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Barutcu AR, Black MB, Andersen ME. Transcriptomic re-analyses of human hepatocyte spheroids treated with PFAS reveals chain length and dose-dependent modes of action. Toxicol Appl Pharmacol 2024; 489:117013. [PMID: 38936668 DOI: 10.1016/j.taap.2024.117013] [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: 03/15/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
To identify pathway perturbations and examine biological modes of action (MOAs) for various perfluoroalkyl substances, we re-analyzed published in vitro gene expression studies from human primary liver spheroids. With treatment times ranging from 10 to 14 days, shorter-chain PFAS (those with 6 or fewer fluorinated carbon atoms in the alkyl chain) showed enrichment for pathways of fatty acid metabolism and fatty acid beta-oxidation with upregulated genes. Longer-chain PFAS compounds, specifically PFOS (perfluorooctane sulfonate), PFDS (perfluorodecane sulfonate), and higher doses of PFOA (perfluorooctanoic acid), had enrichment for pathways involved in steroid metabolism, fatty acid metabolism, and biological oxidation for downregulated genes. Although PFNA (perfluorononanoic acid), PFDA (perfluorodecanoic acid), and PFUnDA (perfluoroundecanoic acid) were more toxic and could only be examined after a 1-day treatment, all three had enrichment patterns similar to those observed with PFOS. With PFOA there were dose-dependent changes in pathway enrichment, shifting from upregulation of fatty acid metabolism and downregulation of steroid metabolism to downregulation of both at higher doses. The response to PFHpS (perfluoroheptanesulfonic acid) was similar to the PFOA pattern at the lower treatment dose. Based on results of transcription factor binding sites analyses, we propose that downregulation of pathways of lipid metabolism by longer chain PFAS may be due to inhibitory interactions of PPARD on genes controlled by PPARA and PPARG. In conclusion, our transcriptomic analysis indicates that the biological MOAs of PFAS compounds differ according to chain length and dose, and that risk assessments for PFAS should consider these differences in biological MOAs when evaluating mixtures of these compounds.
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Affiliation(s)
- A Rasim Barutcu
- ScitoVation LLC, Research Triangle Park, Suite 146, NC, USA.
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2
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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. [PMID: 39046974 DOI: 10.1021/acs.chemrestox.4c00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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.
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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
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Vlasveld M, Callegaro G, Fisher C, Eakins J, Walker P, Lok S, van Oost S, de Jong B, Pellegrino-Coppola D, Burger G, Wink S, van de Water B. The integrated stress response-related expression of CHOP due to mitochondrial toxicity is a warning sign for DILI liability. Liver Int 2024; 44:760-775. [PMID: 38217387 DOI: 10.1111/liv.15822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND AND AIMS Drug-induced liver injury (DILI) is one of the most frequent reasons for failure of drugs in clinical trials or market withdrawal. Early assessment of DILI risk remains a major challenge during drug development. Here, we present a mechanism-based weight-of-evidence approach able to identify certain candidate compounds with DILI liabilities due to mitochondrial toxicity. METHODS A total of 1587 FDA-approved drugs and 378 kinase inhibitors were screened for cellular stress response activation associated with DILI using an imaging-based HepG2 BAC-GFP reporter platform including the integrated stress response (CHOP), DNA damage response (P21) and oxidative stress response (SRXN1). RESULTS In total 389, 219 and 104 drugs were able to induce CHOP-GFP, P21-GFP and SRXN1-GFP expression at 50 μM respectively. Concentration response analysis identified 154 FDA-approved drugs as critical CHOP-GFP inducers. Based on predicted and observed (pre-)clinical DILI liabilities of these drugs, nine antimycotic drugs (e.g. butoconazole, miconazole, tioconazole) and 13 central nervous system (CNS) agents (e.g. duloxetine, fluoxetine) were selected for transcriptomic evaluation using whole-genome RNA-sequencing of primary human hepatocytes. Gene network analysis uncovered mitochondrial processes, NRF2 signalling and xenobiotic metabolism as most affected by the antimycotic drugs and CNS agents. Both the selected antimycotics and CNS agents caused impairment of mitochondrial oxygen consumption in both HepG2 and primary human hepatocytes. CONCLUSIONS Together, the results suggest that early pre-clinical screening for CHOP expression could indicate liability of mitochondrial toxicity in the context of DILI, and, therefore, could serve as an important warning signal to consider during decision-making in drug development.
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Affiliation(s)
- Matthijs Vlasveld
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Giulia Callegaro
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | | | | | | | - Samantha Lok
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Siddh van Oost
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Brechtje de Jong
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Damiano Pellegrino-Coppola
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Gerhard Burger
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Steven Wink
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
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Li R, Zhang Z, Xuan Y, Wang Y, Zhong Y, Zhang L, Zhang J, Chen Q, Yu S, Yuan J. HNF4A as a potential target of PFOA and PFOS leading to hepatic steatosis: Integrated molecular docking, molecular dynamic and transcriptomic analyses. Chem Biol Interact 2024; 390:110867. [PMID: 38199259 DOI: 10.1016/j.cbi.2024.110867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/30/2023] [Accepted: 01/08/2024] [Indexed: 01/12/2024]
Abstract
Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) are indeed among the most well known and extensively studied Per- and polyfluoroalkyl substances (PFASs), and increasing evidence confirm their effects on human health, especially liver steatosis. Nonetheless, the molecular mechanisms of their initiation of hepatic steatosis is still elusive. Therefore, potential targets of PFOA/PFOS must be explored to ameliorate its adverse consequences. This research aims to investigate the molecular mechanisms of PFOA and PFOS-induced liver steatosis, with emphasis on identifying a potential target that links these PFASs to liver steatosis. The potential target that causes PFOA and PFOS-induced liver steatosis have been explored and determined based on molecular docking, molecular dynamics (MD) simulation, and transcriptomics analysis. In silico results show that PFOA/PFOS can form a stable binding conformation with HNF4A, and PFOA/PFOS may interact with HNF4A to affect the downstream conduction mechanism. Transcriptome data from PFOA/PFOS-induced human stem cell spheres showed that HNF4A was inhibited, suggesting that PFOA/PFOS may constrain its function. PFOS mainly down-regulated genes related to cholesterol synthesis while PFOA mainly up-regulated genes related to fatty acid β-oxidation. This study explored the toxicological mechanism of liver steatosis caused by PFOA/PFOS. These compounds might inhibit and down-regulate HNF4A, which is the molecular initiation events (MIE) that induces liver steatosis.
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Affiliation(s)
- Rui Li
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Zijing Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yuxin Xuan
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yulu Wang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yuyan Zhong
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lingyin Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Jinrui Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Qian Chen
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Shuling Yu
- Key Laboratory of Natural Medicine and Immune-Engineering of Henan Province, Henan University, Kaifeng, Henan, 475004, PR China
| | - Jintao Yuan
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
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5
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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.
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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
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6
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Wang J, Novick S. DOSE-L1000: unveiling the intricate landscape of compound-induced transcriptional changes. Bioinformatics 2023; 39:btad683. [PMID: 37952162 PMCID: PMC10663987 DOI: 10.1093/bioinformatics/btad683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 11/14/2023] Open
Abstract
MOTIVATION The LINCS L1000 project has collected gene expression profiles for thousands of compounds across a wide array of concentrations, cell lines, and time points. However, conventional analysis methods often fall short in capturing the rich information encapsulated within the L1000 transcriptional dose-response data. RESULTS We present DOSE-L1000, a database that unravels the potency and efficacy of compound-gene pairs and the intricate landscape of compound-induced transcriptional changes. Our study uses the fitting of over 140 million generalized additive models and robust linear models, spanning the complete spectrum of compounds and landmark genes within the LINCS L1000 database. This systematic approach provides quantitative insights into differential gene expression and the potency and efficacy of compound-gene pairs across diverse cellular contexts. Through examples, we showcase the application of DOSE-L1000 in tasks such as cell line and compound comparisons, along with clustering analyses and predictions of drug-target interactions. DOSE-L1000 fosters applications in drug discovery, accelerating the transition to omics-driven drug development. AVAILABILITY AND IMPLEMENTATION DOSE-L1000 is publicly available at https://doi.org/10.5281/zenodo.8286375.
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Affiliation(s)
- Junmin Wang
- Data Sciences and Quantitative Biology, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, United States
| | - Steven Novick
- Global Statistical Sciences, Eli Lilly, Indianapolis, IN 46285, United States
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7
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Sakolish C, Moyer HL, Tsai HHD, Ford LC, Dickey AN, Wright FA, Han G, Bajaj P, Baltazar MT, Carmichael PL, Stanko JP, Ferguson SS, Rusyn I. Analysis of reproducibility and robustness of a renal proximal tubule microphysiological system OrganoPlate 3-lane 40 for in vitro studies of drug transport and toxicity. Toxicol Sci 2023; 196:52-70. [PMID: 37555834 PMCID: PMC10613961 DOI: 10.1093/toxsci/kfad080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023] Open
Abstract
Microphysiological systems are an emerging area of in vitro drug development, and their independent evaluation is important for wide adoption and use. The primary goal of this study was to test reproducibility and robustness of a renal proximal tubule microphysiological system, OrganoPlate 3-lane 40, as an in vitro model for drug transport and toxicity studies. This microfluidic model was compared with static multiwell cultures and tested using several human renal proximal tubule epithelial cell (RPTEC) types. The model was characterized in terms of the functional transport for various tubule-specific proteins, epithelial permeability of small molecules (cisplatin, tenofovir, and perfluorooctanoic acid) versus large molecules (fluorescent dextrans, 60-150 kDa), and gene expression response to a nephrotoxic xenobiotic. The advantages offered by OrganoPlate 3-lane 40 as compared with multiwell cultures are the presence of media flow, albeit intermittent, and increased throughput compared with other microfluidic models. However, OrganoPlate 3-lane 40 model appeared to offer only limited (eg, MRP-mediated transport) advantages in terms of either gene expression or functional transport when compared with the multiwell plate culture conditions. Although OrganoPlate 3-lane 40 can be used to study cellular uptake and direct toxic effects of small molecules, it may have limited utility for drug transport studies. Overall, this study offers refined experimental protocols and comprehensive comparative data on the function of RPETCs in traditional multiwell culture and microfluidic OrganoPlate 3-lane 40, information that will be invaluable for the prospective end-users of in vitro models of the human proximal tubule.
