1
|
Daley MC, Moreau M, Bronk P, Fisher J, Kofron CM, Mende U, McMullen P, Choi BR, Coulombe K. In vitro to in vivo extrapolation from 3D hiPSC-derived cardiac microtissues and physiologically based pharmacokinetic modeling to inform next-generation arrhythmia risk assessment. Toxicol Sci 2024; 201:145-157. [PMID: 38897660 PMCID: PMC11347779 DOI: 10.1093/toxsci/kfae079] [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: 06/21/2024] Open
Abstract
Proarrhythmic cardiotoxicity remains a substantial barrier to drug development as well as a major global health challenge. In vitro human pluripotent stem cell-based new approach methodologies have been increasingly proposed and employed as alternatives to existing in vitro and in vivo models that do not accurately recapitulate human cardiac electrophysiology or cardiotoxicity risk. In this study, we expanded the capacity of our previously established 3D human cardiac microtissue model to perform quantitative risk assessment by combining it with a physiologically based pharmacokinetic model, allowing a direct comparison of potentially harmful concentrations predicted in vitro to in vivo therapeutic levels. This approach enabled the measurement of concentration responses and margins of exposure for 2 physiologically relevant metrics of proarrhythmic risk (i.e. action potential duration and triangulation assessed by optical mapping) across concentrations spanning 3 orders of magnitude. The combination of both metrics enabled accurate proarrhythmic risk assessment of 4 compounds with a range of known proarrhythmic risk profiles (i.e. quinidine, cisapride, ranolazine, and verapamil) and demonstrated close agreement with their known clinical effects. Action potential triangulation was found to be a more sensitive metric for predicting proarrhythmic risk associated with the primary mechanism of concern for pharmaceutical-induced fatal ventricular arrhythmias, delayed cardiac repolarization due to inhibition of the rapid delayed rectifier potassium channel, or hERG channel. This study advances human-induced pluripotent stem cell-based 3D cardiac tissue models as new approach methodologies that enable in vitro proarrhythmic risk assessment with high precision of quantitative metrics for understanding clinically relevant cardiotoxicity.
Collapse
Affiliation(s)
- Mark C Daley
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI 02912, United States
| | | | - Peter Bronk
- Cardiovascular Research Center, Cardiovascular Institute, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, RI 02903, United States
| | | | - Celinda M Kofron
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI 02912, United States
| | - Ulrike Mende
- Cardiovascular Research Center, Cardiovascular Institute, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, RI 02903, United States
| | | | - Bum-Rak Choi
- Cardiovascular Research Center, Cardiovascular Institute, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, RI 02903, United States
| | - Kareen Coulombe
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI 02912, United States
| |
Collapse
|
2
|
Tsai HHD, Ford LC, Burnett SD, Dickey AN, Wright FA, Chiu WA, Rusyn I. Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human-Induced Pluripotent Stem-Cell-Derived Cardiomyocytes. Chem Res Toxicol 2024; 37:1428-1444. [PMID: 39046974 DOI: 10.1021/acs.chemrestox.4c00193] [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] [Indexed: 07/27/2024]
Abstract
Environmental chemicals may contribute to the global burden of cardiovascular disease, but experimental data are lacking to determine which substances pose the greatest risk. Human-induced pluripotent stem cell (iPSC)-derived cardiomyocytes are a high-throughput cardiotoxicity model that is widely used to test drugs and chemicals; however, most studies focus on exploring electro-physiological readouts. Gene expression data may provide additional molecular insights to be used for both mechanistic interpretation and dose-response analyses. Therefore, we hypothesized that both transcriptomic and functional data in human iPSC-derived cardiomyocytes may be used as a comprehensive screening tool to identify potential cardiotoxicity hazards and risks of the chemicals. To test this hypothesis, we performed concentration-response analysis of 464 chemicals from 12 classes, including both pharmaceuticals and nonpharmaceutical substances. Functional effects (beat frequency, QT prolongation, and asystole), cytotoxicity, and whole transcriptome response were evaluated. Points of departure were derived from phenotypic and transcriptomic data, and risk characterization was performed. Overall, 244 (53%) substances were active in at least one phenotype; as expected, pharmaceuticals with known cardiac liabilities were the most active. Positive chronotropy was the functional phenotype activated by the largest number of tested chemicals. No chemical class was particularly prone to pose a potential hazard to cardiomyocytes; a varying proportion (10-44%) of substances in each class had effects on cardiomyocytes. Transcriptomic data showed that 69 (15%) substances elicited significant gene expression changes; most perturbed pathways were highly relevant to known key characteristics of human cardiotoxicants. The bioactivity-to-exposure ratios showed that phenotypic- and transcriptomic-based POD led to similar results for risk characterization. Overall, our findings demonstrate how the integrative use of in vitro transcriptomic and phenotypic data from iPSC-derived cardiomyocytes not only offers a complementary approach for hazard and risk prioritization, but also enables mechanistic interpretation of the in vitro test results to increase confidence in decision-making.
Collapse
Affiliation(s)
- Han-Hsuan D Tsai
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Lucie C Ford
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Sarah D Burnett
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Allison N Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, United States
| | - Fred A Wright
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, United States
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, United States
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
3
|
Ryoo H, Kimmel H, Rondo E, Underhill GH. Advances in high throughput cell culture technologies for therapeutic screening and biological discovery applications. Bioeng Transl Med 2024; 9:e10627. [PMID: 38818120 PMCID: PMC11135158 DOI: 10.1002/btm2.10627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 06/01/2024] Open
Abstract
Cellular phenotypes and functional responses are modulated by the signals present in their microenvironment, including extracellular matrix (ECM) proteins, tissue mechanical properties, soluble signals and nutrients, and cell-cell interactions. To better recapitulate and analyze these complex signals within the framework of more physiologically relevant culture models, high throughput culture platforms can be transformative. High throughput methodologies enable scientists to extract increasingly robust and broad datasets from individual experiments, screen large numbers of conditions for potential hits, better qualify and predict responses for preclinical applications, and reduce reliance on animal studies. High throughput cell culture systems require uniformity, assay miniaturization, specific target identification, and process simplification. In this review, we detail the various techniques that researchers have used to face these challenges and explore cellular responses in a high throughput manner. We highlight several common approaches including two-dimensional multiwell microplates, microarrays, and microfluidic cell culture systems as well as unencapsulated and encapsulated three-dimensional high throughput cell culture systems, featuring multiwell microplates, micromolds, microwells, microarrays, granular hydrogels, and cell-encapsulated microgels. We also discuss current applications of these high throughput technologies, namely stem cell sourcing, drug discovery and predictive toxicology, and personalized medicine, along with emerging opportunities and future impact areas.
Collapse
Affiliation(s)
- Hyeon Ryoo
- Bioengineering DepartmentUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Hannah Kimmel
- Bioengineering DepartmentUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Evi Rondo
- Bioengineering DepartmentUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Gregory H. Underhill
- Bioengineering DepartmentUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| |
Collapse
|
4
|
Lu EH, Ford LC, Chen Z, Burnett SD, Rusyn I, Chiu WA. Evaluating scientific confidence in the concordance of in vitro and in vivo protective points of departure. Regul Toxicol Pharmacol 2024; 148:105596. [PMID: 38447894 PMCID: PMC11193089 DOI: 10.1016/j.yrtph.2024.105596] [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: 12/15/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
To fulfil the promise of reducing reliance on mammalian in vivo laboratory animal studies, new approach methods (NAMs) need to provide a confident basis for regulatory decision-making. However, previous attempts to develop in vitro NAMs-based points of departure (PODs) have yielded mixed results, with PODs from U.S. EPA's ToxCast, for instance, appearing more conservative (protective) but poorly correlated with traditional in vivo studies. Here, we aimed to address this discordance by reducing the heterogeneity of in vivo PODs, accounting for species differences, and enhancing the biological relevance of in vitro PODs. However, we only found improved in vitro-to-in vivo concordance when combining the use of Bayesian model averaging-based benchmark dose modeling for in vivo PODs, allometric scaling for interspecies adjustments, and human-relevant in vitro assays with multiple induced pluripotent stem cell-derived models. Moreover, the available sample size was only 15 chemicals, and the resulting level of concordance was only fair, with correlation coefficients <0.5 and prediction intervals spanning several orders of magnitude. Overall, while this study suggests several ways to enhance concordance and thereby increase scientific confidence in vitro NAMs-based PODs, it also highlights challenges in their predictive accuracy and precision for use in regulatory decision making.
Collapse
Affiliation(s)
- En-Hsuan Lu
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, 77843, USA
| | - Lucie C Ford
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, 77843, USA
| | - Zunwei Chen
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, 77843, USA
| | - Sarah D Burnett
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, 77843, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, 77843, USA
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
5
|
Ford LC, Lin HC, Tsai HHD, Zhou YH, Wright FA, Sedykh A, Shah RR, Chiu WA, Rusyn I. Hazard and risk characterization of 56 structurally diverse PFAS using a targeted battery of broad coverage assays using six human cell types. Toxicology 2024; 503:153763. [PMID: 38423244 PMCID: PMC11214689 DOI: 10.1016/j.tox.2024.153763] [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: 01/18/2024] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
Per- and poly-fluoroalkyl substances (PFAS) are extensively used in commerce leading to their prevalence in the environment. Due to their chemical stability, PFAS are considered to be persistent and bioaccumulative; they are frequently detected in both the environment and humans. Because of this, PFAS as a class (composed of hundreds to thousands of chemicals) are contaminants of very high concern. Little information is available for the vast majority of PFAS, and regulatory agencies lack safety data to determine whether exposure limits or restrictions are needed. Cell-based assays are a pragmatic approach to inform decision-makers on potential health hazards; therefore, we hypothesized that a targeted battery of human in vitro assays can be used to determine whether there are structure-bioactivity relationships for PFAS, and to characterize potential risks by comparing bioactivity (points of departure) to exposure estimates. We tested 56 PFAS from 8 structure-based subclasses in concentration response (0.1-100 μM) using six human cell types selected from target organs with suggested adverse effects of PFAS - human induced pluripotent stem cell (iPSC)-derived hepatocytes, neurons, and cardiomyocytes, primary human hepatocytes, endothelial and HepG2 cells. While many compounds were without effect; certain PFAS demonstrated cell-specific activity highlighting the necessity of using a compendium of in vitro models to identify potential hazards. No class-specific groupings were evident except for some chain length- and structure-related trends. In addition, margins of exposure (MOE) were derived using empirical and predicted exposure data. Conservative MOE calculations showed that most tested PFAS had a MOE in the 1-100 range; ∼20% of PFAS had MOE<1, providing tiered priorities for further studies. Overall, we show that a compendium of human cell-based models can be used to derive bioactivity estimates for a range of PFAS, enabling comparisons with human biomonitoring data. Furthermore, we emphasize that establishing structure-bioactivity relationships may be challenging for the tested PFAS.
Collapse
Affiliation(s)
- Lucie C Ford
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Hsing-Chieh Lin
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Han-Hsuan D Tsai
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Yi-Hui Zhou
- Department of Biological Sciences and Statistics, North Carolina State University, Raleigh, NC 27695, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Fred A Wright
- Department of Biological Sciences and Statistics, North Carolina State University, Raleigh, NC 27695, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | - Weihsueh A Chiu
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Ivan Rusyn
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
6
|
Tsai HHD, Ford LC, Chen Z, Dickey AN, Wright FA, Rusyn I. Risk-based prioritization of PFAS using phenotypic and transcriptomic data from human induced pluripotent stem cell-derived hepatocytes and cardiomyocytes. ALTEX 2024; 41:363-381. [PMID: 38429992 PMCID: PMC11305846 DOI: 10.14573/altex.2311031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/20/2024] [Indexed: 03/03/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are chemicals with important applications; they are persistent in the environment and may pose human health hazards. Regulatory agencies are considering restrictions and bans of PFAS; however, little data exists for informed decisions. Several prioritization strategies were proposed for evaluation of potential hazards of PFAS. Structure-based grouping could expedite the selection of PFAS for testing; still, the hypothesis that structure-effect relationships exist for PFAS requires confirmation. We tested 26 structurally diverse PFAS from 8 groups using human induced pluripotent stem cell-derived hepatocytes and cardiomyocytes, and tested concentration-response effects on cell function and gene expression. Few phenotypic effects were observed in hepatocytes, but negative chronotropy was observed in cardiomyocytes for 8 PFAS. Substance- and cell type-dependent transcriptomic changes were more prominent but lacked substantial group-specific effects. In hepatocytes, we found upregulation of stress-related and extracellular matrix organization pathways, and down-regulation of fat metabolism. In cardiomyocytes, contractility-related pathways were most affected. We derived phenotypic and transcriptomic points of departure and compared them to predicted PFAS exposures. Conservative estimates for bioactivity and exposure were used to derive a bioactivity-to-exposure ratio (BER) for each PFAS; 23 of 26 PFAS had BER > 1. Overall, these data suggest that structure-based PFAS grouping may not be sufficient to predict their biological effects. Testing of individual PFAS may be needed for scientifically-supported decision-making. Our proposed strategy of using two human cell types and considering phenotypic and transcriptomic effects, combined with dose-response analysis and calculation of BER, may be used for PFAS prioritization.
