PO.ET03.02 · 实验与分子治疗
ELF3驱动的表观遗传重编程在SERD耐药的ER+乳腺癌中造成ERK通路依赖性
ELF3-driven epigenetic reprogramming creates ERK pathway dependency in SERD-resistant ER+ breast cancer
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
选择性雌激素受体降解剂（SERD）如氟维司群（fulvestrant）是治疗内分泌耐药ER+乳腺癌的一种有前景的策略。然而，对SERD的获得性耐药仍是一项重大的临床挑战，而无ESR1突变情况下SERD耐药的潜在机制尚知之甚少。随着新一代口服SERD进入临床，迫切需要了解SERD耐药的机制。我们在亲本和氟维司群耐药的MCF7细胞中运用全基因组CRISPR敲除筛选，鉴定出ELF3是SERD耐药的关键驱动因子。随后，我们进行了包括RNA-seq、ATAC-seq、H3K27ac ChIP-seq、ER ChIP-seq和ELF3 ChIP-seq在内的多组学分析，以表征亲本和氟维司群耐药细胞模型。我们发现，SERD耐药细胞表现出稳定的ER low/ELF3 hi表型，由失调的ERalpha-ELF3相互负反馈回路所驱动。多组学分析显示，在耐药细胞中，ELF3基序在新增的ATAC-seq和H3K27ac峰中均位列富集程度最高的转录因子结合基序。ELF3 ChIP-seq在耐药细胞中鉴定出约5,000个新增结合位点，这些位点与染色质可及性和H3K27ac信号的显著增加共定位，证实了ELF3强劲驱动的对ER非依赖性存活程序的增强子激活。为评估与SERD耐药相关的ELF3驱动的转录变化，我们将ELF3 ChIP-seq数据与来自亲本和SERD耐药细胞的RNA-seq数据进行整合。我们得出了一个由前500个基因组成的ELF3特征，这些基因在耐药细胞中同时表现出ELF3结合增加和表达升高。通路富集分析显示，ELF3靶基因高度富集于ERK信号组分。实验验证表明，耐药细胞表现出显著的ERK通路激活，并对ERK信号产生强烈依赖性，对MEK抑制剂曲美替尼（trametinib）的敏感性增加。对一个转移性乳腺癌队列的单细胞RNA-seq进行重新分析，证实ER low/ELF3 hi肿瘤细胞相较ER hi/ELF3 low细胞表现出ELF3特征的富集和ERK信号的增强。我们定义了一种新的SERD耐药机制，即ER low/ELF3 hi状态通过激活ELF3-ERK信号轴驱动耐药。靶向该通路可能克服ER low/ELF3 hi肿瘤中的耐药。
查看英文原文 English abstract
Selective estrogen receptor degraders (SERDs) such as fulvestrant represent a promising therapeutic strategy for endocrine-resistant ER+ breast cancers. However, acquired resistance to SERDs remains a significant clinical challenge, and mechanisms underlying SERD resistance without ESR1 mutations are poorly understood. With the new generation of oral SERDs entering clinic, there is urgent need to understand the mechanisms of SERD resistance. Using genome-wide CRISPR knockout screens in parental and fulvestrant-resistant MCF7 cells, we identified ELF3 as a critical driver of SERD resistance. We then performed multi-omics profiling including RNA-seq, ATAC-seq, H3K27ac ChIP-seq, ER ChIP-seq and ELF3 ChIP-seq to characterize the parental and fulvestrant-resistant cell models. We found that SERD-resistant cells exhibited a stable ER low /ELF3 hi phenotype driven by a dysregulated ERalpha-ELF3 reciprocal negative feedback circuit. Multi-omics profiling revealed that ELF3 motifs ranked as the top enriched transcription factor binding motif in both gained ATAC-seq and H3K27ac peaks in the resistant cells. ELF3 ChIP-seq identified ~ 5,000 gained binding sites in resistant cells that co-localized with dramatic increases in chromatin accessibility and H3K27ac signals, confirming robust ELF3-driven enhancer activation of ER-independent survival programs. To assess ELF3-driven transcriptional changes associated with SERD resistance, we integrated ELF3 ChIP-seq data with RNA-seq data from both parental and SERD-resistant cells. We derived an ELF3 signature consisting of the top 500 genes that showed both increased ELF3 binding and elevated expression in the resistant cells. Pathway enrichment analysis revealed that ELF3 target genes are highly enriched in ERK signaling components. Experimental validation showed that resistant cells exhibited marked ERK pathway activation and developed strong dependency on ERK signaling, with increased sensitivity to MEK inhibitor trametinib. Re-analysis of single-cell RNA-seq from a metastatic breast cancer cohort confirmed that ER low /ELF3 hi tumor cells show enrichment of the ELF3 signature and increased ERK signaling compared to ER hi /ELF3 low cells. We define a novel mechanism of SERD resistance where the ER low /ELF3 hi state drives resistance by activating an ELF3-ERK signaling axis. Targeting this pathway may overcome resistance in ER low /ELF3 hi tumors.
利益披露 Disclosure
N. Zhang, None..
R. Zheng, None..
K. Chen, None.