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Qualitative and quantitative bioanalytical methods validation of aristolochic acid DNA adducts and application in human formalin-fixed paraffin-embedded hepatocellular carcinoma tissues

Mutation signature of aristolochic acid (AA) found in urothelial or hepatocellular carcinoma causes public concern about the cancer risk of AA. In contrast, direct evidence based on the reliable bioanalytical method for the exposure of AA is still lacking and not universal. Here, we strictly complied with the qualitative and quantitative guidance for forensic toxicological analysis: In the sample preprocessing, DNA from formalin-fixed and paraffin-embedded (FFPE) tissues was digested to single nucleotide by a series of enzymes with 70% enzymatic digestion efficiency. After protein precipitation, the samples were submitted to an ABI6500+ mass spectrometer for LC-MS/MS analysis. Ion pairs 543.2/427.2 and 543.2/395.2 of dA-AAI were selected from 5 ion pairs due to their higher LC-MS/MS response. Both these ion pairs have excellent selectivity and specificity in rat liver DNA matrix, and a linear regression range from 5 pg/mL to 200 pg/mL with the best fit and determination coefficient (r) greater than 0.99. The intra and inter batch accuracy and precision of these two ion pairs are also acceptable with less than 15% variation. The total recovery for ion pair 543.2/427.2 and 543.2/395.2 of dA-AAI was 90.06% and 90.76%, respectively. Our method has a minor matrix effect and good stability under different temperature and time conditions. With signal to noise ratio [&ge;] 3, 2 ion pairs (< 50 % relative abundance variation), the lower limit of quantification (LLOQ) of our method is set to 5 pg/mL([~]3.6 AAI-DNA adducts per 108 DNA bases). By using this validated bioanalytical method of dA-AAI, 165 human HCC FFPE tissues were analyzed, the total ratio of samples with peak543.2/427.2 is 17.0% (28/165), with peak543.2/395.2 is 9.09% (15/165) which yields the total ratio of samples combined peak543.2/427.2 and peak543.2/395.2 is 7.27% (12/165). Two samples are higher than 5 pg/mL under the qualitative requirements. In conclusion, we first reported a fully validated methods to analyze the DNA adducts level of aristolochic acid, which could be qualitatively and quantitatively applied to the investigation of AA exposure in the human and other species.

pharmacology and toxicology↗

Mechanistic characterization of tenuazonic acid-induced cellular stress responses in human esophageal KYSE-510 cells

Tenuazonic acid (TeA) is an emerging Alternaria mycotoxin frequently detected in food and feed commodities, raising concerns about its toxicological relevance. Chronic oral exposure to TeA has been reported to induce dysplastic alterations in the esophageal mucosa of mice, while human biomonitoring data indicate an association between TeA exposure and esophageal cancer, although a causal relationship has not yet been established. At a mechanistic level, the effects of TeA in esophageal cells remain poorly characterized. Therefore, this study investigated the impact of TeA on cytotoxicity, oxidative stress, DNA damage, mitochondrial homeostasis, cell-cycle distribution and transcriptomic stress responses in human esophageal KYSE-510 cells. TeA induced a concentration-dependent reduction in metabolic activity and total protein content after 24 h exposure to 0.1-100 {micro}M. Significant cytotoxicity was measured starting from 20 {micro}M. At sub-cytotoxic concentrations, TeA triggered rapid ROS formation within 5-30 min exposure and induced formamidopyrimidine-DNA glycosylase (FPG) sensitive DNA damage after 1 h exposure (5-7.5 {micro}M), indicating oxidative DNA lesions. In addition, TeA altered mitochondrial morphology after 4 h exposure at 7.5 {micro}M, manifested by shrinkage of the mitochondrial network area and perinuclear redistribution, while mitochondrial respiration showed only a non-significant tendency towards reduced respiratory capacity. RNA sequencing after 6 h exposure to 10 {micro}M TeA revealed oxidative stress-associated transcriptional changes, impaired antioxidant and stress-adaptive responses, and p53-associated stress signaling. Furthermore, TeA induced significant G2/M phase accumulation after 24 h exposure to 1-10 {micro}M. HighlightsO_LITeA triggers rapid oxidative stress in human esophageal KYSE-510 cells C_LIO_LISub-cytotoxic TeA induces FPG-sensitive oxidative DNA lesions C_LIO_LITeA disrupts mitochondrial morphology before overt cytotoxicity occurs C_LIO_LIRNA-seq reveals impaired antioxidant defense and p53-linked stress signaling C_LIO_LITeA promotes G2/M phase accumulation and concentration-dependent cytotoxicity C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/736731v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@a496faorg.highwire.dtl.DTLVardef@1b42072org.highwire.dtl.DTLVardef@be5088org.highwire.dtl.DTLVardef@991b5b_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

On the utilisation and characterisation of external biotransformation systems in in vitro toxicology: a critical review of the scientific literature with guidance recommendations

