Identification of p53 Activators in a Human Microarray Compendium
- DOI
- Language of the publication
- English
- Date
- 2019-08-09
- Type
- Article
- Author(s)
- Corton, Christopher J.
- Witt, Kristine L.
- Yauk, Carole L.
- Publisher
- American Chemical Society
Abstract
Biomarkers predictive of molecular and toxicological effects are needed to interpret emerging high-throughput transcriptomic data streams. The previously characterized 63 gene TGx-DDI biomarker that includes 20 genes known to be regulated by p53 was previously shown to accurately predict DNA damage in chemically treated cells. We comprehensively evaluated whether the molecular basis of the DDI predictions was based on a p53-dependent response. The biomarker was compared to microarray data in a compendium derived from human cells using the Running Fisher test, a nonparametric correlation test. Using the biomarker, we identified conditions that led to p53 activation, including exposure to the chemical nutlin-3 which disrupts interactions between p53 and the negative regulator MDM2 or by knockdown of MDM2. The expression of most of the genes in the biomarker (75%) were found to depend on p53 activation status based on gene behavior after TP53 overexpression or knockdown. The biomarker identified DDI chemicals that were strong inducers of p53 in wild-type cells; these p53 responses were decreased or abolished in cells after p53 knockdown by siRNAs. Using the biomarker, we screened ∼1950 chemicals in ∼9800 human cell line chemical vs control comparisons and identified ∼100 chemicals that caused p53 activation. Among the positive chemicals were many that are known to activate p53 through direct and indirect DNA damaging mechanisms. These results contribute to the evidence that the TGx-DDI biomarker is useful for identifying chemicals that cause DDI and activate p53.
Plain language summary
Health Canada (HC) is responsible for assessing and managing chemicals that may pose a potential health risk to the Canadian population. Chemicals that are genotoxic damage DNA and long-term exposure can cause adverse effects such as cancer and inherited genetic diseases. Thus, genotoxicity testing is a critical component of chemical assessment. HC previously collaborated with members of the Health and Environmental Sciences Institute to develop a test method in human cells in culture that measures changes in gene expression as an indicator of a chemical’s potential to cause DNA damage. The resulting ‘gene expression biomarker’ that was produced in this study has now been extensively validated and applied in a variety of case studies. The current study is part II of a HC collaboration with the US Environmental Protection Agency to explore the application of an alternative computational analysis approach (called the Running Fisher statistical test) to readily screen databases of gene expression changes using the biomarker to assess the potential for chemicals to cause genotoxicity. In this study, the Running Fisher test on the biomarker was evaluated to identify potentially genotoxic agents in a commercial repository of gene expression data. Using the biomarker, ~1950 chemicals in ~9800 human cell line chemical vs. control comparisons were screened, and ~100 chemicals were found as positive for the biomarker. Assessment of these positives supported that the biomarker provides a powerful tool to screen gene expression datasets to identify genotoxic agents in specific cell types and identified unknown potential chemical mutagens. HC is now using this method to assess the potential genotoxicity of chemicals with little conventional data on the Chemicals Management Plan and in other case studies, to determine the best way to use the method to increase the efficiency and accuracy of genotoxicity assessment.
Subject
- Health,
- Health and safety