HT-Toxicogenomics

Based on 15 years of research and development of scientific methods for toxic risk assessment and dedicated biocomputing, Vigilent has hands-on experience in *omics*-based toxicology. Using precisely selected markers, relying on proprietary and automated testing rules, Vigilent introduces novel strategies for fast and cost-effective high throughput (HT) testing. Large data bases derived from parallel, robotized testings involving a series of cell lines, concentrations and exposures, allow to build a chemical-specific deregulation space from which informed regulatory decision can be derived. The goal is to anticipate cellular toxicities of a chemical from its structural descriptors.

Toxic endpoints are intimately related to specific alterations in gene expression. The transcription state of a cell can be revealed by genomics, a technique based on genes derived from genome sequence, DNA array technologies and cell culture. Toxicogenomics identifies genes having their transcription state modified upon exposure of the cell to the test substance.

To date, toxicogenomics is among the most advanced method for scientific toxic risk assessment of chemicals.

However, for reliable hazard assessment, the method requires a vast amount of data for each substance tested. Indeed, for a given substance, several cell lines (derived from tissues and organs most exposed) should be assayed, each with a series of substance concentrations and exposure time points. The study should be replicated to secure data accuracy. The substance should be further tested using cell lines and biomarkers representing major human SNPs. The same series of experiments should be performed to assess metabolite toxicities. As a result, several thousand experiments are required for assessing seriously the cellular toxicities of a single chemical.

To keep cost and labour time within sustainable limits, yet uncompromising the standards for reliability and significance of toxicogenomics data, the HT-Toxicogenomics department has developed a genuine testing process based on:
  • The parallel use of low-cost, low-density minichips, each spotted with a small number (of the order of hundred) of genes known to be deregulated as the cell is driven into selected pathologic pathways. The genes spotted on a minichip is dedicated to a single pathologic pathway (carcinogenicity for instance), or to several, depending on whether the goal of the test is to focus on a specific toxicity endpoint, or provide an overview for several.
  • A self-adaptative, automated testing strategy aiming at minimizing the time required to reveal the toxicity of a given chemical, or of chemicals of closely related structures. Using an incremental toxicogenomic database, the strategy uses the structural description of the tested compound to drive in real time the parallel selection and activation of markers, checking in priority the markers that are most likely to reveal a pathologic pathway within the cell under consideration.
This procedure has two major advantages:
  • reduce considerably the time required for thorough testing of a chemical;
  • derive correlations between substance -characteristic structural descriptors and deregulated marker genes, in view of establishing a "quantitative structure-marker gene deregulation relationship" portfolio.

As a proof of concept, Vigilent has screened some 18.000 annotated human genes and listed 1100 Human Toxicity Markers (HTMs) involved in toxic responses.

The latter were classified into patented families of pathology reporters, i.e. genes characterizing entrance into, or established, pathologic states (genotoxic and non-genotoxic carcinogenesis, immunotoxic, neurotoxic, reprotoxic responses, endocrine proliferation, stress, protein misfolding). Each family is further subclassified for tissue or organ specificity. Based on this list, Vigilent has designed small custom arrays bearing a number of pathology reporter families, each including a small number of the family's most representative pathology markers best adapted to the cell line to be tested.

Partnering with the not-for profit organisation Antidote Europe (see www.antidote-europe.org), the toxicities of a list of chemicals were assessed in two cell lines, using an array bearing 50 cDNA spots representing 6 pathology reporter families (see ArrayExpress database, MIAME accession number E-TOXM-31 for the experiments and A-MEXP-798 for array design).