Application of the Virtual Cell Based Assay for Simulation of in vitro Chemical fate following Acute Exposure

In order to reliably assess the risk of adverse systemic effects of chemicals by using in vitro methods, there is a need to simulate their absorption, distribution, metabolism, and excretion (ADME) in vivo to determine the target organ bioavailable concentration, and to compare this predicted internal concentration with an effective internal concentration. The effective concentration derived from in vitro toxicity studies should ideally take into account the fate of chemicals in the in vitro test system, since there can be significant differences between the applied nominal concentration and the in vitro bioavailable concentration. Whereas PBK models have been developed to simulate ADME properties in vivo, the Virtual Cell Based Assay (VCBA) has been developed to simulate in vitro fate. In this project, the VCBA model in R code, was applied to better interpret previously obtained in vitro acute toxicity data and study how they can be compared to results from acute toxicity in vivo. For 178 chemicals previously tested in vitro with the 3T3 BALB/c cell line using the Neutral Red Uptake cytotoxicity assay, physicochemical parameters were retrieved and curated. Of these chemicals, 83 were run in the VCBA to simulate a 96-well microplate set up with 5% serum supplementation, and their no effect concentration (NEC) and killing rate (Kr) optimized against the experimental data. Analyses of results of partitioning of the chemicals show a strong relation with their lipophilicity, expressed here as the logarithm of the octanol/water partitioning coefficient, with highly lipophilic chemicals binding mostly to medium lipid. Among the chemicals analysed, only benzene and xylene were modelled to evaporate by more than 10 %, and these were also the chemicals with highest degradation rates during the 48 hours assay. Chemical degradation is dependent not only on the air and water degradation rates but also on the extent of binding of the chemical. Due to the strong binding of some chemicals to medium lipids and proteins we analysed the impact of different serum supplementations (0%, 5% and 10%) on the chemical dissolved concentrations. As expected, for the more lipophilic chemicals, different serum levels result in different dissolved concentrations, with lipid and protein binding reducing chemical loss by evaporation. Still the lack of saturation modelling might mislead the 0 % supplementation since the lipids coming solely from cells exudates are able to sequester chemical to a large extent, eg. after 48 hours, 63% (1.2E-5 M) of dimethyldioctadecylammonium chloride was bound to lipid from the cells. Although highly lipophilic chemicals have a very small bioavailable fraction, cellular uptake rate is also dependent on logKow, which compensates for this lack of bioavailability to some extent. Based on the relevance of lipophilicity on in vitro chemical bioavailability, we have developed an alert system based on logKow, creating four classes of chemicals for the experimental condition with 10% serum supplementation: logKow 5- 10 (A), logKow <5 (B), logKow <2.5 (C), and logKow <2 (D). New chemicals from Classes A and B, which will in the future be tested in vitro, were run first on the VCBA, without considering toxicity (NEC and Kr set to 0). VCBA simulations indicated that these chemicals are more than 50% bound to medium proteins, lipids and plastic. Therefore, for chemicals with logKow falling in these classes, special care should be taken when extrapolating the obtained in vitro toxic concentrations to in vivo relevant doses. A comparison of the VCBA-predicted dissolved concentrations corresponding to nominal IC50 values with the available rat oral LD50 values did not improve the previously obtained correlations. This is probably because other in vivo kinetic processes play an important role but were not considered in this in vitro-in vivo extrapolation. The comparison of the VCBA predicted IC50 dissolved concentrations with the available rat oral LD50 values, did not improve the previously obtained correlations. Nevertheless, other in vivo kinetic processes that are not modelled may play an important role. They should be considered in the in vitro-in vivo extrapolations. A local sensitivity analysis showed the relative low impact of Molar Volume and Molecular Diffusion Volume on the final dissolved concentration, supporting the use of approximated values obtained through the herein created QSARs. The logkow and Henry Law Constant showed, as expected, a high impact in partitioning. Killing rate was shown to also have a relative low impact in the final chemical concentration, indicating that although its optimization is important, finding the Kr that leads to the absolute best correlation between experimental and predicted concentration-viability curves, is not imperative. The VCBA can be applied to virtually any chemical as long as the physicochemical data (for the fate model) and the experimental toxicity data (that include cell growth/death) are available. However, being such a generic model, several assumptions had to be made: i) no distinction of chemical classes (inorganic, polar organic chemicals), ii) no consideration of metabolism, iii) saturation kinetics and iv) external in vitro conditions. The advantages of having a generic model are that the VCBA can fit several experimental set ups and should be used in an exploratory manner, to help refinement of experimental conditions. The herein obtained VCBA results should be double checked experimentally the partition with a set of chemical compounds to better understand to what extent VCBA represents chemicals of different properties. In future developments, it would be important to reduce the uncertainties of the model such as binding-saturation and consider inclusion of other endpoints such as metabolic activity.JRC.F.3-Chemicals Safety and Alternative Method