Incorporating biotransformation capabilities into in vitro assays represents one of the most critical challenges in toxicology, facilitating the transition from in vivo models to integrated in vitro strategies. Although emerging technologies show promise, their current limitations in scalability hinder high-throughput applications. In the short to mid-term, externally added biotransformation systems ("BTS": S9 and microsomal liver fractions) used together with in vitro assays offer viable alternatives. However, despite over fifty years of use, BTS are marred by reproducibility issues, raising concerns about their reliability, and raising the question: Are BTS inherently unreliable, or has their reputation been flawed by methodological oversights? This review critically evaluates BTS methodological rigour, applying a deep statistical analysis of the scientific literature. We employed Boolean operator searches across scientific literature repositories to curate a database on BTS research in conjunction with relevant in vitro assays, focusing on endocrine disruption, mutagenicity, and genotoxicity endpoints. Through systematic searches, screening, and eligibility criteria, we identified 229 bibliographic records. Data parameterisation and extraction were conducted across 24 domains of BTS relevance and reliability. Methodological reporting rigour was assessed via scoring (reported vs. non-reported data items) and revealed a lack of reproducible standards. Numerical measures associated with principal BTS reaction components were subjected to meta-regression analyses. No statistically significant correlations were found for BTS and related cofactor concentration-response relationships or time-related elements. Finally, descriptive statistics, multiple correspondence analysis, and Apriori algorithm-based relational networks identified qualitative patterns of methodological robustness and deficiencies. In conclusion, these results emphasise shortcomings across the scientific literature in complying with appropriate methodological reporting. We offer evidence-based recommendations, in the form of a conceptual regulatory guidance framework, to enhance research practices, quality, and reproducibility of BTS applications; designed to strengthen the robustness of BTS research and its integration into regulatory-relevant hazard and risk assessment of chemicals. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/677684v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1a6dd9aorg.highwire.dtl.DTLVardef@1ecb22org.highwire.dtl.DTLVardef@1aa3ee3org.highwire.dtl.DTLVardef@6aaf6_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

Leukemia in Sprague-Dawley Rats Exposed Long-term from Prenatal Life to Glyphosate and Glyphosate-Based Herbicides

BackgroundGlyphosate-based herbicides (GBHs) are the worlds most widely used weed control agents. There has been intense and increasing public health concern about glyphosate and GBHs since the International Agency for Research on Cancer classified glyphosate as a probable human carcinogen in 2015. AimsTo further study the health effects of glyphosate and GBHs, the Ramazzini Institute, in collaboration with an international network of institutes and universities, has launched the Global Glyphosate Study (GGS), the most comprehensive toxicological study ever performed on these compounds. The GGS is an integrated study designed to test a wide range of toxicological outcomes including carcinogenicity, neurotoxicity, multi-generational effects, organ toxicity, endocrine disruption and prenatal developmental toxicity. The present study reports the first definitive results on leukemia incidence and mortality from the carcinogenicity arm of the GGS. MethodGlyphosate and two GBHs, Roundup Bioflow (MON 52276) used in the European Union (EU) and RangerPro (EPA 524-517) used in the U.S., were administered long-term to Sprague-Dawley (SD) rats beginning in prenatal life until 104 weeks of age via drinking water at doses of 0.5, 5, and 50 mg/kg body weight/day. This dose range encompasses both the EU Acceptable Daily Intake (ADI) and the EU No Observed Adverse Effect Level (NOAEL) for glyphosate. Each experimental group was composed of 51 males and 51 females, the total number animals were 1020 (510 males and 510 females). ResultsIn the animals exposed to glyphosate, a significantly increased trend in incidence of lymphoblastic leukemia was observed in males. In the Roundup Bioflow-treated animals, significantly increased trends were observed in incidence of lymphoblastic leukemia (males and females), monocytic leukemia (males), total myeloid leukemia (males), and all leukemias combined (males and females). In the RangerPro-treated animals, significantly increased trends were observed in incidence of lymphoblastic leukemia (males and females), monocytic leukemia (males) and all leukemias combined (males). 43% of leukemias deaths in the glyphosate and GBHs treated groups occurred before the first year of age (52 weeks). ConclusionsGlyphosate and GBHs at exposure levels corresponding to the EU ADI and the EU NOAEL caused significant, dose-related increased trends in incidence of leukemia, a very rare malignancy, in SD rats. Notably, about half of the leukemia deaths seen in the glyphosate and GBH groups occurred at less than one year of age, comparable to less than 35-40 years of age in humans.

pharmacology and toxicology↗

Shotgun metagenomics and metabolomics reveal glyphosate alters the gut microbiome of Sprague-Dawley rats by inhibiting the shikimate pathway

