The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment

Giulia Callegaro, Steven J. Kunnen, Panuwat Trairatphisan, Solène Grosdidier, Marije Niemeijer, Wouter den Hollander, Emre Guney, Janet Piñero Gonzalez, Laura Furlong, Yue W. Webster, Julio Saez-Rodriguez, Jeffrey J. Sutherland, Jennifer Mollon, James L. Stevens*, Bob van de Water*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)
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Abstract

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 mechanisms-revealing data, but interpretative analysis tools 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 network analysis (WGCNA) obtained from the Primary Human Hepatocytes (PHH) TG-GATEs dataset. The 398 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, were perturbed by specific stressors and showed preservation in rat systems (rat primary hepatocytes and rat in vivo liver), with the exception of DNA damage and oxidative stress responses. A subset of 87 well-annotated and preserved modules was used to evaluate mechanisms of toxicity of endoplasmic reticulum (ER) stress and oxidative stress inducers, including cyclosporine A, tunicamycin and acetaminophen. In addition, module responses can be calculated from external datasets obtained with different hepatocyte cells and platforms, including targeted RNA-seq data, therefore, imputing biological responses from a limited gene set. As another application, donors’ sensitivity towards tunicamycin was investigated with the TXG-MAPr, identifying higher basal level of intrinsic immune response in donors with pre-existing liver pathology. 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.

Original languageEnglish
Pages (from-to)3745-3775
Number of pages31
JournalArchives of Toxicology
Volume95
Issue number12
DOIs
Publication statusPublished - 9 Oct 2021

Bibliographical note

Funding Information:
This work was supported by the EU-EFPIA Innovative Medicines Initiative 2 (IMI2) Joint Undertaking TransQST project (grant number 116030) and eTRANSAFE project (grant number 777365) (this Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA), the EC Horizon2020 EU-ToxRisk project (grant number 681002), and the Cosmetics Europe/CEFIC Liver Ontology project.

Funding Information:
JSR received funding from GSK and Sanofi and consultant fees from Travere Therapeutics.

Publisher Copyright:
© 2021, The Author(s).

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