Differences in Tau Seeding in Newborn and Adult Wild-Type Mice

Alzheimer’s disease (AD) and other tauopathies are common neurodegenerative diseases in older adults; in contrast, abnormal tau deposition in neurons and glial cells occurs only exceptionally in children. Sarkosyl-insoluble fractions from sporadic AD (sAD) containing paired helical filaments (PHFs) were inoculated unilaterally into the thalamus in newborn and three-month-old wild-type C57BL/6 mice, which were killed at different intervals from 24 h to six months after inoculation. Tau-positive cells were scanty and practically disappeared at three months in mice inoculated at the age of a newborn. In contrast, large numbers of tau-positive cells, including neurons and oligodendrocytes, were found in the thalamus of mice inoculated at three months and killed at the ages of six months and nine months. Mice inoculated at the age of newborn and re-inoculated at the age of three months showed similar numbers and distribution of positive cells in the thalamus at six months and nine months. This study shows that (a) differences in tau seeding between newborn and young adults may be related to the ratios between 3Rtau and 4Rtau, and the shift to 4Rtau predominance in adults, together with the immaturity of connections in newborn mice, and (b) intracerebral inoculation of sAD PHFs in newborn mice does not protect from tau seeding following intracerebral inoculation of sAD PHFs in young/adult mice

The European Chemicals Bureau: an Overview of 15 Years Experience in EU Chemicals Legislation

From its creation in 1993, the European Chemicals Bureau (ECB) has played a vital role in the conception, development, implementation and monitoring of European Union (EU) legislation on chemicals and in contributing to the European Commission¿s participation in international chemicals programmes. The ECB has housed much of the European Commission¿s experience, capacity and historical memory in chemical risk assessment and safe chemical management. The contribution of ECB to the drafting, development and implementation of the REACH regulation has been an important one. The provision of scientific/technical expertise to the start-up phase of the newly born European Chemicals Agency (ECHA) has been essential for a swift and effective implementation of REACH. The ECB has contributed to that effort not only by selecting, recruiting and training ECHA staff but also by seconding part of its own key staff to the agency. And finally, during 2008 the ECB is completing the hand-over files and transmitting them to the ECHA, which is taking over responsibility for the operational implementation of EU legislation on chemicals.JRC.I-Institute for Health and Consumer Protection (Ispra

Mutations in TP53 and JAK2 are independent prognostic biomarkers in B-cell precursor acute lymphoblastic leukaemia

[EN]Background: In B-cell precursor acute lymphoblastic leukaemia (B-ALL), the identification of additional genetic alterations associated with poor prognosis is still of importance. We determined the frequency and prognostic impact of somatic mutations in children and adult cases with B-ALL treated with Spanish PETHEMA and SEHOP protocols. Methods: Mutational status of hotspot regions of TP53, JAK2, PAX5, LEF1, CRLF2 and IL7R genes was determined by next-generation deep sequencing in 340 B-ALL patients (211 children and 129 adults). The associations between mutation status and clinicopathological features at the time of diagnosis, treatment outcome and survival were assessed. Univariate and multivariate survival analyses were performed to identify independent prognostic factors associated with overall survival (OS), event-free survival (EFS) and relapse rate (RR). Results: A mutation rate of 12.4% was identified. The frequency of adult mutations was higher (20.2% vs 7.6%, P=0.001). TP53 was the most frequently mutated gene (4.1%), followed by JAK2 (3.8%), CRLF2 (2.9%), PAX5 (2.4%), LEF1 (0.6%) and IL7R (0.3%). All mutations were observed in B-ALL without ETV6-RUNX1 (P=0.047) or BCR-ABL1 fusions (P<0.0001). In children, TP53mut was associated with lower OS (5-year OS: 50% vs 86%, P=0.002) and EFS rates (5-year EFS: 50% vs 78.3%, P=0.009) and higher RR (5-year RR: 33.3% vs 18.6% P=0.037), and was independently associated with higher RR (hazard ratio (HR)=4.5; P=0.04). In adults, TP53mut was associated with a lower OS (5-year OS: 0% vs 43.3%, P=0.019) and a higher RR (5-year RR: 100% vs 61.4%, P=0.029), whereas JAK2mut was associated with a lower EFS (5-year EFS: 0% vs 30.6%, P=0.035) and a higher RR (5-year RR: 100% vs 60.4%, P=0.002). TP53mut was an independent risk factor for shorter OS (HR=2.3; P=0.035) and, together with JAK2mut, also were independent markers of poor prognosis for RR (TP53mut: HR=5.9; P=0.027 and JAK2mut: HR=5.6; P=0.036). Conclusions: TP53mut and JAK2mut are potential biomarkers associated with poor prognosis in B-ALL patients.European Commision (EC). Funding FP7/SP1/HEALTH. Project Code: 30624