There is intense debate as to whether glyphosate can interfere with aromatic amino acid biosynthesis in microorganisms inhabiting the gastrointestinal tract, which could potentially lead to negative health outcomes. We have addressed this major gap in glyphosate toxicology by using a multi-omics strategy combining shotgun metagenomics and metabolomics. We tested whether glyphosate (0.5, 50, 175 mg/kg bw/day), or its representative EU commercial herbicide formulation MON 52276 at the same glyphosate equivalent doses, has an effect on the rat gut microbiome in a 90-day subchronic toxicity test. Clinical biochemistry measurements in blood and histopathological evaluations showed that MON 52276 but not glyphosate was associated with statistically significant increase in hepatic steatosis and necrosis. Similar lesions were also present in the liver of glyphosate-treated groups but not in the control group. Caecum metabolomics revealed that glyphosate inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase in the shikimate pathway as evidenced by an accumulation of shikimic acid and 3-dehydroshikimic acid. Levels of caecal microbiome dipeptides involved in the regulation of redox balance ({gamma}-glutamylglutamine, cysteinylglycine, valylglycine) had their levels significantly increased. Shotgun metagenomics showed that glyphosate affected caecum microbial community structure and increased levels of Eggerthella spp. and Homeothermacea spp.. MON 52276, but not glyphosate, increased the relative abundance of Shinella zoogleoides. Since Shinella spp. are known to degrade alkaloids, its increased abundance may explain the decrease in solanidine levels measured with MON 52776 but not glyphosate. Other glyphosate formulations may have different effects since Roundup(R) GT Plus inhibited bacterial growth in vitro at concentrations at which MON 52276 did not present any visible effect. Our study highlights the power of a multiomics approach to investigate effects of pesticides on the gut microbiome. This revealed the first biomarker of glyphosate effects on rat gut microbiome. Although more studies will be needed to ascertain if there are health implications arising from glyphosate inhibition of the shikimate pathway in the gut microbiome, our findings can be used in environmental epidemiological studies to understand if glyphosate can have biological effects in human populations. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/870105v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@66578corg.highwire.dtl.DTLVardef@fddcd9org.highwire.dtl.DTLVardef@ae4ffforg.highwire.dtl.DTLVardef@5f7ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

In vivo characterisation of the toxicological properties of DPhP, one of the main degradation product of aryl phosphate esters.

BackgroundAryl phosphate esters (APEs), a main class of organophosphorus ester molecules, are widely used and commonly present in the environment. Health hazards associated with these compounds remain largely unknown and the effects of diphenyl phosphate (DPhP), one of their most frequent derivatives in human samples, are poorly characterised. ObjectiveOur aim was to investigate whether DPhP per se may represent a more relevant marker of exposure to APEs and determine its potential deleterious biological effects in chronically exposed mice. MethodsConventional animals (FVB mice) were acutely (intravenous or oral gavage) or chronically (0.1 mg.mL-1, 1 mg.mL-1, 10 mg.mL-1 in drink water) exposed to relevant doses of DPhP or triphenyl phosphate (TPhP), one of its main precursors in the environment. Both molecules were measured in blood and other relevant tissues by liquid chromatography-mass spectrometry (LC-MS). Biological effects of chronic DPhP exposure were addressed through liver multi-omics analysis combining mRNA extraction and sequencing to high resolution LC-MS to determine the corresponding metabolic profile. Deep statistical exploration was performed to extract correlated information, guiding further physiological analyses (immunohistochemistry (IHC) and animal growth measurement). ResultsAcute and chronic exposure to DPhP led to significant levels of this molecule in blood and other tissues, an effect missing with TPhP. Multi-omics analysis confirmed the existence of biological effects of DPhP, even at a very low dose of 0.1 mg.mL-1 in drinking water. Chemical structural homology and pathway mapping demonstrated a clear reduction of the fatty-acid catabolic processes centred on acylcarnitine and mitochondrial {beta}-oxidation. Interestingly, mRNA expression confirmed and extended these observations by demonstrating at all tested doses the overall repression of genes involved in lipid catabolic processes and regulated by PPAR, a master regulator of {beta}-oxidation and its associated ketogenesis. IHC analysis confirmed the alteration of these pathways by showing a specific downregulation of Hmgcs2, a kernel target gene of PPAR, at all doses tested, and surprisingly, a strong reduction of the lipid droplet content only at the highest dose. Overall, DPhP absorption led to weight loss, which was significant using the highest dose. ConclusionsOur results suggest that in mice, the effects of chronic exposure to DPhP, even at a low dose, are not negligible. Fatty acid metabolism in the liver in particular is essential for controlling fast and feast periods with adverse consequences on the overall physiology. Therefore, the impact of DPhP on circulating fat, cardiovascular and metabolic disease incidence deserves, in light of our results, further investigations.

pharmacology and toxicology↗

Nicotine measurement on Cambridge Filter PADs: an interlaboratory comparison to evaluate exposure by different electronic devices and traditional cigarette

