From vision toward best practices: Evaluating in vitro transcriptomic points of departure for application in risk assessment using a uniform workflow

Frontiers in Toxicology, Journal Year: 2023, Volume and Issue: 5

Published: May 23, 2023

The growing number of chemicals in the current consumer and industrial markets presents a major challenge for regulatory programs faced with need to assess potential risks they pose human ecological health. increasing demand hazard risk assessment currently exceeds capacity produce toxicity data necessary decision making, applied is commonly generated using traditional approaches animal models that have limited context terms relevance. This scenario provides opportunity implement novel, more efficient strategies purposes. study aims increase confidence implementation new approach methods by parallel analysis identify gaps experimental designs, reveal limitations common deriving transcriptomic points departure, demonstrate strengths high-throughput transcriptomics (HTTr) derive practical endpoints. A uniform workflow was across six curated gene expression datasets from concentration-response studies containing 117 diverse chemicals, three cell types, range exposure durations, determine tPODs based on profiles. After benchmark concentration modeling, used consistent reliable tPODs. High-throughput toxicokinetics were employed translate vitro (µM) human-relevant administered equivalent doses (AEDs, mg/kg-bw/day). most had AEDs lower (i.e., conservative) than apical PODs US EPA CompTox chemical dashboard, suggesting would be protective effects An multiple single revealed longer duration varied culture systems (e.g., 3D vs. 2D) lead decreased tPOD value indicated increased potency. Seven flagged as outliers when comparing ratio POD, thus indicating require further better understand their potential. Our findings build use but also must addressed prior adoption support applications.

Language: Английский

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Progress in toxicogenomics to protect human health

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 2, 2024

Language: Английский

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An updated comparison of microarray and RNA-seq for concentration response transcriptomic study: case studies with two cannabinoids, cannabichromene and cannabinol

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: April 22, 2025

Abstract Background Transcriptomic benchmark concentration (BMC) modeling provides quantitative toxicogenomic information that is increasingly being used in regulatory risk assessment of data poor chemicals. Over the past decade, RNA sequencing (RNA-seq) gradually replacing microarray as major platform for transcriptomic applications due to its higher precision, wider dynamic range, and capability detecting novel transcripts. However, it unclear whether RNA-seq offers substantial advantages over response studies. Results We provide an updated comparison between using two cannabinoids, cannabichromene (CBC) cannabinol (CBN), case The platforms revealed similar overall gene expression patterns with regard both CBC CBN. spite many varieties non-coding transcripts larger numbers differentially expressed genes (DEGs) ranges identified by RNA-seq, displayed equivalent performance identifying functions pathways impacted compound exposure through set enrichment analysis (GSEA). Furthermore, point departure (tPoD) values derived BMC were on same levels Conclusions Considering relatively low cost, smaller size, better availability software public databases interpretation, still a viable method choice traditional such mechanistic pathway identification modeling.

Language: Английский

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Per- and polyfluoroalkyl substances (PFAS) in mixtures show additive effects on transcriptomic points of departure in human liver spheroids

Toxicological Sciences, Journal Year: 2023, Volume and Issue: 194(1), P. 38 - 52

Published: May 17, 2023

Per- and polyfluoroalkyl substances (PFAS) are a wide range of chemicals that used in variety consumer industrial products leading to direct human exposure. Many PFAS chemically nonreactive persistent the environment, resulting additional exposure from water, soil, dietary intake. While some have documented negative health effects, data on simultaneous exposures multiple (PFAS mixtures) inadequate for making informed decisions risk assessment. The current study leverages previous work our group using Templated Oligo-Sequencing (TempO-Seq) high-throughput transcriptomic analysis PFAS-exposed primary liver cell spheroids; herein, we determine potency mixtures. Gene expression single mixture spheroids were subject benchmark concentration (BMC) analysis. We 25th lowest gene BMC as point departure compare potencies mixtures varying complexity composition. Specifically, empirical 8 compared predicted calculated principal addition (ie, dose addition) which component summed by proportion predict potency. In this study, most mixtures, comparable through addition. This supports effects largely follow response suggests these individual not strongly synergistic or antagonistic.

Language: Английский

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Unlocking the Power of Transcriptomic Biomarkers in Qualitative and Quantitative Genotoxicity Assessment of Chemicals

Chemical Research in Toxicology, Journal Year: 2024, Volume and Issue: 37(3), P. 465 - 475

Published: Feb. 26, 2024

To modernize genotoxicity assessment and reduce reliance on experimental animals, new approach methodologies (NAMs) that provide human-relevant dose-response data are needed. Two transcriptomic biomarkers, GENOMARK TGx-DDI, have shown a high classification accuracy for genotoxicity. As these biomarkers were extracted from different training sets, we investigated whether combining the two in human-derived metabolically competent cell line (i.e., HepaRG) provides complementary information of genotoxic hazard identification potency ranking. First, applicability to TempO-Seq, high-throughput technology, was evaluated. HepaRG cells exposed 72 h increasing concentrations 10 chemicals eight known

Language: Английский

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New Approach Methodologies for the Endocrine Activity Toolbox: Environmental Assessment for Fish and Amphibians

Environmental Toxicology and Chemistry, Journal Year: 2023, Volume and Issue: 42(4), P. 757 - 777

