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Negi R, Srivastava A, Srivastava AK, Vatsa P, Ansari UA, Khan B, Singh H, Pandeya A, Pant AB. Proteomic-miRNA Biomics Profile Reveals 2D Cultures of Human iPSC-Derived Neural Progenitor Cells More Sensitive than 3D Spheroid System Against the Experimental Exposure to Arsenic. Mol Neurobiol 2024; 61:5754-5770. [PMID: 38228842 DOI: 10.1007/s12035-024-03924-z] [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: 10/30/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
The iPSC-derived 3D models are considered to be a connective link between 2D culture and in vivo studies. However, the sensitivity of such 3D models is yet to be established. We assessed the sensitivity of the hiPSC-derived 3D spheroids against 2D cultures of neural progenitor cells. The sub-toxic dose of Sodium Arsenite (SA) was used to investigate the alterations in miRNA-proteins in both systems. Though SA exposure induced significant alterations in the proteins in both 2D and 3D systems, these proteins were uncommon except for 20 proteins. The number and magnitude of altered proteins were higher in the 2D system compared to 3D. The association of dysregulated miRNAs with the target proteins showed their involvement primarily in mitochondrial bioenergetics, oxidative and ER stress, transcription and translation mechanism, cytostructure, etc., in both culture systems. Further, the impact of dysregulated miRNAs and associated proteins on these functions and ultrastructural changes was compared in both culture systems. The ultrastructural studies revealed a similar pattern of mitochondrial damage, while the cellular bioenergetics studies confirm a significantly higher energy failure in the 2D system than to 3D. Such a higher magnitude of changes could be correlated with a higher amount of internalization of SA in 2D cultures than in 3D spheroids. Our findings demonstrate that a 2D culture system seems better responsive than a 3D spheroid system against SA exposure.
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Affiliation(s)
- R Negi
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - A Srivastava
- Department of Biochemistry, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India
| | - A K Srivastava
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
| | - P Vatsa
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - U A Ansari
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - B Khan
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
| | - H Singh
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
| | - A Pandeya
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
| | - A B Pant
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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2
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Wang Z, Chen S, Guo Y, Zhang R, Zhang Q, Jiang X, Li M, Jiang Y, Ye L, Guo X, Li C, Zhang G, Li D, Chen L, Chen W. Intestinal carcinogenicity screening of environmental pollutants using organoid-based cell transformation assay. Arch Toxicol 2024; 98:1937-1951. [PMID: 38563870 DOI: 10.1007/s00204-024-03729-y] [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: 12/30/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
The high incidence of colorectal cancer (CRC) is closely associated with environmental pollutant exposure. To identify potential intestinal carcinogens, we developed a cell transformation assay (CTA) using mouse adult stem cell-derived intestinal organoids (mASC-IOs) and assessed the transformation potential on 14 representative chemicals, including Cd, iPb, Cr-VI, iAs-III, Zn, Cu, PFOS, BPA, MEHP, AOM, DMH, MNNG, aspirin, and metformin. We optimized the experimental protocol based on cytotoxicity, amplification, and colony formation of chemical-treated mASC-IOs. In addition, we assessed the accuracy of in vitro study and the human tumor relevance through characterizing interdependence between cell-cell and cell-matrix adhesions, tumorigenicity, pathological feature of subcutaneous tumors, and CRC-related molecular signatures. Remarkably, the results of cell transformation in 14 chemicals showed a strong concordance with epidemiological findings (8/10) and in vivo mouse studies (12/14). In addition, we found that the increase in anchorage-independent growth was positively correlated with the tumorigenicity of tested chemicals. Through analyzing the dose-response relationship of anchorage-independent growth by benchmark dose (BMD) modeling, the potent intestinal carcinogens were identified, with their carcinogenic potency ranked from high to low as AOM, Cd, MEHP, Cr-VI, iAs-III, and DMH. Importantly, the activity of chemical-transformed mASC-IOs was associated with the degree of cellular differentiation of subcutaneous tumors, altered transcription of oncogenic genes, and activated pathways related to CRC development, including Apc, Trp53, Kras, Pik3ca, Smad4 genes, as well as WNT and BMP signaling pathways. Taken together, we successfully developed a mASC-IO-based CTA, which might serve as a potential alternative for intestinal carcinogenicity screening of chemicals.
