Systems pharmacology assessment of the 5-fluorouracil pathway

To assess the impact of the 5-fluorouracil (5-FU) drug-pathway genes on cytotoxicity, and determine whether loss-of-function analyses coupled with functional assays can help prioritize pharmacogenomic candidate genes

A Qualitative Modeling Approach for Whole Genome Prediction Using High-Throughput Toxicogenomics Data and Pathway-Based Validation

Efficient high-throughput transcriptomics (HTT) tools promise inexpensive, rapid assessment of possible biological consequences of human and environmental exposures to tens of thousands of chemicals in commerce. HTT systems have used relatively small sets of gene expression measurements coupled with mathematical prediction methods to estimate genome-wide gene expression and are often trained and validated using pharmaceutical compounds. It is unclear whether these training sets are suitable for general toxicity testing applications and the more diverse chemical space represented by commercial chemicals and environmental contaminants. In this work, we built predictive computational models that inferred whole genome transcriptional profiles from a smaller sample of surrogate genes. The model was trained and validated using a large scale toxicogenomics database with gene expression data from exposure to heterogeneous chemicals from a wide range of classes (the Open TG-GATEs data base). The method of predictor selection was designed to allow high fidelity gene prediction from any pre-existing gene expression data set, regardless of animal species or data measurement platform. Predictive qualitative models were developed with this TG-GATES data that contained gene expression data of human primary hepatocytes with over 941 samples covering 158 compounds. A sequential forward search-based greedy algorithm, combining different fitting approaches and machine learning techniques, was used to find an optimal set of surrogate genes that predicted differential expression changes of the remaining genome. We then used pathway enrichment of up-regulated and down-regulated genes to assess the ability of a limited gene set to determine relevant patterns of tissue response. In addition, we compared prediction performance using the surrogate genes found from our greedy algorithm (referred to as the SV2000) with the landmark genes provided by existing technologies such as L1000 (Genometry) and S1500 (Tox21), finding better predictive performance for the SV2000. The ability of these predictive algorithms to predict pathway level responses is a positive step toward incorporating mode of action (MOA) analysis into the high throughput prioritization and testing of the large number of chemicals in need of safety evaluation

Toxicokinetic Triage for Environmental Chemicals

Toxicokinetic (TK) models link administered doses to plasma, blood, and tissue concentrations. High-throughput TK (HTTK) performs in vitro to in vivo extrapolation to predict TK from rapid in vitro measurements and chemical structure-based properties. A significant toxicological application of HTTK has been “reverse dosimetry,” in which bioactive concentrations from in vitro screening studies are converted into in vivo doses (mg/kg BW/day). These doses are predicted to produce steady-state plasma concentrations that are equivalent to in vitro bioactive concentrations. In this study, we evaluate the impact of the approximations and assumptions necessary for reverse dosimetry and develop methods to determine whether HTTK tools are appropriate or may lead to false conclusions for a particular chemical. Based on literature in vivo data for 87 chemicals, we identified specific properties (eg, in vitro HTTK data, physico-chemical descriptors, and predicted transporter affinities) that correlate with poor HTTK predictive ability. For 271 chemicals we developed a generic HT physiologically based TK (HTPBTK) model that predicts non-steady-state chemical concentration time-courses for a variety of exposure scenarios. We used this HTPBTK model to find that assumptions previously used for reverse dosimetry are usually appropriate, except most notably for highly bioaccumulative compounds. For the thousands of man-made chemicals in the environment that currently have no TK data, we propose a 4-element framework for chemical TK triage that can group chemicals into 7 different categories associated with varying levels of confidence in HTTK predictions. For 349 chemicals with literature HTTK data, we differentiated those chemicals for which HTTK approaches are likely to be sufficient, from those that may require additional data

Incorporating New Technologies Into Toxicity Testing and Risk Assessment: Moving From 21st Century Vision to a Data-Driven Framework