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

CARB-ES-19 Multicenter Study of Carbapenemase-Producing Klebsiella pneumoniae and Escherichia coli From All Spanish Provinces Reveals Interregional Spread of High-Risk Clones Such as ST307/OXA-48 and ST512/KPC-3

ObjectivesCARB-ES-19 is a comprehensive, multicenter, nationwide study integrating whole-genome sequencing (WGS) in the surveillance of carbapenemase-producing K. pneumoniae (CP-Kpn) and E. coli (CP-Eco) to determine their incidence, geographical distribution, phylogeny, and resistance mechanisms in Spain.MethodsIn total, 71 hospitals, representing all 50 Spanish provinces, collected the first 10 isolates per hospital (February to May 2019); CPE isolates were first identified according to EUCAST (meropenem MIC &gt; 0.12 mg/L with immunochromatography, colorimetric tests, carbapenem inactivation, or carbapenem hydrolysis with MALDI-TOF). Prevalence and incidence were calculated according to population denominators. Antibiotic susceptibility testing was performed using the microdilution method (EUCAST). All 403 isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis.ResultsIn total, 377 (93.5%) CP-Kpn and 26 (6.5%) CP-Eco isolates were collected from 62 (87.3%) hospitals in 46 (92%) provinces. CP-Kpn was more prevalent in the blood (5.8%, 50/853) than in the urine (1.4%, 201/14,464). The cumulative incidence for both CP-Kpn and CP-Eco was 0.05 per 100 admitted patients. The main carbapenemase genes identified in CP-Kpn were blaOXA–48 (263/377), blaKPC–3 (62/377), blaVIM–1 (28/377), and blaNDM–1 (12/377). All isolates were susceptible to at least two antibiotics. Interregional dissemination of eight high-risk CP-Kpn clones was detected, mainly ST307/OXA-48 (16.4%), ST11/OXA-48 (16.4%), and ST512-ST258/KPC (13.8%). ST512/KPC and ST15/OXA-48 were the most frequent bacteremia-causative clones. The average number of acquired resistance genes was higher in CP-Kpn (7.9) than in CP-Eco (5.5).ConclusionThis study serves as a first step toward WGS integration in the surveillance of carbapenemase-producing Enterobacterales in Spain. We detected important epidemiological changes, including increased CP-Kpn and CP-Eco prevalence and incidence compared to previous studies, wide interregional dissemination, and increased dissemination of high-risk clones, such as ST307/OXA-48 and ST512/KPC-3

Theoretical and mathematical foundation of the Virtual Cell Based Assay – A Review

There is a need to interpret in vitro concentration-viability data in terms of the actual concentration that the cells are exposed to, rather than the nominal concentration applied to the test system. We have developed a process-based model to simulate the kinetics and dynamics of a chemical compound in cell-based in vitro assays. In the present paper we describe the mathematical equations governing this model as well as the parameters that are needed to run the model. The Virtual Cell Based Assay (VCBA) is an integrated model composed of: [1] a fate and transport model; [2] a cell partitioning model; [3] a cell growth and division model; [4] a toxicity and effects model; [5] the experimental set up. The purpose of the VCBA is to simulate the medium and intracellular concentrations, which can be used on its own to design and interpret in vitro experiments, and in combination with physiologically based kinetic (PBK) models to perform in vitro to in vivo extrapolation. The results can be used in chemical risk assessment to link an external dose to an internal effect or vice versa, using solely in vitro and in silico tools and thereby avoiding animal testing.JRC.F.3-Chemicals Safety and Alternative Method

