Transcriptomic Biomarker Assay Developed for Genetic Toxicology Testing

Currently used follow-up methods, such as animal testing, are expensive and time-consuming, and the development of approaches enabling more accurate mechanism-based risk assessment is essential.

Toward this end, investigators at Georgetown University (Washington, DC, USA) developed an in vitro transcriptomic biomarker-based approach to provide biological relevance to positive genotoxicity assay data, particularly for in vitro chromosome damage assays. Transcriptomics technologies incorporate the techniques used to study an organism’s transcriptome, the sum of all of its RNA transcripts. For this work the transcriptomic biomarker TGx-DDI (previously known as TGx-28.65), which readily distinguishes DNA damage-inducing (DDI) agents from non-DDI agents was used. The TGx-DDI gene set was derived from TK6 cells exposed to a training set of prototypical DNA damage-inducing agents and chemicals with a clean genetic toxicology profile (28 chemicals: 13 DNA damage-inducing, 15 non DNA-damage inducing).

The investigators assessed the ability of this biomarker to classify 45 test agents across a broad set of chemical classes as DDI or non-DDI. In addition, they assessed the biomarker’s utility for correctly classifying the risk of known irrelevant positive agents and evaluated its performance across analytical platforms.

They reported in the December 4, 2017, online edition of the journal Proceedings of the [U.S.] National Academy of Sciences that they had developed a standardized experimental and analytical protocol for the transcriptomics biomarker, as well as an enhanced application of TGx-DDI for high-throughput cell-based genotoxicity testing. Furthermore, they correctly classified 90% (nine of 10) of chemicals with irrelevant positive findings for in vitro chromosome damage assays as negative.

"The lack of an accurate, rapid and high-throughput test that assesses genotoxicity has been a major bottleneck in the development of new drugs as well as the testing of substances by chemical, cosmetic, and agricultural companies," said senior author Dr. Albert J. Fornace Jr., professor of biochemistry and molecular and cellular biology, oncology, and radiation medicine at Georgetown University. “In addition, there is an increasing mandate to reduce animal testing. Compared to older tests, our approach allows for very accurate and high-throughput screening of chemical compounds that cause DNA damage, and potentially, cancer in humans.”

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