Based on existing data and previous work, a series of studies is proposed as a basis toward a pragmatic early step in transforming toxicity testing. These studies were assembled into a data-driven framework that invokes successive tiers of testing with margin of exposure (MOE) as the primary metric. The first tier of the framework integrates data from high-throughput in vitro assays, in vitro-to-in vivo extrapolation (IVIVE) pharmacokinetic modeling, and exposure modeling. The in vitro assays are used to separate chemicals based on their relative selectivity in interacting with biological targets and identify the concentration at which these interactions occur. The IVIVE modeling converts in vitro concentrations into external dose for calculation of the point of departure (POD) and comparisons to human exposure estimates to yield a MOE. The second tier involves short-term in vivo studies, expanded pharmacokinetic evaluations, and refined human exposure estimates. The results from the second tier studies provide more accurate estimates of the POD and the MOE. The third tier contains the traditional animal studies currently used to assess chemical safety. In each tier, the POD for selective chemicals is based primarily on endpoints associated with a proposed mode of action, whereas the POD for nonselective chemicals is based on potential biological perturbation. Based on the MOE, a significant percentage of chemicals evaluated in the first 2 tiers could be eliminated from further testing. The framework provides a risk-based and animal-sparing approach to evaluate chemical safety, drawing broadly from previous experience but incorporating technological advances to increase efficiency

Advancements in Life Cycle Human Exposure and Toxicity Characterization

BACKGROUND: The Life Cycle Initiative, hosted at the United Nations Environment Programme, selected human toxicity impacts from exposure to chemical substances as an impact category that requires global guidance to overcome current assessment challenges. The initiative leadership established the Human Toxicity Task Force to develop guidance on assessing human exposure and toxicity impacts. Based on input gathered at three workshops addressing the main current scientific challenges and questions, the task force built a roadmap for advancing human toxicity characterization, primarily for use in life cycle impact assessment (LCIA). OBJECTIVES: The present paper aims at reporting on the outcomes of the task force workshops along with interpretation of how these outcomes will impact the practice and reliability of toxicity characterization. The task force thereby focuses on two major issues that emerged from the workshops, namely considering near-field exposures and improving dose-response modeling. DISCUSSION: The task force recommended approaches to improve the assessment of human exposure, including capturing missing exposure settings and human receptor pathways by coupling additional fate and exposure processes in consumer and occupational environments (near field) with existing processes in outdoor environments (far field). To quantify overall aggregate exposure, the task force suggested that environments be coupled using a consistent set of quantified chemical mass fractions transferred among environmental compartments. With respect to dose-response, the task force was concerned about the way LCIA currently characterizes human toxicity effects, and discussed several potential solutions. A specific concern is the use of a (linear) dose-response extrapolation to zero. Another concern addresses the challenge of identifying a metric for human toxicity impacts that is aligned with the spatiotemporal resolution of present LCIA methodology, yet is adequate to indicate health impact potential. CONCLUSIONS: Further research efforts are required based on our proposed set of recommendations for improving the characterization of human exposure and toxicity impacts in LCIA and other comparative assessment frameworks. https://doi.org/10.1289/EHP3871