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Affiliation(s)
- Ziwei Wang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
- Stony Brook Cancer Center, Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA
| | - Shen Chen
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Yuzhi Guo
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Rui Zhang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Qi Zhang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Xinhang Jiang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Miao Li
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Yue Jiang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Lizhu Ye
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Xiaoyu Guo
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Chuang Li
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Guangtong Zhang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Daochuan Li
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Liping Chen
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Wen Chen
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China.
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Han X, Cai C, Deng W, Shi Y, Li L, Wang C, Zhang J, Rong M, Liu J, Fang B, He H, Liu X, Deng C, He X, Cao X. Landscape of human organoids: Ideal model in clinics and research. Innovation (N Y) 2024; 5:100620. [PMID: 38706954 PMCID: PMC11066475 DOI: 10.1016/j.xinn.2024.100620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
In the last decade, organoid research has entered a golden era, signifying a pivotal shift in the biomedical landscape. The year 2023 marked a milestone with the publication of thousands of papers in this arena, reflecting exponential growth. However, amid this burgeoning expansion, a comprehensive and accurate overview of the field has been conspicuously absent. Our review is intended to bridge this gap, providing a panoramic view of the rapidly evolving organoid landscape. We meticulously analyze the organoid field from eight distinctive vantage points, harnessing our rich experience in academic research, industrial application, and clinical practice. We present a deep exploration of the advances in organoid technology, underpinned by our long-standing involvement in this arena. Our narrative traverses the historical genesis of organoids and their transformative impact across various biomedical sectors, including oncology, toxicology, and drug development. We delve into the synergy between organoids and avant-garde technologies such as synthetic biology and single-cell omics and discuss their pivotal role in tailoring personalized medicine, enhancing high-throughput drug screening, and constructing physiologically pertinent disease models. Our comprehensive analysis and reflective discourse provide a deep dive into the existing landscape and emerging trends in organoid technology. We spotlight technological innovations, methodological evolution, and the broadening spectrum of applications, emphasizing the revolutionary influence of organoids in personalized medicine, oncology, drug discovery, and other fields. Looking ahead, we cautiously anticipate future developments in the field of organoid research, especially its potential implications for personalized patient care, new avenues of drug discovery, and clinical research. We trust that our comprehensive review will be an asset for researchers, clinicians, and patients with keen interest in personalized medical strategies. We offer a broad view of the present and prospective capabilities of organoid technology, encompassing a wide range of current and future applications. In summary, in this review we attempt a comprehensive exploration of the organoid field. We offer reflections, summaries, and projections that might be useful for current researchers and clinicians, and we hope to contribute to shaping the evolving trajectory of this dynamic and rapidly advancing field.
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Affiliation(s)
- Xinxin Han
- Organ Regeneration X Lab, Lisheng East China Institute of Biotechnology, Peking University, Jiangsu 226200, China
- Shanghai Lisheng Biotech, Shanghai 200092, China
| | - Chunhui Cai
- Shanghai Lisheng Biotech, Shanghai 200092, China
| | - Wei Deng
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, 725 Wanping South Road, Xuhui District, Shanghai 200032, China
- Department of Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Yanghua Shi
- Shanghai Lisheng Biotech, Shanghai 200092, China
| | - Lanyang Li
- Shanghai Lisheng Biotech, Shanghai 200092, China
| | - Chen Wang
- Shanghai Lisheng Biotech, Shanghai 200092, China
| | - Jian Zhang
- Shanghai Lisheng Biotech, Shanghai 200092, China
| | - Mingjie Rong
- Shanghai Lisheng Biotech, Shanghai 200092, China
| | - Jiping Liu
- Shanghai Lisheng Biotech, Shanghai 200092, China
| | - Bangjiang Fang
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, 725 Wanping South Road, Xuhui District, Shanghai 200032, China
| | - Hua He
- Department of Neurosurgery, Third Affiliated Hospital, Naval Medical University, Shanghai 200438, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Chuxia Deng
- Cancer Center, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
- Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau SAR 999078, China
| | - Xiao He
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Cao
- Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Shanghai 200032, China
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Maramraju S, Kowalczewski A, Kaza A, Liu X, Singaraju JP, Albert MV, Ma Z, Yang H. AI-organoid integrated systems for biomedical studies and applications. Bioeng Transl Med 2024; 9:e10641. [PMID: 38435826 PMCID: PMC10905559 DOI: 10.1002/btm2.10641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 03/05/2024] Open
Abstract
In this review, we explore the growing role of artificial intelligence (AI) in advancing the biomedical applications of human pluripotent stem cell (hPSC)-derived organoids. Stem cell-derived organoids, these miniature organ replicas, have become essential tools for disease modeling, drug discovery, and regenerative medicine. However, analyzing the vast and intricate datasets generated from these organoids can be inefficient and error-prone. AI techniques offer a promising solution to efficiently extract insights and make predictions from diverse data types generated from microscopy images, transcriptomics, metabolomics, and proteomics. This review offers a brief overview of organoid characterization and fundamental concepts in AI while focusing on a comprehensive exploration of AI applications in organoid-based disease modeling and drug evaluation. It provides insights into the future possibilities of AI in enhancing the quality control of organoid fabrication, label-free organoid recognition, and three-dimensional image reconstruction of complex organoid structures. This review presents the challenges and potential solutions in AI-organoid integration, focusing on the establishment of reliable AI model decision-making processes and the standardization of organoid research.