Inter-laboratory comparison is widely used to ensure quality control among laboratories. In in vitro toxicology studies for tobacco harm reduction (THR), exposure system performance and laboratory proficiency along with product smoke and aerosol stream are tested for variability to assess accuracy. Here we aim to test a novel inter-laboratory setup created in a new collaborative research group using identical and small footprint systems- in order to minimize variability factors and increase reproducibility. Seven independent laboratories from different geographical areas tested the aerosol and smoke stream and exposure system performance (LM1 and LM4E) using Cambridge Filter Pad (CFP) trapping techniques. We tested 1R6F reference cigarettes, two electronic cigarettes (Vype e-Pen and Vype e-Stick Maxx), and two tobacco heating products (IQOS and Glo) under the appropriate ISO and/or HCI regimes. Nicotine quantification was performed by GC-FID at the laboratory of the leading center. The performance of participant laboratories was assessed by z-score values obtained from results either in relation to the mean and standard deviation of total participants or in relation to the reference leading center. Z-Scores were satisfactory when |z| [&le;] 2, questionable when 2 < |z| < 3 and, unsatisfactory when |z| [&ge;] 3. In the first evaluation, for all the tested devices, Z- scores values generated by dosimetry data ranged from -2 to +2. However, high intra-laboratory variability (RSD> 10%) was observed for almost all laboratories. In the second, data showed borderline and unsatisfactory exposure performances versus LAB-A. Particularly, Z-scores [&ge;] 3 were observed once for LAB-B (e-Stick exposure) and LAB-G (e-Pen exposure), twice for LAB-C (1R6F-ISO and e-Stick exposures) and LAB-E (e-Pen and e-Stick exposures), and three times for LAB-F (1R6F-HCI, e-Pen, and Glo exposures). This study demonstrates that nicotine dosimetry is a fundamental method for quality assurance of smoke/vapor run exposure in the early stage of an interlaboratory study, allowing the identification and possibly the resolution of gaps. Extended practice sessions on exposure runs and several rounds of nicotine dosimetry testing should be planned to keep in check overall equipment and operator performance.

pharmacology and toxicology↗

Chemical augmentation of the validated HepaRGTM CYP induction test method Part 2: Additional laboratory study supported by mRNA analysis

Cytochrome P450 (CYP)-mediated biotransformation of endogenous and xenobiotic substances can lead to altered exposure, toxicological impact, or adverse drug reactions. CYP induction data are fundamental to regulatory chemical toxicity hazard assessment because they directly affect the in vivo fate of xenobiotics, potentially influencing their safety and efficacy of pharmaceuticals, and impacting the safety assessment of industrial chemicals, and environmental contaminants. Here we report on the third laboratory supplementary validation of an established and previously validated human HepaRGTM in vitro method able to detect CYP1A2, CYP2B6, and CYP3A4 induction, to support the expansion of the chemical applicability domain beyond pharmaceuticals. This study was conducted to support the part 1 study with additional robust data. We established the test method in-house using the 10 previously validated pharmaceutical proficiency chemicals, then tested a further 6 proposed augmentation chemicals, tebuconazole, benfuracarb, chlorpyrifos, N, N-Diethyl-meta-toluamide, fipronil, permethrin, as tested in part 1, and then four additional chemicals: prochloraz, atrazine, pyrimethanil, and chlorpyrifos-methyl. LC-MS/MS was utilised to measure the conversion of a cocktail mixture of prototypical selective CYP probe substrates to their metabolites, in parallel with mRNA measurements. We achieved high concordance with expected classifications for proficiency and additional chemicals. Comparisons with mRNA-based measurements suggested gene expression may serve as a cost-effective pre-screening tool for CYP1A2 and CYP3A4, though with greater uncertainty for CYP2B6. The data support the robustness of the HepaRG method for CYP induction testing and the adoption of the test method in 2026 as an Organisation for Economic Cooperation and Development Test Guideline. Plain language summaryCytochrome P450 (CYP) enzymes metabolize drugs, pesticides, and other chemicals. Chemicals that increase or decrease CYP enzyme activity can change internal exposure levels, potentially leading to unexpected toxicity or impact drug effectiveness. Reliable in vitro methods to assess CYP induction are needed for regulatory chemical safety assessment. This study describes results from a third laboratory applying a previously validated human HepaRG cell-based method to assess induction of CYP1A2, CYP2B6, and CYP3A4. After successful in-house implementation using ten reference pharmaceutical compounds, the method was extended to ten more industrial chemicals. CYP induction was evaluated by measuring enzyme activity and changes in gene expression. The test method showed a high level of agreement with expected induction outcomes. Gene expression data supported enzyme activity results, particularly for CYP1A2 and CYP3A4. These results strengthen confidence in the robustness and wider applicability of the method for Organisation for Economic Cooperation and Development Test Guideline adoption.