Antibiotic Use in a Family Practice Setting

ABSTRACT Background: Widespread interest in the appropriate use of antibiotics has led to the publication of anti-infective guidelines for a variety of infectious diseases.Objective: To determine adherence to Ontario’s 1997 Antiinfective Guidelines for Community-Acquired Infections.Methods: This study was a prescriber-blinded, concurrent review of prescriptions over a 2-month period at a university-affiliated family practice clinic. Patients who received antibiotic prescriptions for an infection specified in the guidelines were enrolled. The initial antibiotic regimen (agent, dose, frequency, and duration) was evaluated for adherence to the recommendations. Health records were reviewed over a subsequent 6-week period to determine the occurrence of repeat contact with a health care provider, the outcome of the infection, and antibiotic-related complications.Results: Of the 144 initial regimens assessed, 135 (94%) involved first-, second-, or third-line agents listed in the guidelines; 114 (79%) involved first-line agents. One hundred and five (73%) of the regimens were adherent to the guidelines in terms of agent, dose, frequency, and duration. Among the 98 patients with repeat contact with a health care provider, there was a higher incidence of antibiotic-related complications in association with nonadherent therapy (5 of 26 cases [19%]) than with adherent therapy (2 of 72 cases [3%]) (p = 0.013). There were no differences in outcomes of the diagnosed infections.Conclusions: Adherence to recommendations for antibiotic therapy was high in this family practice clinic. A larger prospective study is necessary to confirm the lower rate of antibiotic-associated complications observed with adherent therapy.RÉSUMÉ Historique : L’intérêt largement répandu pour l’utilisation adéquate des antibiotiques a mené à la publication de lignes directrices sur l’utilisation des antiinfectieux pour différentes maladies infectieuses.Objectif : Évaluer la conformité aux Lignes directrices sur l’utilisation des antiinfectieux dans les infections communautaires de l’Ontario, publiées en 1997.Méthodes : Il s’agit d’une évaluation concurrente en aveugle des ordonnances prescrites sur une période de deux mois à une clinique familiale affiliée à une université. Les patients qui ont reçu des prescriptions d’antibiotiques pour une infection stipulée dans les lignes directrices ont été inscrits à l’étude. Le schéma antibiothérapeutique initial (agent, dose, fréquence et durée) a été évalué pour déterminer dans quelle mesure les recommandations avaient été observées. Les dossiers médicaux ont aussi été examinés au cours d’une période ultérieure de six semaines, pour déterminer l’occurrence des visites répétées auprès d’un prestataire de soins de santé, l’issue de l’infection et les complications liées à l’antibiothérapie.Résultats : Des 144 traitements initiaux évalués, 135 (94 %) mettaient en jeu des agents de première, de deuxième ou de troisième intention listés dans les lignes directrices ; 114 (79 %) des agents de première intention ; et 105 (73 %) étaient conformes aux lignes directrices en termes d’agent utilisé, de dose, de fréquence et de durée. Des 98 patients qui ont visité de façon répétée un prestataire de soins de santé, l’incidence des complications liées aux antibiotiques était plus élevée dans les cas de non-observance thérapeutique (5 cas sur 26 [19 %]) que dans les cas d’observance thérapeutique (2 cas sur 72 [3 %]) (p = 0.013). Aucune différence n’a été observée dans l’issue des infections.Conclusions : La conformité aux recommandations antibiothérapeutiques était élevée à cette clinique familiale. Une étude prospective plus importante est nécessaire pour confirmer l’incidence moindre des complications liées à l’antibiothérapie dans les cas d’observance thérapeutique

Systems pharmacology assessment of the 5-fluorouracil pathway

AIM: To assess the impact of the 5-fluorouracil (5-FU) drug-pathway genes on cytotoxicity, and determine whether loss-of-function analyses coupled with functional assays can help prioritize pharmacogenomic candidate genes. MATERIALS & METHODS: Dose-response experiments were used to quantify the phenotype of sensitivity to 5-FU following the specific knockdown of genes selected from the 5-FU PharmGKB drug pathway in three human colorectal cell lines. Changes in sensitivity were considered significant if the IC(50) for shRNA-exposed cells were three standard deviations outside the mean IC(50) for control-treated cells. RESULTS: Of the 24 genes analyzed, 13 produced significant changes on the phenotype of sensitivity to 5-FU (DHFR, DPYS, DTYMK, DUT, FPGS, GGH, NME1, NT5C, RRM1, TYMS, UCK2, UNG and UMPS). CONCLUSION: The RNAi screening strategy enabled prioritization of the genes from the 5-FU drug pathway. Further validation of the genes credentialed in this study should include gene activity or expression and mutation analyses of clinical samples