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Affiliation(s)
- Sudhiksha Maramraju
- Department of Biomedical EngineeringUniversity of North TexasDentonTexasUSA
- Texas Academy of Mathematics and ScienceUniversity of North TexasDentonTexasUSA
| | - Andrew Kowalczewski
- Department of Biomedical & Chemical EngineeringSyracuse UniversitySyracuseNew YorkUSA
- BioInspired Institute for Material and Living SystemsSyracuse UniversitySyracuseNew YorkUSA
| | - Anirudh Kaza
- Department of Biomedical EngineeringUniversity of North TexasDentonTexasUSA
- Texas Academy of Mathematics and ScienceUniversity of North TexasDentonTexasUSA
| | - Xiyuan Liu
- Department of Mechanical & Aerospace EngineeringSyracuse UniversitySyracuseNew YorkUSA
| | - Jathin Pranav Singaraju
- Department of Biomedical EngineeringUniversity of North TexasDentonTexasUSA
- Texas Academy of Mathematics and ScienceUniversity of North TexasDentonTexasUSA
| | - Mark V. Albert
- Department of Biomedical EngineeringUniversity of North TexasDentonTexasUSA
- Department of Computer Science and EngineeringUniversity of North TexasDentonTexasUSA
| | - Zhen Ma
- Department of Biomedical & Chemical EngineeringSyracuse UniversitySyracuseNew YorkUSA
- BioInspired Institute for Material and Living SystemsSyracuse UniversitySyracuseNew YorkUSA
| | - Huaxiao Yang
- Department of Biomedical EngineeringUniversity of North TexasDentonTexasUSA
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Caipa Garcia AL, Kucab JE, Al-Serori H, Beck RSS, Bellamri M, Turesky RJ, Groopman JD, Francies HE, Garnett MJ, Huch M, Drost J, Zilbauer M, Arlt VM, Phillips DH. Tissue Organoid Cultures Metabolize Dietary Carcinogens Proficiently and Are Effective Models for DNA Adduct Formation. Chem Res Toxicol 2024; 37:234-247. [PMID: 38232180 PMCID: PMC10880098 DOI: 10.1021/acs.chemrestox.3c00255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
Human tissue three-dimensional (3D) organoid cultures have the potential to reproduce in vitro the physiological properties and cellular architecture of the organs from which they are derived. The ability of organoid cultures derived from human stomach, liver, kidney, and colon to metabolically activate three dietary carcinogens, aflatoxin B1 (AFB1), aristolochic acid I (AAI), and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), was investigated. In each case, the response of a target tissue (liver for AFB1; kidney for AAI; colon for PhIP) was compared with that of a nontarget tissue (gastric). After treatment cell viabilities were measured, DNA damage response (DDR) was determined by Western blotting for p-p53, p21, p-CHK2, and γ-H2AX, and DNA adduct formation was quantified by mass spectrometry. Induction of the key xenobiotic-metabolizing enzymes (XMEs) CYP1A1, CYP1A2, CYP3A4, and NQO1 was assessed by qRT-PCR. We found that organoids from different tissues can activate AAI, AFB1, and PhIP. In some cases, this metabolic potential varied between tissues and between different cultures of the same tissue. Similarly, variations in the levels of expression of XMEs were observed. At comparable levels of cytotoxicity, organoids derived from tissues that are considered targets for these carcinogens had higher levels of adduct formation than a nontarget tissue.