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Affiliation(s)
- Courtney Sakolish
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Haley L Moyer
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Han-Hsuan D Tsai
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Lucie C Ford
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Allison N Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Statistics, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Gang Han
- Department of Epidemiology and Biostatistics, Texas A&M University, College Station, Texas 77843, USA
| | - Piyush Bajaj
- Global Investigative Toxicology, Preclinical Safety, Sanofi, Cambridge, Massachusetts 02141, USA
| | - Maria T Baltazar
- Safety & Environmental Assurance Centre (SEAC), Unilever, Bedfordshire MK44 1LQ, UK
| | - Paul L Carmichael
- Safety & Environmental Assurance Centre (SEAC), Unilever, Bedfordshire MK44 1LQ, UK
| | - Jason P Stanko
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Stephen S Ferguson
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Ivan Rusyn
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
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8
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Schürmeyer L, Schorning K, Rahnenführer J. Designs for the simultaneous inference of concentration-response curves. BMC Bioinformatics 2023; 24:393. [PMID: 37858091 PMCID: PMC10588042 DOI: 10.1186/s12859-023-05526-3] [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: 04/06/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND An important problem in toxicology in the context of gene expression data is the simultaneous inference of a large number of concentration-response relationships. The quality of the inference substantially depends on the choice of design of the experiments, in particular, on the set of different concentrations, at which observations are taken for the different genes under consideration. As this set has to be the same for all genes, the efficient planning of such experiments is very challenging. We address this problem by determining efficient designs for the simultaneous inference of a large number of concentration-response models. For that purpose, we both construct a D-optimality criterion for simultaneous inference and a K-means procedure which clusters the support points of the locally D-optimal designs of the individual models. RESULTS We show that a planning of experiments that addresses the simultaneous inference of a large number of concentration-response relationships yields a substantially more accurate statistical analysis. In particular, we compare the performance of the constructed designs to the ones of other commonly used designs in terms of D-efficiencies and in terms of the quality of the resulting model fits using a real data example dealing with valproic acid. For the quality comparison we perform an extensive simulation study. CONCLUSIONS The design maximizing the D-optimality criterion for simultaneous inference improves the inference of the different concentration-response relationships substantially. The design based on the K-means procedure also performs well, whereas a log-equidistant design, which was also included in the analysis, performs poorly in terms of the quality of the simultaneous inference. Based on our findings, the D-optimal design for simultaneous inference should be used for upcoming analyses dealing with high-dimensional gene expression data.
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9
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Tsai HHD, House JS, Wright FA, Chiu WA, Rusyn I. A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo. Toxicol Sci 2023; 193:219-233. [PMID: 37079747 PMCID: PMC10230285 DOI: 10.1093/toxsci/kfad041] [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: 04/22/2023] Open
Abstract
Hazard evaluation of substances of "unknown or variable composition, complex reaction products and biological materials" (UVCBs) remains a major challenge in regulatory science because their chemical composition is difficult to ascertain. Petroleum substances are representative UVCBs and human cell-based data have been previously used to substantiate their groupings for regulatory submissions. We hypothesized that a combination of phenotypic and transcriptomic data could be integrated to make decisions as to selection of group-representative worst-case petroleum UVCBs for subsequent toxicity evaluation in vivo. We used data obtained from 141 substances from 16 manufacturing categories previously tested in 6 human cell types (induced pluripotent stem cell [iPSC]-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, and MCF7 and A375 cell lines). Benchmark doses for gene-substance combinations were calculated, and both transcriptomic and phenotype-derived points of departure (PODs) were obtained. Correlation analysis and machine learning were used to assess associations between phenotypic and transcriptional PODs and to determine the most informative cell types and assays, thus representing a cost-effective integrated testing strategy. We found that 2 cell types-iPSC-derived-hepatocytes and -cardiomyocytes-contributed the most informative and protective PODs and may be used to inform selection of representative petroleum UVCBs for further toxicity evaluation in vivo. Overall, although the use of new approach methodologies to prioritize UVCBs has not been widely adopted, our study proposes a tiered testing strategy based on iPSC-derived hepatocytes and cardiomyocytes to inform selection of representative worst-case petroleum UVCBs from each manufacturing category for further toxicity evaluation in vivo.
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Affiliation(s)
- Han-Hsuan Doris Tsai
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - John S House
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Fred A Wright
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
- Department of Biological Sciences and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
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10
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Wu S, Ellison C, Naciff J, Karb M, Obringer C, Yan G, Shan Y, Smith A, Wang X, Daston GP. Structure-activity relationship read-across and transcriptomics for branched carboxylic acids. Toxicol Sci 2023; 191:343-356. [PMID: 36583546 DOI: 10.1093/toxsci/kfac139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The purpose of this study was to use chemical similarity evaluations, transcriptional profiling, in vitro toxicokinetic data, and physiologically based pharmacokinetic (PBPK) models to support read-across for a series of branched carboxylic acids using valproic acid (VPA), a known developmental toxicant, as a comparator. The chemicals included 2-propylpentanoic acid (VPA), 2-ethylbutanoic acid, 2-ethylhexanoic acid (EHA), 2-methylnonanoic acid, 2-hexyldecanoic acid, 2-propylnonanoic acid (PNA), dipentyl acetic acid or 2-pentylheptanoic acid, octanoic acid (a straight chain alkyl acid), and 2-ethylhexanol. Transcriptomics was evaluated in 4 cell types (A549, HepG2, MCF7, and iCell cardiomyocytes) 6 h after exposure to 3 concentrations of the compounds, using the L1000 platform. The transcriptional profiling data indicate that 2- or 3-carbon alkyl substituents at the alpha position of the carboxylic acid (EHA and PNA) elicit a transcriptional profile similar to the one elicited by VPA. The transcriptional profile is different for the other chemicals tested, which provides support for limiting read-across from VPA to much shorter and longer acids. Molecular docking models for histone deacetylases, the putative target of VPA, provide a possible mechanistic explanation for the activity cliff elucidated by transcriptomics. In vitro toxicokinetic data were utilized in a PBPK model to estimate internal dosimetry. The PBPK modeling data show that as the branched chain increases, predicted plasma Cmax decreases. This work demonstrates how transcriptomics and other mode of action-based methods can improve read-across.
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Affiliation(s)
- Shengde Wu
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Corie Ellison
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Jorge Naciff
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Michael Karb
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Cindy Obringer
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Gang Yan
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Yuqing Shan
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Alex Smith
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Xiaohong Wang
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - George P Daston
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
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11
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Distinct and Dynamic Transcriptome Adaptations of iPSC-Generated Astrocytes after Cytokine Stimulation. Cells 2022; 11:cells11172644. [PMID: 36078052 PMCID: PMC9455058 DOI: 10.3390/cells11172644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Astrocytes (ACs) do not only play a role in normal neurogenesis and brain homeostasis, but also in inflammatory and neurodevelopmental disorders. We studied here the different patterns of inflammatory activation triggered by cytokines in human induced pluripotent stem cell (iPSC)-derived ACs. An optimized differentiation protocol provided non-inflamed ACs. These cells reacted to TNFα with a rapid translocation of NFκB, while AC precursors showed little response. Transcriptome changes were quantified at seven time points (2–72 h) after stimulation with TNFα, IFNγ or TNFα plus IFNγ. TNFα triggered a strong response within 2 h. It peaked from 12–24 h and reverted towards the ground state after 72 h. Activation by IFNγ was also rapid, but the response pattern differed from that of TNFα. For instance, several chemokines up-regulated by TNFα were not affected by IFNγ. Instead, MHC-II-related antigen presentation was drastically enhanced. The combination of the two cytokines led to a stronger and more persistent response. For instance, TRIB3 up-regulation by the combination of TNFα plus IFNγ may have slowed NFκB inactivation. Additionally, highly synergistic regulation was observed for inflammation modifiers, such as CASP4, and for STAT1-controlled genes. The combination of the cytokines also increased oxidative stress markers (e.g., CHAC1), led to phenotypic changes in ACs and triggered markers related to cell death. In summary, these data demonstrate that there is a large bandwidth of pro-inflammatory AC states, and that single markers are not suitable to describe AC activation or their modulation in disease, development and therapy.
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12
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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.
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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
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13
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Duda JC, Kappenberg F, Rahnenführer J. Model selection characteristics when using MCP-Mod for dose-response gene expression data. Biom J 2022; 64:883-897. [PMID: 35187701 DOI: 10.1002/bimj.202000250] [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: 08/19/2020] [Revised: 11/11/2021] [Accepted: 01/12/2022] [Indexed: 11/10/2022]
Abstract
We extend the scope of application for MCP-Mod (Multiple Comparison Procedure and Modeling) to in vitro gene expression data and assess its characteristics regarding model selection for concentration gene expression curves. Precisely, we apply MCP-Mod on single genes of a high-dimensional gene expression data set, where human embryonic stem cells were exposed to eight concentration levels of the compound valproic acid (VPA). As candidate models we consider the sigmoid E max $E_{\max }$ (four-parameter log-logistic), linear, quadratic, E max $E_{\max }$ , exponential, and beta model. Through simulations we investigate the impact of omitting one or more models from the candidate model set to uncover possibly superfluous models and to evaluate the precision and recall rates of selected models. Each model is selected according to Akaike information criterion (AIC) for a considerable number of genes. For less noisy cases the popular sigmoid E max $E_{\max }$ model is frequently selected. For more noisy data, often simpler models like the linear model are selected, but mostly without relevant performance advantage compared to the second best model. Also, the commonly used standard E max $E_{\max }$ model has an unexpected low performance.