pharmacology and toxicology↗

Enabling Transparent Toxicokinetic Modeling for Public Health Risk Assessment

Toxicokinetics describes the absorption, distribution, metabolism, and elimination of chemicals by the body. Predictions from toxicokinetic models provide key information for chemical risk assessment. Traditionally, these predictions extrapolate from experimental animal species data (for example, in rats) to humans. More recently, toxicokinetics has been used for extrapolation from in vitro "new approach methods (NAMs)" for toxicology to in vivo. Chemical-specific in vivo toxicokinetic data are often unavailable for the thousands of chemicals in commerce. Therefore, large amounts of in vitro data measuring chemical-specific toxicokinetics have been collected. These data enable "high-throughput toxicokinetic" or HTTK modeling. The httk R package provides a library of chemical-specific data from peer-reviewed HTTK studies. httk further provides a suite of tools for parameterizing and evaluating toxicokinetic models. httk uses the open-source language MCSim to describe models for compartmental and physiologically based toxicokinetics (PBTK), MCSim can convert the model descriptions into a high-speed C code script. New models are integrated into httk using the open-source package development functionality in R, a model documentation file (R script), and the HTTK model description code file (C script). In addition to HTTK models, httk provides a series of functionalities such as unit conversion, model parameterization, Monte Carlo simulations for uncertainty propagation and biological variability, in vivo-derived data for evaluating model predictions, and other model utility functions. Here, we describe in detail how to add new HTTK models to httk and take advantage of the pre-existing data and functionality in the package. As a demonstration, we describe the integration of the gas inhalation PBTK model into httk. Modern modeling approaches, as exemplified by httk, allow for clear communication, reproducibility, and public scrutiny. The intention of httk is to provide a transparent, open-source tool for toxicokinetics, bioinformatics, and public health risk assessment. Author SummaryWe describe the integration and evaluation of new physiologically based toxicokinetic (PBTK) models into an open-source R package. Adding a new model to the R package allows a modeler to use the existing tools and data for in vitro to in vivo extrapolation (IVIVE). Integration with the R statistical analysis environment further allows model assessment. This workflow is designed to create a more transparent and reproducible approach to toxicokinetic models developed for various exposure scenarios. Here, we demonstrate the model integration and evaluation workflow with an inhalation model. Additionally, we provide an evaluation of the overall package performance as new models, data, and functionality are added over time. Our results show that transparent development of models, and use of existing data within the open-source R package format, allows for improvement of in vitro to in vivo extrapolation estimations. IVIVE is vital for advancement of 21st century human health risk assessment.

pharmacology and toxicology↗

Multiscale Modeling Identifies Cardiovascular Risk from Common Chemical Exposures

BackgroundThe cardiovascular system is significantly affected by exogenous factors, but understanding the risks posed by pharmaceuticals and environmental chemicals is restricted due to limited data availability. New approach methodologies (NAMs) apply in vitro, in chemico, and in silico methods to characterize hazard and risk, thus offering rapid, multiscale human biology-based strategies to overcome regulatory challenges and the potential to complement or replace animal testing for understanding chemical cardiovascular effects. MethodsIn the present study, we applied a systems-based workflow using physiologically based pharmacokinetic (PBPK) models to convert bioactive concentrations from >300 high-throughput screening (HTS) assays with cardiovascular-relevant molecular and cellular targets to human equivalent administered doses (EADs) for >800 substances with widespread human exposure potential. To derive human-relevant risk predictions, the in vitro activity-derived EADs were compared with human exposure estimates and in vivo points of departure (PODs) from toxicological animal studies. For a subset of chemicals, we applied a geospatial analysis to assess the combined risks for populations across regions of the US. ResultsThe combined HTS assay data, human exposure predictions, animal study-based PODs, geospatial exposure data, and PBPK modeling identified compounds with potential cardiovascular toxicity at relevant exposure levels. Personal care product ingredients, flame retardants, herbicides, pesticides, pharmaceuticals, and byproducts of various industrial processes were noted as agents of concern preferentially targeting endothelial cell signaling, nuclear hormone receptors, and other critical cardiovascular targets. Of the 859 chemicals assessed, in vitro CV-relevant assays were more risk protective than animal studies for 96.4% of the chemicals. A set of 17 chemicals had a log10 bioactivity exposure ratio (BER) below -2, indicating estimated human exposure more than 100-fold above the in vitro-derived bioactive dose. ConclusionsThis study establishes an integrative, multiscale framework linking molecular perturbations to population-level cardiovascular risk, enabling systematic identification of potentially cardiotoxic chemicals and the communities most vulnerable to their effects. By bridging mechanistic toxicology with pharmacokinetic modeling and epidemiologic context, this approach enhances the biological relevance and translational impact of human health risk assessment. This scalable, adaptable framework supports timely, evidence-based decision-making and aligns with the growing adoption of NAMs to advance cardiovascular research and disease prevention. Novelty and SignificanceO_ST_ABSWhat is known?C_ST_ABSHigh-throughput screening (HTS) assays can identify chemicals with activity at cardiovascular (CV) relevant molecular targets, but translating in vitro bioactivity concentrations into biologically meaningful human equivalent doses requires physiologically based pharmacokinetic (PBPK) modelling. The bioactivity exposure ratio (BER) provides a data-driven metric for comparing in vitro-derived equivalent administered doses against population exposure estimates, but its application to CV endpoints across a large and chemically diverse environmental chemical landscape has not been demonstrated. Geospatial mapping of CV chemical exposure risk has been demonstrated for a limited set of air pollutants but has not been extended to a broad environmental chemical landscape using human-relevant in vitro bioactivity data. What new information does this article contribute?Integrated in vitro to in vivo extrapolation (IVIVE) across 859 environmental chemicals demonstrates that cardiovascular-relevant in vitro endpoints are sensitive indicators of broader systemic toxicity, 96.4% of chemicals showed positive POD ratios, meaning in vitro CV assays flagged hazard at lower doses than non-specific animal toxicity studies despite the absence of endpoint matching. Seventeen chemicals including PFAS, brominated flame retardants, endocrine disruptors, and agricultural herbicides, had a BER below -2, indicating estimated human exposure more than 100-fold above the in vitro-derived cardiovascular bioactive dose, with convergent evidence from both in vitro and in vivo data supporting regulatory priority. County-level geospatial mapping reveals that cardiovascular chemical exposure risk is geographically heterogeneous across the United States, concentrated in industrially active regions already associated with elevated cardiovascular disease mortality, identifying specific populations for targeted environmental monitoring. SummaryThis study presents a scalable, systems-based IVIVE framework that integrates cardiovascular-relevant in vitro HTS bioactivity data with reverse dosimetry, population exposure predictions, and in vivo animal toxicity data to prioritize environmental chemicals for cardiovascular risk assessment. Applied to 859 chemicals spanning personal care products, flame retardants, pesticides, pharmaceuticals, and industrial compounds, the framework demonstrates that CV-relevant in vitro endpoints are sensitive indicators of systemic toxicity even in the absence of direct endpoint matching with in vivo studies. The BER emerges as a flexible and resource-adaptable prioritization metric, identifying 92 chemicals where estimated human exposure falls within the CV bioactive range, of which 17 represent the highest regulatory priority based on convergent evidence from both data streams. Geospatial mapping further reveals regional heterogeneity in cardiovascular chemical exposure risk concentrated in industrial areas of the central and southeastern United States. This work advances the application of new approach methodologies for cardiovascular chemical risk assessment at a time of accelerating regulatory transition toward human-relevant in vitro-based safety evaluation, providing a reproducible computational workflow directly applicable to chemical prioritization under evolving EPA and FDA regulatory frameworks.