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Affiliation(s)
- Angela L. Caipa Garcia
- Department
of Analytical, Environmental and Forensic Sciences, School of Cancer
& Pharmaceutical Sciences, King’s
College London, London SE1 9NH, U.K.
| | - Jill E. Kucab
- Department
of Analytical, Environmental and Forensic Sciences, School of Cancer
& Pharmaceutical Sciences, King’s
College London, London SE1 9NH, U.K.
| | - Halh Al-Serori
- Department
of Analytical, Environmental and Forensic Sciences, School of Cancer
& Pharmaceutical Sciences, King’s
College London, London SE1 9NH, U.K.
| | - Rebekah S. S. Beck
- Department
of Analytical, Environmental and Forensic Sciences, School of Cancer
& Pharmaceutical Sciences, King’s
College London, London SE1 9NH, U.K.
| | - Madjda Bellamri
- Department
of Medicinal Chemistry, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert J. Turesky
- Department
of Medicinal Chemistry, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Groopman
- Department
of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | | | | | - Meritxell Huch
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jarno Drost
- Princess
Máxima Center for Pediatric Oncology, Oncode Institute, 3584
CS Utrecht, The Netherlands
| | - Matthias Zilbauer
- Department
of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, U.K.
| | - Volker M. Arlt
- Department
of Analytical, Environmental and Forensic Sciences, School of Cancer
& Pharmaceutical Sciences, King’s
College London, London SE1 9NH, U.K.
| | - David H. Phillips
- Department
of Analytical, Environmental and Forensic Sciences, School of Cancer
& Pharmaceutical Sciences, King’s
College London, London SE1 9NH, U.K.
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Nazzari M, Romitti M, Hauser D, Carvalho DJ, Giselbrecht S, Moroni L, Costagliola S, Caiment F. Investigation of the effects of phthalates on in vitro thyroid models with RNA-Seq and ATAC-Seq. Front Endocrinol (Lausanne) 2023; 14:1200211. [PMID: 37810885 PMCID: PMC10556862 DOI: 10.3389/fendo.2023.1200211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/08/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Phthalates are a class of endocrine-disrupting chemicals that have been shown to negatively correlate with thyroid hormone serum levels in humans and to cause a state of hyperactivity in the thyroid. However, their mechanism of action is not well described at the molecular level. Methods We analyzed the response of mouse thyroid organoids to the exposure to a biologically relevant dose range of the phthalates bis(2-ethylhexyl) phthalate (DEHP), di-iso-decylphthalate (DIDP), di-iso-nonylphthalate (DINP), and di-n-octylphthalate (DnOP) for 24 h and simultaneously analyzed mRNA and miRNA expression via RNA sequencing. Using the expression data, we performed differential expression and gene set enrichment analysis. We also exposed the human thyroid follicular epithelial cell line Nthy-ori 3-1 to 1 µM of DEHP or DINP for 5 days and analyzed changes in chromatin accessibility via ATAC-Seq. Results Dose-series analysis showed how the expression of several genes increased or decreased at the highest dose tested. As expected with the low dosing scheme, the compounds induced a modest response on the transcriptome, as we identified changes in only mmu-miR-143-3p after DINP treatment and very few differentially expressed genes. No effect was observed on thyroid markers. Ing5, a component of histones H3 and H4 acetylation complexes, was consistently upregulated in three out of four conditions compared to control, and we observed a partial overlap among the genes differentially expressed by the treatments. Gene set enrichment analysis showed enrichment in the treatment samples of the fatty acid metabolism pathway and in the control of pathways related to the receptor signalling and extracellular matrix organization. ATAC-Seq analysis showed a general increase in accessibility compared to the control, however we did not identify significant changes in accessibility in the identified regions. Discussion With this work, we showed that despite having only a few differentially expressed genes, diverse analysis methods could be applied to retrieve relevant information on phthalates, showing the potential of in vitro thyroid-relevant systems for the analysis of endocrine disruptors.
