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Liu W, Wang Z, Chen J, Tang W, Wang H. Machine Learning Model for Screening Thyroid Stimulating Hormone Receptor Agonists Based on Updated Datasets and Improved Applicability Domain Metrics. Chem Res Toxicol 2023. [PMID: 37209109 DOI: 10.1021/acs.chemrestox.3c00074] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Machine learning (ML) models for screening endocrine-disrupting chemicals (EDCs), such as thyroid stimulating hormone receptor (TSHR) agonists, are essential for sound management of chemicals. Previous models for screening TSHR agonists were built on imbalanced datasets and lacked applicability domain (AD) characterization essential for regulatory application. Herein, an updated TSHR agonist dataset was built, for which the ratio of active to inactive compounds greatly increased to 1:2.6, and chemical spaces of structure-activity landscapes (SALs) were enhanced. Resulting models based on 7 molecular representations and 4 ML algorithms were proven to outperform previous ones. Weighted similarity density (ρs) and weighted inconsistency of activities (IA) were proposed to characterize the SALs, and a state-of-the-art AD characterization methodology ADSAL{ρs, IA} was established. An optimal classifier developed with PubChem fingerprints and the random forest algorithm, coupled with ADSAL{ρs ≥ 0.15, IA ≤ 0.65}, exhibited good performance on the validation set with the area under the receiver operating characteristic curve being 0.984 and balanced accuracy being 0.941 and identified 90 TSHR agonist classes that could not be found previously. The classifier together with the ADSAL{ρs, IA} may serve as efficient tools for screening EDCs, and the AD characterization methodology may be applied to other ML models.
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Affiliation(s)
- Wenjia Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhongyu Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Weihao Tang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Haobo Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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Simond AE, Houde M, Lesage V, Michaud R, Zbinden D, Verreault J. Associations between organohalogen exposure and thyroid- and steroid-related gene responses in St. Lawrence Estuary belugas and minke whales. MARINE POLLUTION BULLETIN 2019; 145:174-184. [PMID: 31590774 DOI: 10.1016/j.marpolbul.2019.05.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 05/12/2019] [Accepted: 05/13/2019] [Indexed: 06/10/2023]
Abstract
Elevated concentrations of persistent organic pollutants (POPs) and emerging halogenated flame retardants (HFRs) have been reported in tissues of the endangered St. Lawrence Estuary (Canada) beluga population as well as in minke whales visiting that same feeding area. This study examined the linkages between blubber concentrations of POPs and emerging HFRs, and transcription in skin of genes involved in the regulation of thyroid and steroid axes in belugas and minke whales from the St. Lawrence Estuary. In belugas, concentrations of PCBs, OCs and hexabromobenzene (HBB) were positively correlated with the transcription of thyroid- and/or steroid-related genes, while Dec-604 CB concentrations were negatively associated with the transcription of glucocorticoid and thyroid genes. In minke whales, PBDE concentrations changed positively with Esrβ transcript levels and HBB concentrations negatively with Nr3c1 transcripts. Present results suggest that several biological functions including reproduction and energetic metabolism may represent potential targets for organohalogens in these whales.
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Affiliation(s)
- Antoine E Simond
- Centre de recherche en toxicologie de l'environnement (TOXEN), Département des sciences biologiques, Université du Québec à Montréal, P.O. Box 8888, Succursale Centre-ville, Montreal, QC H3C 3P8, Canada
| | - Magali Houde
- Environment and Climate Change Canada, 105 McGill Street, Montreal, QC H2Y 2E7, Canada
| | - Véronique Lesage
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, P.O. Box 1000, 850 route de la Mer, Mont-Joli, QC G5H 3Z4, Canada
| | - Robert Michaud
- Groupe de Recherche et d'Éducation sur les Mammifères Marins (GREMM), 870 avenue Salaberry, Bureau R24, Québec, QC G1R 2T9, Canada
| | - Dany Zbinden
- Mériscope, 833 rue du Quai, Portneuf-sur-Mer, QC G0T 1P0, Canada
| | - Jonathan Verreault
- Centre de recherche en toxicologie de l'environnement (TOXEN), Département des sciences biologiques, Université du Québec à Montréal, P.O. Box 8888, Succursale Centre-ville, Montreal, QC H3C 3P8, Canada.