pharmacology and toxicology↗

Evidences of a cytotoxic activity of S-adenosylmethionine on OCI-AML3 cells

BackgroundThe acute myeloid leukemia (AML) cell line OCI-AML3, carrying both NPM1 mutation A and the heterozygous DNMT3A R882C mutation, represents the model for in vitro studies on AML with mutated NPM11. AML with mutated NPM1 harbours a hypo-methylated profile distinct from those of the other AML subtypes2. This characteristic is probably related to the inhibitory effect of the mutant DNMT3A on the wild type protein3. S-adenosylmethionine (SAM) is a universal methyl donor acting as a coenzyme of DNMT3A. There are growing evidences of the antineoplastic effect of SAM in vitro and in murine models of gastric cancer, colon cancer and hepatocellular carcinoma, where SAM induces the downregulation of several oncogenes4-10. Moreover SAM upregulates the expression of DNMT enzymes in lung cancer cells11. In our knowledge there are no published data exploring the effect of SAM on the growth of OCI-AML3 cells and its ability to modulate DNMT3A activity in this cell line. Study design and methodsThe present data have been generated between August 2013 and April 2014 at the VITROSCREEN facilities in Milan-ITALY. We used a 3-(4,5-dimethylthiazol-2-yl)-2,5-dephenyl tetrazolium bromide (MTT) assay to assess the cytotoxic effect of SAM iodide (Sigma-Aldrich) on OCI-AML3 cells (DSMZ Leibniz Institut). We analyzed then the ability of SAM to induce apoptosis by Tali Image-Based Cytometer (green Annexin V - Alexa Fluor 488 for apoptotic cells, red propidium and green Annexin V-Alexa Fluor 488 for necrotic cells). ResultsThe MTT assays were performed after having treated the OCI-AML3 cells with various concentrations of the indicated drug for 24 hours. We observed no significant effects on cells viability using 0.5M, 10 M and 100 M of SAM (data not shown). In contrast, a dose dependent cytotoxic effect of SAM on OCI-AML3 cells was evident for concentrations equal or superior to 500 M, with an IC50 of 500 M (Figure 1). Since a Cmax of 211(SD 94)M after single intravenous infusion of SAM was previously reported in healthy voluntarees12, we decided to investigate the cytotoxic effect of SAM for concentrations close to 211 M using the MTT test. A significant dose dependent reduction of the cells viability was observed with SAM 200M (62,74% viable cells) and SAM 300M (53.32% viable cells), (Figure 2). The Apoptosis assay after 24 hours of treatment with SAM showed no differences in the percentages of apoptotic cells between the OCI-AML3 cells treated with SAM 300-500-2500 M and the untreated cells (data not shown). After 72 hours, only a minimal effect on the amount of apoptotic cells was obtained, while a clear dose dependent increase in the proportion of dead cells was noted (Figure 3), confirming the results of the aforementioned MTT tests. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/004978v1_fig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@5e4195org.highwire.dtl.DTLVardef@23bd30org.highwire.dtl.DTLVardef@59a9c5org.highwire.dtl.DTLVardef@98e377_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO MTT assay after 24 h exposure of OCI-AML3 cells to SAM at 0.5 mM, 2.5 mM and 10 mM. CN= negative control, untreated cells. SAM=S-Adenosylmethionine. Percentages of viable cells are reported. Both SAM treated cells and CN were tested in triplicate samples. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/004978v1_fig2.gif" ALT="Figure 2"> View larger version (16K): org.highwire.dtl.DTLVardef@17dab5forg.highwire.dtl.DTLVardef@17e1d00org.highwire.dtl.DTLVardef@a213c5org.highwire.dtl.DTLVardef@c01c13_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO MTT assay after 24 h exposure of OCI-AML3 cells to SAM at 200 M (0.2mM), 300 M, 400 M, 500 M, 1000 M, 2500M. CN=negative control, untreated cells. SAM=S-Adenosylmethionine. Percentages of viable cells are reported. Both SAM treated cells and CN were tested in triplicate samples. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/004978v1_fig3.gif" ALT="Figure 3"> View larger version (31K): org.highwire.dtl.DTLVardef@733c66org.highwire.dtl.DTLVardef@1825707org.highwire.dtl.DTLVardef@1f99a6org.highwire.dtl.DTLVardef@a08020_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3.C_FLOATNO Percentages of Living, Dead and Apoptotic OCI-AML3 cells assessed by Tali image based cytometer after 72 hours treatment with different concentrations of SAM, and after 72 hours in medium (CN=negative control). Both SAM treated cells and CN were tested in duplicate samples. C_FIG ConclusionsSAM showed remarkable in vitro cytotoxic activity on OCI-AML3 cells at concentrations similar to those achievable in humans after intravenous administration. SAM is not able to induce apoptosis of OCI-AML3 cells in vitro after 72 hours of treatment. However, the increase in the amount of dead cells after SAM treatment may be due to mechanisms other than apoptosis. In order to verify if the observed cytotoxicity was mediated by the enzymatic activity of DNMT3A, we planned to repeat the cytotoxicity assays after DNMT3A silencing. The in vivo antineoplastic effect of SAM could be assessed in NOD/SCID mice engrafted with OCI-AML3 cells. Authors contributionKAvH wrote the study rationale, designed the study, interpreted the data and wrote the article; IP revised the article, MM and BDS planned and interpreted the experiments and BDS performed the experiments.