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Affiliation(s)
- Marta Nazzari
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Mírian Romitti
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Duncan Hauser
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Daniel J. Carvalho
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
| | - Stefan Giselbrecht
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
| | - Lorenzo Moroni
- Department of Complex Tissue Regeneration, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
| | - Sabine Costagliola
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
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Horánszky A, Shashikadze B, Elkhateib R, Lombardo SD, Lamberto F, Zana M, Menche J, Fröhlich T, Dinnyés A. Proteomics and disease network associations evaluation of environmentally relevant Bisphenol A concentrations in a human 3D neural stem cell model. Front Cell Dev Biol 2023; 11:1236243. [PMID: 37664457 PMCID: PMC10472293 DOI: 10.3389/fcell.2023.1236243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Bisphenol A (BPA) exposure is associated with a plethora of neurodevelopmental abnormalities and brain disorders. Previous studies have demonstrated BPA-induced perturbations to critical neural stem cell (NSC) characteristics, such as proliferation and differentiation, although the underlying molecular mechanisms remain under debate. The present study evaluated the effects of a repeated-dose exposure of environmentally relevant BPA concentrations during the in vitro 3D neural induction of human induced pluripotent stem cells (hiPSCs), emulating a chronic exposure scenario. Firstly, we demonstrated that our model is suitable for NSC differentiation during the early stages of embryonic brain development. Our morphological image analysis showed that BPA exposure at 0.01, 0.1 and 1 µM decreased the average spheroid size by day 21 (D21) of the neural induction, while no effect on cell viability was detected. No alteration to the rate of the neural induction was observed based on the expression of key neural lineage and neuroectodermal transcripts. Quantitative proteomics at D21 revealed several differentially abundant proteins across all BPA-treated groups with important functions in NSC proliferation and maintenance (e.g., FABP7, GPC4, GAP43, Wnt-8B, TPPP3). Additionally, a network analysis demonstrated alterations to the glycolytic pathway, potentially implicating BPA-induced changes to glycolytic signalling in NSC proliferation impairments, as well as the pathophysiology of brain disorders including intellectual disability, autism spectrum disorders, and amyotrophic lateral sclerosis (ALS). This study enhances the current understanding of BPA-related NSC aberrations based mostly on acute, often high dose exposures of rodent in vivo and in vitro models and human GWAS data in a novel human 3D cell-based model with real-life scenario relevant prolonged and low-level exposures, offering further mechanistic insights into the ramifications of BPA exposure on the developing human brain and consequently, later life neurological disorders.
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Affiliation(s)
- Alex Horánszky
- BioTalentum Ltd., Gödöllő, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Bachuki Shashikadze
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Radwa Elkhateib
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Salvo Danilo Lombardo
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Federica Lamberto
- BioTalentum Ltd., Gödöllő, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | | | - Jörg Menche
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - András Dinnyés
- BioTalentum Ltd., Gödöllő, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Department of Cell Biology and Molecular Medicine, University of Szeged, Szeged, Hungary
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Wang Z, Chen S, Pang Y, Ye L, Zhang Q, Jiang X, Zhang R, Li M, Guo Z, Jiang Y, Li D, Xing X, Chen L, Aschner M, Chen W. Morphological alterations in C57BL/6 mouse intestinal organoids as a tool for predicting chemical-induced toxicity. Arch Toxicol 2023; 97:1133-1146. [PMID: 36806895 PMCID: PMC10045874 DOI: 10.1007/s00204-023-03451-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/24/2023] [Indexed: 02/23/2023]
Abstract
Intestinal organoid may serve as an alternative model for toxicity testing. However, the linkage between specific morphological alterations in organoids and chemical-induced toxicity has yet to be defined. Here, we generated C57BL/6 mouse intestinal organoids and conducted a morphology-based analysis on chemical-induced toxicity. Alterations in morphology were characterized by large spheroids, hyperplastic organoids, small spheroids, and protrusion-loss organoids, which responded in a concentration-dependent manner to the treatment of four metal(loid)s including cadmium (Cd), lead (Pb), hexavalent chromium (Cr-VI), and inorganic trivalent arsenic (iAs-III). Notably, alterations in organoid morphology characterized by abnormal morphology rate were correlated with specific intestinal toxic effects, including reduction in cell viability and differentiation, induction of apoptosis, dysfunction of mucus production, and damage to epithelial barrier upon repeated administration. The benchmark dose (BMDL10) values of morphological alterations (0.007-0.195 μM) were lower than those of conventional bioassays (0.010-0.907 μM). We also established that the morphologic features of organoids upon Cd, Pb, Cr-VI, or iAs-III treatment were metal specific, and mediated by Wnt, bone morphogenetic protein, apoptosis induction, and Notch signaling pathways, respectively. Collectively, these findings provide novel insights into the relevance of morphological alterations in organoids to specific toxic endpoints and identify specific morphological alterations as potential indicators of enterotoxicity.
