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

Abstract

Background: There are profound racial disparities in breast cancer incidence and outcomes in the United States and the impact of chemical exposures remains poorly characterized. Objectives: Analyzing the US Center for Disease Control's National Health and Nutrition Examination Survey chemical biomarker data, we identified a suite of toxicants, including metals, pesticides, and personal care product compounds, to which non-Hispanic Black women are disproportionately exposed. To characterize the impact of these toxicants on breast cancer pathways, we performed high throughput transcriptomic analysis of toxicant exposed breast cells. Methods: We treated non-tumorigenic mammary epithelial cells, MCF10A, with 21 chemicals prioritized for exposure disparities, at four doses (25nM, 250nM, 2.5uM, 25uM) 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. 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 a more basal-like characteristics for some chemicals, including p,p'-DDE, lead, copper, and methyl paraben. Discussion: These analyses revealed that chemicals with exposure disparities induce significant changes in pathways involved in breast cancer initiation and progression at human exposure relevant doses.