Collapse
Affiliation(s)
- Han-Hsuan D Tsai
- Interdisciplinary Faculty of Toxicology, College Station, TX, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| | - Lucie C Ford
- Interdisciplinary Faculty of Toxicology, College Station, TX, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| | - Zunwei Chen
- Interdisciplinary Faculty of Toxicology, College Station, TX, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
- Current address: Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Allison N Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Fred A Wright
- Interdisciplinary Faculty of Toxicology, College Station, TX, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, College Station, TX, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| |
Collapse
|
7
|
Chehelgerdi M, Behdarvand Dehkordi F, Chehelgerdi M, Kabiri H, Salehian-Dehkordi H, Abdolvand M, Salmanizadeh S, Rashidi M, Niazmand A, Ahmadi S, Feizbakhshan S, Kabiri S, Vatandoost N, Ranjbarnejad T. Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy. Mol Cancer 2023; 22:189. [PMID: 38017433 PMCID: PMC10683363 DOI: 10.1186/s12943-023-01873-0] [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: 07/04/2023] [Accepted: 09/27/2023] [Indexed: 11/30/2023] Open
Abstract
The advent of iPSCs has brought about a significant transformation in stem cell research, opening up promising avenues for advancing cancer treatment. The formation of cancer is a multifaceted process influenced by genetic, epigenetic, and environmental factors. iPSCs offer a distinctive platform for investigating the origin of cancer, paving the way for novel approaches to cancer treatment, drug testing, and tailored medical interventions. This review article will provide an overview of the science behind iPSCs, the current limitations and challenges in iPSC-based cancer therapy, the ethical and social implications, and the comparative analysis with other stem cell types for cancer treatment. The article will also discuss the applications of iPSCs in tumorigenesis, the future of iPSCs in tumorigenesis research, and highlight successful case studies utilizing iPSCs in tumorigenesis research. The conclusion will summarize the advancements made in iPSC-based tumorigenesis research and the importance of continued investment in iPSC research to unlock the full potential of these cells.
Collapse
Affiliation(s)
- Matin Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Fereshteh Behdarvand Dehkordi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran.
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Hamidreza Kabiri
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | | | - Mohammad Abdolvand
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Sharareh Salmanizadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar-Jereeb Street, Isfahan, 81746-73441, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Anoosha Niazmand
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Saba Ahmadi
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Sara Feizbakhshan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Saber Kabiri
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Nasimeh Vatandoost
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tayebeh Ranjbarnejad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| |
Collapse
|
8
|
Cordova AC, Klaren WD, Ford LC, Grimm FA, Baker ES, Zhou YH, Wright FA, Rusyn I. Integrative Chemical-Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams. TOXICS 2023; 11:586. [PMID: 37505552 PMCID: PMC10385386 DOI: 10.3390/toxics11070586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/24/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Human cell-based test methods can be used to evaluate potential hazards of mixtures and products of petroleum refining ("unknown or variable composition, complex reaction products, or biological materials" substances, UVCBs). Analyses of bioactivity and detailed chemical characterization of petroleum UVCBs were used separately for grouping these substances; a combination of the approaches has not been undertaken. Therefore, we used a case example of representative high production volume categories of petroleum UVCBs, 25 lower olefin substances from low benzene naphtha and resin oils categories, to determine whether existing manufacturing-based category grouping can be supported. We collected two types of data: nontarget ion mobility spectrometry-mass spectrometry of both neat substances and their organic extracts and in vitro bioactivity of the organic extracts in five human cell types: umbilical vein endothelial cells and induced pluripotent stem cell-derived hepatocytes, endothelial cells, neurons, and cardiomyocytes. We found that while similarity in composition and bioactivity can be observed for some substances, existing categories are largely heterogeneous. Strong relationships between composition and bioactivity were observed, and individual constituents that determine these associations were identified. Overall, this study showed a promising approach that combines chemical composition and bioactivity data to better characterize the variability within manufacturing categories of petroleum UVCBs.
Collapse
Affiliation(s)
- Alexandra C Cordova
- Interdisciplinary Faculty of Toxicology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - William D Klaren
- Interdisciplinary Faculty of Toxicology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Lucie C Ford
- Interdisciplinary Faculty of Toxicology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Fabian A Grimm
- Interdisciplinary Faculty of Toxicology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Erin S Baker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yi-Hui Zhou
- Departments of Statistics and Biological Sciences and Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
| | - Fred A Wright
- Departments of Statistics and Biological Sciences and Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
9
|
Cordova AC, Ford LC, Valdiviezo A, Roman-Hubers AT, McDonald TJ, Chiu WA, Rusyn I. Dosing Methods to Enable Cell-Based In Vitro Testing of Complex Substances: A Case Study with a PAH Mixture. TOXICS 2022; 11:19. [PMID: 36668745 PMCID: PMC9866728 DOI: 10.3390/toxics11010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Cell-based testing of multi-constituent substances and mixtures for their potential adverse health effects is difficult due to their complex composition and physical-chemical characteristics. Various extraction methods are typically used to enable studies in vitro; however, a limited number of solvents are biocompatible with in vitro studies and the extracts may not fully represent the original test article's composition. While the methods for dosing with "difficult-to-test" substances in aquatic toxicity studies are well defined and widely used, they are largely unsuited for small-volume (100 microliters or less) in vitro studies with mammalian cells. Therefore, we aimed to evaluate suitability of various scaled-down dosing methods for high-throughput in vitro testing by using a mixture of polycyclic aromatic hydrocarbons (PAH). Specifically, we compared passive dosing via silicone micro-O-rings, cell culture media-accommodated fraction, and traditional solvent (dimethyl sulfoxide) extraction procedures. Gas chromatography-tandem mass spectrometry (GC-MS/MS) was used to evaluate kinetics of PAH absorption to micro-O-rings, as well as recovery of PAH and the extent of protein binding in cell culture media with and without cells for each dosing method. Bioavailability of the mixture from different dosing methods was also evaluated by characterizing in vitro cytotoxicity of the PAH mixture using EA.hy926 and HepG2 human cell lines. Of the tested dosing methods, media accommodated fraction (MAF) was determined to be the most appropriate method for cell-based studies of PAH-containing complex substances and mixtures. This conclusion is based on the observation that the highest fraction of the starting materials can be delivered using media accommodated fraction approach into cell culture media and thus enable concentration-response in vitro testing.
Collapse
Affiliation(s)
- Alexandra C. Cordova
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Lucie C. Ford
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Alan Valdiviezo
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Alina T. Roman-Hubers
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Thomas J. McDonald
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Departments of Environmental and Occupational Health, Texas A&M University, College Station, TX 77843, USA
| | - Weihsueh A. Chiu
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
10
|
MacDonnell S, Megna J, Ruan Q, Zhu O, Halasz G, Jasewicz D, Powers K, E H, del Pilar Molina-Portela M, Jin X, Zhang D, Torello J, Feric NT, Graziano MP, Shekhar A, Dunn ME, Glass D, Morton L. Activin A directly impairs human cardiomyocyte contractile function indicating a potential role in heart failure development. Front Cardiovasc Med 2022; 9:1038114. [PMID: 36440002 PMCID: PMC9685658 DOI: 10.3389/fcvm.2022.1038114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/10/2022] [Indexed: 09/27/2023] Open
Abstract
Activin A has been linked to cardiac dysfunction in aging and disease, with elevated circulating levels found in patients with hypertension, atherosclerosis, and heart failure. Here, we investigated whether Activin A directly impairs cardiomyocyte (CM) contractile function and kinetics utilizing cell, tissue, and animal models. Hydrodynamic gene delivery-mediated overexpression of Activin A in wild-type mice was sufficient to impair cardiac function, and resulted in increased cardiac stress markers (N-terminal pro-atrial natriuretic peptide) and cardiac atrophy. In human-induced pluripotent stem cell-derived (hiPSC) CMs, Activin A caused increased phosphorylation of SMAD2/3 and significantly upregulated SERPINE1 and FSTL3 (markers of SMAD2/3 activation and activin signaling, respectively). Activin A signaling in hiPSC-CMs resulted in impaired contractility, prolonged relaxation kinetics, and spontaneous beating in a dose-dependent manner. To identify the cardiac cellular source of Activin A, inflammatory cytokines were applied to human cardiac fibroblasts. Interleukin -1β induced a strong upregulation of Activin A. Mechanistically, we observed that Activin A-treated hiPSC-CMs exhibited impaired diastolic calcium handling with reduced expression of calcium regulatory genes (SERCA2, RYR2, CACNB2). Importantly, when Activin A was inhibited with an anti-Activin A antibody, maladaptive calcium handling and CM contractile dysfunction were abrogated. Therefore, inflammatory cytokines may play a key role by acting on cardiac fibroblasts, causing local upregulation of Activin A that directly acts on CMs to impair contractility. These findings demonstrate that Activin A acts directly on CMs, which may contribute to the cardiac dysfunction seen in aging populations and in patients with heart failure.
Collapse
Affiliation(s)
| | - Jake Megna
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | - Qin Ruan
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | - Olivia Zhu
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | - Gabor Halasz
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | - Dan Jasewicz
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | - Kristi Powers
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | - Hock E
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | | | - Ximei Jin
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | - Dongqin Zhang
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | | | - Nicole T. Feric
- TARA Biosystems Inc., Alexandria Center for Life Sciences, New York, NY, United States
| | - Michael P. Graziano
- TARA Biosystems Inc., Alexandria Center for Life Sciences, New York, NY, United States
| | | | | | - David Glass
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| | - Lori Morton
- Regeneron Pharmaceuticals, Tarrytown, NY, United States
| |
Collapse
|
11
|
Valdiviezo A, Brown GE, Michell AR, Trinconi CM, Bodke VV, Khetani SR, Luo YS, Chiu WA, Rusyn I. Reanalysis of Trichloroethylene and Tetrachloroethylene Metabolism to Glutathione Conjugates Using Human, Rat, and Mouse Liver in Vitro Models to Improve Precision in Risk Characterization. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:117009. [PMID: 36445294 PMCID: PMC9707501 DOI: 10.1289/ehp12006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/16/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Both trichloroethylene (TCE) and tetrachloroethylene (PCE) are high-priority chemicals subject to numerous human health risk evaluations by a range of agencies. Metabolism of TCE and PCE determines their ultimate toxicity; important uncertainties exist in quantitative characterization of metabolism to genotoxic moieties through glutathione (GSH) conjugation and species differences therein. OBJECTIVES This study aimed to address these uncertainties using novel in vitro liver models, interspecies comparison, and a sensitive assay for quantification of GSH conjugates of TCE and PCE, S-(1,2-dichlorovinyl)glutathione (DCVG) and S-(1,2,2-trichlorovinyl) glutathione (TCVG), respectively. METHODS Liver in vitro models used herein were suspension, 2-D culture, and micropatterned coculture (MPCC) with primary human, rat, and mouse hepatocytes, as well as human induced pluripotent stem cell (iPSC)-derived hepatocytes (iHep). RESULTS We found that, although efficiency of metabolism varied among models, consistent with known differences in their metabolic capacity, formation rates of DCVG and TCVG generally followed the patterns human ≥ rat ≥ mouse , and primary hepatocytes > iHep . Data derived from MPCC were most consistent with estimates from physiologically based pharmacokinetic models calibrated to in vivo data. DISCUSSION For TCE, the new data provided additional empirical support for inclusion of GSH conjugation-mediated kidney effects as critical for the derivation of noncancer toxicity values. For PCE, the data reduced previous uncertainties regarding the extent of TCVG formation in humans; this information was used to update several candidate kidney-specific noncancer toxicity values. Overall, MPCC-derived data provided physiologically relevant estimates of GSH-mediated metabolism of TCE and PCE to reduce uncertainties in interspecies extrapolation that constrained previous risk evaluations, thereby increasing the precision of risk characterizations of these high-priority toxicants. https://doi.org/10.1289/EHP12006.