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Affiliation(s)
- Ziwei Wang
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Shen Chen
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Yaqin Pang
- Faculty of Toxicology, School of Public Health, Youjiang Medical College for Nationalities, Guangxi, China
| | - Lizhu Ye
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Qi Zhang
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Xinhang Jiang
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Rui Zhang
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Miao Li
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Zhanyu Guo
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Yue Jiang
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Daochuan Li
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Xiumei Xing
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Liping Chen
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Wen Chen
- Department of Toxicology, School of Public Health, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou, 510080, China.
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Park SB, Jung WH, Choi KJ, Koh B, Kim KY. A Comparative Systematic Analysis of The Influence of Microplastics on Colon Cells, Mouse and Colon Organoids. Tissue Eng Regen Med 2023; 20:49-58. [PMID: 36374371 PMCID: PMC9852409 DOI: 10.1007/s13770-022-00496-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Microplastics (MPs) are small fragments from any type of plastic formed from various sources, including plastic waste and microfibers from clothing. MPs degrades slowly, resulting in a high probability of human inhalation, ingestion and accumulation in bodies and tissues. As its impact on humans is a prolonged event, the evaluation of its toxicity and influence on human health are critical. In particular, MPs can enter the human digestive system through food and beverage consumption, and its effect on the human colon needs to be carefully examined. METHODS We monitored the influence of small MPs (50 and 100 nm) on human colon cells, human colon organoids and also examined their toxicity and changes in gene expression in vivo in a mouse model. RESULTS The data suggested that 5 mg/mL concentrations of 50 and 100 nm MPs induced a > 20% decrease in colon organoid viability and an increase in the expression of inflammatory-, apoptosis- and immunity-related genes. In addition, in vivo data suggested that 50 nm MPs accumulate in various mouse organs, including the colon, liver, pancreas and testicles after 7 d of exposure. CONCLUSION Taken together, our data suggest that smaller MPs can induce more toxic effects in the human colon and that human colon organoids have the potential to be used as a predictive tool for colon toxicity.
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Affiliation(s)
- Sung Bum Park
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Won Hoon Jung
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Kyoung Jin Choi
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Byumseok Koh
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea.
| | - Ki Young Kim
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea.
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10
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Park SB, Kim EA, Kim KY, Koh B. Induction of toxicity in human colon cells and organoids by size- and composition-dependent road dust. RSC Adv 2023; 13:2833-2840. [PMID: 36756445 PMCID: PMC9845984 DOI: 10.1039/d2ra07500h] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Environmental pollution, including the annual resurgence of particulate matter derived from road dust, is a serious issue worldwide. Typically, the size of road dust is less than 10 μm; thus, road dust can penetrate into human organs, including the brain, through inhalation and intake by mouth. Therefore, the toxicity of road dust has been intensively studied in vitro and in vivo. However, in vitro systems, including 2D cell cultures, cannot mimic complex human organs, and there are several discrepancies between in vivo and human systems. Here, we used human colon cells and organoids to evaluate the cytotoxicity of particulate matter derived from road dust. The toxicity of road dust collected in industrialized and high traffic areas and NIST urban particulate matter reference samples were evaluated in 2D and 3D human colon cells as well as colon organoids and their characteristics were carefully examined. Data suggest that the size and elemental compositions of road dust can correlate with colon organoid toxicity, and thus, a more careful assessment of the size and elemental compositions of road dust should be conducted to predict its effect on human health.
