Mutational profiling in human cells as an in vitro alternative to in vivo mutagenicity assessments

Project Summary A significant shift in the safety assessment of new drug candidates and environmental chemicals that can revolutionize the practice of regulatory toxicology is ongoing. This shift includes a reduction, or in some cases elimination, of traditional toxicity testing in animals with the implementation of higher-throughput testing schemes using human cell systems. Knowledge regarding the potential of new chemicals, food additives, and pharmaceuticals to damage the human genome and cause mutations remains critical to public health. Mutations are heritable changes in the cellular genome and are key events in the induction of cancer, birth defects, and neurological diseases. Screening chemicals for their potential to cause mutation in a human relevant assay offers an effective strategy for improving public health. The lack of a mutagenicity bioassay in human cells is a major data gap in the genetic toxicology test battery used by regulatory agencies for hazard identification and quantitative risk assessments. Our novel methods, initially developed to identify genetic subclones within cancers, permits analytical assessment of mutagenicity and precise quantification of these very rare events (1 in 100,000 - 1,000,000). These methods can be integrated with human cells as a genetic toxicology assay that can replace 50 yr. old clonal selection techniques to assess mutation. Although duplex sequencing is highly innovative and a “game changer”, without integration into a well-defined human cell-based system and careful validation studies, its application in regulatory Genetic Toxicology will be limited. The focus of this SBIR Phase I application is to develop a New Approach Methodologies (NAM) combining human cells and duplex sequencing as an in vitro alternative to in vivo mutation assays. We will accomplish this by conducting “proof of principle” experiments using a well-established human cell line, as outlined in two specific aims. In Specific Aim 1, we will determine the time course for the induction of mutations at multiple loci using duplex sequencing for a prototypic mutagenic compound. In Specific Aim 2, we will determine the dose response for the induction of mutations at multiple loci using duplex sequencing for two prototypic mutagenic compounds. Completion of this Phase I SBIR will lead to development of a human cell-based mutation assay that can be used as a follow up to bacterial mutation assays and as a NAM to reduce reliance on current in vivo gene mutation assays in rodents. This data will also support a Phase II application to validate this assay and adapt these methods to quantify mutation in human CD34+ cells and HepaRG™ cells.Project Narrative The practice of regulatory toxicology is shifting towards a reduction, or in some cases elimination, of traditional toxicity testing in animals with the implementation of higher-throughput testing schemes using human cell systems. DNA damage and mutation have a key role in a broad spectrum of human disease. The purpose of this SBIR application is to develop a mutational profiling assay in human cells to fill a data gap in the Genetic Toxicology testing programs and as an alternative to animal studies.