Characterizing heterogeneous cis-regulatory elements in gene regulatory programs associated with breast cancer

Background: Cis-regulatory elements (CREs) control oncogene expression and malignant phenotypes. The high clinicopathological heterogeneity of cancer cannot be explained by gene expression alone, being attributed to CRE heterogeneity. However, characterizing cancer-associated CRE is challenging. To address this issue, we performed a single-cell epigenomic analysis of clinical specimens. Methods: To map the multicellular ecosystem of BC and identify candidate CREs (cCREs), we performed a single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) of 38 prospectively collected breast cancer (BC) samples with various clinicopathological characteristics. Results: First, we performed single-cell chromatin accessibility profiling of a high-quality set of 22,775 cells from BC samples. Cells were accurately annotated using marker gene accessibility and integration with existing single-cell RNA sequencing data. By predicting copy number variants, epithelial cells were classified into non-malignant and malignant cells. The chromatin accessibility patterns exhibited by malignant cells were consistent with the clinicopathological features of each tumor. We identified 224,585 cCREs across the BC ecosystem. By identifying cluster-specific differentially accessible cCREs (DA-cCREs) and constructing a putative enhancer-promoter network, we mapped the cis-regulatory landscape for cancer cells and the tumor microenvironment. In this dataset, we identified changes in the cis-regulatory landscape associated with cancer progression. In particular, estrogen receptor (ER)-positive tumors have increased accessibility of ER binding motifs during the cell transition from non-cancerous to cancerous and increased accessibility of Kruppel like factor motifs during the transition from cancerous to metastatic. Furthermore, the accessibility of putative enhancers targeting the same gene differed within or between tumors, highlighting intra- and inter-cis-regulatory tumor heterogeneity. Conclusions: This study provides a valuable resource for future epigenetic research on BC and highlights the diverse regulatory landscape within or among tumor(s), suggesting that cCREs regulate tumor progression and intra- and inter-tumor heterogeneity.