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Affiliation(s)
- Sung Bum Park
- Biotechnology and Therapeutics Division, Korea Research Institute of Chemical Technology 141 Gajeong-ro, Yuseong-gu Daejeon 34114 Republic of Korea
| | - Eun-Ah Kim
- National Assembly Futures InstituteMembers Office Bldg, 1 Uisadang-daero, Yeongdeungpo-guSeoul07233Republic of Korea
| | - Ki Young Kim
- Biotechnology and Therapeutics Division, Korea Research Institute of Chemical Technology 141 Gajeong-ro, Yuseong-gu Daejeon 34114 Republic of Korea
| | - Byumseok Koh
- Biotechnology and Therapeutics Division, Korea Research Institute of Chemical Technology 141 Gajeong-ro, Yuseong-gu Daejeon 34114 Republic of Korea
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11
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Caipa Garcia AL, Kucab JE, Al-Serori H, Beck RSS, Fischer F, Hufnagel M, Hartwig A, Floeder A, Balbo S, Francies H, Garnett M, Huch M, Drost J, Zilbauer M, Arlt VM, Phillips DH. Metabolic Activation of Benzo[ a]pyrene by Human Tissue Organoid Cultures. Int J Mol Sci 2022; 24:ijms24010606. [PMID: 36614051 PMCID: PMC9820386 DOI: 10.3390/ijms24010606] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Organoids are 3D cultures that to some extent reproduce the structure, composition and function of the mammalian tissues from which they derive, thereby creating in vitro systems with more in vivo-like characteristics than 2D monocultures. Here, the ability of human organoids derived from normal gastric, pancreas, liver, colon and kidney tissues to metabolise the environmental carcinogen benzo[a]pyrene (BaP) was investigated. While organoids from the different tissues showed varied cytotoxic responses to BaP, with gastric and colon organoids being the most susceptible, the xenobiotic-metabolising enzyme (XME) genes, CYP1A1 and NQO1, were highly upregulated in all organoid types, with kidney organoids having the highest levels. Furthermore, the presence of two key metabolites, BaP-t-7,8-dihydrodiol and BaP-tetrol-l-1, was detected in all organoid types, confirming their ability to metabolise BaP. BaP bioactivation was confirmed both by the activation of the DNA damage response pathway (induction of p-p53, pCHK2, p21 and γ-H2AX) and by DNA adduct formation. Overall, pancreatic and undifferentiated liver organoids formed the highest levels of DNA adducts. Colon organoids had the lowest responses in DNA adduct and metabolite formation, as well as XME expression. Additionally, high-throughput RT-qPCR explored differences in gene expression between organoid types after BaP treatment. The results demonstrate the potential usefulness of organoids for studying environmental carcinogenesis and genetic toxicology.
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Affiliation(s)
- Angela L. Caipa Garcia
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, King’s College London, London SE1 9NH, UK
| | - Jill E. Kucab
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, King’s College London, London SE1 9NH, UK
| | - Halh Al-Serori
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, King’s College London, London SE1 9NH, UK
| | - Rebekah S. S. Beck
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, King’s College London, London SE1 9NH, UK
| | - Franziska Fischer
- Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, Institute of Applied Biosciences, 76131 Karlsruhe, Germany
| | - Matthias Hufnagel
- Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, Institute of Applied Biosciences, 76131 Karlsruhe, Germany
| | - Andrea Hartwig
- Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, Institute of Applied Biosciences, 76131 Karlsruhe, Germany
| | - Andrew Floeder
- Division of Environmental Health Sciences, School of Public Health and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Silvia Balbo
- Division of Environmental Health Sciences, School of Public Health and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, 3584 CS Utrecht, The Netherlands
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Volker M. Arlt
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, King’s College London, London SE1 9NH, UK
| | - David H. Phillips
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, King’s College London, London SE1 9NH, UK
- Correspondence:
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Evaluation of Biological Activity of Natural Compounds: Current Trends and Methods. Molecules 2022; 27:molecules27144490. [PMID: 35889361 PMCID: PMC9324072 DOI: 10.3390/molecules27144490] [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: 05/14/2022] [Revised: 06/26/2022] [Accepted: 07/04/2022] [Indexed: 02/08/2023] Open
Abstract
Natural compounds have diverse structures and are present in different forms of life. Metabolites such as tannins, anthocyanins, and alkaloids, among others, serve as a defense mechanism in live organisms and are undoubtedly compounds of interest for the food, cosmetic, and pharmaceutical industries. Plants, bacteria, and insects represent sources of biomolecules with diverse activities, which are in many cases poorly studied. To use these molecules for different applications, it is essential to know their structure, concentrations, and biological activity potential. In vitro techniques that evaluate the biological activity of the molecules of interest have been developed since the 1950s. Currently, different methodologies have emerged to overcome some of the limitations of these traditional techniques, mainly via reductions in time and costs. These emerging technologies continue to appear due to the urgent need to expand the analysis capacity of a growing number of reported biomolecules. This review presents an updated summary of the conventional and relevant methods to evaluate the natural compounds’ biological activity in vitro.
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