Biology subjects

Kunnen, S. J.

Publications and source records attributed to Kunnen, S. J..

4 recordsLinked to original sources

bioRxiv2023

Utilizing gene co-expression networks with the rat kidney TXG-MAPr tool to enhance safety assessment, biomarker identification and human translation

Toxicogenomic data represent a valuable source of biological information at molecular and cellular level to understand unanticipated organ toxicities. Weighted gene co-expression networks analysis can reduce the complexity of gene-level transcriptomic data to a set of biological response-networks useful for providing insights into mechanisms of drug-induced adverse outcomes. In this study, we have built co-regulated gene networks (modules) from the TG-GATEs and DrugMatrix rat kidney datasets consisting of time- and dose-response data for 180 compounds, including nephrotoxicants. Data from the 347 modules were incorporated into the rat kidney TXG-MAPr web tool, a user-friendly interface that enables visualization and analysis of module perturbations, quantified by a module eigengene score (EGS) for each treatment condition. Several modules annotated for cellular stress, renal injury and inflammation were statistically associated with concurrent renal pathologies, including modules that contain both well-known and novel renal biomarker genes. In addition, many rat kidney modules contain well annotated, robust gene networks that are preserved across transcriptome datasets, suggesting that these biological networks translate to other (drug-induced) kidney injury cases. Moreover, preservation analysis of human kidney transcriptomic data provided a quantitative metric to assess the likelihood that rat kidney modules, and the associated biological interpretation, translate from non-clinical species to human. In conclusion, the rat kidney TXG-MAPr enables uploading and analysis of kidney gene expression data in the context of rat kidney co-expression networks, which could identify possible safety liabilities and/or mechanisms that can lead to adversity for chemical or drug candidates. Translational StatementGene co-expression networks (modules) were generated using rat kidney toxicogenomics data, which reduced data complexity and retained quantitative mechanisms to enhance safety assessment. Several stress, injury and inflammation modules were statistically associated with renal pathologies, useful for biomarker identification. Moreover, many rat kidney modules contained well-annotated, robust gene-networks that were preserved in human patients transcriptome data after renal transplantation, suggesting that these biological networks translate to human relevant kidney-injury. So, the rat kidney TXG-MAPr tool enables transcriptome analysis in the context of kidney co-expression networks, which could identify chemical-induced safety liabilities and/or mechanisms leading to adversity, relevant for human risk-assessment.

pharmacology and toxicology↗

bioRxiv2023

Systematic comparison of temporal transcriptional responses to hepatotoxicants in primary human hepatocytes (PHH) and HepaRG cells using concentration-response modelling of gene co-expression networks

Next generation risk assessment of chemicals revolves around the use of mechanistic information without animal experimentation. In this regard, toxicogenomics has proven to be a useful tool to elucidate the underlying mechanisms of adverse effects of xenobiotics. In the present study, two widely used human in vitro hepatocyte culture systems, namely primary human hepatocytes (PHH) and human hepatoma HepaRG cells, were exposed to liver toxicants known to induce liver cholestasis, steatosis or necrosis. Benchmark concentration-response modelling was applied to transcriptomics gene co-expression networks (modules) in order to derive benchmark concentrations (BMCs) and to gain mechanistic insight into the hepatotoxic effects. BMCs derived by concentration-response modelling of gene co-expression modules recapitulated concentration-response modelling of individual genes. Although PHH and HepaRG cells showed overlap in deregulated genes and modules by the liver toxicants, PHH demonstrated a higher responsiveness, based on the lower BMCs of co-regulated gene modules. Such BMCs can be used as transcriptomics point of departure (tPOD) for assessing module-associated cellular (stress) pathways/processes. This approach identified clear tPODs of around maximum systemic concentration (Cmax) levels for the tested drugs, while for cosmetics ingredients the BMCs were 10-100 fold higher than the estimated plasma concentrations. This approach could serve next generation risk assessment practice to identify early responsive modules at low BMCs, that could be linked to key events in liver adverse outcome pathways. In turn, this can assist in delineating potential hazards of new test chemicals using in vitro systems and used in a risk assessment when BMCs are paired with chemical exposure assessment.

pharmacology and toxicology↗

bioRxiv2022

Rats exhibit higher hepatic stress response pathway capacities compared with mice and humans

To minimise unexpected toxicities in early phase clinical studies of new drugs, it is vital to understand fundamental similarities and differences between preclinical test species and humans. We have used physiologically-based pharmacokinetic modelling to identify doses of the model hepatotoxin acetaminophen yielding similar hepatic burdens of the reactive metabolite N-acetyl-p-benzoquinoneimine in mice and rats, to enable comparison of tissue adaptive responses under conditions of equivalent chemical insult. Mice exhibited a greater degree of liver injury than rats, despite the equivalent hepatic NAPQI burden. Transcriptomic and proteomic analyses highlighted the stronger activation of stress response pathways (including the Nrf2 oxidative stress response and autophagy) in the livers of rats. Components of these pathways were also found to be expressed at a higher basal level in the livers of rats compared with both mice and humans. Our findings exemplify a systems approach to understanding differential species sensitivity to hepatotoxicity, and have important implications for species selection and human translation in the safety testing of new drug candidates.

pharmacology and toxicology↗

bioRxiv2021

The human hepatocyte TXG-MAPr: WGCNA transcriptomic modules to support mechanism-based risk assessment

Mechanism-based risk assessment is urged to advance and fully permeate into current safety assessment practices, possibly at early phases of drug safety testing. Toxicogenomics is a promising source of comprehensive and mechanisms-revealing data, but analysis tools to interpret mechanisms of toxicity and specific for the testing systems (e.g. hepatocytes) are lacking. In this study we present the TXG-MAPr webtool (available at https://txg-mapr.eu/WGCNA_PHH/TGGATEs_PHH/), an R-Shiny-based implementation of weighted gene co-expression networks (WGCNA) obtained from the Primary Human Hepatocytes (PHH) TG-GATEs dataset. Gene co-expression networks (modules) were annotated with functional information (pathway enrichment, transcription factor) to reveal their mechanistic interpretation. Several well-known stress response pathways were captured in the modules, are perturbed by specific stressors and show preserved in rat systems (rat primary hepatocytes and rat in vivo liver), highlighting stress responses that translate across species/testing systems. The TXG-MAPr tool was successfully applied to investigate the mechanism of toxicity of TG-GATEs compounds and using external datasets obtained from different hepatocyte cells and microarray platforms. Additionally, we suggest that module responses can be calculated from targeted RNA-seq data therefore imputing biological responses from a limited gene. By analyzing 50 different PHH donors responses to a common stressor, tunicamycin, we were able to suggest modules associated with donors traits, e.g. pre-existing disease state, therefore connected to donors variability. In conclusion, we demonstrated that gene co-expression analysis coupled to an interactive visualization environment, the TXG-MAPr, is a promising approach to achieve mechanistic relevant, cross-species and cross-platform evaluation of toxicogenomic data.

pharmacology and toxicology↗