雌激素受体α（ER/ESR1）突变在30-40%的内分泌耐药性ER阳性（ER+）乳腺癌中发生。Forkhead Box A1（FOXA1）是介导ER+乳腺癌中ER染色质相互作用和内分泌反应的关键先驱因子，但其在ESR1突变乳腺癌中的作用尚不清楚。我们之前的FOXA1 ChIP-seq表明在T47D基因编辑的Y537S和D538G ESR1突变细胞中，出现了大量重定向的结合位点。在此基础上，我们将FOXA1基因组结合谱与同构的ER染色体组、可访问基因组和T47D细胞模型的转录组数据进一步整合。FOXA1的重定向与ESR1突变引起的转录组改变显著相关。此外，在ESR1突变细胞中，FOXA1结合位点与ER的重叠频率较低，并且差异表达基因与经典的FOXA1-ER轴的关联性较弱。基序分析显示，ESR1突变细胞的FOXA1结合位点中存在独特的视黄酸X受体（RXR）基序富集。一致地，ESR1突变细胞对RXR激动剂LG268的生长刺激作用更为敏感。突变特异性的响应依赖于两种RXR亚型，RXR-α和RXR-β，对后者的依赖性更强。此外，甲状腺激素受体激动剂T3在ESR1突变细胞中也表现出类似的促进生长作用。重要的是，RXR拮抗剂HX531阻止了ESR1突变细胞和患者来源的异种移植物（PDX）衍生的带ESR1 D538G突变的器官肿瘤的生长。总体而言，我们的数据支持了与FOXA1重编程相关的更强烈的RXR响应的证据，并提示针对具有ESR1突变的乳腺肿瘤的RXR途径的治疗策略的发展。意义：提供了FOXA1在ESR1突变乳腺癌中的作用全面的表征，以及通过阻断RXR激活的潜在治疗策略。

Estrogen receptor alpha (ER/ESR1) mutations occur in 30-40% of endocrine resistant ER-positive (ER+) breast cancer. Forkhead Box A1 (FOXA1) is a key pioneer factor mediating ER-chromatin interactions and endocrine response in ER+ breast cancer, but its role in ESR1 mutant breast cancer remains unclear. Our previous FOXA1 ChIP-seq identified a large portion of redistributed binding sites in T47D genome-edited Y537S and D538G ESR1 mutant cells. Here, we further integrated FOXA1 genomic binding profile with the isogenic ER cistrome, accessible genome and transcriptome data of T47D cell model. FOXA1 redistribution was significantly associated with transcriptomic alterations caused by ESR1 mutations. Furthermore, in ESR1 mutant cells, FOXA1 binding sites less frequently overlapped with ER, and differential gene expression was less associated with the canonical FOXA1-ER axis. Motif analysis revealed a unique enrichment of retinoid X receptor (RXR) motifs in FOXA1 binding sites of ESR1 mutant cells. Consistently, ESR1 mutant cells were more sensitive to growth stimulation with the RXR agonist LG268. The mutant-specific response was dependent on two RXR isoforms, RXR-α and RXR-β, with a stronger dependency on the latter. In addition, T3, the agonist of thyroid receptor also showed a similar growth-promoting effect in ESR1 mutant cells. Importantly, RXR antagonist HX531 blocked growth of ESR1 mutant cells and a patient derived xenograft (PDX)-derived organoid with an ESR1 D538G mutation. Collectively, our data support evidence for a stronger RXR response associated with FOXA1 reprogramming in ESR1 mutant cells, suggesting development of therapeutic strategies targeting RXR pathways in breast tumors with ESR1 mutation. Implications: It provides comprehensive characterization of the role of FOXA1 in ESR1 mutant breast cancer and potential therapeutic strategy through blocking RXR activation.