FOXA1 Shapes the Chromatin State of ILC and Drives Differential Response to Aromatase Inhibitors and Tamoxifen [GATA3 ChIP-seq]

Invasive lobular breast cancer (ILC) is the second most common histological sub-type of breast cancer. Although the majority of ILC are strongly hormone receptor positive and are of low-intermediate grade, they present a number of clinical challenges. These challenges include limitations in physical exam and breast imaging for early detection, decreased response to chemotherapy and prospective evidence for differences in the benefit from specific adjuvant endocrine treatment regimens when compared to invasive ductal cancer (IDC). In addition to loss of e-cadherin, ILCs possess genetic alterations that are suggestive of a unique estrogen receptor(ER) axis, including an increase in the frequency of FOXA1 mutations and decrease in GATA3 truncating mutations. We performed a randomized Phase II clinical trial, Palbociclib and Endocrine therapy for LObular breast cancer Preoperative Study (PELOP), in which patients were stratified by histological subtype and found that the magnitude of the difference between the benefit from letrozole compared tamoxifen is significantly higher in ILC versus IDC. To elucidate the mechanism underlying this divergent response we comprehensively studied the ER axis in experimental models of ILC and IDC and clinical samples and show that ILC harbors a unique ER transcriptional axis that stems from increased FOXA1 chromatin binding and an altered chromatin state. These findings provide insights to the unique pattern of response to endocrine treatment in ILC and mechanisms of resistance to endocrine treatment, and offer new treatment strategies to improve outcomes for patients with this breast cancer subtype." Overall design: GATA3 ChIP-seq of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) cells in hormone deprivided condition (WM) plus estrogen; in duplicates, using Illumina NextSeq500.

浸润性小叶乳腺癌（Invasive lobular breast cancer）是乳腺癌第二常见的组织学亚型。尽管多数浸润性小叶乳腺癌为激素受体强阳性且分级处于低至中级水平，但其临床诊疗仍面临多重挑战：包括体格检查与乳腺影像检查用于早期筛查存在局限、化疗应答率降低，以及相较于浸润性导管癌（Invasive ductal cancer, IDC），特定辅助内分泌治疗方案的获益存在差异的前瞻性证据。除E-钙粘蛋白（e-cadherin）缺失外，浸润性小叶乳腺癌还携带有提示其雌激素受体（Estrogen receptor, ER）通路独特的遗传改变，具体表现为FOXA1突变频率升高，以及GATA3截短突变频率降低。
我们开展了一项随机II期临床试验——小叶乳腺癌术前帕博西尼联合内分泌治疗研究（PELOP），该试验按组织学亚型对患者进行分层，结果证实来曲唑对比他莫昔芬的获益差异幅度在浸润性小叶乳腺癌组中显著高于浸润性导管癌组。
为阐明这种应答差异的潜在机制，我们在浸润性小叶乳腺癌与浸润性导管癌的实验模型及临床样本中全面研究了ER通路，并证实浸润性小叶乳腺癌存在独特的ER转录调控通路，该通路源于FOXA1染色质结合能力增强以及染色质状态改变。
上述发现为浸润性小叶乳腺癌内分泌治疗应答的独特模式及内分泌治疗耐药机制提供了全新见解，并为改善该乳腺癌亚型患者的预后提供了新型治疗策略。
实验整体设计：在激素剥夺培养条件（WM）下添加雌激素，对导管型（MCF7与T47D）与小叶型（MDA134与SUM44）细胞开展GATA3染色质免疫沉淀测序（ChIP-seq），设置生物学重复，采用Illumina NextSeq500平台完成测序。