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Rossi M, Taddei AR, Fasciani I, Maggio R, Giorgi F. The cell biology of the thyroid-disrupting mechanism of dichlorodiphenyltrichloroethane (DDT). J Endocrinol Invest 2018. [PMID: 28639207 DOI: 10.1007/s40618-017-0716-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Dichlorodiphenyltrichloroethane (DDT) is an organochlorine known for its pesticide properties and for its negative effects on human health. It was banned in most countries for its toxicity to the endocrine system, but due to its persistence at clinically relevant concentrations in both soil and animal tissues, DDT is still linked to several health and social problems. METHODS We have previously shown that DDT exposure is causally related to the extracellular release of vesicular organelles such as microvesicles and/or exosomes by using immunocytochemistry with gold-tagged antibodies and various fluorescent membrane markers. RESULTS It is now well recognized that microvesicles and/or exosomes organelles are implicated in cell-to-cell communication, and that they are fundamental elements for transferring proteins, RNA, DNA, lipids and transcriptional factors among cells. In this short review, we discussed the role of extracellular vesicle formation in the thyroid-disrupting mechanism of DDT. In particular, we described how DDT, by dislodging the thyrotropin hormone (TSH) receptor from the raft containing compartments of the cells, prevents its activation and internalization. CONCLUSION Based on our earlier finding and on the large body of evidence here reviewed, we propose that DDT-induced formation of extracellular vesicles containing the TSH receptor could be directly involved in the development of autoimmune responses against the TSH receptor and that, therefore, their release could lead to the development of the Graves' disease.
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Affiliation(s)
- M Rossi
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - A R Taddei
- Section of Electron Microscopy, Great Equipment Center, University of Tuscia, Viterbo, Italy
| | - I Fasciani
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - R Maggio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - F Giorgi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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Leto K, Arancillo M, Becker EBE, Buffo A, Chiang C, Ding B, Dobyns WB, Dusart I, Haldipur P, Hatten ME, Hoshino M, Joyner AL, Kano M, Kilpatrick DL, Koibuchi N, Marino S, Martinez S, Millen KJ, Millner TO, Miyata T, Parmigiani E, Schilling K, Sekerková G, Sillitoe RV, Sotelo C, Uesaka N, Wefers A, Wingate RJT, Hawkes R. Consensus Paper: Cerebellar Development. CEREBELLUM (LONDON, ENGLAND) 2016; 15:789-828. [PMID: 26439486 PMCID: PMC4846577 DOI: 10.1007/s12311-015-0724-2] [Citation(s) in RCA: 250] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The development of the mammalian cerebellum is orchestrated by both cell-autonomous programs and inductive environmental influences. Here, we describe the main processes of cerebellar ontogenesis, highlighting the neurogenic strategies used by developing progenitors, the genetic programs involved in cell fate specification, the progressive changes of structural organization, and some of the better-known abnormalities associated with developmental disorders of the cerebellum.
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Affiliation(s)
- Ketty Leto
- Department of Neuroscience Rita Levi Montalcini, University of Turin, via Cherasco 15, 10026, Turin, Italy.
- Neuroscience Institute Cavalieri-Ottolenghi, University of Turin, Regione Gonzole 10, 10043, Orbassano, Torino, Italy.
| | - Marife Arancillo
- Departments of Pathology & Immunology and Neuroscience, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Esther B E Becker
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Annalisa Buffo
- Department of Neuroscience Rita Levi Montalcini, University of Turin, via Cherasco 15, 10026, Turin, Italy
- Neuroscience Institute Cavalieri-Ottolenghi, University of Turin, Regione Gonzole 10, 10043, Orbassano, Torino, Italy
| | - Chin Chiang
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, 4114 MRB III, Nashville, TN, 37232, USA
| | - Baojin Ding
- Department of Microbiology and Physiological Systems and Program in Neuroscience, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-2324, USA
| | - William B Dobyns
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, USA
- Department of Pediatrics, Genetics Division, University of Washington, Seattle, WA, USA
| | - Isabelle Dusart
- Sorbonne Universités, Université Pierre et Marie Curie Univ Paris 06, Institut de Biologie Paris Seine, France, 75005, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR8246, INSERM U1130, Neuroscience Paris Seine, France, 75005, Paris, France
| | - Parthiv Haldipur
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, USA
| | - Mary E Hatten
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, 10065, USA
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Daniel L Kilpatrick
- Department of Microbiology and Physiological Systems and Program in Neuroscience, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-2324, USA
| | - Noriyuki Koibuchi
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Salvador Martinez
- Department Human Anatomy, IMIB-Arrixaca, University of Murcia, Murcia, Spain
| | - Kathleen J Millen
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, USA
| | - Thomas O Millner
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Takaki Miyata
- Department of Anatomy and Cell Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Elena Parmigiani
- Department of Neuroscience Rita Levi Montalcini, University of Turin, via Cherasco 15, 10026, Turin, Italy
- Neuroscience Institute Cavalieri-Ottolenghi, University of Turin, Regione Gonzole 10, 10043, Orbassano, Torino, Italy
| | - Karl Schilling
- Anatomie und Zellbiologie, Anatomisches Institut, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Gabriella Sekerková
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Roy V Sillitoe
- Departments of Pathology & Immunology and Neuroscience, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Constantino Sotelo
- Institut de la Vision, UPMC Université de Paris 06, Paris, 75012, France
| | - Naofumi Uesaka
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Annika Wefers
- Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
| | - Richard J T Wingate
- MRC Centre for Developmental Neurobiology, King's College London, London, UK
| | - Richard Hawkes
- Department of Cell Biology & Anatomy and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, T2N 4NI, AB, Canada
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