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Affiliation(s)
- Julia C Duda
- Department of Statistics, TU Dortmund University, Dortmund, Germany
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14
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Djidrovski I, Georgiou M, Tasinato E, Leonard MO, Van den Bor J, Lako M, Armstrong L. Direct transcriptomic comparison of xenobiotic metabolism and toxicity pathway induction of airway epithelium models at an air-liquid interface generated from induced pluripotent stem cells and primary bronchial epithelial cells. Cell Biol Toxicol 2022; 39:1-18. [PMID: 35641671 PMCID: PMC10042770 DOI: 10.1007/s10565-022-09726-0] [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: 10/15/2021] [Accepted: 05/11/2022] [Indexed: 11/25/2022]
Abstract
The airway epithelium represents the main barrier between inhaled air and the tissues of the respiratory tract and is therefore an important point of contact with xenobiotic substances into the human body. Several studies have recently shown that in vitro models of the airway grown at an air-liquid interface (ALI) can be particularly useful to obtain mechanistic information about the toxicity of chemical compounds. However, such methods are not very amenable to high throughput since the primary cells cannot be expanded indefinitely in culture to obtain a sustainable number of cells. Induced pluripotent stem cells (iPSCs) have become a popular option in the recent years for modelling the airways of the lung, but despite progress in the field, such models have so far not been assessed for their ability to metabolise xenobiotic compounds and how they compare to the primary bronchial airway model (pBAE). Here, we report a comparative analysis by TempoSeq (oligo-directed sequencing) of an iPSC-derived airway model (iBAE) with a primary bronchial airway model (pBAE). The iBAE and pBAE were differentiated at an ALI and then evaluated in a 5-compound screen with exposure to a sub-lethal concentration of each compound for 24 h. We found that despite lower expression of xenobiotic metabolism genes, the iBAE similarly predicted the toxic pathways when compared to the pBAE model. Our results show that iPSC airway models at ALI show promise for inhalation toxicity assessments with further development.
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Affiliation(s)
- Ivo Djidrovski
- The Biosphere, Newcells Biotech Ltd., Draymans way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK.,Biosciences Institute, The International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Maria Georgiou
- Biosciences Institute, The International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Elena Tasinato
- The Biosphere, Newcells Biotech Ltd., Draymans way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
| | - Martin O Leonard
- Toxicology Department, Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Harwell Campus, Chilton, OX11 0RQ, UK
| | - Jelle Van den Bor
- Department of Medicinal Chemistry, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Majlinda Lako
- Biosciences Institute, The International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Lyle Armstrong
- The Biosphere, Newcells Biotech Ltd., Draymans way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK. .,Biosciences Institute, The International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK.
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15
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Everett LJ, Mav D, Phadke DP, Balik-Meisner MR, Shah RR. Impact of Aligner, Normalization Method, and Sequencing Depth on TempO-seq Accuracy. Bioinform Biol Insights 2022; 16:11779322221095216. [PMID: 35515009 PMCID: PMC9067045 DOI: 10.1177/11779322221095216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
High-throughput transcriptomics has advanced through the introduction of TempO-seq, a targeted alternative to traditional RNA-seq. TempO-seq platforms use 50 nucleotide probes, each specifically designed to target a known transcript, thus allowing for reduced sequencing depth per sample compared with RNA-seq without compromising the accuracy of results. Thus far, studies using the TempO-seq method have relied on existing tools for processing the resulting short read data. However, these tools were originally designed for other data types. While they have been used for processing of early TempO-seq data, they have not been systematically assessed for accuracy or compared to determine an optimal framework for processing and analyzing TempO-seq data. In this work, we re-analyze several publicly available TempO-seq data sets covering a range of experimental designs and use corresponding RNA-seq data sets as a gold standard to rigorously assess accuracy at multiple levels. We compare 6 aligners and 5 normalization methods across various accuracy and performance metrics. Our results demonstrate the overall robust accuracy of the TempO-seq platform, independent of data processing methods. Complex aligners and advanced normalization methods do not appear to have any general advantage over simpler methods when it comes to analyzing TempO-seq data. The reduced complexity of the sequencing space, and the fact that TempO-seq probes are all equal length, appears to reduce the need for elaborate bioinformatic or statistical methods used to address these factors in RNA-seq data.
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Affiliation(s)
| | - Deepak Mav
- Sciome LLC, Research Triangle Park, NC, USA
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16
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Speen AM, Murray JR, Krantz QT, Davies D, Evansky P, Harrill JA, Everett LJ, Bundy JL, Dailey LA, Hill J, Zander W, Carlsten E, Monsees M, Zavala J, Higuchi MA. Benchmark Dose Modeling Approaches for Volatile Organic Chemicals using a Novel Air-Liquid Interface In Vitro Exposure System. Toxicol Sci 2022; 188:88-107. [PMID: 35426944 DOI: 10.1093/toxsci/kfac040] [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: 11/14/2022] Open
Abstract
Inhalation is the most relevant route of volatile organic chemical (VOC) exposure; however, due to unique challenges posed by their chemical properties and poor solubility in aqueous solutions, in vitro chemical safety testing is predominantly performed using direct application dosing/submerged exposures. To address the difficulties in screening toxic effects of VOCs, our cell culture exposure system permits cells to be exposed to multiple concentrations at air-liquid interface (ALI) in a 24-well format. ALI exposure methods permit direct chemical-to-cell interaction with the test article at physiological conditions. In the present study, BEAS-2B and primary normal human bronchial epithelial cells (pHBEC) are used to assess gene expression, cytotoxicity, and cell viability responses to a variety of volatile chemicals including acrolein, formaldehyde, 1,3-butadiene, acetaldehyde, 1-bromopropane, carbon tetrachloride, dichloromethane, and trichloroethylene. BEAS-2B cells were exposed to all the test agents, while pHBECs were only exposed to the latter four listed above. The VOC concentrations tested elicited only slight cell viability changes in both cell types. Gene expression changes were analyzed using benchmark dose (BMD) modeling. The BMD for the most sensitive gene set was within one order of magnitude of the threshold-limit value reported by the American Conference of Governmental Industrial Hygienists, and the most sensitive gene sets impacted by exposure correlate to known adverse health effects recorded in epidemiologic and in vivo exposure studies. Overall, our study outlines a novel in vitro approach for evaluating molecular-based points-of-departure in human airway epithelial cell exposure to volatile chemicals.
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Affiliation(s)
- Adam M Speen
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee 37830, USA
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Jessica R Murray
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Quentin Todd Krantz
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - David Davies
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Paul Evansky
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Joshua A Harrill
- CCTE, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Logan J Everett
- CCTE, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Joseph L Bundy
- CCTE, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Lisa A Dailey
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Jazzlyn Hill
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Associated Universities (ORAU), Oak Ridge, Tennessee 37830, USA
| | - Wyatt Zander
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Associated Universities (ORAU), Oak Ridge, Tennessee 37830, USA
| | - Elise Carlsten
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Associated Universities (ORAU), Oak Ridge, Tennessee 37830, USA
| | - Michael Monsees
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Associated Universities (ORAU), Oak Ridge, Tennessee 37830, USA
| | - Jose Zavala
- MedTec BioLab Inc., Hillsborough, North Carolina 27278, USA
| | - Mark A Higuchi
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
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17
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Lagunas‐Rangel FA, Linnea‐Niemi JV, Kudłak B, Williams MJ, Jönsson J, Schiöth HB. Role of the Synergistic Interactions of Environmental Pollutants in the Development of Cancer. GEOHEALTH 2022; 6:e2021GH000552. [PMID: 35493962 PMCID: PMC9036628 DOI: 10.1029/2021gh000552] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/01/2022] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
There is a growing awareness that the large number of environmental pollutants we are exposed to on a daily basis are causing major health problems. Compared to traditional studies that focus on individual pollutants, there are relatively few studies on how pollutants mixtures interact. Several studies have reported a relationship between environmental pollutants and the development of cancer, even when pollutant levels are below toxicity reference values. The possibility of synergistic interactions between different pollutants could explain how even low concentrations can cause major health problems. These intricate that molecular interactions can occur through a wide variety of mechanisms, and our understanding of the physiological effects of mixtures is still limited. The purpose of this paper is to discuss recent reports that address possible synergistic interactions between different types of environmental pollutants that could promote cancer development. Our literature studies suggest that key biological pathways are frequently implicated in such processes. These include increased production of reactive oxygen species, activation by cytochrome P450, and aryl hydrocarbon receptor signaling, among others. We discuss the need to understand individual pathological vulnerability not only in relation to basic genetics and gene expression, but also in terms of measurable exposure to contaminants. We also mention the need for significant improvements in future studies using a multitude of disciplines, such as the development of high-throughput study models, better tools for quantifying pollutants in cancer patients, innovative pharmacological and toxicological studies, and high-efficiency computer analysis, which allow us to analyze the molecular mechanisms of mixtures.
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Affiliation(s)
| | - Jenni Viivi Linnea‐Niemi
- Department of Surgical Sciences, Functional Pharmacology and NeuroscienceUppsala UniversityUppsalaSweden
| | - Błażej Kudłak
- Faculty of ChemistryDepartment of Analytical ChemistryGdańsk University of TechnologyGdańskPoland
| | - Michael J. Williams
- Department of Surgical Sciences, Functional Pharmacology and NeuroscienceUppsala UniversityUppsalaSweden
| | - Jörgen Jönsson
- Department of Surgical Sciences, Functional Pharmacology and NeuroscienceUppsala UniversityUppsalaSweden
| | - Helgi B. Schiöth
- Department of Surgical Sciences, Functional Pharmacology and NeuroscienceUppsala UniversityUppsalaSweden
- Institute of Translational Medicine and BiotechnologyI. M. Sechenov First Moscow State Medical UniversityMoscowRussia
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18
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Holzer AK, Suciu I, Karreman C, Goj T, Leist M. Specific Attenuation of Purinergic Signaling during Bortezomib-Induced Peripheral Neuropathy In Vitro. Int J Mol Sci 2022; 23:ijms23073734. [PMID: 35409095 PMCID: PMC8998302 DOI: 10.3390/ijms23073734] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 12/18/2022] Open
Abstract
Human peripheral neuropathies are poorly understood, and the availability of experimental models limits further research. The PeriTox test uses immature dorsal root ganglia (DRG)-like neurons, derived from induced pluripotent stem cells (iPSC), to assess cell death and neurite damage. Here, we explored the suitability of matured peripheral neuron cultures for the detection of sub-cytotoxic endpoints, such as altered responses of pain-related P2X receptors. A two-step differentiation protocol, involving the transient expression of ectopic neurogenin-1 (NGN1) allowed for the generation of homogeneous cultures of sensory neurons. After >38 days of differentiation, they showed a robust response (Ca2+-signaling) to the P2X3 ligand α,β-methylene ATP. The clinical proteasome inhibitor bortezomib abolished the P2X3 signal at ≥5 nM, while 50−200 nM was required in the PeriTox test to identify neurite damage and cell death. A 24 h treatment with low nM concentrations of bortezomib led to moderate increases in resting cell intracellular Ca2+ concentration but signaling through transient receptor potential V1 (TRPV1) receptors or depolarization-triggered Ca2+ influx remained unaffected. We interpreted the specific attenuation of purinergic signaling as a functional cell stress response. A reorganization of tubulin to form dense structures around the cell somata confirmed a mild, non-cytotoxic stress triggered by low concentrations of bortezomib. The proteasome inhibitors carfilzomib, delanzomib, epoxomicin, and MG-132 showed similar stress responses. Thus, the model presented here may be used for the profiling of new proteasome inhibitors in regard to their side effect (neuropathy) potential, or for pharmacological studies on the attenuation of their neurotoxicity. P2X3 signaling proved useful as endpoint to assess potential neurotoxicants in peripheral neurons.
