Single cell RNA sequencing of primary breast cancer.

We performed single cell RNA sequencing (RNA-seq) for 549 primary breast cancer cells and lymph node metastases from 11 patients with distinct molecular subtypes (BC01-BC02, estrogen receptor positive (ER+); BC03, double positive (ER+ and HER2+); BC03LN, lymph node metastasis of BC03; BC04-BC06, human epidermal growth factor receptor 2 positive (HER2+); BC07-BC11, triple-negative breast cancer (TNBC); BC07LN, lymph node metastasis of BC07) and matched bulk tumors. We separated these single cells into epithelial tumor and tumor-infiltrating immune cells using inferred CNVs from RNA-seq. The refined single cell profiles for the tumor and immune cells provide key expression signatures of breast cancer and the surrounding microenvironment. Overall design: All single-cell mRNA expression profiles were acquired from eleven patients (BC01-BC11) including two lymph node metastases (BC03LN, BC07LN) (549 samples). We applied four filtering criteria so as to remove samples with low sequencing quality and finally obtained 515 single cell sequencing data. Matched bulk tumor tissues and/or pooled cells were also sequenced and analyzed by the single cell RNA-seq pipeline (14 samples). Bulk tumor transcriptomes showed significant correlations with the average of single cell transcriptomes.

我们对来自11例具有不同分子亚型的患者的549个原发性乳腺癌细胞和淋巴结转移灶（BC01-BC02：雌激素受体阳性（ER+）；BC03：双阳性（ER+和HER2+）；BC03LN：BC03的淋巴结转移灶；BC04-BC06：人表皮生长因子受体2阳性（HER2+）；BC07-BC11：三阴性乳腺癌（TNBC）；BC07LN：BC07的淋巴结转移灶）及匹配的批量肿瘤进行了单细胞RNA测序（RNA-seq）。我们利用RNA-seq推断的拷贝数变异（copy number variations, CNVs）将这些单细胞分为上皮肿瘤细胞和肿瘤浸润免疫细胞。经过优化的肿瘤细胞和免疫细胞单细胞谱提供了乳腺癌及其周围微环境的关键表达特征。
整体设计：所有单细胞mRNA表达谱均来自11例患者（BC01-BC11），包括2个淋巴结转移灶（BC03LN、BC07LN），共549个样本。我们采用四项过滤标准以去除测序质量较低的样本，最终获得515个单细胞测序数据。匹配的批量肿瘤组织和/或混合细胞也通过单细胞RNA-seq流程进行测序和分析（14个样本）。批量肿瘤转录组与单细胞转录组的平均值呈显著相关性。