alternatives to animals including new approach methodologies, and to promote practices to help refine animal experiments where alternatives are not available. This report presents the proceedings of the conference, which was held in hybrid mode (i.e. virtual and in-person) in November 2021.
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Affiliation(s)
| | | | | | - Helena Kandarova
- Centre of Experimental Medicine, Slovak Academy of Science, Slovakia
| | | | | | - Tuli Dey
- Savitribai Phule Pune University, India
| | | | - Lena Smirnova
- Johns Hopkins Bloomberg School of Public Health, USA
| | | | | | | | | | | | - Montip Gettayacamin
- Association for Accreditation of Laboratory Animal Care (AAALAC international), USA
| | - Arti Ahluwalia
- University of Pisa, and Interuniversity Center for the Promotion of 3Rs Principles in Teaching and Research (Centro 3R), Italy
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20
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Rajagopal R, Baltazar MT, Carmichael PL, Dent MP, Head J, Li H, Muller I, Reynolds J, Sadh K, Simpson W, Spriggs S, White A, Kukic P. Beyond AOPs: A Mechanistic Evaluation of NAMs in DART Testing. FRONTIERS IN TOXICOLOGY 2022; 4:838466. [PMID: 35295212 PMCID: PMC8915803 DOI: 10.3389/ftox.2022.838466] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
New Approach Methodologies (NAMs) promise to offer a unique opportunity to enable human-relevant safety decisions to be made without the need for animal testing in the context of exposure-driven Next Generation Risk Assessment (NGRA). Protecting human health against the potential effects a chemical may have on embryo-foetal development and/or aspects of reproductive biology using NGRA is particularly challenging. These are not single endpoint or health effects and risk assessments have traditionally relied on data from Developmental and Reproductive Toxicity (DART) tests in animals. There are numerous Adverse Outcome Pathways (AOPs) that can lead to DART, which means defining and developing strict testing strategies for every AOP, to predict apical outcomes, is neither a tenable goal nor a necessity to ensure NAM-based safety assessments are fit-for-purpose. Instead, a pragmatic approach is needed that uses the available knowledge and data to ensure NAM-based exposure-led safety assessments are sufficiently protective. To this end, the mechanistic and biological coverage of existing NAMs for DART were assessed and gaps to be addressed were identified, allowing the development of an approach that relies on generating data relevant to the overall mechanisms involved in human reproduction and embryo-foetal development. Using the knowledge of cellular processes and signalling pathways underlying the key stages in reproduction and development, we have developed a broad outline of endpoints informative of DART. When the existing NAMs were compared against this outline to determine whether they provide comprehensive coverage when integrated in a framework, we found them to generally cover the reproductive and developmental processes underlying the traditionally evaluated apical endpoint studies. The application of this safety assessment framework is illustrated using an exposure-led case study.
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