Integrated Molecular Analysis of Tamoxifen-Resistant Invasive Lobular Breast Cancer Cells

Invasive lobular breast cancer (ILC) is an understudied malignancy with distinct clinical, pathological, and molecular features that distinguish it from the more common invasive ductal carcinoma (IDC). Mounting evidence suggests that estrogen receptor-alpha positive (ER+) ILC has a poor response to Tamoxifen (TAM), but the mechanistic drivers of this are undefined. In the current work, we comprehensively characterize the SUM44/LCCTam ILC model system through integrated analysis of gene expression, copy number, and mutation, with the goal of identifying actionable alterations relevant to clinical ILC that can be co-targeted along with ER to improve treatment outcomes. We show that TAM has several distinct effects on the transcriptome of LCCTam cells, that this resistant cell model has acquired copy number alterations and mutations that impinge on MAPK and metabotropic glutamate receptor (GRM/mGluR) signaling networks, and that pharmacological inhibition of either improves or restores the growth-inhibitory actions of endocrine therapy. These samples form a SuperSeries with GSE12708. Total RNA was extracted from sub-confluent T-25 cm^2 tissue culture flasks of SUM44 and LCCTam cells, then processed and arrayed. Microarray data quality was then assessed using several tools, including those recommended by Affymetrix and a series of additional QC measures. The Robust Multiple-Array Average (RMA) method was used to preprocess the raw gene expression data, as implemented in the Bioconductor project (http://bioconductor.org).

浸润性小叶癌（Invasive lobular breast cancer, ILC）是一类尚未被充分研究的恶性肿瘤，其临床、病理及分子特征均与更为常见的浸润性导管癌（Invasive Ductal Carcinoma, IDC）存在显著差异。日益增多的研究证据表明，雌激素受体α阳性（Estrogen Receptor-alpha Positive, ER+）的ILC对他莫昔芬（Tamoxifen, TAM）应答不佳，但其背后的机制驱动因素仍未明确。本研究通过整合分析基因表达、拷贝数变异与突变特征，对SUM44/LCCTam ILC模型系统开展全面表征，旨在识别与临床ILC相关的可靶向治疗靶点改变，从而可与雌激素受体靶向治疗联合应用以改善治疗结局。

我们证实，他莫昔芬对LCCTam细胞的转录组存在多种独特调控作用；该耐药细胞模型已获得影响丝裂原活化蛋白激酶（Mitogen-Activated Protein Kinase, MAPK）及代谢型谷氨酸受体（Metabotropic Glutamate Receptor, GRM/mGluR）信号通路的拷贝数变异与突变；且任一通路的药理学抑制均可增强或恢复内分泌治疗的生长抑制效应。

本数据集与GSE12708共同构成超级系列数据集（SuperSeries）。我们从培养于T-25 cm²组织培养瓶、处于亚汇合状态的SUM44与LCCTam细胞中提取总RNA，随后完成样本处理并制备为微阵列芯片。我们采用Affymetrix推荐的分析工具及一系列额外质控标准，对微阵列数据质量进行评估。原始基因表达数据采用Bioconductor项目（http://bioconductor.org）中实现的稳健多阵列平均（Robust Multiple-Array Average, RMA）方法完成预处理。