Collapse
Affiliation(s)
- Alan Valdiviezo
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Grace E. Brown
- Department of Biomedical Engineering, University of Illinois Chicago, Illinois, USA
| | - Ashlin R. Michell
- Department of Biomedical Engineering, University of Illinois Chicago, Illinois, USA
| | | | - Vedant V. Bodke
- Department of Biomedical Engineering, University of Illinois Chicago, Illinois, USA
| | - Salman R. Khetani
- Department of Biomedical Engineering, University of Illinois Chicago, Illinois, USA
| | - Yu-Syuan Luo
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Weihsueh A. Chiu
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| |
Collapse
|
12
|
Ouyang Q, Yang W, Wu Y, Xu Z, Hu Y, Hu N, Zhang D. Multi-labeled neural network model for automatically processing cardiomyocyte mechanical beating signals in drug assessment. Biosens Bioelectron 2022; 209:114261. [DOI: 10.1016/j.bios.2022.114261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/09/2022] [Accepted: 04/05/2022] [Indexed: 11/16/2022]
|
13
|
House JS, Grimm FA, Klaren WD, Dalzell A, Kuchi S, Zhang SD, Lenz K, Boogaard PJ, Ketelslegers HB, Gant TW, Rusyn I, Wright FA. Grouping of UVCB substances with dose-response transcriptomics data from human cell-based assays. ALTEX 2022; 39:388–404. [PMID: 35288757 PMCID: PMC9344966 DOI: 10.14573/altex.2107051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 02/22/2022] [Indexed: 12/18/2022]
Abstract
The application of in vitro biological assays as new approach methodologies (NAMs) to support grouping of UVCB (unknown or variable composition, complex reaction products, and biological materials) substances has recently been demonstrated. In addition to cell-based phenotyping as NAMs, in vitro transcriptomic profiling is used to gain deeper mechanistic understanding of biological responses to chemicals and to support grouping and read-across. However, the value of gene expression profiling for characterizing complex substances like UVCBs has not been explored. Using 141 petroleum substance extracts, we performed dose-response transcriptomic profiling in human induced pluripotent stem cell (iPSC)-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, as well as cell lines MCF7 and A375. The goal was to determine whether transcriptomic data can be used to group these UVCBs and to further characterize the molecular basis for in vitro biological responses. We found distinct transcriptional responses for petroleum substances by manufacturing class. Pathway enrichment informed interpretation of effects of substances and UVCB petroleum-class. Transcriptional activity was strongly correlated with concentration of polycyclic aromatic compounds (PAC), especially in iPSC-derived hepatocytes. Supervised analysis using transcriptomics, alone or in combination with bioactivity data collected on these same substances/cells, suggest that transcriptomics data provide useful mechanistic information, but only modest additional value for grouping. Overall, these results further demonstrate the value of NAMs for grouping of UVCBs, identify informative cell lines, and provide data that could be used for justifying selection of substances for further testing that may be required for registration.
Collapse
Affiliation(s)
- John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, RTP, NC, USA
| | - Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - William D Klaren
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.,current address: ToxStrategies, Inc., Asheville, NC, USA
| | - Abigail Dalzell
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Harwell Science Campus, Oxon, UK
| | - Srikeerthana Kuchi
- Northern Ireland Centre for Stratified Medicine, Ulster University, L/Derry, Northern Ireland, UK.,current address: MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Ulster University, L/Derry, Northern Ireland, UK
| | - Klaus Lenz
- SYNCOM Forschungs und Entwicklungsberatung GmbH, Ganderkesee, Germany
| | | | | | - Timothy W Gant
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Harwell Science Campus, Oxon, UK
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| |
Collapse
|
14
|
Assessing Drug-Induced Mitochondrial Toxicity in Cardiomyocytes: Implications for Preclinical Cardiac Safety Evaluation. Pharmaceutics 2022; 14:pharmaceutics14071313. [PMID: 35890211 PMCID: PMC9319223 DOI: 10.3390/pharmaceutics14071313] [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: 05/10/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 02/07/2023] Open
Abstract
Drug-induced cardiotoxicity not only leads to the attrition of drugs during development, but also contributes to the high morbidity and mortality rates of cardiovascular diseases. Comprehensive testing for proarrhythmic risks of drugs has been applied in preclinical cardiac safety assessment for over 15 years. However, other mechanisms of cardiac toxicity have not received such attention. Of them, mitochondrial impairment is a common form of cardiotoxicity and is known to account for over half of cardiovascular adverse-event-related black box warnings imposed by the U.S. Food and Drug Administration. Although it has been studied in great depth, mitochondrial toxicity assessment has not yet been incorporated into routine safety tests for cardiotoxicity at the preclinical stage. This review discusses the main characteristics of mitochondria in cardiomyocytes, drug-induced mitochondrial toxicities, and high-throughput screening strategies for cardiomyocytes, as well as their proposed integration into preclinical safety pharmacology. We emphasize the advantages of using adult human primary cardiomyocytes for the evaluation of mitochondrial morphology and function, and the need for a novel cardiac safety testing platform integrating mitochondrial toxicity and proarrhythmic risk assessments in cardiac safety evaluation.
Collapse
|
15
|
Luo YS, Chen Z, Hsieh NH, Lin TE. Chemical and biological assessments of environmental mixtures: A review of current trends, advances, and future perspectives. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128658. [PMID: 35290896 DOI: 10.1016/j.jhazmat.2022.128658] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/21/2022] [Accepted: 03/07/2022] [Indexed: 05/28/2023]
Abstract
Considering the chemical complexity and toxicity data gaps of environmental mixtures, most studies evaluate the chemical risk individually. However, humans are usually exposed to a cocktail of chemicals in real life. Mixture health assessment remains to be a research area having significant knowledge gaps. Characterization of chemical composition and bioactivity/toxicity are the two critical aspects of mixture health assessments. This review seeks to introduce the recent progress and tools for the chemical and biological characterization of environmental mixtures. The state-of-the-art techniques include the sampling, extraction, rapid detection methods, and the in vitro, in vivo, and in silico approaches to generate the toxicity data of an environmental mixture. Application of these novel methods, or new approach methodologies (NAMs), has increased the throughput of generating chemical and toxicity data for mixtures and thus refined the mixture health assessment. Combined with computational methods, the chemical and biological information would shed light on identifying the bioactive/toxic components in an environmental mixture.
Collapse
Affiliation(s)
- Yu-Syuan Luo
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, Taipei City, Taiwan.
| | - Zunwei Chen
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nan-Hung Hsieh
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Tzu-En Lin
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| |
Collapse
|
16
|
Daley MC, Mende U, Choi BR, McMullen PD, Coulombe KLK. Beyond pharmaceuticals: Fit-for-purpose new approach methodologies for environmental cardiotoxicity testing. ALTEX 2022; 40:103-116. [PMID: 35648122 PMCID: PMC10502740 DOI: 10.14573/altex.2109131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 05/16/2022] [Indexed: 11/23/2022]
Abstract
Environmental factors play a substantial role in determining cardiovascular health, but data informing the risks presented by environmental toxicants is insufficient. In vitro new approach methodologies (NAMs) offer a promising approach with which to address the limitations of traditional in vivo and in vitro assays for assessing cardiotoxicity. Driven largely by the needs of pharmaceutical toxicity testing, considerable progress in developing NAMs for cardiotoxicity analysis has already been made. As the scientific and regulatory interest in NAMs for environmental chemicals continues to grow, a thorough understanding of the unique features of environmental cardiotoxicants and their associated cardiotoxicities is needed. Here, we review the key characteristics of as well as important regulatory and biological considerations for fit-for-purpose NAMs for environmental cardiotoxicity. By emphasizing the challenges and opportunities presented by NAMs for environmental cardiotoxicity we hope to accelerate their development, acceptance, and application.
Collapse
Affiliation(s)
- Mark C Daley
- Center for Biomedical Engineering, School of Engineering and Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Ulrike Mende
- Cardiovascular Research Center, Cardiovascular Institute, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Bum-Rak Choi
- Cardiovascular Research Center, Cardiovascular Institute, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | | | - Kareen L K Coulombe
- Center for Biomedical Engineering, School of Engineering and Division of Biology and Medicine, Brown University, Providence, RI, USA
| |
Collapse
|
17
|
Kwok CK, Sébastien I, Hariharan K, Meiser I, Wihan J, Altmaier S, Karnatz I, Bauer D, Fischer B, Feile A, Cabrera-Socorro A, Rasmussen M, Holst B, Neubauer JC, Clausen C, Verfaillie C, Ebneth A, Hansson M, Steeg R, Zimmermann H. Scalable expansion of iPSC and their derivatives across multiple lineages. Reprod Toxicol 2022; 112:23-35. [PMID: 35595152 DOI: 10.1016/j.reprotox.2022.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 12/30/2022]
Abstract
Induced pluripotent stem cell (iPSC) technology enabled the production of pluripotent stem cell lines from somatic cells from a range of known genetic backgrounds. Their ability to differentiate and generate a wide variety of cell types has resulted in their use for various biomedical applications, including toxicity testing. Many of these iPSC lines are now registered in databases and stored in biobanks such as the European Bank for induced pluripotent Stem Cells (EBiSC), which can streamline the quality control and distribution of these individual lines. To generate the quantities of cells for banking and applications like high-throughput toxicity screening, scalable and robust methods need to be developed to enable the large-scale production of iPSCs. 3D suspension culture platforms are increasingly being used by stem cell researchers, owing to a higher cell output in a smaller footprint, as well as simpler scaling by increasing culture volume. Here we describe our strategies for successful scalable production of iPSCs using a benchtop bioreactor and incubator for 3D suspension cultures, while maintaining quality attributes expected of high-quality iPSC lines. Additionally, to meet the increasing demand for "ready-to-use" cell types, we report recent work to establish robust, scalable differentiation protocols to cardiac, neural, and hepatic fate to enable EBiSC to increase available research tools.
Collapse
Affiliation(s)
- Chee Keong Kwok
- Cell Therapy R&D, Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Isabelle Sébastien
- Fraunhofer Project Center for Stem Cell Process Engineering, Fraunhofer Institute for Biomedical Engineering IBMT, Neunerplatz 2, 97082 Würzburg, Germany
| | - Krithika Hariharan
- Fraunhofer Project Center for Stem Cell Process Engineering, Fraunhofer Institute for Biomedical Engineering IBMT, Neunerplatz 2, 97082 Würzburg, Germany
| | - Ina Meiser
- Fraunhofer Institute for Biomedical Engineering IBMT, Joseph-von-Fraunhofer-Weg 1, 66820 Sulzbach, Germany
| | - Jeanette Wihan
- Fraunhofer Project Center for Stem Cell Process Engineering, Fraunhofer Institute for Biomedical Engineering IBMT, Neunerplatz 2, 97082 Würzburg, Germany
| | - Saskia Altmaier
- Fraunhofer Institute for Biomedical Engineering IBMT, Joseph-von-Fraunhofer-Weg 1, 66820 Sulzbach, Germany
| | - Isabell Karnatz
- Fraunhofer Project Center for Stem Cell Process Engineering, Fraunhofer Institute for Biomedical Engineering IBMT, Neunerplatz 2, 97082 Würzburg, Germany
| | - Dominic Bauer
- Fraunhofer Project Center for Stem Cell Process Engineering, Fraunhofer Institute for Biomedical Engineering IBMT, Neunerplatz 2, 97082 Würzburg, Germany
| | - Benjamin Fischer
- Fraunhofer Project Center for Stem Cell Process Engineering, Fraunhofer Institute for Biomedical Engineering IBMT, Neunerplatz 2, 97082 Würzburg, Germany
| | - Alexander Feile
- Fraunhofer Project Center for Stem Cell Process Engineering, Fraunhofer Institute for Biomedical Engineering IBMT, Neunerplatz 2, 97082 Würzburg, Germany
| | - Alfredo Cabrera-Socorro
- Neuroscience Therapeutic Area, Janssen Research & Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Bjørn Holst
- Bioneer A/S, Kogle Allé 2, 2970 Hørsholm, Denmark
| | - Julia C Neubauer
- Fraunhofer Project Center for Stem Cell Process Engineering, Fraunhofer Institute for Biomedical Engineering IBMT, Neunerplatz 2, 97082 Würzburg, Germany; Fraunhofer Institute for Biomedical Engineering IBMT, Joseph-von-Fraunhofer-Weg 1, 66820 Sulzbach, Germany
| | | | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, UZ Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - Andreas Ebneth
- Neuroscience Therapeutic Area, Janssen Research & Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Mattias Hansson
- Cell Therapy R&D, Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Rachel Steeg
- Fraunhofer UK Research Ltd, Technology and Innovation Centre, 99 George Street, G1 1RD Glasgow, United Kingdom
| | - Heiko Zimmermann
- Fraunhofer Project Center for Stem Cell Process Engineering, Fraunhofer Institute for Biomedical Engineering IBMT, Neunerplatz 2, 97082 Würzburg, Germany; Fraunhofer Institute for Biomedical Engineering IBMT, Joseph-von-Fraunhofer-Weg 1, 66820 Sulzbach, Germany; Department of Molecular and Cellular Biotechnology, Saarland University, 66123 Saarbrücken, Germany; Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
| |
Collapse
|
18
|
Cromwell EF, Sirenko O, Nikolov E, Hammer M, Brock CK, Matossian MD, Alzoubi MS, Collins-Burow BM, Burow ME. Multifunctional profiling of triple-negative breast cancer patient-derived tumoroids for disease modeling. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:191-200. [PMID: 35124274 DOI: 10.1016/j.slasd.2022.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
3D cell models derived from patient tumors are highly translational tools that can recapitulate the complex genetic and molecular compositions of solid cancers and accelerate identification of drug targets and drug testing. However, the complexity of performing assays with such models remains a hurdle for their wider adoption. In the present study, we describe methods for processing and multi-functional profiling of tumoroid samples to test compound effects using a novel flowchip system in combination with high content imaging and metabolite analysis. Tumoroids were formed from primary cells isolated from a patient-derived tumor explant, TU-BcX-4IC, that represents metaplastic breast cancer with a triple-negative breast cancer subtype. Assays were performed in a microfluidics-based device (Pu⋅MA System) that allows automated exchange of media and treatments of tumoroids in a tissue culture incubator environment. Multi-functional assay profiling was performed on tumoroids treated with anti-cancer drugs. High-content imaging was used to evaluate drug effects on cell viability and expression of E-cadherin and CD44. Lactate secretion was used to measure tumoroid metabolism as a function of time and drug concentration. Observed responses included loss of cell viability, decrease in E-cadherin expression, and increase of lactate production. Importantly, the tumoroids were sensitive to romidepsin and trametinib, while showed significantly reduced sensitivity to paclitaxel and cytarabine, consistent with the primary tumor response. These methods for multi-parametric profiling of drug effects in patient-derived tumoroids provide an in depth understanding of drug sensitivity of individual tumor types, with important implications for the future development of personalized medicine.