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Affiliation(s)
- Anna-Katharina Holzer
- In Vitro Toxicology and Biomedicine, Dept Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (A.-K.H.); (I.S.); (C.K.); (T.G.)
| | - Ilinca Suciu
- In Vitro Toxicology and Biomedicine, Dept Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (A.-K.H.); (I.S.); (C.K.); (T.G.)
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - Christiaan Karreman
- In Vitro Toxicology and Biomedicine, Dept Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (A.-K.H.); (I.S.); (C.K.); (T.G.)
| | - Thomas Goj
- In Vitro Toxicology and Biomedicine, Dept Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (A.-K.H.); (I.S.); (C.K.); (T.G.)
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Dept Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (A.-K.H.); (I.S.); (C.K.); (T.G.)
- CAAT-Europe, University of Konstanz, 78457 Konstanz, Germany
- Correspondence: ; Tel.: +49-(0)-7531-88-5037
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19
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Basili D, Reynolds J, Houghton J, Malcomber S, Chambers B, Liddell M, Muller I, White A, Shah I, Everett LJ, Middleton A, Bender A. Latent Variables Capture Pathway-Level Points of Departure in High-Throughput Toxicogenomic Data. Chem Res Toxicol 2022; 35:670-683. [PMID: 35333521 PMCID: PMC9019810 DOI: 10.1021/acs.chemrestox.1c00444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Estimation
of points of departure (PoDs) from high-throughput transcriptomic
data (HTTr) represents a key step in the development of next-generation
risk assessment (NGRA). Current approaches mainly rely on single key
gene targets, which are constrained by the information currently available
in the knowledge base and make interpretation challenging as scientists
need to interpret PoDs for thousands of genes or hundreds of pathways.
In this work, we aimed to address these issues by developing a computational
workflow to investigate the pathway concentration–response
relationships in a way that is not fully constrained by known biology
and also facilitates interpretation. We employed the Pathway-Level
Information ExtractoR (PLIER) to identify latent variables (LVs) describing
biological activity and then investigated in vitro LVs’ concentration–response
relationships using the ToxCast pipeline. We applied this methodology
to a published transcriptomic concentration–response data set
for 44 chemicals in MCF-7 cells and showed that our workflow can capture
known biological activity and discriminate between estrogenic and
antiestrogenic compounds as well as activity not aligning with the
existing knowledge base, which may be relevant in a risk assessment
scenario. Moreover, we were able to identify the known estrogen activity
in compounds that are not well-established ER agonists/antagonists
supporting the use of the workflow in read-across. Next, we transferred
its application to chemical compounds tested in HepG2, HepaRG, and
MCF-7 cells and showed that PoD estimates are in strong agreement
with those estimated using a recently developed Bayesian approach
(cor = 0.89) and in weak agreement with those estimated using a well-established
approach such as BMDExpress2 (cor = 0.57). These results demonstrate
the effectiveness of using PLIER in a concentration–response
scenario to investigate pathway activity in a way that is not fully
constrained by the knowledge base and to ease the biological interpretation
and support the development of an NGRA framework with the ability
to improve current risk assessment strategies for chemicals using
new approach methodologies.
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Affiliation(s)
- Danilo Basili
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.,Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Joe Reynolds
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Jade Houghton
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Sophie Malcomber
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Bryant Chambers
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Mark Liddell
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Iris Muller
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Andrew White
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Logan J Everett
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Alistair Middleton
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Andreas Bender
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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20
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Holzer AK, Karreman C, Suciu I, Furmanowsky LS, Wohlfarth H, Loser D, Dirks WG, Pardo González E, Leist M. OUP accepted manuscript. Stem Cells Transl Med 2022; 11:727-741. [PMID: 35689659 PMCID: PMC9299516 DOI: 10.1093/stcltm/szac031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/09/2022] [Indexed: 11/12/2022] Open
Abstract
In vitro models of the peripheral nervous system would benefit from further refinements to better support studies on neuropathies. In particular, the assessment of pain-related signals is still difficult in human cell cultures. Here, we harnessed induced pluripotent stem cells (iPSCs) to generate peripheral sensory neurons enriched in nociceptors. The objective was to generate a culture system with signaling endpoints suitable for pharmacological and toxicological studies. Neurons generated by conventional differentiation protocols expressed moderate levels of P2X3 purinergic receptors and only low levels of TRPV1 capsaicin receptors, when maturation time was kept to the upper practically useful limit of 6 weeks. As alternative approach, we generated cells with an inducible NGN1 transgene. Ectopic expression of this transcription factor during a defined time window of differentiation resulted in highly enriched nociceptor cultures, as determined by functional (P2X3 and TRPV1 receptors) and immunocytochemical phenotyping, complemented by extensive transcriptome profiling. Single cell recordings of Ca2+-indicator fluorescence from >9000 cells were used to establish the “fraction of reactive cells” in a stimulated population as experimental endpoint, that appeared robust, transparent and quantifiable. To provide an example of application to biomedical studies, functional consequences of prolonged exposure to the chemotherapeutic drug oxaliplatin were examined at non-cytotoxic concentrations. We found (i) neuronal (allodynia-like) hypersensitivity to otherwise non-activating mechanical stimulation that could be blocked by modulators of voltage-gated sodium channels; (ii) hyper-responsiveness to TRPV1 receptor stimulation. These findings and several other measured functional alterations indicate that the model is suitable for pharmacological and toxicological studies related to peripheral neuropathies.
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Affiliation(s)
- Anna-Katharina Holzer
- In vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
- Graduate School Biological Sciences (GBS), University of Konstanz, Konstanz, Germany
| | - Christiaan Karreman
- In vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Ilinca Suciu
- In vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Lara-Seline Furmanowsky
- In vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Harald Wohlfarth
- In vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Dominik Loser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Lines, DSMZ, German Collection of Microorganisms and Cell Cultures and German Biological Resource Center, Braunschweig, Germany
| | - Emilio Pardo González
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Marcel Leist
- Corresponding author: Marcel Leist, PhD, In Vitro Toxicology and Biomedicine, Dept Inaugurated by the Doerenkamp-Zbinden Foundation at the University of Konstanz, Universitaetsstr. 10, Konstanz 78457, Germany.
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21
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Reardon AJF, Rowan-Carroll A, Ferguson SS, Leingartner K, Gagne R, Kuo B, Williams A, Lorusso L, Bourdon-Lacombe JA, Carrier R, Moffat I, Yauk CL, Atlas E. Potency Ranking of Per- and Polyfluoroalkyl Substances Using High-Throughput Transcriptomic Analysis of Human Liver Spheroids. Toxicol Sci 2021; 184:154-169. [PMID: 34453843 DOI: 10.1093/toxsci/kfab102] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Per- and polyfluoroalkyl substances (PFAS) are some of the most prominent organic contaminants in human blood. Although the toxicological implications of human exposure to perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) are well established, data on lesser-understood PFAS are limited. New approach methodologies (NAMs) that apply bioinformatic tools to high-throughput data are being increasingly considered to inform risk assessment for data-poor chemicals. The aim of this study was to compare the potencies (ie, benchmark concentrations: BMCs) of PFAS in primary human liver microtissues (3D spheroids) using high-throughput transcriptional profiling. Gene expression changes were measured using TempO-seq, a templated, multiplexed RNA-sequencing platform. Spheroids were exposed for 1 or 10 days to increasing concentrations of 23 PFAS in 3 subgroups: carboxylates (PFCAs), sulfonates (PFSAs), and fluorotelomers and sulfonamides. PFCAs and PFSAs exhibited trends toward increased transcriptional potency with carbon chain-length. Specifically, longer-chain compounds (7-10 carbons) were more likely to induce changes in gene expression and have lower transcriptional BMCs. The combined high-throughput transcriptomic and bioinformatic analyses support the capability of NAMs to efficiently assess the effects of PFAS in liver microtissues. The data enable potency ranking of PFAS for human liver cell spheroid cytotoxicity and transcriptional changes, and assessment of in vitro transcriptomic points of departure. These data improve our understanding of the possible health effects of PFAS and will be used to inform read-across for human health risk assessment.
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Affiliation(s)
- Anthony J F Reardon
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Stephen S Ferguson
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Karen Leingartner
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Remi Gagne
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Luigi Lorusso
- Chemicals and Environmental Health Management Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Julie A Bourdon-Lacombe
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Richard Carrier
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Ivy Moffat
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada.,Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada.,Department of Biochemistry, University of Ottawa, Ottawa, Ontario, Canada
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22
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Reardon AJF, Rowan-Carroll A, Ferguson SS, Leingartner K, Gagne R, Kuo B, Williams A, Lorusso L, Bourdon-Lacombe JA, Carrier R, Moffat I, Yauk CL, Atlas E. Potency Ranking of Per- and Polyfluoroalkyl Substances Using High-Throughput Transcriptomic Analysis of Human Liver Spheroids. Toxicol Sci 2021; 184:154-169. [PMID: 34453843 DOI: 10.1101/2020.10.15.341362] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Per- and polyfluoroalkyl substances (PFAS) are some of the most prominent organic contaminants in human blood. Although the toxicological implications of human exposure to perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) are well established, data on lesser-understood PFAS are limited. New approach methodologies (NAMs) that apply bioinformatic tools to high-throughput data are being increasingly considered to inform risk assessment for data-poor chemicals. The aim of this study was to compare the potencies (ie, benchmark concentrations: BMCs) of PFAS in primary human liver microtissues (3D spheroids) using high-throughput transcriptional profiling. Gene expression changes were measured using TempO-seq, a templated, multiplexed RNA-sequencing platform. Spheroids were exposed for 1 or 10 days to increasing concentrations of 23 PFAS in 3 subgroups: carboxylates (PFCAs), sulfonates (PFSAs), and fluorotelomers and sulfonamides. PFCAs and PFSAs exhibited trends toward increased transcriptional potency with carbon chain-length. Specifically, longer-chain compounds (7-10 carbons) were more likely to induce changes in gene expression and have lower transcriptional BMCs. The combined high-throughput transcriptomic and bioinformatic analyses support the capability of NAMs to efficiently assess the effects of PFAS in liver microtissues. The data enable potency ranking of PFAS for human liver cell spheroid cytotoxicity and transcriptional changes, and assessment of in vitro transcriptomic points of departure. These data improve our understanding of the possible health effects of PFAS and will be used to inform read-across for human health risk assessment.
