Enhancer RNA Transcription Is Essential for a Novel CSF1 Enhancer in Triple-Negative Breast Cancer

SIMPLE SUMMARY: In cancer, regulatory regions of the genome are hijacked by the tumor cells for the activation of oncogenes that lead to cancer initiation and progression. One of the most salient regulatory elements of the genome are called enhancers, which are characterized by their ability to increase the expression of their target genes. In this study, we identified a novel enhancer that drives the expression of the oncogene CSF1 in triple-negative breast cancer patients, the most aggressive subtype of breast cancer. We demonstrate that this enhancer is specifically active in triple-negative breast cancer patients compared to other breast cancer subtypes and show that its target genes portend a worse clinical outcome in patients. We then use innovative CRISPR-based genome engineering techniques to systematically perturb various features of this enhancer to elucidate its mechanisms of action and determine the consequences on tumor cell growth. Furthermore, we test our model for CSF1 enhancer function in ovarian cancer cells and demonstrate that our findings can apply to other cancer types. These results demonstrate the significant impact of enhancers in cancer biology and highlight their potential as tractable targets for therapeutic intervention. ABSTRACT: Enhancers are critical regulatory elements in the genome that help orchestrate spatiotemporal patterns of gene expression during development and normal physiology. In cancer, enhancers are often rewired by various genetic and epigenetic mechanisms for the activation of oncogenes that lead to initiation and progression. A key feature of active enhancers is the production of non-coding RNA molecules called enhancer RNAs, whose functions remain unknown but can be used to specify active enhancers de novo. Using a combination of eRNA transcription and chromatin modifications, we have identified a novel enhancer located 30 kb upstream of Colony Stimulating Factor 1 (CSF1). Notably, CSF1 is implicated in the progression of breast cancer, is overexpressed in triple-negative breast cancer (TNBC) cell lines, and its enhancer is primarily active in TNBC patient tumors. Genomic deletion of the enhancer (via CRISPR/Cas9) enabled us to validate this regulatory element as a bona fide enhancer of CSF1 and subsequent cell-based assays revealed profound effects on cancer cell proliferation, colony formation, and migration. Epigenetic silencing of the enhancer via CRISPR-interference assays (dCas9-KRAB) coupled to RNA-sequencing, enabled unbiased identification of additional target genes, such as RSAD2, that are predictive of clinical outcome. Additionally, we repurposed the RNA-guided RNA-targeting CRISPR-Cas13 machinery to specifically degrade the eRNAs transcripts produced at this enhancer to determine the consequences on CSF1 mRNA expression, suggesting a post-transcriptional role for these non-coding transcripts. Finally, we test our eRNA-dependent model of CSF1 enhancer function and demonstrate that our results are extensible to other forms of cancer. Collectively, this work describes a novel enhancer that is active in the TNBC subtype, which is associated with cellular growth, and requires eRNA transcripts for proper enhancer function. These results demonstrate the significant impact of enhancers in cancer biology and highlight their potential as tractable targets for therapeutic intervention.