Collapse
|
19
|
Ivanov SM, Lagunin AA, Filimonov DA, Poroikov VV. Relationships between the Structure and Severe Drug-Induced Liver Injury for Low, Medium, and High Doses of Drugs. Chem Res Toxicol 2022; 35:402-411. [PMID: 35172101 DOI: 10.1021/acs.chemrestox.1c00307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Assessment of structure-activity relationships (SARs) for predicting severe drug-induced liver injury (DILI) is essential since in vivo and in vitro preclinical methods cannot detect many druglike compounds disrupting liver functions. To date, plenty of SAR models for the prediction of DILI have been developed; however, none of them considered the route of drug administration and daily dose, which may introduce significant bias into prediction results. We have created a dataset of 617 drugs with parenteral and oral administration routes and consistent information on DILI severity. We have found a clear relationship between route, dose, and DILI severity. According to SAR, nearly 40% of moderate- and non-DILI-causing drugs would cause severe DILI if they were administered at high oral doses. We have proposed the following approach to predict severe DILI. New compounds recommended to be used at low oral doses (<∼10 mg daily), or parenterally, can be considered not causing severe DILI. DILI for compounds administered at medium oral doses (∼10-100 mg daily; 22.2% of drugs under consideration) can be considered unpredictable because reasonable SAR models were not obtained due to the small size and heterogeneity of the corresponding dataset. The DILI potential of the compounds recommended to be used at high oral doses (more than ∼100 mg daily) can be estimated using SAR modeling. The balanced accuracy of the approach calculated by a 10-fold cross-validation procedure is 0.803. The developed approach can be used to estimate severe DILI for druglike compounds proposed to use at low and high oral doses or parenterally at the early stages of drug development.
Collapse
Affiliation(s)
- Sergey M Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow 119121, Russia.,Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, Moscow 117997, Russia
| | - Alexey A Lagunin
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow 119121, Russia.,Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, Moscow 117997, Russia
| | - Dmitry A Filimonov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow 119121, Russia
| | - Vladimir V Poroikov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow 119121, Russia
| |
Collapse
|
20
|
Tricot T, Verfaillie CM, Kumar M. Current Status and Challenges of Human Induced Pluripotent Stem Cell-Derived Liver Models in Drug Discovery. Cells 2022; 11:442. [PMID: 35159250 PMCID: PMC8834601 DOI: 10.3390/cells11030442] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 02/08/2023] Open
Abstract
The pharmaceutical industry is in high need of efficient and relevant in vitro liver models, which can be incorporated in their drug discovery pipelines to identify potential drugs and their toxicity profiles. Current liver models often rely on cancer cell lines or primary cells, which both have major limitations. However, the development of human induced pluripotent stem cells (hiPSCs) has created a new opportunity for liver disease modeling, drug discovery and liver toxicity research. hiPSCs can be differentiated to any cell of interest, which makes them good candidates for disease modeling and drug discovery. Moreover, hiPSCs, unlike primary cells, can be easily genome-edited, allowing the creation of reporter lines or isogenic controls for patient-derived hiPSCs. Unfortunately, even though liver progeny from hiPSCs has characteristics similar to their in vivo counterparts, the differentiation of iPSCs to fully mature progeny remains highly challenging and is a major obstacle for the full exploitation of these models by pharmaceutical industries. In this review, we discuss current liver-cell differentiation protocols and in vitro iPSC-based liver models that could be used for disease modeling and drug discovery. Furthermore, we will discuss the challenges that still need to be overcome to allow for the successful implementation of these models into pharmaceutical drug discovery platforms.
Collapse
Affiliation(s)
| | | | - Manoj Kumar
- Stem Cell Institute, KU Leuven, 3000 Leuven, Belgium; (T.T.); (C.M.V.)
| |
Collapse
|
21
|
Chen Z, Jang S, Kaihatu JM, Zhou YH, Wright FA, Chiu WA, Rusyn I. Potential Human Health Hazard of Post-Hurricane Harvey Sediments in Galveston Bay and Houston Ship Channel: A Case Study of Using In Vitro Bioactivity Data to Inform Risk Management Decisions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:13378. [PMID: 34948986 PMCID: PMC8702027 DOI: 10.3390/ijerph182413378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 01/14/2023]
Abstract
Natural and anthropogenic disasters may be associated with redistribution of chemical contaminants in the environment; however, current methods for assessing hazards and risks of complex mixtures are not suitable for disaster response. This study investigated the suitability of in vitro toxicity testing methods as a rapid means of identifying areas of potential human health concern. We used sediment samples (n = 46) from Galveston Bay and the Houston Ship Channel (GB/HSC) areas after hurricane Harvey, a disaster event that led to broad redistribution of chemically-contaminated sediments, including deposition of the sediment on shore due to flooding. Samples were extracted with cyclohexane and dimethyl sulfoxide and screened in a compendium of human primary or induced pluripotent stem cell (iPSC)-derived cell lines from different tissues (hepatocytes, neuronal, cardiomyocytes, and endothelial) to test for concentration-dependent effects on various functional and cytotoxicity phenotypes (n = 34). Bioactivity data were used to map areas of potential concern and the results compared to the data on concentrations of polycyclic aromatic hydrocarbons (PAHs) in the same samples. We found that setting remediation goals based on reducing bioactivity is protective of both "known" risks associated with PAHs and "unknown" risks associated with bioactivity, but the converse was not true for remediation based on PAH risks alone. Overall, we found that in vitro bioactivity can be used as a comprehensive indicator of potential hazards and is an example of a new approach method (NAM) to inform risk management decisions on site cleanup.
Collapse
Affiliation(s)
- Zunwei Chen
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, TX 77843, USA; (Z.C.); (S.J.); (W.A.C.)
| | - Suji Jang
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, TX 77843, USA; (Z.C.); (S.J.); (W.A.C.)
| | - James M. Kaihatu
- Civil & Environmental Engineering and Ocean Engineering, Texas A&M University, College Station, TX 77843, USA;
| | - Yi-Hui Zhou
- Biological Sciences and Statistics, North Carolina State University, Raleigh, NC 27695, USA; (Y.-H.Z.); (F.A.W.)
| | - Fred A. Wright
- Biological Sciences and Statistics, North Carolina State University, Raleigh, NC 27695, USA; (Y.-H.Z.); (F.A.W.)
| | - Weihsueh A. Chiu
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, TX 77843, USA; (Z.C.); (S.J.); (W.A.C.)
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, TX 77843, USA; (Z.C.); (S.J.); (W.A.C.)
| |
Collapse
|
22
|
Matsui T, Shinozawa T. Human Organoids for Predictive Toxicology Research and Drug Development. Front Genet 2021; 12:767621. [PMID: 34790228 PMCID: PMC8591288 DOI: 10.3389/fgene.2021.767621] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/11/2021] [Indexed: 12/11/2022] Open
Abstract
Organoids are three-dimensional structures fabricated in vitro from pluripotent stem cells or adult tissue stem cells via a process of self-organization that results in the formation of organ-specific cell types. Human organoids are expected to mimic complex microenvironments and many of the in vivo physiological functions of relevant tissues, thus filling the translational gap between animals and humans and increasing our understanding of the mechanisms underlying disease and developmental processes. In the last decade, organoid research has attracted increasing attention in areas such as disease modeling, drug development, regenerative medicine, toxicology research, and personalized medicine. In particular, in the field of toxicology, where there are various traditional models, human organoids are expected to blaze a new path in future research by overcoming the current limitations, such as those related to differences in drug responses among species. Here, we discuss the potential usefulness, limitations, and future prospects of human liver, heart, kidney, gut, and brain organoids from the viewpoints of predictive toxicology research and drug development, providing cutting edge information on their fabrication methods and functional characteristics.
Collapse
Affiliation(s)
- Toshikatsu Matsui
- Drug Safety Research and Evaluation, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Tadahiro Shinozawa
- Drug Safety Research and Evaluation, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| |
Collapse
|
23
|
Huang MF, Pang LK, Chen YH, Zhao R, Lee DF. Cardiotoxicity of Antineoplastic Therapies and Applications of Induced Pluripotent Stem Cell-Derived Cardiomyocytes. Cells 2021; 10:2823. [PMID: 34831045 PMCID: PMC8616116 DOI: 10.3390/cells10112823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023] Open
Abstract
The therapeutic landscape for the treatment of cancer has evolved significantly in recent decades, aided by the development of effective oncology drugs. However, many cancer drugs are often poorly tolerated by the body and in particular the cardiovascular system, causing adverse and sometimes fatal side effects that negate the chemotherapeutic benefits. The prevalence and severity of chemotherapy-induced cardiotoxicity warrants a deeper investigation of the mechanisms and implicating factors in this phenomenon, and a consolidation of scientific efforts to develop mitigating strategies. Aiding these efforts is the emergence of induced pluripotent stem cells (iPSCs) in recent years, which has allowed for the generation of iPSC-derived cardiomyocytes (iPSC-CMs): a human-based, patient-derived, and genetically variable platform that can be applied to the study of chemotherapy-induced cardiotoxicity and beyond. After surveying chemotherapy-induced cardiotoxicity and the associated chemotherapeutic agents, we discuss the use of iPSC-CMs in cardiotoxicity modeling, drug screening, and other potential applications. Improvements to the iPSC-CM platform, such as the development of more adult-like cardiomyocytes and ongoing advances in biotechnology, will only enhance the utility of iPSC-CMs in both basic science and clinical applications.
Collapse
Affiliation(s)
- Mo-Fan Huang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.-F.H.); (L.K.P.)
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Lon Kai Pang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.-F.H.); (L.K.P.)
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi-Hung Chen
- Department and Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
| | - Ruiying Zhao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.-F.H.); (L.K.P.)
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.-F.H.); (L.K.P.)
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| |
Collapse
|
24
|
Ashraf M, Khalilitousi M, Laksman Z. Applying Machine Learning to Stem Cell Culture and Differentiation. Curr Protoc 2021; 1:e261. [PMID: 34529356 DOI: 10.1002/cpz1.261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Machine learning techniques are increasingly becoming incorporated into biological research workflows in a variety of disciplines, most notably cancer research and drug discovery. Efforts in stem cell research comparatively lag behind. We detail key paradigms in machine learning, with a focus on equipping stem cell biologists with the understanding necessary to begin conceptualizing and designing machine learning workflows within their own domain of expertise. Supervised approaches in both regression and classification as well as unsupervised clustering techniques are all covered, with examples from across the biological sciences. High-throughput, high-content, multiplex assays for data acquisition are also discussed in the form of single-cell RNA sequencing and image-based approaches. Lastly, potential applications in stem cell biology, including the development of novel cell types, and improving model maturation are also discussed. Machine learning approaches applied in stem cell biology show promise in accelerating progress in developmental biology, drug screening, disease modeling, and personalized medicine. © 2021 Wiley Periodicals LLC.