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Affiliation(s)
- Anthony J F Reardon
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Stephen S Ferguson
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Karen Leingartner
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Remi Gagne
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Luigi Lorusso
- Chemicals and Environmental Health Management Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Julie A Bourdon-Lacombe
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Richard Carrier
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Ivy Moffat
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, University of Ottawa, Ottawa, Ontario, Canada
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23
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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24
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Rowan-Carroll A, Reardon A, Leingartner K, Gagné R, Williams A, Meier MJ, Kuo B, Bourdon-Lacombe J, Moffat I, Carrier R, Nong A, Lorusso L, Ferguson SS, Atlas E, Yauk C. High-Throughput Transcriptomic Analysis of Human Primary Hepatocyte Spheroids Exposed to Per- and Polyfluoroalkyl Substances as a Platform for Relative Potency Characterization. Toxicol Sci 2021; 181:199-214. [PMID: 33772556 DOI: 10.1093/toxsci/kfab039] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Per- and poly-fluoroalkyl substances (PFAS) are widely found in the environment because of their extensive use and persistence. Although several PFAS are well studied, most lack toxicity data to inform human health hazard and risk assessment. This study focused on 4 model PFAS: perfluorooctanoic acid (PFOA; 8 carbon), perfluorobutane sulfonate (PFBS; 4 carbon), perfluorooctane sulfonate (PFOS; 8 carbon), and perfluorodecane sulfonate (PFDS; 10 carbon). Human primary liver cell spheroids (pooled from 10 donors) were exposed to 10 concentrations of each PFAS and analyzed at 4 time points. The approach aimed to: (1) identify gene expression changes mediated by the PFAS, (2) identify similarities in biological responses, (3) compare PFAS potency through benchmark concentration analysis, and (4) derive bioactivity exposure ratios (ratio of the concentration at which biological responses occur, relative to daily human exposure). All PFAS induced transcriptional changes in cholesterol biosynthesis and lipid metabolism pathways, and predicted PPARα activation. PFOS exhibited the most transcriptional activity and had a highly similar gene expression profile to PFDS. PFBS induced the least transcriptional changes and the highest benchmark concentration (ie, was the least potent). The data indicate that these PFAS may have common molecular targets and toxicities, but that PFOS and PFDS are the most similar. The transcriptomic bioactivity exposure ratios derived here for PFOA and PFOS were comparable to those derived using rodent apical endpoints in risk assessments. These data provide a baseline level of toxicity for comparison with other known PFAS using this testing strategy.
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Affiliation(s)
- Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Anthony Reardon
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Karen Leingartner
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Remi Gagné
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Julie Bourdon-Lacombe
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Ivy Moffat
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Richard Carrier
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Andy Nong
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Luigi Lorusso
- Chemicals and Environmental Health Management Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Stephen S Ferguson
- U.S. National Institute of Environmental Health Sciences (NIEHS), Ottawa, Ontario K1N 6N5, Canada
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada
| | - Carole Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K1N 6N5, Canada.,Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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25
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Sakolish C, House JS, Chramiec A, Liu Y, Chen Z, Halligan SP, Vunjak-Novakovic G, Rusyn I. Tissue-Engineered Bone Tumor as a Reproducible Human in Vitro Model for Studies of Anticancer Drugs. Toxicol Sci 2021; 173:65-76. [PMID: 31626302 DOI: 10.1093/toxsci/kfz220] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Studies of anticancer therapies in traditional cell culture models can demonstrate efficacy of direct-acting compounds but lack the 3-dimensional arrangement of the tumor cells and their tissue-specific microenvironments, both of which are important modulators of treatment effects in vivo. Bone cells reside in complex environments that regulate their fate and function. A bioengineered human bone-tumor model has been shown to provide a microphysiological niche for studies of cancer cell behavior. Here, we demonstrate successful transfer between 2 laboratories and utility of this model in efficacy studies using well-established chemotherapeutic agents. The bioengineered human bone-tumor model consisted of Ewing sarcoma (RD-ES) cancer cell aggregates infused into tissue-engineered bone that was grown from human mesenchymal stem cell-derived differentiated into osteoblasts within mineralized bone scaffolds. The tumor model was maintained in culture for over 5 weeks and subjected to clinically relevant doses of linsitinib, doxorubicin, cisplatin, methotrexate, vincristine, dexamethasone, or MAP (methotrexate, doxorubicin, and cisplatin combination). Drug administration cycles were designed to mimic clinical treatment regimens. The bioengineered tumors were evaluated days to weeks after the cessation of treatment to monitor the potential for relapse, using bioengineered bone and ES cell monolayers as controls. Drug binding to the scaffolds and media proteins and gene expression were also evaluated. We show that a bioengineered human bone tumor can be used as a microphysiological model for preclinical studies of anticancer drugs. We found that anticancer efficacy was achieved at concentrations approximating the human Cmax, in contrast to traditional ES cell monolayers. These studies show that the bone-tumor model can be successfully transferred between laboratories and has predictive power in preclinical studies. The effects of drugs on the bone tumors and healthy bone were studied in parallel, in support of the utility of this model for identification of new therapeutic targets.
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Affiliation(s)
- Courtney Sakolish
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695
| | - Alan Chramiec
- Department of Biomedical Engineering, Columbia University, New York, New York 10032
| | - Yizhong Liu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843
| | - Zunwei Chen
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843
| | - Susan P Halligan
- Department of Biomedical Engineering, Columbia University, New York, New York 10032
| | | | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843
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26
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Harrill JA, Everett LJ, Haggard DE, Sheffield T, Bundy JL, Willis CM, Thomas RS, Shah I, Judson RS. High-Throughput Transcriptomics Platform for Screening Environmental Chemicals. Toxicol Sci 2021; 181:68-89. [PMID: 33538836 DOI: 10.1093/toxsci/kfab009] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
New approach methodologies (NAMs) that efficiently provide information about chemical hazard without using whole animals are needed to accelerate the pace of chemical risk assessments. Technological advancements in gene expression assays have made in vitro high-throughput transcriptomics (HTTr) a feasible option for NAMs-based hazard characterization of environmental chemicals. In this study, we evaluated the Templated Oligo with Sequencing Readout (TempO-Seq) assay for HTTr concentration-response screening of a small set of chemicals in the human-derived MCF7 cell model. Our experimental design included a variety of reference samples and reference chemical treatments in order to objectively evaluate TempO-Seq assay performance. To facilitate analysis of these data, we developed a robust and scalable bioinformatics pipeline using open-source tools. We also developed a novel gene expression signature-based concentration-response modeling approach and compared the results to a previously implemented workflow for concentration-response analysis of transcriptomics data using BMDExpress. Analysis of reference samples and reference chemical treatments demonstrated highly reproducible differential gene expression signatures. In addition, we found that aggregating signals from individual genes into gene signatures prior to concentration-response modeling yielded in vitro transcriptional biological pathway altering concentrations (BPACs) that were closely aligned with previous ToxCast high-throughput screening assays. Often these identified signatures were associated with the known molecular target of the chemicals in our test set as the most sensitive components of the overall transcriptional response. This work has resulted in a novel and scalable in vitro HTTr workflow that is suitable for high-throughput hazard evaluation of environmental chemicals.
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Affiliation(s)
- Joshua A Harrill
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Logan J Everett
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Derik E Haggard
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA.,Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - Thomas Sheffield
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA.,Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - Joseph L Bundy
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Clinton M Willis
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA.,Oak Ridge Associated Universities (ORAU), Oak Ridge, Tennessee, USA
| | - Russell S Thomas
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Richard S Judson
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
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27
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Loser D, Hinojosa MG, Blum J, Schaefer J, Brüll M, Johansson Y, Suciu I, Grillberger K, Danker T, Möller C, Gardner I, Ecker GF, Bennekou SH, Forsby A, Kraushaar U, Leist M. Functional alterations by a subgroup of neonicotinoid pesticides in human dopaminergic neurons. Arch Toxicol 2021; 95:2081-2107. [PMID: 33778899 PMCID: PMC8166715 DOI: 10.1007/s00204-021-03031-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/17/2021] [Indexed: 12/16/2022]
Abstract
Neonicotinoid pesticides, originally developed to target the insect nervous system, have been reported to interact with human receptors and to activate rodent neurons. Therefore, we evaluated in how far these compounds may trigger signaling in human neurons, and thus, affect the human adult or developing nervous system. We used SH-SY5Y neuroblastoma cells as established model of nicotinic acetylcholine receptor (nAChR) signaling. In parallel, we profiled dopaminergic neurons, generated from LUHMES neuronal precursor cells, as novel system to study nAChR activation in human post-mitotic neurons. Changes of the free intracellular Ca2+ concentration ([Ca2+]i) were used as readout, and key findings were confirmed by patch clamp recordings. Nicotine triggered typical neuronal signaling responses that were blocked by antagonists, such as tubocurarine and mecamylamine. Pharmacological approaches suggested a functional expression of α7 and non-α7 nAChRs on LUHMES cells. In this novel test system, the neonicotinoids acetamiprid, imidacloprid, clothianidin and thiacloprid, but not thiamethoxam and dinotefuran, triggered [Ca2+]i signaling at 10-100 µM. Strong synergy of the active neonicotinoids (at low micromolar concentrations) with the α7 nAChR-positive allosteric modulator PNU-120596 was observed in LUHMES and SH-SY5Y cells, and specific antagonists fully inhibited such signaling. To provide a third line of evidence for neonicotinoid signaling via nAChR, we studied cross-desensitization: pretreatment of LUHMES and SH-SY5Y cells with active neonicotinoids (at 1-10 µM) blunted the signaling response of nicotine. The pesticides (at 3-30 µM) also blunted the response to the non-α7 agonist ABT 594 in LUHMES cells. These data show that human neuronal cells are functionally affected by low micromolar concentrations of several neonicotinoids. An effect of such signals on nervous system development is a toxicological concern.
