Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer [ChIP_seq]. Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer [ChIP_seq]

A subset of triple negative breast cancers (TNBC) are characterized by genetic alterations in fibroblast growth factor receptors (FGFR) including amplifications, activating mutations or gene fusions. However, despite this genetic evidence of FGFR-dependency, FGFR inhibitors have shown only limited clinical efficacy in TNBC, suggesting the presence of intrinsic or adaptive resistance mechanisms. Using genome-wide CRISPR screens, we found that resistance to FGFR inhibition is mediated by activation of the mTORC1 and YAP pathways. Prolonged FGFR inhibition increased expression of several amino acid transporters resulting in increased cellular level of certain amino acids and activation of the mTORC1 amino acid sensing pathway. Epigenomic analyses revealed that FGFR inhibition reorganized YAP/TEAD associated enhancers leading to the upregulation of YAP target genes including the amino acid transporters upstream of mTORC1. Remarkably, mTORC1 and FGFR inhibitors synergistically blocked the growth of TNBC cells in vitro and in patient-derived xenografts. These findings define a novel epigenetic feedback mechanism involving intracellular amino acid levels leading to targeted therapy resistance in TNBC, and offers a combinatorial drug treatment strategy to improve clinical outcomes for this aggressive breast cancer subtype. Overall design: ATAC-seq, H3K27ac ChIP-seq, YAP ChIP-seq and BRG1 ChIP-seq in CAL-120 cells treated with DMSO or infigratinib

三阴性乳腺癌（triple negative breast cancer, TNBC）的一个亚群，以成纤维细胞生长因子受体（fibroblast growth factor receptor, FGFR）的遗传改变为特征，包括基因扩增、激活突变或基因融合。尽管存在FGFR依赖的遗传学证据，但FGFR抑制剂在TNBC中仅表现出有限的临床疗效，这提示存在内在或适应性耐药机制。本研究通过全基因组CRISPR筛选发现，FGFR抑制剂耐药由哺乳动物雷帕霉素靶蛋白复合物1（mTORC1）与Yes相关蛋白（YAP）通路的激活所介导。持续FGFR抑制可上调多种氨基酸转运蛋白的表达，导致特定氨基酸的细胞内水平升高，并激活mTORC1的氨基酸感知通路。表观基因组分析显示，FGFR抑制会重塑YAP/TEAD结合的增强子区域，进而上调YAP靶基因的表达，其中包括mTORC1上游的氨基酸转运蛋白。尤为重要的是，mTORC1抑制剂与FGFR抑制剂在体外及患者来源异种移植物中，可协同阻断TNBC细胞的增殖。本研究揭示了一种全新的表观遗传反馈机制：细胞内氨基酸水平的变化可导致TNBC的靶向治疗耐药，并提出了联合用药策略，以改善这一侵袭性乳腺癌亚型的临床结局。总体实验设计：在经二甲基亚砜（DMSO）或英菲格拉替尼（infigratinib）处理的CAL-120细胞中，开展转座酶可及性测序（ATAC-seq）、组蛋白H3赖氨酸27乙酰化染色质免疫共沉淀测序（H3K27ac ChIP-seq）、YAP染色质免疫共沉淀测序（YAP ChIP-seq）及BRG1染色质免疫共沉淀测序（BRG1 ChIP-seq）实验。