Published: Feb. 15, 2023

Multiple in vivo test guidelines focusing on the estrogen, androgen, thyroid, and steroidogenesis pathways have been developed validated for mammals, amphibians, or fish. However, these tests are resource-intensive often use a large number of laboratory animals. Developing alternatives is consistent with replacement, reduction, refinement principles animal welfare considerations, which supported by increasing mandates to move toward an "animal-free" testing paradigm worldwide. New approach methodologies (NAMs) hold great promise identify molecular, cellular, tissue changes that can be used predict effects reliably more efficiently at individual level (and potentially populations) while reducing animals (eco)toxicological endocrine disruption. In collaborative effort, experts from government, academia, industry met 2020 discuss current challenges activity assessment fish amphibians. Continuing this cross-sector initiative, our review focuses state science regarding NAMs chemical-induced effects. The present study highlights using safety what work needed reduce their uncertainties increase acceptance regulatory processes. We reviewed available including silico, vitro, eleutheroembryo models. integrated as part weight-of-evidence hazard risk adverse outcome pathway framework. development utilization not only allows but also provide robust fit-for-purpose methods chemicals acting via mechanisms. Environ Toxicol Chem 2023;42:757-777. © 2023 Authors. Environmental Toxicology Chemistry published Wiley Periodicals LLC behalf SETAC.

Language: Английский

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From Pipeline to Plant Protection Products: Using New Approach Methodologies (NAMs) in Agrochemical Safety Assessment

Journal of Agricultural and Food Chemistry, Journal Year: 2024, Volume and Issue: 72(19), P. 10710 - 10724

Published: April 30, 2024

The human population will be approximately 9.7 billion by 2050, and food security has been identified as one of the key issues facing global population. Agrochemicals are an important tool available to farmers that enable high crop yields continued access healthy foods, but average new agrochemical active ingredient takes more than ten years, 350 million dollars, 20,000 animals develop register. time, monetary, animal costs incentivize use New Approach Methodologies (NAMs) in early-stage screening prioritize chemical candidates. This review outlines NAMs currently or can adapted for programs. It covers vitro screens on horizon areas regulatory concern. Overall, with enables prioritization development agrochemicals without environmental health concerns through a directed, agile, iterative program before animal-based testing is even considered.

Language: Английский

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The dose disrupts the pathway: application of Paracelsus principle to mechanistic toxicology

Toxicological Sciences, Journal Year: 2024, Volume and Issue: 200(2), P. 228 - 234

Published: May 7, 2024

Abstract Arguably the most famous principle of toxicology is “The dose makes poison” formulated by Paracelsus in 16th century. Application Paracelsus’s to mechanistic may be challenging as one compound affect many molecular pathways at different doses with and often nonlinear dose-response relationships. As a result, studies environmental occupational compounds use high xenobiotics motivated need see clear signal indicating disruption particular pathway. This approach ignores possibility that same xenobiotic mechanism(s) much lower relevant human exposures. To amend simple concise guiding principle, I suggest recontextualization following its letter spirit: disrupts pathway”. Justification this statement includes observations broad range cascades, are sensitive chemical exposures, compound. become useful guidance educational tool toxicological applications, including experimental design, comparative analysis hypotheses, evaluation quality studies, risk assessment.

Language: Английский

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Transcriptomic point of departure determination: a comparison of distribution-based and gene set-based approaches

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: May 9, 2024

A key step in assessing the potential human and environmental health risks of industrial agricultural chemicals is to determine toxicity point departure (POD), which highest dose level that causes no adverse effect. Transcriptomic POD (tPOD) values have been suggested accurately estimate values. One most common approach for tPOD determination involves mapping genes annotated gene sets, a process might lead substantial information loss particularly species with poor annotation. Alternatively, methods calculate directly from distribution individual omit this step. Using rat transcriptome data 79 molecules obtained Open TG-GATEs (Toxicogenomics Project Genomics Assisted Toxicity Evaluation System), hypothesis was tested based on all will give similar value via set-based method. Gene using four different set structures were compared five methods. Results revealed high concordance tested, especially at least 300 dose-responsive probesets: 90% those molecules, within 4-fold each other. In addition, random sets upon structure biological knowledge-derived produced median absolute fold change 1.3–1.4 when original counterparts, suggesting little used generation approach. These findings indicate distributions viable parsimonious alternative sets. Importantly, distribution-based do not require knowledge organization can be applied any including poorly

Language: Английский

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Comparison on the mechanism and potency of hepatotoxicity among hemp extract and its four major constituent cannabinoids

Toxicology, Journal Year: 2024, Volume and Issue: 506, P. 153885 - 153885

Published: July 14, 2024

Cannabidiol (CBD) has been reported to induce hepatotoxicity in clinical trials and research studies; however, little is known about the safety of other nonintoxicating cannabinoids. New approach methodologies (NAMs) based on bioinformatic analysis high-throughput transcriptomic data are gaining increasing importance risk assessment regulatory decision-making data-poor chemicals. In current study, we conducted a concentration response hemp extract its four major constituent cannabinoids [CBD, cannabichromene (CBC), cannabigerol (CBG), cannabinol (CBN)] hepatocytes derived from human induced pluripotent stem cells (iPSCs). Each compound impacted distinctive combination biological functions pathways. However, all impaired liver metabolism caused oxidative stress cells. Benchmark (BMC) showed potencies transcriptional activity were order CBN > CBD CBC CBG, consistent with their cytotoxicity IC

Language: Английский

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