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Affiliation(s)
- Dominik Loser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
- NMI TT GmbH, 72770, Reutlingen, Germany
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Konstanz, Germany
| | - Maria G Hinojosa
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Jonathan Blum
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Konstanz, Germany
| | - Jasmin Schaefer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
- NMI TT GmbH, 72770, Reutlingen, Germany
| | - Markus Brüll
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Konstanz, Germany
| | - Ylva Johansson
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Ilinca Suciu
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Konstanz, Germany
| | - Karin Grillberger
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Timm Danker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
- NMI TT GmbH, 72770, Reutlingen, Germany
| | - Clemens Möller
- Life Sciences Faculty, Albstadt-Sigmaringen University, 72488, Sigmaringen, Germany
| | - Iain Gardner
- CERTARA UK Limited, Simcyp Division, Level 2-Acero, 1 Concourse Way, Sheffield, S1 2BJ, UK
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | - Anna Forsby
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Udo Kraushaar
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Konstanz, Germany.
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A human stem cell-derived test system for agents modifying neuronal N-methyl-D-aspartate-type glutamate receptor Ca 2+-signalling. Arch Toxicol 2021; 95:1703-1722. [PMID: 33713149 PMCID: PMC8113295 DOI: 10.1007/s00204-021-03024-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
Methods to assess neuronal receptor functions are needed in toxicology and for drug development. Human-based test systems that allow studies on glutamate signalling are still scarce. To address this issue, we developed and characterized pluripotent stem cell (PSC)-based neural cultures capable of forming a functional network. Starting from a stably proliferating neuroepithelial stem cell (NESC) population, we generate “mixed cortical cultures” (MCC) within 24 days. Characterization by immunocytochemistry, gene expression profiling and functional tests (multi-electrode arrays) showed that MCC contain various functional neurotransmitter receptors, and in particular, the N-methyl-d-aspartate subtype of ionotropic glutamate receptors (NMDA-R). As this important receptor is found neither on conventional neural cell lines nor on most stem cell-derived neurons, we focused here on the characterization of rapid glutamate-triggered Ca2+ signalling. Changes of the intracellular free calcium ion concentration ([Ca2+]i) were measured by fluorescent imaging as the main endpoint, and a method to evaluate and quantify signals in hundreds of cells at the same time was developed. We observed responses to glutamate in the low µM range. MCC responded to kainate and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), and a subpopulation of 50% had functional NMDA-R. The receptor was modulated by Mg2+, Zn2+ and Pb2+ in the expected ways, and various toxicologically relevant agonists (quinolinic acid, ibotenic acid, domoic acid) triggered [Ca2+]i responses in MCC. Antagonists, such as phencyclidine, ketamine and dextromethorphan, were also readily identified. Thus, the MCC developed here may fill an important gap in the panel of test systems available to characterize the effects of chemicals on neurotransmitter receptors.
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Loser D, Schaefer J, Danker T, Möller C, Brüll M, Suciu I, Ückert AK, Klima S, Leist M, Kraushaar U. Human neuronal signaling and communication assays to assess functional neurotoxicity. Arch Toxicol 2021; 95:229-252. [PMID: 33269408 PMCID: PMC7811517 DOI: 10.1007/s00204-020-02956-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/16/2020] [Indexed: 01/08/2023]
Abstract
Prediction of drug toxicity on the human nervous system still relies mainly on animal experiments. Here, we developed an alternative system allowing assessment of complex signaling in both individual human neurons and on the network level. The LUHMES cultures used for our approach can be cultured in 384-well plates with high reproducibility. We established here high-throughput quantification of free intracellular Ca2+ concentrations [Ca2+]i as broadly applicable surrogate of neuronal activity and verified the main processes by patch clamp recordings. Initially, we characterized the expression pattern of many neuronal signaling components and selected the purinergic receptors to demonstrate the applicability of the [Ca2+]i signals for quantitative characterization of agonist and antagonist responses on classical ionotropic neurotransmitter receptors. This included receptor sub-typing and the characterization of the anti-parasitic drug suramin as modulator of the cellular response to ATP. To exemplify potential studies on ion channels, we characterized voltage-gated sodium channels and their inhibition by tetrodotoxin, saxitoxin and lidocaine, as well as their opening by the plant alkaloid veratridine and the food-relevant marine biotoxin ciguatoxin. Even broader applicability of [Ca2+]i quantification as an end point was demonstrated by measurements of dopamine transporter activity based on the membrane potential-changing activity of this neurotransmitter carrier. The substrates dopamine or amphetamine triggered [Ca2+]i oscillations that were synchronized over the entire culture dish. We identified compounds that modified these oscillations by interfering with various ion channels. Thus, this new test system allows multiple types of neuronal signaling, within and between cells, to be assessed, quantified and characterized for their potential disturbance.
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Affiliation(s)
- Dominik Loser
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
- NMI TT GmbH, 72770, Reutlingen, Germany
- Life Sciences Faculty, Albstadt-Sigmaringen University, 72488, Sigmaringen, Germany
| | - Jasmin Schaefer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
- NMI TT GmbH, 72770, Reutlingen, Germany
| | | | - Clemens Möller
- Life Sciences Faculty, Albstadt-Sigmaringen University, 72488, Sigmaringen, Germany
| | - Markus Brüll
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany
| | - Ilinca Suciu
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany
| | - Anna-Katharina Ückert
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany
| | - Stefanie Klima
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany.
| | - Udo Kraushaar
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
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de Boer A, Krul L, Fehr M, Geurts L, Kramer N, Tabernero Urbieta M, van der Harst J, van de Water B, Venema K, Schütte K, Hepburn PA. Animal-free strategies in food safety & nutrition: What are we waiting for? Part I: Food safety. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.10.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bushel PR, Ferguson SS, Ramaiahgari SC, Paules RS, Auerbach SS. Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data. Front Genet 2020; 11:594. [PMID: 32655620 PMCID: PMC7325690 DOI: 10.3389/fgene.2020.00594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022] Open
Abstract
Analysis of bulk RNA sequencing (RNA-Seq) data is a valuable tool to understand transcription at the genome scale. Targeted sequencing of RNA has emerged as a practical means of assessing the majority of the transcriptomic space with less reliance on large resources for consumables and bioinformatics. TempO-Seq is a templated, multiplexed RNA-Seq platform that interrogates a panel of sentinel genes representative of genome-wide transcription. Nuances of the technology require proper preprocessing of the data. Various methods have been proposed and compared for normalizing bulk RNA-Seq data, but there has been little to no investigation of how the methods perform on TempO-Seq data. We simulated count data into two groups (treated vs. untreated) at seven-fold change (FC) levels (including no change) using control samples from human HepaRG cells run on TempO-Seq and normalized the data using seven normalization methods. Upper Quartile (UQ) performed the best with regard to maintaining FC levels as detected by a limma contrast between treated vs. untreated groups. For all FC levels, specificity of the UQ normalization was greater than 0.84 and sensitivity greater than 0.90 except for the no change and +1.5 levels. Furthermore, K-means clustering of the simulated genes normalized by UQ agreed the most with the FC assignments [adjusted Rand index (ARI) = 0.67]. Despite having an assumption of the majority of genes being unchanged, the DESeq2 scaling factors normalization method performed reasonably well as did simple normalization procedures counts per million (CPM) and total counts (TCs). These results suggest that for two class comparisons of TempO-Seq data, UQ, CPM, TC, or DESeq2 normalization should provide reasonably reliable results at absolute FC levels ≥2.0. These findings will help guide researchers to normalize TempO-Seq gene expression data for more reliable results.
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Affiliation(s)
- Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences of National Institutes of Health, Durham, NC, United States.,Massive Genome Informatics Group, National Institute of Environmental Health Sciences of National Institutes of Health, Durham, NC, United States.,Biomolecular Screening Branch, National Institute of Environmental Health Sciences of National Institutes of Health, Durham, NC, United States
| | - Stephen S Ferguson
- Biomolecular Screening Branch, National Institute of Environmental Health Sciences of National Institutes of Health, Durham, NC, United States
| | - Sreenivasa C Ramaiahgari
- Biomolecular Screening Branch, National Institute of Environmental Health Sciences of National Institutes of Health, Durham, NC, United States
| | - Richard S Paules
- Biomolecular Screening Branch, National Institute of Environmental Health Sciences of National Institutes of Health, Durham, NC, United States
| | - Scott S Auerbach
- Biomolecular Screening Branch, National Institute of Environmental Health Sciences of National Institutes of Health, Durham, NC, United States
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Renner S, Bergsdorf C, Bouhelal R, Koziczak-Holbro M, Amati AM, Techer-Etienne V, Flotte L, Reymann N, Kapur K, Hoersch S, Oakeley EJ, Schuffenhauer A, Gubler H, Lounkine E, Farmer P. Gene-signature-derived IC 50s/EC 50s reflect the potency of causative upstream targets and downstream phenotypes. Sci Rep 2020; 10:9670. [PMID: 32541899 PMCID: PMC7295968 DOI: 10.1038/s41598-020-66533-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/19/2020] [Indexed: 02/02/2023] Open
Abstract
Multiplexed gene-signature-based phenotypic assays are increasingly used for the identification and profiling of small molecule-tool compounds and drugs. Here we introduce a method (provided as R-package) for the quantification of the dose-response potency of a gene-signature as EC50 and IC50 values. Two signaling pathways were used as models to validate our methods: beta-adrenergic agonistic activity on cAMP generation (dedicated dataset generated for this study) and EGFR inhibitory effect on cancer cell viability. In both cases, potencies derived from multi-gene expression data were highly correlated with orthogonal potencies derived from cAMP and cell growth readouts, and superior to potencies derived from single individual genes. Based on our results we propose gene-signature potencies as a novel valid alternative for the quantitative prioritization, optimization and development of novel drugs.
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Affiliation(s)
- Steffen Renner
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland.
| | - Christian Bergsdorf
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | - Rochdi Bouhelal
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | | | - Andrea Marco Amati
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland.,Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Valerie Techer-Etienne
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | | | - Nicole Reymann
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | | | | | | | - Ansgar Schuffenhauer
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | | | - Eugen Lounkine
- Chemical Biology & Therapeutics, NIBR, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.,Modeling and Informatics, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Pierre Farmer
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland.
