Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling

Annotation of the cis-regulatory elements mediating oncogenic transcription is essential to understanding breast cancer biology. In this work, we quantitatively linked variation in chromatin accessibility to gene expression within human breast tumors, normal mammary reduction tissue samples, and breast cancer cell lines using single-cell chromatin accessibility sequencing (scATAC-seq) and single-cell transcriptomic sequencing (scRNA-seq). Our analysis resolved the underlying cellular heterogeneity in chromatin accessibility and transcriptional output for each patient sample. We also showed that our findings were recapitulated in the breast cancer cell line samples. These data will serve as an important resource for the single-cell genomics and breast cancer research communities.