Human Bioaccumulation Potential simulated in R and implemented in the KNIME Interface

The assessment of human bioaccumulation potential is an important element in the risk assessment of chemicals. Tonnelier et al. (Arch Toxicol (2012) 86: 393–403) developed a generic physiologically based toxicokinetic (PBTK) model which, based on in vitro human liver metabolism data, minimal renal excretion and a constant exposure scenario, was able to predict the bioaccumulation potential of a chemical, expressed as the human bio concentration factor (hBCF). This model was designed to incorporate not only the chemical properties of the compounds, but also the processes that tend to decrease the concentration of the compound, such as metabolism. Following this work we have implemented the generic PBTK model, now written in R, in the open source KNIME interface. The KNIME workflow consists of several nodes: (1) a database connector (with biophysical properties of specific compound) with a query filter node to select the values for the simulated chemical; (2) an XLS reader node that provides the model input parameters (e.g. flow rates, organ volume); (3) an R node where the PBTK model is described mathematically; and (4) an R view node for output. The outputs are: a figure expressed as concentration versus time and the hBCF. The hBCF values can be used to rank chemicals for their potency which can assist in risk making decisions. Examples applied to selected chemicals will be shown. This open source approach will help in performing in vitro–in vivo extrapolation (IVIVE) in the risk assessment process without the use of animal experiments.JRC.I.5-Systems Toxicolog

Practical use of the Virtual Cell Based Assay: Simulation of repeated exposure experiments in liver cell lines

The Virtual Cell Based Assay (VCBA) was applied to simulate the long-term (repeat dose) toxic effects of chemicals, including substances in cosmetics and personal care products. The presented model is an extension of the original VCBA for simulation of single exposure and is implemented in a KNIME workflow. This work illustrates the steps taken to simulate the repeated dose effects of two reference compounds, caffeine and amiodarone. Using caffeine, in vitro experimental viability data in single exposure from two human liver cell lines, HepG2 and HepaRG, were measured and used to optimize the VCBA, subsequently repeated exposure simulations were run. Amiodarone was then tested and simulations were performed under repeated exposure conditions in HepaRG. The results show that the VCBA can adequately predict repeated exposure experiments in liver cell lines. The refined VCBA model can be used not only to support the design of long term in vitro experiments but also practical applications in risk assessment. Our model is a step towards the development of in silico predictive approaches to replace, refine, and reduce the in vivo repeated dose systemic toxicity studies in the assessment of human safety.JRC.F.3-Chemicals Safety and Alternative Method

In vitro-to-in vivo correlation of the skin penetration, liver clearance and hepatotoxicity of caffeine

This work illustrates the use of Physiologically-Based Toxicokinetic (PBTK) modelling in in vitro-to-in vivo correlation (IVIVC) of kinetic measures of caffeine skin penetration and liver metabolism, as well as dose metrics of caffeine-induced HepaRG toxicity. We applied a PBTK model calibrated for the Caucasian population to quantify the differences in in vitro and in vivo skin absorption and liver metabolism rates by means of a simple correlation factor. We developed a multi-scale computational approach by linking the PBTK model with a Virtual Cell-Based (VCB) Assay to relate an external oral and dermal dose with an internal dose-dependent liver toxicity, measured in vitro as HepaRG cell viability. The results revealed higher in vivo skin permeation profiles than those determined in vitro using identical in vitro and in vivo exposure conditions. Literature in vitro liver metabolism rates were higher than the optimized in vivo rates with respect to available caffeine plasma concentrations. Finally, HepaRG cell viability was shown to decrease only slightly for external caffeine doses in the 5-200 mg range, assuming a 4.56 mg/mL in ethanol/propylene glycol vehicle after both exposure types. We modelled single human exposure to single doses of caffeine only. The approaches described in the present paper provide a promising means of performing in vitro -to- in vivo correlations that may contribute to a reduction of animal experimentation in the chemical risk assessment process.JRC.I.5-Systems Toxicolog