Characterization and Interlaboratory Comparison of a Gene Expression Signature for Differentiating Genotoxic Mechanisms

Abstract

The genotoxicity testing battery is highly sensitive for detection of chemical carcinogens. However, it features a low specificity and provides only limited mechanistic information required for risk assessment of positive findings. This is especially important in case of positive findings in the in vitro chromosome damage assays, because chromosome damage may be also induced secondarily to cell death. An increasing body of evidence indicates that toxicogenomic analysis of cellular stress responses provides an insight into mechanisms of action of genotoxicants. To evaluate the utility of such a toxicogenomic analysis we evaluated gene expression profiles of TK6 cells treated with four model genotoxic agents using a targeted high density real-time PCR approach in a multilaboratory project coordinated by the Health and Environmental Sciences Institute Committee on the Application of Genomics in Mechanism-based Risk Assessment. We show that this gene profiling technology produced reproducible data across laboratories allowing us to conclude that expression analysis of a relevant gene set is capable of distinguishing compounds that cause DNA adducts or double strand breaks from those that interfere with mitotic spindle function or that cause chromosome damage as a consequence of cytotoxicity. Furthermore, our data suggest that the gene expression profiles at early time points are most likely to provide information relevant to mechanisms of genotoxic damage and that larger gene expression arrays will likely provide richer information for differentiating molecular mechanisms of action of genotoxicants. Although more compounds need to be tested to identify a robust molecular signature, this study confirms the potential of toxicogenomic analysis for investigation of genotoxic mechanisms.

Selectively Targeting the DNA-binding Domain of the Androgen Receptor as a Prospective Therapy for Prostate Cancer

“…Finally, to identify any potential genotoxic effect from the two chemicals, up-regulated genes by either VPC-14449 or enzalutamide were compared with a list of 31 genes, the expression of which has previously been shown to increase in the presence of genotoxins (34). This set of genotoxin-responsive genes includes a number of p53 target genes and others involved in apoptosis, DNA repair, DNA damage response, and stress response.…”

Gene and protein analysis reveals that p53 pathway is functionally inactivated in cytogenetically normal Acute Myeloid Leukemia and Acute Promyelocytic Leukemia

“…The analysis of several literature-based signatures related to cell cycle, apoptosis and oxidative stress defense [71–74, 78, 85] was presented above. Analysis of additional 5 signatures is summarized in Table 3.…”

Utilization of CDKN1A/p21 gene for class discrimination of DNA damage-induced clastogenicity

“…While this 2007 study successfully demonstrated the usefulness of toxicogenomics in genotoxic testing, it only focused on anticancer drugs. Expression analysis of a relevant gene set can reportedly be used to distinguish DNA-damaging compounds that cause DNA adducts or double-strand breaks (DSB) from compounds that do not damage DNA but do interfere with mitotic spindle function or cause chromosome damage as a consequence of cytotoxicity by using only four compounds, cisplatin, etoposide, paclitaxel and sodium chloride (Ellinger-Ziegelbauer et al, 2009). While these previous findings demonstrate that toxicogenomics can be used for genotoxic risk assessment, there are still unmet needs in this field of research for applying the diverse mechanisms and a large number of compounds.…”