A predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells

Andrew Williams,Carol D Swartz,Albert J Fornace,Daniel R Hyduke,Julie K Buick,Heng-Hong Li,Leslie Recio,Jiri Aubrecht,Ivy Moffat,Carole L Yauk

doi:10.1016/j.dib.2015.08.013

Abstract

Genotoxicity testing is a critical component of chemical assessment. The use of integrated approaches in genetic toxicology, including the incorporation of gene expression data to determine the DNA damage response pathways involved in response, is becoming more common. In companion papers previously published in Environmental and Molecular Mutagenesis, Li et al. (2015) [6] developed a dose optimization protocol that was based on evaluating expression changes in several well-characterized stress-response genes using quantitative real-time PCR in human lymphoblastoid TK6 cells in culture. This optimization approach was applied to the analysis of TK6 cells exposed to one of 14 genotoxic or 14 non-genotoxic agents, with sampling 4 h post-exposure. Microarray-based transcriptomic analyses were then used to develop a classifier for genotoxicity using the nearest shrunken centroids method. A panel of 65 genes was identified that could accurately classify toxicants as genotoxic or non-genotoxic. In Buick et al. (2015) [1], the utility of the biomarker for chemicals that require metabolic activation was evaluated. In this study, TK6 cells were exposed to increasing doses of four chemicals (two genotoxic that require metabolic activation and two non-genotoxic chemicals) in the presence of rat liver S9 to demonstrate that S9 does not impair the ability to classify genotoxicity using this genomic biomarker in TK6cells.

Highlights

Genotoxicity testing is a critical component of chemical assessment
In companion papers previously published in Environmental and Molecular Mutagenesis, Li et al (2015) [6] developed a dose optimization protocol that was based on evaluating expression changes in several well-characterized stress-response genes using quantitative real-time PCR in human lymphoblastoid TK6 cells in culture
TK6 cells were exposed to increasing doses of four chemicals in the presence of rat liver S9 to demonstrate that S9 does not impair the ability to classify genotoxicity using this genomic biomarker in TK6 cells. & 2015 Published by Elsevier Inc

Summary

Experimental design

Transcriptome measurements were performed using a two-color dye swap design [4]. Cyanine-3 and cyanine-5 labeled cRNA for treated and untreated samples were co-hybridized to two Agilent oligonucleotide microarrays. One microarray was hybridized with the treated cyanine-3 labeled cRNA co-hybridized with the untreated cyanine-5 labeled cRNA. The second slide was hybridized with the treated and untreated samples having the reversed cyanine-3 and cyanine-5 labeling. A summary of the workflow for the subsequent steps are presented as Fig. 1

Hybridization and data quantification

Data processing and normalization

Findings

PCA analysis