Chromatin Accessibility differentiates Invasive Lobular from Invasive Ductal Breast cancer and Dictates Response to Endocrine Treatment

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: ATAC-seq of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) cells, as well as MDA134 witn and without an shRNA for FOXA1, in hormone deprivided condition (WM) plus estrogen; in duplicates, using Illumina NextSeq500.

浸润性小叶癌（Invasive lobular breast cancer, ILC）是乳腺癌第二常见的组织学亚型。尽管绝大多数ILC均为强激素受体阳性且处于中低级别，但该亚型仍存在诸多临床挑战：包括早期筛查时体格检查与乳腺影像学检查存在局限性、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临床证据。除E-钙粘蛋白（e-cadherin）表达缺失外，ILC还携带提示其存在独特雌激素受体（estrogen receptor, ER）信号轴的遗传改变，包括FOXA1突变频率升高以及GATA3截短突变发生率降低。本研究开展了一项随机Ⅱ期临床试验——帕博西尼联合内分泌治疗用于小叶乳腺癌术前研究（Palbociclib and Endocrine therapy for LObular breast cancer Preoperative Study, PELOP），试验按组织学亚型对患者进行分层，结果显示相较于他莫昔芬，来曲唑的获益差异幅度在ILC组中显著高于IDC组。为阐明这种应答差异的潜在机制，本研究在ILC与IDC的实验模型及临床样本中对ER信号轴开展了全面分析，结果表明ILC拥有独特的ER转录轴，该轴源于FOXA1染色质结合能力增强以及染色质状态改变。上述发现揭示了ILC对内分泌治疗的独特应答模式以及内分泌治疗耐药机制，为改善该乳腺癌亚型患者的预后提供了全新的治疗策略。整体实验设计：在激素剥夺培养条件（WM）添加雌激素的环境中，对导管型细胞系（MCF7、T47D）、小叶型细胞系（MDA134与SUM44），以及带有/不带有FOXA1短发夹RNA（shRNA）的MDA134细胞进行ATAC测序（ATAC-seq）；实验设置双重复，采用Illumina NextSeq500测序平台完成测序。