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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
Published on: September 20, 2018
Chromatin insulation orchestrates matrix metalloproteinase gene cluster expression reprogramming in aggressive breast
Pere Llinàs-Arias1, Miquel Ensenyat-Mendez1, Sandra Íñiguez-Muñoz1
1Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain.
Background:
Triple-negative breast cancer (TNBC) is an aggressive subtype that exhibits a high incidence of distant metastases and lacks targeted therapeutic options. Here we explored how the epigenome contributes to matrix metalloprotease (MMP) dysregulation impacting tumor invasion, which is the first step of the metastatic process.
Methods:
We combined RNA expression and chromatin interaction data to identify insulator elements potentially associated with MMP gene expression and invasion. We employed CRISPR/Cas9 to disrupt the CCCTC-Binding Factor (CTCF) binding site on an insulator element downstream of the MMP8 gene (IE8) in two TNBC cellular models. We characterized these models by combining Hi-C, ATAC-seq, and RNA-seq with functional experiments to determine invasive ability. The potential of our findings to predict the progression of ductal carcinoma in situ (DCIS), was tested in data from clinical specimens.
Results:
We explored the clinical relevance of an insulator element located within the Chr11q22.2 locus, downstream of the MMP8 gene (IE8). This regulatory element resulted in a topologically associating domain (TAD) boundary that isolated nine MMP genes into two anti-correlated expression clusters. This expression pattern was associated with worse relapse-free (HR = 1.57 [1.06 - 2.33]; p = 0.023) and overall (HR = 2.65 [1.31 - 5.37], p = 0.005) survival of TNBC patients. After CRISPR/Cas9-mediated disruption of IE8, cancer cells showed a switch in the MMP expression signature, specifically downregulating the pro-invasive MMP1 gene and upregulating the antitumorigenic MMP8 gene, resulting in reduced invasive ability and collagen degradation. We observed that the MMP expression pattern predicts DCIS that eventually progresses into invasive ductal carcinomas (AUC = 0.77, p < 0.01).
Conclusion:
Our study demonstrates how the activation of an IE near the MMP8 gene determines the regional transcriptional regulation of MMP genes with opposing functional activity, ultimately influencing the invasive properties of aggressive forms of breast cancer.
Insights
This study reveals how an insulator element near the MMP8 gene regulates matrix metalloprotease (MMP) genes, impacting triple-negative breast cancer (TNBC) invasion. Modifying this element reduced cancer cell invasiveness and predicted disease progression.
Area of Science:
- Genomics and Epigenetics
- Cancer Biology
- Molecular Oncology
Background:
- Triple-negative breast cancer (TNBC) is aggressive, prone to metastasis, and lacks targeted therapies.
- Tumor invasion, the initial step in metastasis, is linked to dysregulated matrix metalloproteases (MMPs).
- Epigenetic mechanisms influencing MMP dysregulation in TNBC invasion require further investigation.
Purpose of the Study:
- To investigate the epigenetic regulation of MMPs in TNBC invasion.
- To identify insulator elements controlling MMP gene expression and their role in tumor metastasis.
- To assess the potential of MMP expression patterns in predicting breast cancer progression.
Main Methods:
- Combined RNA expression and chromatin interaction data to identify MMP-associated insulator elements.
- Utilized CRISPR/Cas9 to disrupt a specific insulator element (IE8) downstream of the MMP8 gene in TNBC models.
- Employed Hi-C, ATAC-seq, and RNA-seq, alongside functional assays, to characterize cellular models and invasive ability.
- Validated findings using clinical specimens of ductal carcinoma in situ (DCIS).
Main Results:
- Identified an insulator element (IE8) at Chr11q22.2 acting as a topologically associating domain (TAD) boundary, segregating nine MMP genes into distinct expression clusters.
- Disruption of IE8 altered MMP expression, downregulating pro-invasive MMP1 and upregulating antitumorigenic MMP8, leading to reduced cancer cell invasion and collagen degradation.
- The identified MMP expression pattern significantly correlated with poorer relapse-free and overall survival in TNBC patients.
- MMP expression patterns effectively predicted the progression of DCIS to invasive ductal carcinomas.
Conclusions:
- Activation of the IE8 insulator element near MMP8 drives regional transcriptional regulation of MMP genes with opposing functions.
- This epigenetic regulation of MMPs significantly influences the invasive properties of aggressive breast cancers.
- Targeting such epigenetic regulators offers potential therapeutic strategies for TNBC.
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