Using a gene expression biomarker to identify DNA damage-inducing agents in microarray profiles
- DOI
- Language of the publication
- English
- Date
- 2018-10-17
- Type
- Article
- Author(s)
- Corton, Christopher J.
- Williams, Andrew
- Yauk, Carole L.
- Publisher
- Wiley
Abstract
High-throughput transcriptomic technologies are increasingly being used to screen environmental chemicals in vitro to provide mechanistic context for regulatory testing. The TGx-DDI biomarker is a 64-gene expression profile generated from testing 28 model chemicals or treatments (13 that cause DNA damage and 15 that do not) in human TK6 cells. While the biomarker is very accurate at predicting DNA damage inducing (DDI) potential using the nearest shrunken centroid method, the broad utility of the biomarker using other computational methods is not fully known. Here, we determined the accuracy of the biomarker used with the Running Fisher test, a nonparametric correlation test. In TK6 cells, the methods could readily differentiate DDI and non-DDI compounds with balanced accuracies of 87–97%, depending on the threshold for determining DDI positives. The methods identified DDI agents in the metabolically competent hepatocyte cell line HepaRG (accuracy = 90%) but not in HepG2 cells or hepatocytes derived from embryonic stem cells (60 and 80%, respectively). DDI was also accurately classified when the gene expression changes were derived using the nCounter technology (accuracy = 89%). In addition, we found: (1) not all genes contributed equally to the correlations; (2) the minimal overlap in genes between the biomarker and the individual comparisons required for significant positive correlation was 10 genes, but usually was much higher; and (3) different sets of genes in the biomarker can by themselves contribute to the significant correlations. Overall, these results demonstrate the utility of the biomarker to accurately classify DDI agents.
Plain language summary
Health Canada 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. Health Canada previously collaborated with members of the Health and Environmental Sciences Institute (HESI) 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. In the current study Health Canada collaborated with the US Environmental Protection Agency to develop an alternative computational analysis approach to readily screen databases of gene expression changes using the biomarker to assess the potential for chemicals to cause DNA damage. Applying a statistical test called the Running Fisher test, the team found that the approach was between 87-97% accurate in identifying positive agents, and worked across a variety of technologies and human cell culture models. The data show that this approach has the potential to add significant value to the existing genotoxicity testing system as it can be rapidly applied to large data sets. It also demonstrates that the biomarker is robust with respect to different analytical approaches. Health Canada 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