Multiplatform Analysis of Primary and Metastatic Breast Tumors from the AURORA US Network identifies microenvironment and epigenetics differences as drivers of metastasis [RNA-Seq]. Multiplatform Analysis of Primary and Metastatic Breast Tumors from the AURORA US Network identifies microenvironment and epigenetics differences as drivers of metastasis [RNA-Seq]

Patients with metastatic breast cancer (MBC) typically have short survival times and their successful treatment represents one of the most challenging aspects of patient care. This poor prognostic behavior is in part due to molecular features including increased tumor cell clonal heterogeneity, multiple drug resistance mechanisms, and alterations of the tumor microenvironment. The AURORA US Metastasis Project was established with the goal to identify molecular features specifically associated with metastasis. We therefore collected and molecularly characterized specimens from 55 metastatic breast cancer (BC) patients representing 51 primary cancers and 102 metastases. The 153 unique tumors were assayed using RNAseq, tumor/germline DNA exomes and low pass whole genome sequencing, and global DNA methylation microarrays. We found intrinsic molecular subtype differences between primary tumors and their matched metastases to be rare in triple negative breast cancer (TNBC)/Basal-like subtype tumors. Conversely, tumor subtype changes were relatively frequent in estrogen receptor positive (ER+) cancers where ~30% of Luminal A cases switched to Luminal B or HER2-enriched (HER2E) subtypes. Clonal evolution studies identified changes in expression subtype coincident with DNA clonality shifts, especially involving HER2 amplification and/or the HER2E expression subtype. In contrast, we found remarkable conservation of cancer-associated DNA hypermethylation profiles within primary tumor-metastasis pairs. We further found evidence for ER-mediated downregulation of genes involved in cell-cell adhesion in metastases. Microenvironment differences varied according to tumor subtype where ER+/Luminal metastases had lower fibroblast and endothelial cell content, while TNBC/Basal-like metastases showed a dramatic decrease in B cells and T cells. In 17% of metastatic tumors, we identified DNA hypermethylation and/or focal DNA deletions near HLA-A that were associated with its significantly reduced expression, and with lower immune cell infiltrates. We also identified low immune cell features in brain and liver metastases when compared to other metastatic sites, even within the same patient. These findings have implications for the treatment of metastatic breast cancer patients with immune- and HER2-targeting therapies and suggest potential novel therapeutic avenues for the improvement of outcomes for some patients with MBC Overall design: Comparative gene expression profiling analysis of RNA-seq data of breast primary and matched metastatic tumors NOTE FROM THE SUBMITTER: the raw files (BAMs) which will be submitted to dbGAP

转移性乳腺癌（metastatic breast cancer, MBC）患者通常生存期较短，其成功治疗堪称临床护理中最具挑战性的课题之一。该不良预后特征在一定程度上源于多种分子特性，包括肿瘤细胞克隆异质性升高、多重耐药机制以及肿瘤微环境改变。本研究依托AURORA美国转移项目（AURORA US Metastasis Project），旨在明确与肿瘤转移特异性相关的分子特征。为此，我们收集了55例转移性乳腺癌（breast cancer, BC）患者的样本并完成分子表征，其中涵盖51例原发性肿瘤与102处转移灶，共计153例独特肿瘤样本。我们通过RNA测序（RNAseq）、肿瘤/生殖系DNA外显子组测序、低覆盖度全基因组测序以及全基因组DNA甲基化微阵列对上述样本进行了检测分析。研究结果显示，三阴性乳腺癌（triple negative breast cancer, TNBC）/基底样亚型肿瘤中，原发性肿瘤与其匹配转移灶之间的内在分子亚型差异极为罕见。与之相反，雌激素受体阳性（estrogen receptor positive, ER+）乳腺癌的肿瘤亚型改变相对常见，约30%的管腔A型（Luminal A）病例会向管腔B型（Luminal B）或人表皮生长因子受体2富集型（HER2-enriched, HER2E）亚型转换。克隆进化研究表明，表达亚型的改变与DNA克隆性变化高度契合，尤其涉及人表皮生长因子受体2（HER2）扩增和/或HER2E表达亚型。与之形成对比的是，我们观察到原发性肿瘤-转移灶配对样本中，癌症相关DNA高甲基化谱呈现显著的保守性。我们还发现了转移灶中雌激素受体介导的细胞间黏附相关基因表达下调的证据。肿瘤微环境差异因肿瘤亚型而异：ER+/管腔型转移灶的成纤维细胞与内皮细胞含量较低，而TNBC/基底样转移灶的B细胞与T细胞含量显著降低。在17%的转移性肿瘤中，我们检测到HLA-A基因区域附近存在DNA高甲基化和/或局灶性DNA缺失，该改变与HLA-A表达水平显著降低以及免疫细胞浸润减少显著相关。相较于其他转移部位，即使是同一患者，脑转移与肝转移灶的免疫细胞特征也普遍偏低。上述研究结果对转移性乳腺癌患者的免疫靶向治疗与HER2靶向治疗具有重要指导意义，同时为改善部分转移性乳腺癌患者的预后提供了潜在的新型治疗策略。整体研究设计：对乳腺原发性肿瘤与其匹配转移灶的RNA测序数据开展比较基因表达谱分析。提交者备注：原始数据文件（BAM文件）将提交至dbGAP数据库。