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

Frontiers in Toxicology, Год журнала: 2023, Номер 5

Опубликована: Май 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.

Язык: Английский

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Progress in toxicogenomics to protect human health

Nature Reviews Genetics, Год журнала: 2024, Номер unknown

Опубликована: Сен. 2, 2024

Язык: 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, Год журнала: 2023, Номер 194(1), С. 38 - 52

Опубликована: Май 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.

Язык: Английский

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

Chemical Research in Toxicology, Год журнала: 2024, Номер 37(3), С. 465 - 475

Опубликована: Фев. 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

Язык: 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, Год журнала: 2025, Номер 26(1)

Опубликована: Апрель 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.

Язык: Английский

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

Environmental Toxicology and Chemistry, Год журнала: 2023, Номер 42(4), С. 757 - 777

Опубликована: Фев. 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.

Язык: Английский

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In vitrotranscriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals

Toxicological Sciences, Год журнала: 2022, Номер 191(2), С. 266 - 275

Опубликована: Дек. 19, 2022

Since initial regulatory action in 2010 Canada, bisphenol A (BPA) has been progressively replaced by structurally related alternative chemicals. Unfortunately, many of these chemicals are data-poor, limiting toxicological risk assessment. We used high-throughput transcriptomics to evaluate potential hazards and compare potencies BPA 15 cultured breast cancer cells. MCF-7 cells were exposed (0.0005-100 µM) for 48 h. TempO-Seq (BioSpyder Inc) was examine global transcriptomic changes estrogen receptor alpha (ERα)-associated transcriptional changes. Benchmark concentration (BMC) analysis conducted identify 2 points departure: (1) the lowest pathway median gene BMC (2) 25th rank-ordered BMC. ERα activation evaluated using a published biomarker an ERα-specific point departure derived. Genes fitting models subjected upstream regulator canonical Ingenuity Pathway Analysis. Biomarker identified 8 as active. Global produced highly similar potency rankings with AF most potent chemical tested, followed C. Further, transcriptionally active enriched sets associated increased cell division cancer-related processes. These data provide support future read-across applications profiling assessment data-poor suggest that several may cause at concentrations BPA.

Язык: Английский

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The contribution of larval zebrafish transcriptomics to chemical risk assessment

Regulatory Toxicology and Pharmacology, Год журнала: 2023, Номер 138, С. 105336 - 105336

Опубликована: Янв. 13, 2023

In Canada, the Canadian Environmental Protection Act (1999) requires human health and environmental risk assessments be conducted for new substances prior to their manufacture or import. While this toxicity data is historically obtained using rodents, in response international effort eliminate animal testing, Health Canada collaborating with National Research Council (NRC) of develop a New Approach Method by refining existing NRC zebrafish models. The embryo/larval model evaluates systemic (whole body) general which currently unachievable cell-based testing. strengthened behavioral, toxicokinetic transcriptomic responses assess non-visible indicators following chemical exposure at sub-phenotypic concentrations. paper, predictive power transcriptomics demonstrated two chemicals; Raloxifene Resorcinol. produced darkening liver malformation nose/mandible, while Resorcinol increased locomotor activity. Transcriptomic analysis correlated differentially expressed genes phenotypic effects benchmark dose calculations determined that Point Departure (POD) occurred subphenotypic Correlating gene expression apical (phenotypic) strengthens confidence evaluation toxicity, thereby demonstrating significant advancement larval represents assessment.

Язык: Английский

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Risk-based prioritization of PFAS using phenotypic and transcriptomic data from human induced pluripotent stem cell-derived hepatocytes and cardiomyocytes

ALTEX, Год журнала: 2024, Номер unknown

Опубликована: Янв. 1, 2024

Per- and polyfluoroalkyl substances (PFAS) are chemicals with important applications; they persistent in the environment may pose human health hazards. Regulatory agencies considering restrictions bans of PFAS; however, little data exists for informed decisions. Several prioritization strategies were proposed evaluation potential hazards PFAS. Structure-based grouping could expedite selection PFAS testing; still, hypothesis that structure-effect relationships exist requires confirmation. We tested 26 structurally diverse from 8 groups using human-induced pluripotent stem cell-derived hepatocytes cardiomyocytes, concentration-response effects on cell function gene expression. Few phenotypic observed hepatocytes, but negative chronotropy was Substance- type-dependent transcriptomic changes more prominent lacked substantial group-specific effects. In we found up-regulation stress-related extracellular matrix organization pathways, down-regulation fat metabolism. contractility-related pathways most affected. derived points departure compared them to predicted exposures. The conservative estimates bioactivity exposure used derive bioactivity-to-exposure ratio (BER) each PFAS, (23 26) had BER>1. Overall, these suggests structure-based not be sufficient predict their biological Testing individual needed scientific-based decision-making. Our strategy two types effects, combined dose-response analysis calculation BER, prioritization. Plain language summaryPer- man-made many products. However, have been safety, concerns harmful and/or environment. This study aimed use cell-based models investigate if some exhibit hazardous properties similarities among observed. liver cells, a decrease beating frequency heart cells Gene expression substance- type-dependent. did find convincing this testing necessary future inform showed test types, heart, without need animals.

Язык: 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, Год журнала: 2024, Номер 72(19), С. 10710 - 10724

Опубликована: Апрель 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.

Язык: Английский

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