Pharmacology and Toxicology↗

Novel Natural Product Discovery from Marine Sponges and their Obligate Symbiotic Organisms

Discovery of novel natural products is an accepted method for the elucidation of pharmacologically active molecules and drug leads. Best known sources for such discovery have been terrestrial plants and microbes, accounting for about 85% of the approved natural products in pharmaceutical use (1), and about 60% of approved pharmaceuticals and new drug applications annually (2). Discovery in the marine environment has lagged due to the difficulty of exploration in this ecological niche. Exploration began in earnest in the 1950s, after technological advances such as scuba diving allowed collection of marine organisms, primarily at a depth to about 15m.\n\nNatural products from filter feeding marine invertebrates and in particular, sponges, have proven to be a rich source of structurally unique pharmacologically active compounds, with over 16,000 molecules isolated thus far (3, 1) and a continuing pace of discovery at hundreds of novel bioactive molecules per year. All classes of pharmaceuticals have been represented in this discovery process, including antiprotazoals, pesticides, TGF-beta inhibitors, cationic channel blockers, anticancer, cytotoxic, antiviral, anti-inflammatory and antibacterial compounds. Important biosynthetic pathways found in sponges which give rise to these compounds include the terpenoid (4), fatty acid, polyketoid, quinone reductase, alkaloid, isoprenoid (5), and non-ribosomal protein synthase pathways.

Pharmacology and Toxicology↗

Rapid quantitative pharmacodynamic imaging with Bayesian estimation

We recently described rapid quantitative pharmacodynamic imaging, a novel method for estimating sensitivity of a biological system to a drug. We tested its accuracy in simulated biological signals with varying receptor sensitivity and varying levels of random noise, and presented initial proof-of-concept data from functional MRI (fMRI) studies in primate brain. However, the initial simulation testing used a simple iterative approach to estimate pharmacokinetic-pharmacodynamic (PKPD) parameters, an approach that was computationally efficient but returned parameters only from a small, discrete set of values chosen a priori.\n\nHere we revisit the simulation testing using a Bayesian method to estimate the PKPD parameters. This improved accuracy compared to our previous method, and noise without intentional signal was never interpreted as signal. We also reanalyze the fMRI proof-of-concept data. The success with the simulated data, and with the limited fMRI data, is a necessary first step toward further testing of rapid quantitative pharmacodynamic imaging.

