Riaz Muhammad, van Jaarsveld Marijn T M, Hollestelle Antoinette, Prager-van der Smissen Wendy J C, Heine Anouk A J, Boersma Antonius W M, Liu Jingjing, Helmijr Jean, Ozturk Bahar, Smid Marcel, Wiemer Erik A, Foekens John A, Martens John W M
Breast Cancer Res. 2013 Apr 19;15(2):R33. doi: 10.1186/bcr3415.
Breast cancer is a genetically and phenotypically complex disease. To understand the role of miRNAs in this molecular complexity, we performed miRNA expression analysis in a cohort of molecularly well-characterized human breast cancer cell lines to identify miRNAs associated with the most common molecular subtypes and the most frequent genetic aberrations.
Using a microarray carrying LNA™ modified oligonucleotide capture probes), expression levels of 725 human miRNAs were measured in 51 breast cancer cell lines. Differential miRNA expression was explored by unsupervised cluster analysis and was then associated with the molecular subtypes and genetic aberrations commonly present in breast cancer.
Unsupervised cluster analysis using the most variably expressed miRNAs divided the 51 breast cancer cell lines into a major and a minor cluster predominantly mirroring the luminal and basal intrinsic subdivision of breast cancer cell lines. One hundred and thirteen miRNAs were differentially expressed between these two main clusters. Forty miRNAs were differentially expressed between basal-like and normal-like/claudin-low cell lines. Within the luminal-group, 39 miRNAs were associated with ERBB2 overexpression and 24 with E-cadherin gene mutations, which are frequent in this subtype of breast cancer cell lines. In contrast, 31 miRNAs were associated with E-cadherin promoter hypermethylation, which, contrary to E-cadherin mutation, is exclusively observed in breast cancer cell lines that are not of luminal origin. Thirty miRNAs were associated with p16INK4 status while only a few miRNAs were associated with BRCA1, PIK3CA/PTEN and TP53 mutation status. Twelve miRNAs were associated with DNA copy number variation of the respective locus.
Luminal-basal and epithelial-mesenchymal associated miRNAs determine the subdivision of miRNA transcriptome of breast cancer cell lines. Specific sets of miRNAs were associated with ERBB2 overexpression, p16INK4a or E-cadherin mutation or E-cadherin methylation status, which implies that these miRNAs may contribute to the driver role of these genetic aberrations. Additionally, miRNAs, which are located in a genomic region showing recurrent genetic aberrations, may themselves play a driver role in breast carcinogenesis or contribute to a driver gene in their vicinity. In short, our study provides detailed molecular miRNA portraits of breast cancer cell lines, which can be exploited for functional studies of clinically important miRNAs.
乳腺癌是一种基因和表型复杂的疾病。为了解微小RNA（miRNA）在这种分子复杂性中的作用，我们对一组分子特征明确的人乳腺癌细胞系进行了miRNA表达分析，以鉴定与最常见分子亚型和最频繁遗传畸变相关的miRNA。
使用携带锁核酸（LNA™）修饰寡核苷酸捕获探针的微阵列，在51个人乳腺癌细胞系中测量725种人类miRNA的表达水平。通过无监督聚类分析探索miRNA的差异表达，然后将其与乳腺癌中常见的分子亚型和遗传畸变相关联。
使用表达变化最大的miRNA进行无监督聚类分析，将51个人乳腺癌细胞系分为一个主要聚类和一个次要聚类，主要反映了乳腺癌细胞系的管腔型和基底型内在分类。这两个主要聚类之间有113种miRNA差异表达。基底样细胞系与正常样/克劳丁低细胞系之间有40种miRNA差异表达。在管腔型组内，39种miRNA与ERBB2过表达相关，24种与E-钙黏蛋白基因突变相关，这在这种亚型的乳腺癌细胞系中很常见。相比之下，31种miRNA与E-钙黏蛋白启动子高甲基化相关，与E-钙黏蛋白突变相反，这仅在非管腔型起源的乳腺癌细胞系中观察到。30种miRNA与p16INK4状态相关，而只有少数miRNA与BRCA1、PIK3CA/PTEN和TP53突变状态相关。12种miRNA与各自基因座的DNA拷贝数变异相关。
管腔型-基底型和上皮-间质相关的miRNA决定了乳腺癌细胞系miRNA转录组的分类。特定的miRNA组与ERBB2过表达、p16INK4a或E-钙黏蛋白突变或E-钙黏蛋白甲基化状态相关，这意味着这些miRNA可能有助于这些遗传畸变发挥驱动作用。此外，位于显示反复遗传畸变的基因组区域的miRNA本身可能在乳腺癌发生中起驱动作用，或对其附近的驱动基因起作用。简而言之，我们的研究提供了乳腺癌细胞系详细的分子miRNA图谱，可用于对临床重要miRNA的功能研究。