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Ramaiahgari SC, Auerbach SS, Saddler TO, Rice JR, Dunlap PE, Sipes NS, DeVito MJ, Shah RR, Bushel PR, Merrick BA, Paules RS, Ferguson SS. The Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals Using High-throughput Transcriptomics and Benchmark Concentration Modeling. Toxicol Sci 2020; 169:553-566. [PMID: 30850835 DOI: 10.1093/toxsci/kfz065] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Prediction of human response to chemical exposures is a major challenge in both pharmaceutical and toxicological research. Transcriptomics has been a powerful tool to explore chemical-biological interactions, however, limited throughput, high-costs, and complexity of transcriptomic interpretations have yielded numerous studies lacking sufficient experimental context for predictive application. To address these challenges, we have utilized a novel high-throughput transcriptomics (HTT) platform, TempO-Seq, to apply the interpretive power of concentration-response modeling with exposures to 24 reference compounds in both differentiated and non-differentiated human HepaRG cell cultures. Our goals were to (1) explore transcriptomic characteristics distinguishing liver injury compounds, (2) assess impacts of differentiation state of HepaRG cells on baseline and compound-induced responses (eg, metabolically-activated), and (3) identify and resolve reference biological-response pathways through benchmark concentration (BMC) modeling. Study data revealed the predictive utility of this approach to identify human liver injury compounds by their respective BMCs in relation to human internal exposure plasma concentrations, and effectively distinguished drug analogs with varied associations of human liver injury (eg, withdrawn therapeutics trovafloxacin and troglitazone). Impacts of cellular differentiation state (proliferated vs differentiated) were revealed on baseline drug metabolizing enzyme expression, hepatic receptor signaling, and responsiveness to metabolically-activated toxicants (eg, cyclophosphamide, benzo(a)pyrene, and aflatoxin B1). Finally, concentration-response modeling enabled efficient identification and resolution of plausibly-relevant biological-response pathways through their respective pathway-level BMCs. Taken together, these findings revealed HTT paired with differentiated in vitro liver models as an effective tool to model, explore, and interpret toxicological and pharmacological interactions.
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Affiliation(s)
- Sreenivasa C Ramaiahgari
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Scott S Auerbach
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Trey O Saddler
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Julie R Rice
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Paul E Dunlap
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Nisha S Sipes
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Michael J DeVito
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Ruchir R Shah
- Sciome, LLC, Research Triangle Park, Durham, North Carolina 27709
| | - Pierre R Bushel
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709.,Division of Intramural Research, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Bruce A Merrick
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Richard S Paules
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
| | - Stephen S Ferguson
- *Biomolecular Screening Branch, Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, North Carolina 27709
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Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. NANOMATERIALS 2020; 10:nano10040750. [PMID: 32326418 PMCID: PMC7221878 DOI: 10.3390/nano10040750] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 02/07/2023]
Abstract
The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms' responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics integrates classical toxicology with omics assays, thus allowing the characterization of the mechanism of action (MOA) of chemical compounds, novel small molecules, and engineered nanomaterials (ENMs). Lack of standardization in data generation and analysis currently hampers the full exploitation of toxicogenomics-based evidence in risk assessment. To fill this gap, TGx methods need to take into account appropriate experimental design and possible pitfalls in the transcriptomic analyses as well as data generation and sharing that adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data. We provide guidelines on exposure time, dose and complex endpoint selection, sample quality considerations and sample randomization. Furthermore, we summarize publicly available data resources and highlight applications of TGx data to understand and predict chemical toxicity potential. Additionally, we discuss the efforts to implement TGx into regulatory decision making to promote alternative methods for risk assessment and to support the 3R (reduction, refinement, and replacement) concept. This review is the first part of a three-article series on Transcriptomics in Toxicogenomics. These initial considerations on Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects, are the starting point for further rigorous and reliable data preprocessing and modeling, described in the second and third part of the review series.
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Xia P, Zhang H, Peng Y, Shi W, Zhang X. Pathway-based assessment of single chemicals and mixtures by a high-throughput transcriptomics approach. ENVIRONMENT INTERNATIONAL 2020; 136:105455. [PMID: 31945694 DOI: 10.1016/j.envint.2019.105455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/12/2019] [Accepted: 12/26/2019] [Indexed: 05/23/2023]
Abstract
The ever-increasing number of chemicals and complex mixtures demands a high-throughput and cost-effective approach for chemical safety assessment. High-throughput transcriptomics (HTT) is promising in investigating genome-scale perturbation of chemical exposure in concentration-dependent manner. However, the application of HTT has been limited due to lack of methodology for single chemicals and mixture assessment. This study aimed to evaluate the ability of a newly-developed human reduced transcriptomics (RHT) approach to assess pathway-based profiles of single chemicals, and to develop a biological pathway-based approach for benchmarking mixture potency using single chemical-based prediction model. First, concentration-dependent RHT were used to qualitatively and quantitatively differentiate pathway-based patterns of different chemicals, using three model toxicants, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), triclosan (TCS) and 5-Chloro-6-hydroxy-2,2',4,4'-tetrabromodiphenyl ether (5-Cl-6-OH-BDE-47). AHR-regulated genes and pathways were most sensitively induced by TCDD, while TCS and 5-Cl-6-OH-BDE-47 were much less potent in AHR-associated activation, which was concordant with known MoA of each single chemical. Second, two artificial mixtures and their components of twelve individual chemicals were performed with concentration-dependent RHT. Concentration addition (CA) and independent action (IA) models were used to predict transcriptional potency of mixtures from transcriptomics of individual chemicals. For overall bioactivity, CA and IA models can both predict potency of observed responses within 95% confidence interval. For specific biological processes, multiple biological processes such as hormone signaling and DNA damage can be predicted using CA models for mixtures. The concentration-dependent RHT can provide a powerful approach for qualitative and quantitative assessment of biological pathway perturbated by environment chemical and mixtures.
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Affiliation(s)
- Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Hanxin Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Ying Peng
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Wei Shi
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China.
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Harrill J, Shah I, Setzer RW, Haggard D, Auerbach S, Judson R, Thomas RS. Considerations for Strategic Use of High-Throughput Transcriptomics Chemical Screening Data in Regulatory Decisions. CURRENT OPINION IN TOXICOLOGY 2019; 15:64-75. [PMID: 31501805 DOI: 10.1016/j.cotox.2019.05.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, numerous organizations, including governmental regulatory agencies in the U.S. and abroad, have proposed using data from New Approach Methodologies (NAMs) for augmenting and increasing the pace of chemical assessments. NAMs are broadly defined as any technology, methodology, approach or combination thereof that can be used to provide information on chemical hazard and risk assessment that avoids the use of intact animals. High-throughput transcriptomics (HTTr) is a type of NAM that uses gene expression profiling as an endpoint for rapidly evaluating the effects of large numbers of chemicals on in vitro cell culture systems. As compared to targeted high-throughput screening (HTS) approaches that measure the effect of chemical X on target Y, HTTr is a non-targeted approach that allows researchers to more broadly characterize the integrated response of an intact biological system to chemicals that may affect a specific biological target or many biological targets under a defined set of treatment conditions (time, concentration, etc.). HTTr screening performed in concentration-response mode can provide potency estimates for the concentrations of chemicals that produce perturbations in cellular response pathways. Here, we discuss study design considerations for HTTr concentration-response screening and present a framework for the use of HTTr-based biological pathway-altering concentrations (BPACs) in a screening-level, risk-based chemical prioritization approach. The framework involves concentration-response modeling of HTTr data, mapping gene level responses to biological pathways, determination of BPACs, in vitro-to-in vivo extrapolation (IVIVE) and comparison to human exposure predictions.
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Affiliation(s)
- Joshua Harrill
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - R Woodrow Setzer
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Derik Haggard
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, USA
| | - Scott Auerbach
- National Toxicology Program, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC, USA
| | - Richard Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Russell S Thomas
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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Trejo CL, Babić M, Imler E, Gonzalez M, Bibikov SI, Shepard PJ, VanSteenhouse HC, Yeakley JM, Seligmann BE. Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue. PLoS One 2019; 14:e0212031. [PMID: 30794557 PMCID: PMC6386473 DOI: 10.1371/journal.pone.0212031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/26/2019] [Indexed: 02/06/2023] Open
Abstract
We describe the use of a ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq, to profile formalin-fixed paraffin-embedded (FFPE) tissue, including H&E stained FFPE tissue, by directly lysing tissue scraped from slides without extracting RNA or converting the RNA to cDNA. The correlation of measured gene expression changes in unfixed and fixed samples using blocks prepared from a pellet of a single cell type was R2 = 0.97, demonstrating that no significant artifacts were introduced by fixation. Fixed and fresh samples prepared in an equivalent manner produced comparable sequencing depth results (+/- 20%), with similar %CV (11.5 and 12.7%, respectively), indicating no significant loss of measurable RNA due to fixation. The sensitivity of the TempO-Seq assay was the same whether the tissue section was fixed or not. The assay performance was equivalent for human, mouse, or rat whole transcriptome. The results from 10 mm2 and 2 mm2 areas of tissue obtained from 5 μm thick sections were equivalent, thus demonstrating high sensitivity and ability to profile focal areas of histology within a section. Replicate reproducibility of separate areas of tissue ranged from R2 = 0.83 (lung) to 0.96 (liver) depending on the tissue type, with an average correlation of R2 = 0.90 across nine tissue types. The average %CVs were 16.8% for genes expressed at greater than 200 counts, and 20.3% for genes greater than 50 counts. Tissue specific differences in gene expression were identified and agreed with the literature. There was negligible impact on assay performance using FFPE tissues that had been archived for up to 30 years. Similarly, there was negligible impact of H&E staining, facilitating accurate visualization for scraping and assay of small focal areas of specific histology within a section.