Collapse
Affiliation(s)
- Mishal Ashraf
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mohammadali Khalilitousi
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zachary Laksman
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
25
|
Chen Z, Lloyd D, Zhou YH, Chiu WA, Wright FA, Rusyn I. Risk Characterization of Environmental Samples Using In Vitro Bioactivity and Polycyclic Aromatic Hydrocarbon Concentrations Data. Toxicol Sci 2021; 179:108-120. [PMID: 33165562 DOI: 10.1093/toxsci/kfaa166] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Methods to assess environmental exposure to hazardous chemicals have primarily focused on quantification of individual chemicals, although chemicals often occur in mixtures, presenting challenges to the traditional risk characterization framework. Sampling sites in a defined geographic region provide an opportunity to characterize chemical contaminants, with spatial interpolation as a tool to provide estimates for non-sampled sites. At the same time, the use of in vitro bioactivity measurements has been shown to be informative for rapid risk-based decisions. In this study, we measured in vitro bioactivity in 39 surface soil samples collected immediately after flooding associated with Hurricane Harvey in Texas in a residential area known to be inundated with polycyclic aromatic hydrocarbon (PAH) contaminants. Bioactivity data were from a number of functional and toxicity assays in 5 human cell types, such as induced pluripotent stem cell-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, as well as human umbilical vein endothelial cells. Data on concentrations of PAH in these samples were also available and the combination of data sources offered a unique opportunity to assess the joint spatial variation of PAH components and bioactivity. We found significant evidence of spatial correlation of a subset of PAH contaminants and of cell-based phenotypes. In addition, we show that the cell-based bioactivity data can be used to predict environmental concentrations for several PAH contaminants, as well as overall PAH summaries and cancer risk. This study's impact lies in its demonstration that cell-based profiling can be used for rapid hazard screening of environmental samples by anchoring the bioassays to concentrations of PAH. This work sets the stage for identification of the areas of concern and direct quantitative risk characterization based on bioactivity data, thereby providing an important supplement to traditional individual chemical analyses by shedding light on constituents that may be missed from targeted chemical monitoring.
Collapse
Affiliation(s)
- Zunwei Chen
- Interdisciplinary Faculty of Toxicology.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843
| | - Dillon Lloyd
- Bioinformatics Research Center.,Departments of Biological Sciences and Statistics, North Carolina State University, Raleigh, North Carolina 27695
| | - Yi-Hui Zhou
- Bioinformatics Research Center.,Departments of Biological Sciences and Statistics, North Carolina State University, Raleigh, North Carolina 27695
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843
| | - Fred A Wright
- Bioinformatics Research Center.,Departments of Biological Sciences and Statistics, North Carolina State University, Raleigh, North Carolina 27695
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843
| |
Collapse
|
26
|
Blanchette AD, Burnett SD, Grimm FA, Rusyn I, Chiu WA. A Bayesian Method for Population-wide Cardiotoxicity Hazard and Risk Characterization Using an In Vitro Human Model. Toxicol Sci 2021; 178:391-403. [PMID: 33078833 DOI: 10.1093/toxsci/kfaa151] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes are an established model for testing potential chemical hazards. Interindividual variability in toxicodynamic sensitivity has also been demonstrated in vitro; however, quantitative characterization of the population-wide variability has not been fully explored. We sought to develop a method to address this gap by combining a population-based iPSC-derived cardiomyocyte model with Bayesian concentration-response modeling. A total of 136 compounds, including 54 pharmaceuticals and 82 environmental chemicals, were tested in iPSC-derived cardiomyocytes from 43 nondiseased humans. Hierarchical Bayesian population concentration-response modeling was conducted for 5 phenotypes reflecting cardiomyocyte function or viability. Toxicodynamic variability was quantified through the derivation of chemical- and phenotype-specific variability factors. Toxicokinetic modeling was used for probabilistic in vitro-to-in vivo extrapolation to derive population-wide margins of safety for pharmaceuticals and margins of exposure for environmental chemicals. Pharmaceuticals were found to be active across all phenotypes. Over half of tested environmental chemicals showed activity in at least one phenotype, most commonly positive chronotropy. Toxicodynamic variability factor estimates for the functional phenotypes were greater than those for cell viability, usually exceeding the generally assumed default of approximately 3. Population variability-based margins of safety for pharmaceuticals were correctly predicted to be relatively narrow, including some below 10; however, margins of exposure for environmental chemicals, based on population exposure estimates, generally exceeded 1000, suggesting they pose little risk at current general population exposures even to sensitive subpopulations. Overall, this study demonstrates how a high-throughput, human population-based, in vitro-in silico model can be used to characterize toxicodynamic population variability in cardiotoxic risk.
Collapse
Affiliation(s)
- Alexander D Blanchette
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458
| | - Sarah D Burnett
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458
| | - Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458
| |
Collapse
|
27
|
Kang SY, Joshi P, Lee MY. High-Throughput Screening of Compound Neurotoxicity Using 3D-Cultured Neural Stem Cells on a 384-Pillar Plate. Curr Protoc 2021; 1:e107. [PMID: 33887124 DOI: 10.1002/cpz1.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Assessing the neurotoxicity of test chemicals has typically been performed using two-dimensionally (2D)-cultured neuronal cell monolayers and animal models. The in vitro 2D cell models are simple and straightforward compared to animal models, which have the disadvantage of being relatively low throughput, expensive, and time consuming. Despite their extensive use in this area of neurotoxicology research, both models often do not accurately recapitulate human outcomes. To bridge this gap and attempt to better replicate what happens in vivo, three-dimensionally (3D) cultured neural stem cells (NSCs) encapsulated in hydrogels on a 384-pillar plate have been developed via miniature 3D bioprinting. This technology allows users to print NSCs on a pillar plate for rapid 3D cell culture as well as high-throughput compound screening. For this, the 384-pillar plate with bioprinted NSCs is sandwiched with a standard 384-well plate with growth medium for 3D culture, allowing researchers to expose the cells to test compounds and stain them with various fluorescent dyes for a suite of high-content imaging assays, including assays for DNA damage, mitochondrial impairment, cell membrane integrity, intracellular glutathione levels, and apoptosis. After acquiring cell images from an automated fluorescence microscope and extracting fluorescence intensities, researchers can obtain the IC50 value of each compound to evaluate critical parameters in neurotoxicity. Here, we provide a detailed description of protocols for cell printing on a 384-pillar plate, 3D NSC culture, compound testing, 3D cell staining, and image acquisition and analysis, which altogether will allow researchers to investigate mechanisms of compound neurotoxicity with 3D-cultured NSCs in a high-throughput manner. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Three-dimensional neural stem cell culture on a 384-pillar plate Basic Protocol 2: Compound treatment and cell staining Basic Protocol 3: Image acquisition, processing, and data analysis.
Collapse
Affiliation(s)
- Soo-Yeon Kang
- Department of Chemical and Biomedical Engineering, Cleveland State University, Cleveland, Ohio
| | - Pranav Joshi
- Department of Chemical and Biomedical Engineering, Cleveland State University, Cleveland, Ohio
| | - Moo-Yeal Lee
- Department of Chemical and Biomedical Engineering, Cleveland State University, Cleveland, Ohio
| |
Collapse
|
28
|
Qosa H, Ribeiro AJS, Hartman NR, Volpe DA. Characterization of a commercially available line of iPSC hepatocytes as models of hepatocyte function and toxicity for regulatory purposes. J Pharmacol Toxicol Methods 2021; 110:107083. [PMID: 34098110 DOI: 10.1016/j.vascn.2021.107083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/11/2021] [Accepted: 06/01/2021] [Indexed: 10/25/2022]
Abstract
It has recently become possible to produce hepatocytes from human induced pluripotent stem cells (iPSC-heps), which may offer some advantages over primary human hepatocytes (Prim-heps) in the regulatory environment. The aim of this research was to assess similarities and differences between commercially available iPSC-heps and Prim-heps in preliminary assays of drug metabolism, hepatotoxicity, and drug transport. Hepatocytes were either cultured in collagen-coated 96-well plates (Prim-heps and 2d-iPSC-heps) or in ultra-low adhesion plates as spheroids (3d-iPSC-heps). 3d-iPSC-heps were used to enhance physiological cell-cell contacts, which is essential to maintain the phenotype of mature hepatocytes. Cytochrome P450 (CYP) 3A4, CYP1A2, and CYP2B6 activity levels were evaluated using fluorescent assays. Phase II metabolism was assessed by HPLC measurement of formation of glucuronides and sulfates of 4-methylumbelliferone, 1-naphthol, and estradiol. The toxicity of acetaminophen, amiodarone, aspirin, clozapine, tacrine, tamoxifen, and troglitazone was monitored using a luminescent cell viability assay. Canaliculi formation was monitored by following the fluorescence of 5,6-carboxy-2',7'-dichlorofluorescein diacetate. All culture models showed similar levels of basal CYP3A4, CYP1A2 and CYP2B6 activity. However, while Prim-heps showed a vigorous response to CYP inducing agents, 2d-iPSC-heps showed no response and 3d-iPSC-heps displayed an inconclusive response. 2d-iPSC-heps showed reduced, yet appreciable, glucuronide and sulfate formation compared to Prim-heps. All culture models showed similar activity in tests of hepatotoxicity, with Prim-heps generally being more sensitive. All models formed canaliculi capable of transporting carboxy-2',7'-dichlorofluorescein. The iPSC-heps appear to be useful for toxicity and transport studies, but metabolic activity is not optimum, and metabolism studies would benefit from a more mature model.
Collapse
Affiliation(s)
- Hisham Qosa
- United States Food and Drug Administration, Center for Drug Evaluation and Research, Office of Translational Sciences, Office of Clinical Pharmacology, Division of Applied Regulatory Science, 10903 New Hampshire Ave, Silver Spring, MD 20993-0002, United States of America
| | - Alexandre J S Ribeiro
- United States Food and Drug Administration, Center for Drug Evaluation and Research, Office of Translational Sciences, Office of Clinical Pharmacology, Division of Applied Regulatory Science, 10903 New Hampshire Ave, Silver Spring, MD 20993-0002, United States of America
| | - Neil R Hartman
- United States Food and Drug Administration, Center for Drug Evaluation and Research, Office of Translational Sciences, Office of Clinical Pharmacology, Division of Applied Regulatory Science, 10903 New Hampshire Ave, Silver Spring, MD 20993-0002, United States of America
| | - Donna A Volpe
- United States Food and Drug Administration, Center for Drug Evaluation and Research, Office of Translational Sciences, Office of Clinical Pharmacology, Division of Applied Regulatory Science, 10903 New Hampshire Ave, Silver Spring, MD 20993-0002, United States of America.
| |
Collapse
|
29
|
Human Pluripotent Stem-Cell-Derived Models as a Missing Link in Drug Discovery and Development. Pharmaceuticals (Basel) 2021; 14:ph14060525. [PMID: 34070895 PMCID: PMC8230131 DOI: 10.3390/ph14060525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs), have the potential to accelerate the drug discovery and development process. In this review, by analyzing each stage of the drug discovery and development process, we identified the active role of hPSC-derived in vitro models in phenotypic screening, target-based screening, target validation, toxicology evaluation, precision medicine, clinical trial in a dish, and post-clinical studies. Patient-derived or genome-edited PSCs can generate valid in vitro models for dissecting disease mechanisms, discovering novel drug targets, screening drug candidates, and preclinically and post-clinically evaluating drug safety and efficacy. With the advances in modern biotechnologies and developmental biology, hPSC-derived in vitro models will hopefully improve the cost-effectiveness and the success rate of drug discovery and development.
Collapse
|
30
|
Alle Q, Le Borgne E, Milhavet O, Lemaitre JM. Reprogramming: Emerging Strategies to Rejuvenate Aging Cells and Tissues. Int J Mol Sci 2021; 22:3990. [PMID: 33924362 PMCID: PMC8070588 DOI: 10.3390/ijms22083990] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Aging is associated with a progressive and functional decline of all tissues and a striking increase in many "age-related diseases". Although aging has long been considered an inevitable process, strategies to delay and potentially even reverse the aging process have recently been developed. Here, we review emerging rejuvenation strategies that are based on reprogramming toward pluripotency. Some of these approaches may eventually lead to medical applications to improve healthspan and longevity.