Pharmacology and Toxicology↗

MDMA impairs response to water intake in healthy volunteers

Hyponatremia is a serious complication of 3,4-methylenedioxymethamphetamine (MDMA) use. We investigated potential mechanisms in two double-blind, placebo-controlled studies. In study 1, healthy drug-experienced volunteers received MDMA or placebo alone and in combination with the alpha-1 adrenergic inverse agonist prazosin, used as a positive control to release antidiuretic hormone (ADH). In study 2, volunteers received MDMA or placebo followed by standardized water intake. MDMA lowered serum sodium, but did not increase ADH or copeptin, although the control prazosin did increase ADH. Water loading reduced serum sodium more after MDMA than after placebo. There was a trend for women to have lower baseline serum sodium than men, but there were no significant interactions with drug condition. Combining studies, MDMA potentiated the ability of water to lower serum sodium. Thus, hyponatremia appears to be a significant risk when hypotonic fluids are consumed during MDMA use. Clinical trials and events where MDMA use is common should anticipate and mitigate this risk.

Pharmacology and Toxicology↗

Effects of MDMA on socioemotional feelings, authenticity, and autobiographical disclosure in healthy volunteers in a controlled setting

The drug 3,4-methylenedioxymethamphetamine (MDMA, \"ecstasy\", \"molly\") is a widely used illicit drug and experimental adjunct to psychotherapy. MDMA has unusual, poorly understood socioemotional effects, including feelings of interpersonal closeness and sociability. To better understand these effects, we conducted a within-subjects double-blind placebo controlled study of the effects of 1.5 mg/kg oral MDMA on social emotions and autobiographical disclosure in a controlled setting. MDMA displayed both sedative- and stimulant-like effects, including increased self-report anxiety. At the same time, MDMA positively altered evaluation of the self (i.e., increasing feelings of authenticity) while decreasing concerns about negative evaluation by others (i.e., decreasing social anxiety). Consistent with these feelings, MDMA increased how comfortable participants felt describing emotional memories. Overall, MDMA produced a prosocial syndrome that seemed to facilitate emotional disclosure and that appears consistent with the suggestion that it represents a novel pharmacological class.

Pharmacology and Toxicology↗

Efficient Generation and Selection of Virtual Populations in Quantitative Systems Pharmacology Models

Quantitative systems pharmacology models mechanistically describe a biological system and the effect of drug treatment on system behavior. Because these models rarely are identifiable from the available data, the uncertainty in physiological parameters may be sampled to create alternative parameterizations of the model, sometimes termed Virtual Patients. In order to reproduce the statistics of a clinical population, Virtual Patients are often weighted to form a Virtual Population that reflects the baseline characteristics of the clinical cohort. Here we introduce a novel technique to efficiently generate Virtual Patients and, from this ensemble, demonstrate how to select a Virtual Population that matches the observed data without the need for weighting. This approach improves confidence in model predictions by mitigating the risk that spurious Virtual Patients become over-represented in Virtual Populations.

Pharmacology and Toxicology↗

Evaluation of antimalarial properties from Azores deep-sea invertebrate extracts: a first contribution

Several deep-sea marine invertebrates were collected from hydrothermal vents, seamounts and cold coral assemblages in the North Atlantic Ocean, near the Azores islands. The effect of their lipid crude extracts against two strains of malaria parasite P. falciparum (Dd2 and 3D7) was measured in vitro in order to establish the potential of these invertebrates as new sources for antimalarial compounds. Extracts that presented higher antimalarial activity potential were gorgonian Callogorgia verticillata and the hydrothermal vent shrimp Mirocaris fortunata, presenting the lowest value of IC50 and the highest selectivity index for both evaluated stains. To our knowledge this is the first report on the antimalarial activity of crude lipid extracts considering species collected at depths higher then 100 m.

Pharmacology and Toxicology↗

Best Practices in Docking and Activity Prediction

During the last decade we witnessed how computational docking methods became a crucial tool in the search for new drug candidates. The central dogma of small molecule docking is that compounds that dock correctly into the receptor are more likely to display biological activity than those that do not dock. This dogma, however, possesses multiple twists and turns that may not be obvious to novice dockers. The first premise is that the compounds must dock; this implies: (i) availability of data, (ii) realistic representation of the chemical entities in a form that can be understood by the computer and the software, and, (iii) exhaustive sampling of the protein-ligand conformational space. The second premise is that, after the sampling, all docking solutions must be ranked correctly with a score representing the physico-chemical foundations of binding. The third premise is that correctness must be defined unambiguously, usually by comparison with static experimental data (or lack thereof). Each of these premises involves some degree of simplification of reality, and overall loss in the accuracy of the docking predictions.\n\nIn this chapter we will revise our latest experiences in receptor-based docking when dealing with all three above-mentioned issues. First, we will explain the theoretical foundation of ICM docking, along with a brief explanation on how we measure performance. Second, we will contextualize ICM by showing its performance in single and multiple receptor conformation schemes with the Directory of Useful Decoys (DUD) and the Pocketome. Third, we will describe which strategies we are using to represent protein plasticity, like using multiple crystallographic structures or Monte Carlo (MC) and Normal Mode Analysis (NMA) sampling methods, emphasizing how to overcome the associated pitfalls (e.g., increased number of false positives). In the last section, we will describe ALiBERO, a new tool that is helping us to improve the discriminative power of X-ray structures and homology models in screening campaigns.

Pharmacology and Toxicology↗