CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia

The ability to deduce carcinogenic potential from subchronic, repeat dose rodent studies would constitute a major advance in chemical safety assessment and drug development. This study investigated an error-corrected NGS method (CarcSeq) for quantifying cancer driver mutations (CDMs) and deriving a metric of clonal expansion predictive of future neoplastic potential. CarcSeq was designed to interrogate subsets of amplicons encompassing hotspot CDMs applicable to a variety of cancers. Previously, normal human breast DNA was analyzed by CarcSeq and metrics based on mammary-specific CDMs were correlated with tissue donor age, a surrogate of breast cancer risk. Here we report development of parallel methodologies for rat. The utility of the rat CarcSeq method for predicting neoplastic potential was investigated by analyzing mammary tissue of 16-week-old untreated rats with known differences in spontaneous mammary neoplasia (Fischer 344, Wistar Han, and Sprague Dawley). Hundreds of mutants with mutant fractions ≥ 10-4 were quantified in each strain, most were recurrent mutations, and 42.5% of the nonsynonymous mutations have human homologs. Mutants in the mammary-specific target of the most tumor-sensitive strain (Sprague Dawley) showed the greatest nonsynonymous/synonymous mutation ratio, indicative of positive selection consistent with clonal expansion. For the mammary-specific target (Hras, Pik3ca, and Tp53 amplicons), median absolute deviation correlated with percentages of rats that develop spontaneous mammary neoplasia at 104 weeks (Pearson r = 1.0000, 1-tailed p = .0010). Therefore, this study produced evidence CarcSeq analysis of spontaneously occurring CDMs can be used to derive an early metric of clonal expansion relatable to long-term neoplastic outcome.

Assessment of clonal expansion using CarcSeq measurement of lung cancer driver mutations and correlation with mouse strain- and sex-related incidence of spontaneous lung neoplasia

Quantification of variation in levels of spontaneously occurring cancer driver mutations (CDMs) was developed to assess clonal expansion and predict future risk of neoplasm development. Specifically, an error-corrected next generation sequencing method, CarcSeq, and a mouse CarcSeq panel (analogous to human and rat panels) were developed and used to quantify low-frequency mutations in a panel of amplicons enriched in hotspot CDMs. Mutations in a subset of panel amplicons, Braf, Egfr, Kras, Stk11 and Tp53, were related to incidence of lung neoplasms at two years. This was achieved by correlating median absolute deviation (MAD) from the overall median mutant fraction (MF) measured in the lung DNA of 16-week-old male and female, B6C3F1 and CD-1 mice (10 mice/sex/strain) with percentages of spontaneous alveolar/bronchioloalveolar adenomas and carcinomas reported in bioassay control groups. 1,586 mouse lung mutants with MFs >1 x 10-4 were recovered. The ratio of non-synonymous to synonymous mutations was used to assess the proportion of recovered mutations conferring a positive selective advantage. The greatest ratio was observed in what is considered the most lung tumor-sensitive model examined, male B6C3F1 mice. Of the recurrent, non-synonymous mouse mutations recovered, 55.5% have been reported in human tumors, with many located in or around the mouse equivalent of human cancer hotspot codons. MAD for the same subset of amplicons measured in normal human lung DNA samples showed a correlation of moderate strength and borderline significance) with age (a cancer risk factor), as well as age-related cumulative lung cancer risk, suggesting MAD may inform species extrapolation.

The 2-year rodent bioassay in drug and chemical carcinogenesis testing: Sensitivity, according to the framework of carcinogenic action

The long-term rodent bioassay (RCB) has been the gold-standard for the pre-marketing prediction of chemical and drug carcinogenicity to humans. Nonetheless, the validity of this toxicity test has remained elusive for several decades. In the quest to uncover the performance of the RCB, its sensitivity (SEN) was charted as the first step. This appraisal was based on (a) chemicals with sufficient epidemiological evidence of carcinogenicity, and (b) other substances with limited epidemiological evidence, or remarkable classifications of carcinogenicity based on mechanistic or pharmacological data. In the present study, chemicals evaluated for their carcinogenicity to humans in IARC Monographs volumes 1-123, U.S. EPA IRIS Assessments, and U.S. NTP RoC were considered. This investigation gathered additional evidence supporting that, in hazard identification, the RCB is unwarranted for mutagenic or direct-acting genotoxicants. However, for purposes of risk assessment or management, the RCB might be justified whenever there is a lack of reliable and/or comprehensive epidemiological data. The RCB exhibited a significantly different SEN for threshold-based human carcinogens compared to non-threshold-based ones. With threshold-based chemicals, to increase the SEN of the testing from 80% (rat-RCB) to 90%, the 2-species RCB might be warranted. Nevertheless, the resolve would depend on the viewpoint, and on the future analysis of the overall performance of the RCB. In terms of SEN, and cancer hazard identification, the comparison between the RCB and alternative methods (e.g. rasH2 mouse, Tg.AC mouse) is now enabled.