Abstract P5-14-02: Identifying oncogenic enhancer elements in TNBC of the Basal-like subtype using single-cell ATAC-seq and RNA-seq
Authors: Regner Matthew J. , Thennavan Aatish , Wisniewska Kamila , Garcia-Recio Susana , Mendez-Giraldez Raul , Spanheimer Philip , Perou Charles M. , Franco Hector L. 
Published: March 2023

Identification of the cis-regulatory elements controlling oncogenic transcriptional programs is critical to understanding tumor biology. To find cis-regulatory elements (i.e. gene enhancers) of oncogenic dependencies in Triple-Negative Breast Cancers (TNBC) of the Basal-like gene expression subtype, we generated matched single-cell transcriptome (scRNA-seq) and chromatin accessibility (scATAC-seq) profiles for two human Basal-like tumors and four normal mammary reduction samples. This unique dataset enabled us to correlate variations in chromatin structure with variations in gene expression revealing putative enhancers that are specifically active within cancer cells, but not within normal mammary ductal epithelial cells. We then leveraged the Cancer Dependency Map (DepMap) portal at the BROAD Institute to infer gene expression dependencies in breast cancer cell lines of the Basal-like molecular subtype. Putative cancer-specific enhancers were prioritized based on the transcriptional dependency of their target gene(s) in Basal-like cell lines as reported by the DepMap portal. Based on our preliminary analyses, we report several cancer-specific enhancers that drive the expression of important transcription factors such as EN1 and SOX4. These transcription factors are known to have profound effects on tumor biology, especially considering that high expression of EN1 is associated with brain metastasis and SOX4 is known to regulate immune evasion and PI3K/Akt signaling. Moreover, both of these transcription factors portend a worse outcome in TNBC patients. Thus, our analysis suggests that high levels of expression of these transcription factors is sustained specifically within the malignant cell types of these tumors, by the activity of these cancer-specific enhancers that are not typically active in normal epithelial cells. We are now performing CRISPR dCas9-KRAB experiments to epigenetically silence these cancer-specific enhancers and measure the consequences on expression of their predicted target genes. Additionally, we are investigating the trans-acting transcription factors that may physically bind to these enhancers to further regulate oncogenic transcription. By defining the regulatory logic of cancer cells at single-cell resolution, our work highlights the importance of cancer-specific and clinically relevant oncogenic regulatory elements in TNBC of the Basal-like subtype.

Citation Format: Matthew J. Regner, Aatish Thennavan, Kamila Wisniewska, Susana Garcia-Recio, Raul Mendez-Giraldez, Philip Spanheimer, Charles M. Perou, Hector L. Franco. Identifying oncogenic enhancer elements in TNBC of the Basal-like subtype using single-cell ATAC-seq and RNA-seq [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-14-02.