基于单细胞ATAC测序数据的乳腺癌上皮细胞转录因子研究  

Analysis of Transcription Factors in Breast Cancer Epithelial Cells Based on Single-cell ATAC-seq Data

作　　者：张雅娜 牟苑菁 李苇祥 赵俊焱 郭志云[1] ZHANG Yana;MOU Yuanjing;LI Weixiang;ZHAO Junyan;GUO Zhiyun(School of Life Science and Engineering,Southwest Jiaotong University,Chengdu 610031,Sichuan,China)

机构地区：[1]西南交通大学生命科学与工程学院,中国四川成都610031

出　　处：《生命科学研究》2024年第2期171-178,共8页Life Science Research

基　　金：四川省科技厅自然科学基金项目(2022NSFSC0779);传染病防治科技重大专项(2018ZX10101-003-001-008);西南交通大学大学生创新创业训练计划(2023133);第十七期个性化实验项目(GX202316027)。

摘　　要：研究表明,乳腺肿瘤细胞染色质开放区域上的转录因子显著影响乳腺癌患者的临床表型和预后。然而,在单细胞层面,这些调控元件如何调控乳腺癌发生发展尚不明确。为此,本研究从GEO数据库中下载了45216个正常和肿瘤乳腺组织的单细胞染色质可及性测序(single-cell ATAC sequencing,scATAC-seq)数据,并对其进行了分析。根据标记基因在细胞群的基因活性得分进行细胞类型注释后得到7种乳腺细胞类型。皮尔逊相关性分析表明,肿瘤和正常乳腺样本的上皮细胞存在明显的染色质可及性差异,且乳腺上皮细胞存在高度样本间异质性(PCC=-0.07),暗示其是乳腺肿瘤的主要恶性细胞类型。为了探究正常和恶性乳腺上皮细胞的差异可及性区域中转录因子结合基序的富集情况,在提取上皮细胞群后对4个上皮细胞亚型的特征开放区域进行了转录因子结合基序富集分析。结果表明,恶性乳腺上皮细胞有194个转录因子显著富集(P<0.001),它们可能涉及乳腺肿瘤发展和转移等调控过程。对上皮细胞亚型中富集程度较高的转录因子进行活性分数计算及转录组数据验证,结果进一步显示这些差异调控元件可能与乳腺细胞恶性发展相关。此外,对转录因子结合基序在不同乳腺癌亚型中的可及性差异进行了分析,发现SNAI2在三阴性乳腺癌样本中具有显著高的可及性,提示SNAI2在三阴性乳腺癌中具有潜在的特异性调控作用。Studies have shown that transcription factors binding to open chromatin regions in breast tumor cells significantly influence the clinical phenotype and prognosis of breast cancer patients.However,it is unclear how these regulatory elements regulate the occurrence and development of breast cancer at the sin-gle-cell level.Herein,single-cell chromatin accessibility sequencing(single-cell ATAC sequencing,scATAC-seq)data of 45216 normal and tumor breast tissues were downloaded from the GEO database,and seven breast cell types were obtained after cell type annotation based on gene activity scores of marker genes in cell populations.Pearson correlation analysis showed significant differences in chromatin accessibility be-tween tumor and normal breast epithelial cells,and a high degree of inter-sample heterogeneity of breast epithelial cells(PCC=-0.07),implying that they are the main malignant cell type in breast tumors.To explore the enrichment of transcription factor motifs in the differentially accessible regions of normal and malignant mammary epithelial cells,motif enrichment analysis was performed on the characteristic open regions of the four epithelial cell subtypes after extraction of the epithelial cell populations.The results showed that malig-nant breast epithelial cells were significantly enriched for 194 transcription factors(P<0.001),which may be involved in regulatory processes of breast tumor development and metastasis.Calculation of activity scores and validation of transcriptome data for transcription factors highly enriched in epithelial cell subtypes fur-ther showed that these differential regulatory elements may be associated with malignant development of breast cells.In addition,differences in the accessibility of transcription factor binding motifs in different breast can-cer subtypes were analyzed,and SNAI2 was found to have significantly high accessibility in triple-negative breast cancer samples,suggesting that SNAI2 has a potential specific regulatory role in triple-negative breast cancer.

关 键 词：乳腺癌 单细胞 单细胞染色质可及性测序(scATAC-seq) 转录因子 

分 类 号：Q523.1[生物学—生物化学] Q811.4[医药卫生—肿瘤] R737.9[医药卫生—临床医学]