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Affiliation(s)
- Christy L. Trejo
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Miloš Babić
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Elliot Imler
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Migdalia Gonzalez
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Sergei I. Bibikov
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Peter J. Shepard
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | | | - Joanne M. Yeakley
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
| | - Bruce E. Seligmann
- BioSpyder Technologies, Inc., Carlsbad, California, United States of America
- * E-mail:
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Grimm FA, House JS, Wilson MR, Sirenko O, Iwata Y, Wright FA, Ball N, Rusyn I. Multi-dimensional in vitro bioactivity profiling for grouping of glycol ethers. Regul Toxicol Pharmacol 2019; 101:91-102. [PMID: 30471335 PMCID: PMC6333527 DOI: 10.1016/j.yrtph.2018.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/23/2018] [Accepted: 11/20/2018] [Indexed: 01/01/2023]
Abstract
High-content screening data derived from physiologically-relevant in vitro models promise to improve confidence in data-integrative groupings for read-across in human health safety assessments. The biological data-based read-across concept is especially applicable to bioactive chemicals with defined mechanisms of toxicity; however, the challenge of data-derived groupings for chemicals that are associated with little or no bioactivity has not been explored. In this study, we apply a suite of organotypic and population-based in vitro models for comprehensive bioactivity profiling of twenty E-Series and P-Series glycol ethers, solvents with a broad variation in toxicity ranging from relatively non-toxic to reproductive and hematopoetic system toxicants. Both E-Series and P-Series glycol ethers elicited cytotoxicity only at high concentrations (mM range) in induced pluripotent stem cell-derived hepatocytes and cardiomyocytes. Population-variability assessment comprised a study of cytotoxicity in 94 human lymphoblast cell lines from 9 populations and revealed differences in inter-individual variability across glycol ethers, but did not indicate population-specific effects. Data derived from various phenotypic and transcriptomic assays revealed consistent bioactivity trends between both cardiomyocytes and hepatocytes, indicating a more universal, rather than cell-type specific mode-of-action for the tested glycol ethers in vitro. In vitro bioactivity-based similarity assessment using Toxicological Priority Index (ToxPi) showed that glycol ethers group according to their alcohol chain length, longer chains were associated with increased bioactivity. While overall in vitro bioactivity profiles did not correlate with in vivo toxicity data on glycol ethers, in vitro bioactivity of E-series glycol ethers were indicative of and correlated with in vivo irritation scores.
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Affiliation(s)
- Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Melinda R Wilson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | | | - Yasuhiro Iwata
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Nicholas Ball
- Toxicology and Environmental Research and Consulting (TERC), Environment, Health and Safety (EH&S), The Dow Chemical Company, Horgen, Zurich, 8810, Switzerland
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA.
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Bushel PR, Paules RS, Auerbach SS. A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. Front Genet 2018; 9:485. [PMID: 30420870 PMCID: PMC6217592 DOI: 10.3389/fgene.2018.00485] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/28/2018] [Indexed: 11/13/2022] Open
Abstract
The TempO-SeqTM platform allows for targeted transcriptomic analysis and is currently used by many groups to perform high-throughput gene expression analysis. Herein we performed a comparison of gene expression characteristics measured using 45 purified RNA samples from the livers of rats exposed to chemicals that fall into one of five modes of action (MOAs). These samples have been previously evaluated using AffymetrixTM rat genome 230 2.0 microarrays and Illumina® whole transcriptome RNA-Seq. Comparison of these data with TempO-Seq analysis using the rat S1500+ beta gene set identified clear differences in the platforms related to signal to noise, root mean squared error, and/or sources of variability. Microarray and TempO-Seq captured the most variability in terms of MOA and chemical treatment whereas RNA-Seq had higher noise and larger differences between samples within a MOA. However, analysis of the data by hierarchical clustering, gene subnetwork connectivity and biological process representation of MOA-varying genes revealed that the samples clearly grouped by treatment as opposed to gene expression platform. Overall these findings demonstrate that the results from the TempO-Seq platform are consistent with findings on other more established approaches for measuring the genome-wide transcriptome.
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Affiliation(s)
- Pierre R Bushel
- Biostatistics and Computational Biology Branch, NIEHS, Research Triangle Park, Durham, NC, United States
| | - Richard S Paules
- Biomolecular Screening Branch, National Toxicology Program, NIEHS, Research Triangle Park, Durham, NC, United States
| | - Scott S Auerbach
- Biomolecular Screening Branch, National Toxicology Program, NIEHS, Research Triangle Park, Durham, NC, United States
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Haider S, Black MB, Parks BB, Foley B, Wetmore BA, Andersen ME, Clewell RA, Mansouri K, McMullen PD. A Qualitative Modeling Approach for Whole Genome Prediction Using High-Throughput Toxicogenomics Data and Pathway-Based Validation. Front Pharmacol 2018; 9:1072. [PMID: 30333746 PMCID: PMC6176017 DOI: 10.3389/fphar.2018.01072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/05/2018] [Indexed: 01/05/2023] Open
Abstract
Efficient high-throughput transcriptomics (HTT) tools promise inexpensive, rapid assessment of possible biological consequences of human and environmental exposures to tens of thousands of chemicals in commerce. HTT systems have used relatively small sets of gene expression measurements coupled with mathematical prediction methods to estimate genome-wide gene expression and are often trained and validated using pharmaceutical compounds. It is unclear whether these training sets are suitable for general toxicity testing applications and the more diverse chemical space represented by commercial chemicals and environmental contaminants. In this work, we built predictive computational models that inferred whole genome transcriptional profiles from a smaller sample of surrogate genes. The model was trained and validated using a large scale toxicogenomics database with gene expression data from exposure to heterogeneous chemicals from a wide range of classes (the Open TG-GATEs data base). The method of predictor selection was designed to allow high fidelity gene prediction from any pre-existing gene expression data set, regardless of animal species or data measurement platform. Predictive qualitative models were developed with this TG-GATES data that contained gene expression data of human primary hepatocytes with over 941 samples covering 158 compounds. A sequential forward search-based greedy algorithm, combining different fitting approaches and machine learning techniques, was used to find an optimal set of surrogate genes that predicted differential expression changes of the remaining genome. We then used pathway enrichment of up-regulated and down-regulated genes to assess the ability of a limited gene set to determine relevant patterns of tissue response. In addition, we compared prediction performance using the surrogate genes found from our greedy algorithm (referred to as the SV2000) with the landmark genes provided by existing technologies such as L1000 (Genometry) and S1500 (Tox21), finding better predictive performance for the SV2000. The ability of these predictive algorithms to predict pathway level responses is a positive step toward incorporating mode of action (MOA) analysis into the high throughput prioritization and testing of the large number of chemicals in need of safety evaluation.
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Affiliation(s)
- Saad Haider
- ScitoVation, Research Triangle Park, NC, United States
| | | | | | - Briana Foley
- ScitoVation, Research Triangle Park, NC, United States
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Sakolish C, Weber EJ, Kelly EJ, Himmelfarb J, Mouneimne R, Grimm FA, House JS, Wade T, Han A, Chiu WA, Rusyn I. Technology Transfer of the Microphysiological Systems: A Case Study of the Human Proximal Tubule Tissue Chip. Sci Rep 2018; 8:14882. [PMID: 30291268 PMCID: PMC6173737 DOI: 10.1038/s41598-018-33099-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023] Open
Abstract
The adoption of a new technology into basic research, and industrial and clinical settings requires rigorous testing to build confidence in the reproducibility, reliability, robustness, and relevance of these models. Tissue chips are promising new technology, they have the potential to serve as a valuable tool in biomedical research, as well as pharmaceutical development with regards to testing for efficacy and safety. The principal goals of this study were to validate a previously established proximal tubule tissue chip model in an independent laboratory and to extend its utility to testing of nephrotoxic compounds. Here, we evaluated critical endpoints from the tissue chip developer laboratory, focusing on biological relevance (long-term viability, baseline protein and gene expression, ammoniagenesis, and vitamin D metabolism), and toxicity biomarkers. Tissue chip experiments were conducted in parallel with traditional 2D culture conditions using two different renal proximal tubule epithelial cell sources. The results of these studies were then compared to the findings reported by the tissue chip developers. While the overall transferability of this advanced tissue chip platform was a success, the reproducibility with the original report was greatly dependent on the cell source. This study demonstrates critical importance of developing microphysiological platforms using renewable cell sources.
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Affiliation(s)
- Courtney Sakolish
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Elijah J Weber
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Edward J Kelly
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Jonathan Himmelfarb
- Division of Nephrology, University of Washington Kidney Research Institute, Seattle, WA, USA
| | - Roula Mouneimne
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Terry Wade
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Biomedical Engineering, 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.
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Grimm FA, Blanchette A, House JS, Ferguson K, Hsieh NH, Dalaijamts C, Wright AA, Anson B, Wright FA, Chiu WA, Rusyn I. A human population-based organotypic in vitro model for cardiotoxicity screening. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION 2018; 35:441-452. [PMID: 29999168 PMCID: PMC6231908 DOI: 10.14573/altex.1805301] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/05/2018] [Indexed: 12/11/2022]
Abstract
Assessing inter-individual variability in responses to xenobiotics remains a substantial challenge, both in drug development with respect to pharmaceuticals and in public health with respect to environmental chemicals. Although approaches exist to characterize pharmacokinetic variability, there are no methods to routinely address pharmacodynamic variability. In this study, we aimed to demonstrate the feasibility of characterizing inter-individual variability in a human in vitro model. Specifically, we hypothesized that genetic variability across a population of iPSC-derived cardiomyocytes translates into reproducible variability in both baseline phenotypes and drug responses. We measured baseline and drug-related effects in iPSC-derived cardiomyocytes from 27 healthy donors on kinetic Ca2+ flux and high-content live cell imaging. Cells were treated in concentration-response with cardiotoxic drugs: isoproterenol (β-adrenergic receptor agonist/positive inotrope), propranolol (β-adrenergic receptor antagonist/negative inotrope), and cisapride (hERG channel inhibitor/QT prolongation). Cells from four of the 27 donors were further evaluated in terms of baseline and treatment-related gene expression. Reproducibility of phenotypic responses was evaluated across batches and time. iPSC-derived cardiomyocytes exhibited reproducible donor-specific differences in baseline function and drug-induced effects. We demonstrate the feasibility of using a panel of population-based organotypic cells from healthy donors as an animal replacement experimental model. This model can be used to rapidly screen drugs and chemicals for inter-individual variability in cardiotoxicity. This approach demonstrates the feasibility of quantifying inter-individual variability in xenobiotic responses and can be expanded to other cell types for which in vitro populations can be derived from iPSCs.
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Affiliation(s)
- Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Alexander Blanchette
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Kyle Ferguson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Nan-Hung Hsieh
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Chimeddulam Dalaijamts
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Alec A Wright
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Blake Anson
- Cellular Dynamics International, Madison, WI, USA
| | - Fred A Wright
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Department of Statistics, 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
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Andersen ME, Pendse SN, Black MB, McMullen PD. Application of transcriptomic data, visualization tools and bioinformatics resources for informing mode of action. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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