Collapse
Affiliation(s)
- Quentin Alle
- IRMB, University of Montpellier, INSERM, 34295 Montpellier, France; (Q.A.); (E.L.B.)
| | - Enora Le Borgne
- IRMB, University of Montpellier, INSERM, 34295 Montpellier, France; (Q.A.); (E.L.B.)
| | - Ollivier Milhavet
- IRMB, University of Montpellier, INSERM, CNRS, 34295 Montpellier, France
| | - Jean-Marc Lemaitre
- IRMB, University of Montpellier, INSERM, 34295 Montpellier, France; (Q.A.); (E.L.B.)
| |
Collapse
|
31
|
Fritsche E, Haarmann-Stemmann T, Kapr J, Galanjuk S, Hartmann J, Mertens PR, Kämpfer AAM, Schins RPF, Tigges J, Koch K. Stem Cells for Next Level Toxicity Testing in the 21st Century. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006252. [PMID: 33354870 DOI: 10.1002/smll.202006252] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/13/2020] [Indexed: 06/12/2023]
Abstract
The call for a paradigm change in toxicology from the United States National Research Council in 2007 initiates awareness for the invention and use of human-relevant alternative methods for toxicological hazard assessment. Simple 2D in vitro systems may serve as first screening tools, however, recent developments infer the need for more complex, multicellular organotypic models, which are superior in mimicking the complexity of human organs. In this review article most critical organs for toxicity assessment, i.e., skin, brain, thyroid system, lung, heart, liver, kidney, and intestine are discussed with regards to their functions in health and disease. Embracing the manifold modes-of-action how xenobiotic compounds can interfere with physiological organ functions and cause toxicity, the need for translation of such multifaceted organ features into the dish seems obvious. Currently used in vitro methods for toxicological applications and ongoing developments not yet arrived in toxicity testing are discussed, especially highlighting the potential of models based on embryonic stem cells and induced pluripotent stem cells of human origin. Finally, the application of innovative technologies like organs-on-a-chip and genome editing point toward a toxicological paradigm change moves into action.
Collapse
Affiliation(s)
- Ellen Fritsche
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
- Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | | | - Julia Kapr
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Saskia Galanjuk
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Julia Hartmann
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Peter R Mertens
- Department of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke-University Magdeburg, Magdeburg, 39106, Germany
| | - Angela A M Kämpfer
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Roel P F Schins
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Julia Tigges
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Katharina Koch
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| |
Collapse
|
32
|
Cromwell EF, Leung M, Hammer M, Thai A, Rajendra R, Sirenko O. Disease Modeling with 3D Cell-Based Assays Using a Novel Flowchip System and High-Content Imaging. SLAS Technol 2021; 26:237-248. [PMID: 33783259 DOI: 10.1177/24726303211000688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
There is an increasing interest in using three-dimensional (3D) cell structures for modeling tumors, organs, and tissue to accelerate translational research. We describe here a novel automated organoid assay system (the Pu·MA System) combined with microfluidic-based flowchips that can facilitate 3D cell-based assays. The flowchip is composed of sample wells, which contain organoids, connected to additional multiple wells that can hold various assay reagents. Organoids are positioned in a protected chamber in sample wells, and fluids are exchanged from side reservoirs using pressure-driven flow. Media exchange, sample staining, wash steps, and other processes can be performed without disruption to or loss of 3D sample. The bottom of the sample chamber is thin, optically clear plastic compatible with high-content imaging (HCI). The whole system can be kept in an incubator, allowing long-term cellular assays to be performed. We present two examples of use of the system for biological research. In the first example, cytotoxicity effects of anticancer drugs were evaluated on HeLa and HepG2 spheroids using HCI and vascular endothelial growth factor expression. In the second application, the flowchip system was used for the functional evaluation of Ca2+ oscillations in neurospheroids. Neurospheres were incubated with neuroactive compounds, and neuronal activity was assessed using Ca2+-sensitive dyes and fast kinetic fluorescence imaging. This novel assay system using microfluidics enables automation of 3D cell-based cultures that mimic in vivo conditions, performs multidosing protocols and multiple media exchanges, provides gentle handling of spheroids and organoids, and allows a wide range of assay detection modalities.
Collapse
|
33
|
Ahmed U, Ahmed R, Masoud MS, Tariq M, Ashfaq UA, Augustine R, Hasan A. Stem cells based in vitro models: trends and prospects in biomaterials cytotoxicity studies. Biomed Mater 2021; 16:042003. [PMID: 33686970 DOI: 10.1088/1748-605x/abe6d8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Advanced biomaterials are increasingly used for numerous medical applications from the delivery of cancer-targeted therapeutics to the treatment of cardiovascular diseases. The issues of foreign body reactions induced by biomaterials must be controlled for preventing treatment failure. Therefore, it is important to assess the biocompatibility and cytotoxicity of biomaterials on cell culture systems before proceeding to in vivo studies in animal models and subsequent clinical trials. Direct use of biomaterials on animals create technical challenges and ethical issues and therefore, the use of non-animal models such as stem cell cultures could be useful for determination of their safety. However, failure to recapitulate the complex in vivo microenvironment have largely restricted stem cell cultures for testing the cytotoxicity of biomaterials. Nevertheless, properties of stem cells such as their self-renewal and ability to differentiate into various cell lineages make them an ideal candidate for in vitro screening studies. Furthermore, the application of stem cells in biomaterials screening studies may overcome the challenges associated with the inability to develop a complex heterogeneous tissue using primary cells. Currently, embryonic stem cells, adult stem cells, and induced pluripotent stem cells are being used as in vitro preliminary biomaterials testing models with demonstrated advantages over mature primary cell or cell line based in vitro models. This review discusses the status and future directions of in vitro stem cell-based cultures and their derivatives such as spheroids and organoids for the screening of their safety before their application to animal models and human in translational research.
Collapse
Affiliation(s)
- Uzair Ahmed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000 Punjab, Pakistan
| | | | | | | | | | | | | |
Collapse
|
34
|
Burnett SD, Blanchette AD, Chiu WA, Rusyn I. Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes as an in vitro model in toxicology: strengths and weaknesses for hazard identification and risk characterization. Expert Opin Drug Metab Toxicol 2021; 17:887-902. [PMID: 33612039 DOI: 10.1080/17425255.2021.1894122] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes is one of the most widely used cell-based models that resulted from the discovery of how non-embryonic stem cells can be differentiated into multiple cell types. In just one decade, iPSC-derived cardiomyocytes went from a research lab to widespread use in biomedical research and preclinical safety evaluation for drugs and other chemicals. AREAS COVERED This manuscript reviews data on toxicology applications of human iPSC-derived cardiomyocytes. We detail the outcome of a systematic literature search on their use (i) in hazard assessment for cardiotoxicity liabilities, (ii) for risk characterization, (iii) as models for population variability, and (iv) in studies of personalized medicine and disease. EXPERT OPINION iPSC-derived cardiomyocytes are useful to increase the accuracy, precision, and efficiency of cardiotoxicity hazard identification for both drugs and non-pharmaceuticals, with recent efforts beginning to demonstrate their utility for risk characterization. Notable limitations include the needs to improve the maturation of cells in culture, to better understand their potential use identifying structural cardiotoxicity, and for additional case studies involving population-wide and disease-specific risk characterization. Ultimately, the greatest future benefits are likely for non-pharmaceutical chemicals, filling a critical gap where no routine testing for cardiotoxicity is currently performed.
Collapse
Affiliation(s)
- Sarah D Burnett
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Alexander D Blanchette
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| |
Collapse
|
35
|
Thomas D, Shenoy S, Sayed N. Building Multi-Dimensional Induced Pluripotent Stem Cells-Based Model Platforms to Assess Cardiotoxicity in Cancer Therapies. Front Pharmacol 2021; 12:607364. [PMID: 33679396 PMCID: PMC7930625 DOI: 10.3389/fphar.2021.607364] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular disease (CVD) complications have contributed significantly toward poor survival of cancer patients worldwide. These complications that result in myocardial and vascular damage lead to long-term multisystemic disorders. In some patient cohorts, the progression from acute to symptomatic CVD state may be accelerated due to exacerbation of underlying comorbidities such as obesity, diabetes and hypertension. In such situations, cardio-oncologists are often left with a clinical predicament in finding the optimal therapeutic balance to minimize cardiovascular risks and maximize the benefits in treating cancer. Hence, prognostically there is an urgent need for cost-effective, rapid, sensitive and patient-specific screening platform to allow risk-adapted decision making to prevent cancer therapy related cardiotoxicity. In recent years, momentous progress has been made toward the successful derivation of human cardiovascular cells from induced pluripotent stem cells (iPSCs). This technology has not only provided deeper mechanistic insights into basic cardiovascular biology but has also seamlessly integrated within the drug screening and discovery programs for early efficacy and safety evaluation. In this review, we discuss how iPSC-derived cardiovascular cells have been utilized for testing oncotherapeutics to pre-determine patient predisposition to cardiovascular toxicity. Lastly, we highlight the convergence of tissue engineering technologies and precision medicine that can enable patient-specific cardiotoxicity prognosis and treatment on a multi-organ level.
Collapse
Affiliation(s)
- Dilip Thomas
- Stanford Cardiovascular Institute, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, United States
| | - Sushma Shenoy
- Stanford Cardiovascular Institute, Stanford, CA, United States
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, United States.,Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
| |
Collapse
|
36
|
MacFarlane EM, Bruin JE. Human Pluripotent Stem Cells: A Unique Tool for Toxicity Testing in Pancreatic Progenitor and Endocrine Cells. Front Endocrinol (Lausanne) 2021; 11:604998. [PMID: 33542706 PMCID: PMC7851047 DOI: 10.3389/fendo.2020.604998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022] Open
Abstract
Diabetes prevalence is increasing worldwide, and epidemiological studies report an association between diabetes incidence and environmental pollutant exposure. There are >84,000 chemicals in commerce, many of which are released into the environment without a clear understanding of potential adverse health consequences. While in vivo rodent studies remain an important tool for testing chemical toxicity systemically, we urgently need high-throughput screening platforms in biologically relevant models to efficiently prioritize chemicals for in depth toxicity analysis. Given the increasing global burden of obesity and diabetes, identifying chemicals that disrupt metabolism should be a high priority. Pancreatic endocrine cells are key regulators of systemic metabolism, yet often overlooked as a target tissue in toxicology studies. Immortalized β-cell lines and primary human, porcine, and rodent islets are widely used for studying the endocrine pancreas in vitro, but each have important limitations in terms of scalability, lifespan, and/or biological relevance. Human pluripotent stem cell (hPSC) culture is a powerful tool for in vitro toxicity testing that addresses many of the limitations with other β-cell models. Current in vitro differentiation protocols can efficiently generate glucose-responsive insulin-secreting β-like cells that are not fully mature, but still valuable for high-throughput toxicity screening in vitro. Furthermore, hPSCs can be applied as a model of developing pancreatic endocrine cells to screen for chemicals that influence endocrine cell formation during critical windows of differentiation. Given their versatility, we recommend using hPSCs to identify potential β-cell toxins, which can then be prioritized as chemicals of concern for metabolic disruption.
Collapse
Affiliation(s)
| | - Jennifer E. Bruin
- Department of Biology & Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
| |
Collapse
|
37
|
Luo YS, Chen Z, Blanchette AD, Zhou YH, Wright FA, Baker ES, Chiu WA, Rusyn I. Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes. Food Chem Toxicol 2021; 149:111979. [PMID: 33450301 DOI: 10.1016/j.fct.2021.111979] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/24/2022]
Abstract
Consumption of energy drinks has been associated with adverse cardiovascular effects; however, little is known about the ingredients that may contribute to these effects. We therefore characterized the chemical profiles and in vitro effects of energy drinks and their ingredients on human induced pluripotent stem cell (iPSC)-derived cardiomyocytes, and identified the putative active ingredients using a multivariate prediction model. Energy drinks from 17 widely-available over-the-counter brands were evaluated in this study. The concentrations of six common ingredients (caffeine, taurine, riboflavin, pantothenic acid, adenine, and L-methionine) were quantified by coupling liquid chromatography with a triple quadrupole mass spectrometer for the acquisition of LC-MS/MS spectra. In addition, untargeted analyses for each beverage were performed with a platform combining LC, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) measurements. Approximately 300 features were observed across samples in the untargeted studies, and of these ~100 were identified. In vitro effects of energy drinks and some of their ingredients were then tested in iPSC-derived cardiomyocytes. Data on the beat rate (positive and negative chronotropy), ion channel function (QT prolongation), and cytotoxicity were collected in a dilution series. We found that some of the energy drinks elicited adverse effects on the cardiomyocytes with the most common being an increase in the beat rate, while QT prolongation was also observed at the lowest concentrations. Finally, concentration addition modeling using quantitative data from the 6 common ingredients and multivariate prediction modeling was used to determine potential ingredients responsible for the adverse effects on the cardiomyocytes. These analyses suggested theophylline, adenine, and azelate as possibly contributing to the in vitro effects of energy drinks on QT prolongation in cardiomyocytes.
