Cancer researchAug 26, 2024

Identifying Key Gene Regulators That Drive Progression of Triple-Negative Breast Cancer

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗

Updated Mar 11, 2026

Abstract

Deletion of an identified super-enhancer controlling the PODXL gene led to profound inhibitory effects on target gene expression, cell proliferation, and migration.

Triple-negative breast cancer (TNBC) has limited targeted therapies, making it a particularly challenging subtype of breast cancer.
A systematic analysis of regulatory elements, specifically transcriptional enhancers and their noncoding eRNA transcripts, was conducted.
High-throughput CRISPR-interference assays and RNA sequencing revealed the functions of the top 30 eRNA-producing super-enhancers.
Direct target genes of these super-enhancers were associated with worse clinical outcomes in TNBC patients.
Single-cell RNA sequencing indicated that the activity of one specific super-enhancer was enhanced in malignant TNBC cells compared to nonmalignant cells.
Loss of the identified super-enhancer not only inhibited tumor growth and metastasis in mouse models but also affected cell proliferation and migration.

Simplified

Triple-negative breast cancer (TNBC) is the most therapeutically recalcitrant form of breast cancer, which is due in part to the paucity of targeted therapies. A systematic analysis of regulatory elements that extend beyond protein-coding genes could uncover avenues for therapeutic intervention. To this end, we analyzed the regulatory mechanisms of TNBC-specific transcriptional enhancers together with their noncoding enhancer RNA (eRNA) transcripts. The functions of the top 30 eRNA-producing super-enhancers were systematically probed using high-throughput CRISPR-interference assays coupled to RNA sequencing that enabled unbiased detection of target genes genome-wide. Generation of high-resolution Hi-C chromatin interaction maps enabled annotation of the direct target genes for each super-enhancer, which highlighted their proclivity for genes that portend worse clinical outcomes in patients with TNBC. Illustrating the utility of this dataset, deletion of an identified super-enhancer controlling the nearby PODXL gene or specific degradation of its eRNAs led to profound inhibitory effects on target gene expression, cell proliferation, and migration. Furthermore, loss of this super-enhancer suppressed tumor growth and metastasis in TNBC mouse xenograft models. Single-cell RNA sequencing and assay for transposase-accessible chromatin with high-throughput sequencing analyses demonstrated the enhanced activity of this super-enhancer within the malignant cells of TNBC tumor specimens compared with nonmalignant cell types. Collectively, this work examines several fundamental questions about how regulatory information encoded into eRNA-producing super-enhancers drives gene expression networks that underlie the biology of TNBC. Significance: Integrative analysis of eRNA-producing super-enhancers defines molecular mechanisms controlling global patterns of gene expression that regulate clinical outcomes in breast cancer, highlighting the potential of enhancers as biomarkers and therapeutic targets.

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Identifying Key Gene Regulators That Drive Progression of Triple-Negative Breast Cancer

Abstract

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