Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain.
Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA.
Mol Cancer. 2023 Nov 28;22(1):190. doi: 10.1186/s12943-023-01906-8.
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.
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.
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).
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.
三阴性乳腺癌（TNBC）是一种侵袭性亚型，其远处转移的发生率较高，且缺乏靶向治疗选择。在这里，我们探讨了表观基因组如何导致基质金属蛋白酶（MMP）失调，从而影响肿瘤侵袭，这是转移过程的第一步。
我们结合 RNA 表达和染色质相互作用数据，鉴定可能与 MMP 基因表达和侵袭相关的绝缘子元件。我们在两种 TNBC 细胞模型中，使用 CRISPR/Cas9 破坏 MMP8 基因下游的绝缘子元件（IE8）上的 CCCTC 结合因子（CTCF）结合位点。我们通过结合 Hi-C、ATAC-seq 和 RNA-seq 以及功能实验来对这些模型进行表征，以确定侵袭能力。我们还在临床标本的数据分析中测试了我们发现预测导管原位癌（DCIS）进展的潜力。
我们探索了位于 Chr11q22.2 位置 MMP8 基因下游的一个绝缘子元件的临床相关性（IE8）。该调节元件产生了一个拓扑关联域（TAD）边界，将九个 MMP 基因隔离成两个反相关表达簇。这种表达模式与 TNBC 患者无复发生存（HR=1.57[1.06-2.33]；p=0.023）和总生存（HR=2.65[1.31-5.37]，p=0.005）较差相关。在 CRISPR/Cas9 介导的 IE8 破坏后，癌细胞的 MMP 表达特征发生了转变，具体表现为下调促侵袭性 MMP1 基因和上调抗肿瘤 MMP8 基因，从而降低了侵袭能力和胶原降解。我们观察到 MMP 表达模式预测了最终进展为浸润性导管癌的 DCIS（AUC=0.77，p<0.01）。
我们的研究表明，MMP8 基因附近的 IE 激活如何决定 MMP 基因的区域转录调控，具有相反的功能活性，最终影响侵袭性乳腺癌的侵袭特性。