Collapse
Affiliation(s)
- Yu-Syuan Luo
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Zunwei Chen
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Alexander D Blanchette
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Yi-Hui Zhou
- Departments of Statistics and Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Fred A Wright
- Departments of Statistics and Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
38
|
Hsieh NH, Chen Z, Rusyn I, Chiu WA. Risk Characterization and Probabilistic Concentration-Response Modeling of Complex Environmental Mixtures Using New Approach Methodologies (NAMs) Data from Organotypic in Vitro Human Stem Cell Assays. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:17004. [PMID: 33395322 PMCID: PMC7781439 DOI: 10.1289/ehp7600] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Risk assessment of chemical mixtures or complex substances remains a major methodological challenge due to lack of available hazard or exposure data. Therefore, risk assessors usually infer hazard or risk from data on the subset of constituents with available toxicity values. OBJECTIVES We evaluated the validity of the widely used traditional mixtures risk assessment paradigms, Independent Action (IA) and Concentration Addition (CA), with new approach methodologies (NAMs) data from human cell-based in vitro assays. METHODS A diverse set of 42 chemicals was tested both individually and as mixtures for functional and cytotoxic effects in vitro. A panel of induced pluripotent stem cell (iPSCs)-derived models (hepatocytes, cardiomyocytes, endothelial, and neurons) and one primary cell type (HUVEC) were used. Bayesian concentration-response modeling of individual chemicals or their mixtures was performed for a total of 47 phenotypes to derive point-of-departure (POD) values. Probabilistic IA or CA was conducted to estimate the mixture effects based on the bioactivity profiles from the individual chemicals and compared with mixture bioactivity. RESULTS All mixtures showed significant bioactivity, even though some were constructed using individual chemical concentrations considered "low" or "safe." Even though CA is much more accurate as a predictor of mixture effects in comparison with IA, with CA-based POD typically within an order of magnitude of the actual mixture, in some cases, the bioactivity of the mixtures appeared to be much greater than that of their components under either additivity assumption. DISCUSSION These results suggest that CA is a preferred first approximation for predicting mixture toxicity when data for all constituents are available. However, because the accuracy of additivity assumptions varies greatly across phenotypes, we posit that mixtures and complex substances need to be directly tested for their hazard potential. NAMs provide a practical solution that rapidly yields highly informative data for mixtures risk assessment. https://doi.org/10.1289/EHP7600.
Collapse
Affiliation(s)
- Nan-Hung Hsieh
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Zunwei Chen
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Weihsueh A. Chiu
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| |
Collapse
|
39
|
Talikka M, Belcastro V, Boué S, Marescotti D, Hoeng J, Peitsch MC. Applying Systems Toxicology Methods to Drug Safety. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11522-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
40
|
Analysis of reproducibility and robustness of a human microfluidic four-cell liver acinus microphysiology system (LAMPS). Toxicology 2020; 448:152651. [PMID: 33307106 DOI: 10.1016/j.tox.2020.152651] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/06/2020] [Accepted: 11/27/2020] [Indexed: 02/07/2023]
Abstract
A human microfluidic four-cell liver acinus microphysiology system (LAMPS), was evaluated for reproducibility and robustness as a model for drug pharmacokinetics and toxicology. The model was constructed using primary human hepatocytes or human induced pluripotent stem cell (iPSC)-derived hepatocytes and 3 human cell lines for the endothelial, Kupffer and stellate cells. The model was tested in two laboratories and demonstrated to be reproducible in terms of basal function of hepatocytes, Terfenadine metabolism, and effects of Tolcapone (88 μM), Troglitazone (150 μM), and caffeine (600 μM) over 9 days in culture. Additional experiments compared basal outputs of albumin, urea, lactate dehydrogenase (LDH) and tumor necrosis factor (TNF)α, as well as drug metabolism and toxicity in the LAMPS model, and in 2D cultures seeded with either primary hepatocytes or iPSC-hepatocytes. Further experiments to study the effects of Terfenadine (10 μM), Tolcapone (88 μM), Trovafloxacin (150 μM with or without 1 μg/mL lipopolysaccharide), Troglitazone (28 μM), Rosiglitazone (0.8 μM), Pioglitazone (3 μM), and caffeine (600 μM) were carried out over 10 days. We found that both primary human hepatocytes and iPSC-derived hepatocytes in 3D culture maintained excellent basal liver function and Terfenadine metabolism over 10 days compared the same cells in 2D cultures. In 2D, non-overlay monolayer cultures, both cell types lost hepatocyte phenotypes after 48 h. With respect to drug effects, both cell types demonstrated comparable and more human-relevant effects in LAMPS, as compared to 2D cultures. Overall, these studies show that LAMPS is a robust and reproducible in vitro liver model, comparable in performance when seeded with either primary human hepatocytes or iPSC-derived hepatocytes, and more physiologically and clinically relevant than 2D monolayer cultures.
Collapse
|
41
|
Lee G, Kim H, Park JY, Kim G, Han J, Chung S, Yang JH, Jeon JS, Woo DH, Han C, Kim SK, Park HJ, Kim JH. Generation of uniform liver spheroids from human pluripotent stem cells for imaging-based drug toxicity analysis. Biomaterials 2020; 269:120529. [PMID: 33257114 DOI: 10.1016/j.biomaterials.2020.120529] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022]
Abstract
Recent advances in pluripotent stem cell technology provide an alternative source of human hepatocytes to overcome the limitations of current toxicity tests. However, this approach requires optimization and standardization before it can be used as a fast and reliable toxicity screening system. Here, we designed and tested microwell culture platforms with various diameters. We found that large quantities of uniformly-sized hepatocyte-like cell (HLC) spheroids (3D-uniHLC-Ss) could be efficiently and reproducibly generated in a short period time from a small number of differentiating human pluripotent stem cells (hPSCs). The hPSC-3D-uniHLC-Ss that were produced in 500-μm diameter microwells consistently exhibited high expressions of hepatic marker genes and had no significant signs of cell death. Importantly, a hepatic master gene hepatocyte nuclear factor 4α (HNF4α) was maintained at high levels, and the epithelial-mesenchymal transition was significantly attenuated in hPSC-3D-uniHLC-Ss. Additionally, when compared with 3D-HLC-Ss that were produced in other 3D platforms, hPSC-3D-uniHLC-Ss showed significantly higher hepatic gene expressions and drug-metabolizing activity of the enzyme, CYP3A4. Imaging-based drug toxicity studies demonstrated that hPSC-3D-uniHLC-Ss exhibited enhanced sensitivity to various hepatotoxicants, compared to HLCs, which were differentiated under 2D conditions. Precise prediction of drug-induced hepatotoxicity is a crucial step in the early phases of drug discovery. Thus, the hPSC-3D-uniHLC-Ss produced using our microwell platform could be used as an imaging-based toxicity screening system to predict drug hepatotoxicity.
Collapse
Affiliation(s)
- Gyunggyu Lee
- Laboratory of Stem Cells and Tissue Regeneration, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Hyemin Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, South Korea
| | - Ji Young Park
- Laboratory of Stem Cells and Tissue Regeneration, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Gyeongmin Kim
- Laboratory of Stem Cells and Tissue Regeneration, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Jiyou Han
- Department of Biological Sciences, Hyupsung University, Hwasung-si, 18330, South Korea
| | - Seok Chung
- School of Mechanical Engineering, Korea University, Seoul, 20841, South Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, South Korea
| | - Ji Hun Yang
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, South Korea
| | - Jang Su Jeon
- Chungnam National University, Daejeon, 34134, South Korea
| | - Dong-Hun Woo
- Laboratory of Stem Cells, NEXEL Co., Ltd., Seoul, 02580, South Korea
| | - Choongseong Han
- Laboratory of Stem Cells, NEXEL Co., Ltd., Seoul, 02580, South Korea
| | - Sang Kyum Kim
- Chungnam National University, Daejeon, 34134, South Korea.
| | - Han-Jin Park
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, South Korea.
| | - Jong-Hoon Kim
- Laboratory of Stem Cells and Tissue Regeneration, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea.
| |
Collapse
|
42
|
Truong KM, Feng W, Pessah IN. Ryanodine Receptor Type 2: A Molecular Target for Dichlorodiphenyltrichloroethane- and Dichlorodiphenyldichloroethylene-Mediated Cardiotoxicity. Toxicol Sci 2020; 178:159-172. [PMID: 32894766 PMCID: PMC7850024 DOI: 10.1093/toxsci/kfaa139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Dichlorodiphenyltrichloroethane (DDT) and its metabolite dichlorodiphenyl-dichloroethylene (DDE) are ubiquitously found in the environment and linked to cardiovascular diseases-with a majority of the work focused on hypertension. Studies investigating whether DDx can interact with molecular targets on cardiac tissue to directly affect cardiac function are lacking. Therefore, we investigated whether o,p'-DDT, p,p'-DDT, o,p'-DDE, or p,p'-DDE (DDx, collectively) can directly alter the function of human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) by assessing their effect(s) on hiPSC-CMs Ca2+ dynamics. DDx (0.1-10 µM) affected hiPSC-CMs synchronous Ca2+ oscillation frequency in a concentration-dependent manner, with p,p'-DDT and p,p'-DDE also decreasing Ca2+ stores. HEK-RyR2 cells cultured under antibiotic selection to induce expression of wild-type mouse ryanodine receptor type 2 (RyR2) are used to further investigate whether DDx alters hiPSC-CMs Ca2+ dynamics through engagement with RyR2, a protein critical for cardiac muscle excitation-contraction coupling (ECC). Acute treatment with 10 µM DDx failed to induce Ca2+ release in HEK293-RyR2, whereas pretreatment with DDx (0.1-10 µM) for 12- or 24-h significantly decreased sarcoplasmic reticulum Ca2+ stores in HEK-RyR2 cells challenged with caffeine (1 mM), an RyR agonist. [3H]ryanodine-binding analysis using murine cardiac RyR2 homogenates further confirmed that all DDx isomers (10 µM) can directly engage with RyR2 to favor an open (leaky) confirmation, whereas only the DDT isomers (10 µM) modestly (≤10%) inhibited SERCA2a activity. The data demonstrate that DDx increases heart rate and depletes Ca2+ stores in human cardiomyocytes through a mechanism that impairs RyR2 function and Ca2+ dynamics. IMPACT STATEMENT DDT/DDE interactions with RyR2 alter cardiomyocyte Ca2+ dynamics that may contribute to adverse cardiovascular outcomes associated with exposures.
Collapse
Affiliation(s)
- Kim M Truong
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616-5270
| | - Wei Feng
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616-5270
| | - Isaac N Pessah
- To whom correspondence should be addressed at Department of Molecular Biosciences, School of Veterinary Medicine, University of California, 1089 Veterinary Medicine Drive, Davis, CA 95616. E-mail:
| |
Collapse
|
43
|
Constantinou C, Miranda AMA, Chaves P, Bellahcene M, Massaia A, Cheng K, Samari S, Rothery SM, Chandler AM, Schwarz RP, Harding SE, Punjabi P, Schneider MD, Noseda M. Human pluripotent stem cell-derived cardiomyocytes as a target platform for paracrine protection by cardiac mesenchymal stromal cells. Sci Rep 2020; 10:13016. [PMID: 32747668 PMCID: PMC7400574 DOI: 10.1038/s41598-020-69495-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
Ischemic heart disease remains the foremost cause of death globally, with survivors at risk for subsequent heart failure. Paradoxically, cell therapies to offset cardiomyocyte loss after ischemic injury improve long-term cardiac function despite a lack of durable engraftment. An evolving consensus, inferred preponderantly from non-human models, is that transplanted cells benefit the heart via early paracrine signals. Here, we tested the impact of paracrine signals on human cardiomyocytes, using human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) as the target of mouse and human cardiac mesenchymal stromal cells (cMSC) with progenitor-like features. In co-culture and conditioned medium studies, cMSCs markedly inhibited human cardiomyocyte death. Little or no protection was conferred by mouse tail tip or human skin fibroblasts. Consistent with the results of transcriptomic profiling, functional analyses showed that the cMSC secretome suppressed apoptosis and preserved cardiac mitochondrial transmembrane potential. Protection was independent of exosomes under the conditions tested. In mice, injecting cMSC-conditioned media into the infarct border zone reduced apoptotic cardiomyocytes > 70% locally. Thus, hPSC-CMs provide an auspicious, relevant human platform to investigate extracellular signals for cardiac muscle survival, substantiating human cardioprotection by cMSCs, and suggesting the cMSC secretome or its components as potential cell-free therapeutic products.
Collapse
Affiliation(s)
- Chrystalla Constantinou
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Antonio M A Miranda
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London, W12 0NN, UK
| | - Patricia Chaves
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London, W12 0NN, UK
| | - Mohamed Bellahcene
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London, W12 0NN, UK
| | - Andrea Massaia
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London, W12 0NN, UK
| | - Kevin Cheng
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Sara Samari
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London, W12 0NN, UK
| | - Stephen M Rothery
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Anita M Chandler
- Kardia Therapeutics, Houston, TX, 77030, USA
- Department of Bioengineering, BioScience Research Collaborative, Rice University, Houston, TX, 77005, USA
| | - Richard P Schwarz
- Kardia Therapeutics, Houston, TX, 77030, USA
- CV Ventures, LLC, Blue Bell, PA, 19422, USA
| | - Sian E Harding
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London, W12 0NN, UK
| | - Prakash Punjabi
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London, W12 0NN, UK
- Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Michael D Schneider
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London, W12 0NN, UK.
