High Throughput Transcriptomics to Understand Chemical Drivers of Aggressive Breast Cancer Subtypes

Background The impact of chemical exposures on breast cancer progression is poorly characterized and may influence the development of more severe and aggressive subtypes. Objectives There is a suite of toxicants, including metals, pesticides, and personal care product compounds, which are commonly detected at high levels in US Center for Disease Control’s National Health and Nutrition Examination Survey (NHANES) chemical biomarker screens. To characterize the impact of these toxicants on breast cancer pathways, we performed high throughput dose-response transcriptomic analysis of toxicant exposed breast cells. Methods We treated non-tumorigenic mammary epithelial cells, MCF10A, with 21 chemicals at four doses (25nM, 250nM, 2.5µM, 25µM) for 48 hours. We conducted RNA-sequencing for these 408 samples, adapting the PlexWell plate-based RNA-sequencing method to analyze changes in gene expression resulting from these exposures. For each chemical, we calculated gene and biological pathway specific benchmark doses using BMDExpress2, identifying differentially expressed genes and generating the best fit benchmark dose models for each gene. We employed enrichment testing to test whether each chemical’s upregulated or downregulated genes were over-represented in a biological process or pathway. We contextualized benchmark doses relative to human population biomarker concentrations in NHANES. Results Overall, significant changes in gene expression varied across doses of each chemical and benchmark dose modeling revealed dose-responsive alterations of thousands of different genes. Comparison of benchmark data to NHANES chemical biomarker concentrations indicated an overlap between actual exposure levels and levels sufficient to cause a gene expression response. Enrichment and cell deconvolution analyses showed benchmark dose responses correlated with changes in cancer and breast cancer related pathways, including induction of basal-like characteristics for some chemicals, including p,p’-DDE, lead, copper, and methyl paraben. Discussion These analyses revealed that these 21 chemicals induce significant changes in pathways involved in breast cancer initiation and progression at human exposure relevant doses.