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London, W12 0NN, UK.
| |
Collapse
|
44
|
Maddah M, Mandegar MA, Dame K, Grafton F, Loewke K, Ribeiro AJS. Quantifying drug-induced structural toxicity in hepatocytes and cardiomyocytes derived from hiPSCs using a deep learning method. J Pharmacol Toxicol Methods 2020; 105:106895. [PMID: 32629158 DOI: 10.1016/j.vascn.2020.106895] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022]
Abstract
Cardiac and hepatic toxicity result from induced disruption of the functioning of cardiomyocytes and hepatocytes, respectively, which is tightly related to the organization of their subcellular structures. Cellular structure can be analyzed from microscopy imaging data. However, subtle or complex structural changes that are not easily perceived may be missed by conventional image-analysis techniques. Here we report the evaluation of PhenoTox, an image-based deep-learning method of quantifying drug-induced structural changes using human hepatocytes and cardiomyocytes derived from human induced pluripotent stem cells. We assessed the ability of the deep learning method to detect variations in the organization of cellular structures from images of fixed or live cells. We also evaluated the power and sensitivity of the method for detecting toxic effects of drugs by conducting a set of experiments using known toxicants and other methods of screening for cytotoxic effects. Moreover, we used PhenoTox to characterize the effects of tamoxifen and doxorubicin-which cause liver toxicity-on hepatocytes. PhenoTox revealed differences related to loss of cytochrome P450 3A4 activity, for which it showed greater sensitivity than a caspase 3/7 assay. Finally, PhenoTox detected structural toxicity in cardiomyocytes, which was correlated with contractility defects induced by doxorubicin, erlotinib, and sorafenib. Taken together, the results demonstrated that PhenoTox can capture the subtle morphological changes that are early signs of toxicity in both hepatocytes and cardiomyocytes.
Collapse
Affiliation(s)
| | | | - Keri Dame
- Division of Applied Regulatory Science, Office of Translational Science, Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | | | | | - Alexandre J S Ribeiro
- Division of Applied Regulatory Science, Office of Translational Science, Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| |
Collapse
|
45
|
Grimm FA, Klaren WD, Li X, Lehmler HJ, Karmakar M, Robertson LW, Chiu WA, Rusyn I. Cardiovascular Effects of Polychlorinated Biphenyls and Their Major Metabolites. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:77008. [PMID: 32701041 PMCID: PMC7377239 DOI: 10.1289/ehp7030] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND Xenobiotic metabolism is complex, and accounting for bioactivation and detoxification processes of chemicals remains among the most challenging aspects for decision making with in vitro new approach methods data. OBJECTIVES Considering the physiological relevance of human organotypic culture models and their utility for high-throughput screening, we hypothesized that multidimensional chemical-biological profiling of chemicals and their major metabolites is a sensible alternative for the toxicological characterization of parent molecules vs. metabolites in vitro. METHODS In this study, we tested 25 polychlorinated biphenyls (PCBs) [PCB 3, 11, 52, 126, 136, and 153 and their relevant metabolites (hydroxylated, methoxylated, sulfated, and quinone)] in concentration-response (10 nM-100μM) for effects in human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (CMs) and endothelial cells (ECs) (iPSC-derived and HUVECs). Functional phenotypic end points included effects on beating parameters and intracellular Ca2+ flux in CMs and inhibition of tubulogenesis in ECs. High-content imaging was used to evaluate cytotoxicity, mitochondrial integrity, and oxidative stress. RESULTS Data integration of a total of 19 physicochemical descriptors and 36 in vitro phenotypes revealed that chlorination status and metabolite class are strong predictors of the in vitro cardiovascular effects of PCBs. Oxidation of PCBs, especially to di-hydroxylated and quinone metabolites, was associated with the most pronounced effects, whereas sulfation and methoxylation of PCBs resulted in diminished bioactivity. DISCUSSION Risk characterization analysis showed that although in vitro derived effective concentrations exceeded the levels measured in the general population, risks cannot be ruled out due to the potential for population variability in susceptibility and the need to fill data gaps using read-across approaches. This study demonstrated a strategy for how in vitro data can be used to characterize human health risks from PCBs and their metabolites. https://doi.org/10.1289/EHP7030.
Collapse
Affiliation(s)
- Fabian A. Grimm
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - William D. Klaren
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Xueshu Li
- Department of Occupational and Environmental Health, College of Public Health, The University of Iowa, Iowa City, Iowa, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, College of Public Health, The University of Iowa, Iowa City, Iowa, USA
| | - Moumita Karmakar
- Department of Statistics, College of Science, Texas A&M University, College Station, Texas, USA
| | - Larry W. Robertson
- Department of Occupational and Environmental Health, College of Public Health, The University of Iowa, Iowa City, Iowa, USA
| | - Weihsueh A. Chiu
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| |
Collapse
|
46
|
Optimum concentration-response curve metrics for supervised selection of discriminative cellular phenotypic endpoints for chemical hazard assessment. Arch Toxicol 2020; 94:2951-2964. [PMID: 32601827 DOI: 10.1007/s00204-020-02813-3] [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: 03/01/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
High-content imaging (HCI) provides quantitative and information-rich measurements of chemical effects on human in vitro cell models. Identification of discriminative phenotypic endpoints from cellular features obtained from HCI is required for accurate assessments of potential chemical hazards. However, the use of suboptimal metrics to quantify the concentration-response curves (CRC) of chemicals based on these features may obscure discriminative features, and lead to non-predictive endpoints and poor chemical classifications or hazard assessments. Here, we present a systematic and data-driven study on the performances of different CRC metrics in identifying image-based phenotypic features that can accurately classify the effects of reference chemicals with known in vivo toxicities. We studied four previous HCI in vitro nephro- or pulmono-toxicity datasets, which contain phenotypic feature measurements from different cell and feature types. Within a feature type, we found that efficacy metrics at higher chemical concentrations tend to give higher classification accuracy, whereas potency metrics do not have obvious trends across different response levels. Across different cell and feature types, efficacy metrics generally gave higher classification accuracy than potency metrics and area under the curve (AUC). Our results suggest that efficacy metrics, especially at higher concentrations, are more likely to help us to identify discriminative phenotypic endpoints. Therefore, HCI experiments for toxicological applications should include measurements at sufficiently high chemical concentrations, and efficacy metrics should always be analyzed. The identified features may be used as specific toxicity endpoints for further chemical hazard assessment.
Collapse
|
47
|
Chen Z, Liu Y, Wright FA, Chiu WA, Rusyn I. Rapid hazard characterization of environmental chemicals using a compendium of human cell lines from different organs. ALTEX 2020; 37:623-638. [PMID: 32521033 PMCID: PMC7941183 DOI: 10.14573/altex.2002291] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023]
Abstract
The lack of adequate toxicity data for the vast majority of chemicals in the environment has spurred the development of new approach methodologies (NAMs). This study aimed to develop a practical high-throughput in vitro model for rapidly evaluating potential hazards of chemicals using a small number of human cells. Forty-two compounds were tested using human induced pluripotent stem cell (iPSC)-derived cells (hepatocytes, neurons, cardiomyocytes and endothelial cells), and a primary endothelial cell line. Both functional and cytotoxicity endpoints were evaluated using high-content imaging. Concentration-response was used to derive points-of-departure (POD). PODs were integrated with ToxPi and used as surrogate NAM-based PODs for risk characterization. We found chemical class-specific similarity among the chemicals tested; metal salts exhibited the highest overall bioactivity. We also observed cell type-specific patterns among classes of chemicals, indicating the ability of the proposed in vitro model to recognize effects on different cell types. Compared to available NAM datasets, such as ToxCast/Tox21 and chemical structure-based descriptors, we found that the data from the five-cell-type model was as good or even better in assigning compounds to chemical classes. Additionally, the PODs from this model performed well as a conservative surrogate for regulatory in vivo PODs and were less likely to underestimate in vivo potency and potential risk compared to other NAM-based PODs. In summary, we demonstrate the potential of this in vitro screening model to inform rapid risk-based decision-making through ranking, clustering, and assessment of both hazard and risks of diverse environmental chemicals.
Collapse
Affiliation(s)
- Zunwei Chen
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Yizhong Liu
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Fred A. Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Departments of Statistics and Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Weihsueh A. Chiu
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| |
Collapse
|
48
|
Herholt A, Galinski S, Geyer PE, Rossner MJ, Wehr MC. Multiparametric Assays for Accelerating Early Drug Discovery. Trends Pharmacol Sci 2020; 41:318-335. [PMID: 32223968 DOI: 10.1016/j.tips.2020.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 02/07/2023]
Abstract
Drug discovery campaigns are hampered by substantial attrition rates largely due to a lack of efficacy and safety reasons associated with candidate drugs. This is true in particular for genetically complex diseases, where insufficient knowledge of the modulatory actions of candidate drugs on targets and entire target pathways further adds to the problem of attrition. To better profile compound actions on targets, potential off-targets, and disease-linked pathways, new innovative technologies need to be developed that can elucidate the complex cellular signaling networks in health and disease. Here, we discuss progress in genetically encoded multiparametric assays and mass spectrometry (MS)-based proteomics, which both represent promising toolkits to profile multifactorial actions of drug candidates in disease-relevant cellular systems to promote drug discovery and personalized medicine.
Collapse
Affiliation(s)
- Alexander Herholt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Sabrina Galinski
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; OmicEra Diagnostics GmbH, Am Klopferspitz 19, 82152, Planegg, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Michael C Wehr
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany.
| |
Collapse
|
49
|
Hepatotoxicity Modeling Using Counter-Propagation Artificial Neural Networks: Handling an Imbalanced Classification Problem. Molecules 2020; 25:molecules25030481. [PMID: 31979300 PMCID: PMC7037161 DOI: 10.3390/molecules25030481] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
Drug-induced liver injury is a major concern in the drug development process. Expensive and time-consuming in vitro and in vivo studies do not reflect the complexity of the phenomenon. Complementary to wet lab methods are in silico approaches, which present a cost-efficient method for toxicity prediction. The aim of our study was to explore the capabilities of counter-propagation artificial neural networks (CPANNs) for the classification of an imbalanced dataset related to idiosyncratic drug-induced liver injury and to develop a model for prediction of the hepatotoxic potential of drugs. Genetic algorithm optimization of CPANN models was used to build models for the classification of drugs into hepatotoxic and non-hepatotoxic class using molecular descriptors. For the classification of an imbalanced dataset, we modified the classical CPANN training algorithm by integrating random subsampling into the training procedure of CPANN to improve the classification ability of CPANN. According to the number of models accepted by internal validation and according to the prediction statistics on the external set, we concluded that using an imbalanced set with balanced subsampling in each learning epoch is a better approach compared to using a fixed balanced set in the case of the counter-propagation artificial neural network learning methodology.
Collapse
|
50
|
High-content imaging of 3D-cultured neural stem cells on a 384-pillar plate for the assessment of cytotoxicity. Toxicol In Vitro 2020; 65:104765. [PMID: 31923580 DOI: 10.1016/j.tiv.2020.104765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 12/20/2019] [Accepted: 01/05/2020] [Indexed: 12/17/2022]
Abstract
The assessment of neurotoxicity has been performed traditionally with animals. However, in vivo studies are highly expensive and time-consuming, and often do not correlate to human outcomes. Thus, there is a need for cost-effective, high-throughput, highly predictive alternative in vitro test methods based on early markers of mechanisms of toxicity. High-content imaging (HCI) assays performed on three-dimensionally (3D) cultured cells could provide better understanding of the mechanism of toxicity needed to predict neurotoxicity in humans. However, current 3D cell culture systems lack the throughput required for screening neurotoxicity against a large number of chemicals. Therefore, we have developed miniature 3D neural stem cell (NSC) culture on a unique 384-pillar plate, which is complementary to conventional 384-well plates. Mitochondrial membrane impairment, intracellular glutathione level, cell membrane integrity, DNA damage, and apoptosis have been tested against 3D-cultured ReNcell VM on the 384-pillar plate with four model compounds rotenone, 4-aminopyridine, digoxin, and topotecan. The HCI assays performed in 3D-cultured ReNcell VM on the 384-pillar plates were highly robust and reproducible as indicated by the average Z' factor of 0.6 and CV values around 12%. From concentration-response curves and IC50 values, mitochondrial membrane impairment appears to be the early stage marker of cell death by the compounds.
Collapse
|