MCF-10A Exome sequencing. Homo sapiens

We have compared the proteome, transcriptome and metabolome of two isogenic cell lines: MCF-10A, derived from human breast epithelium, and the mutant MCF-10A-H1047R. These cell lines differ by a single amino acid substitution (H1047R) caused by single nucleotide change in one allele of the PIK3CA gene which encodes the catalytic subunit p110α of phosphatidylinositol 3-kinase (PI3K). The H1047R mutation of PIK3CA is one of the most frequently encountered somatic cancer-specific mutations. In MCF-10A, this mutation induces an extensive cellular reorganization that far exceeds the known signaling activities of PI3K. The changes are highly diverse; with examples in structural protein levels, the DNA repair machinery and sterol synthesis. Gene set enrichment analysis reveals a highly significant concordance of the genes differentially expressed in MCF-10A-H1047R cells and the established protein and RNA signatures of basal breast cancer. No such concordance was found with the specific gene signatures of other histological types of breast cancer. Our data document the power of a single base mutation, inducing an extensive remodeling of the cell toward the phenotype of a specific cancer. This set of samples is whole exome sequencing to demonstrate the variants between MCF-10A and the MCF-10A-H1047R knock-in cell lines.

本研究对两株同基因细胞系的蛋白质组（proteome）、转录组（transcriptome）与代谢组（metabolome）进行了比较分析，两株细胞系分别为源自人乳腺上皮的MCF-10A，以及突变株MCF-10A-H1047R。二者仅存在一处单氨基酸替换（H1047R），该变异由编码磷脂酰肌醇3-激酶（PI3K）催化亚基p110α的PIK3CA基因的单个等位基因发生单核苷酸突变所导致。PIK3CA基因的H1047R突变是最常见的体细胞癌症特异性突变之一。在MCF-10A细胞中，该突变可诱导广泛的细胞重构，其影响远超PI3K已知的信号活性。此类变化具有高度多样性，涉及结构蛋白水平、DNA修复机制以及固醇合成等多个层面。基因集富集分析（gene set enrichment analysis）结果显示，MCF-10A-H1047R细胞中差异表达的基因与已确立的基底型乳腺癌（basal breast cancer）的蛋白及RNA特征谱具有极高显著性的一致性；而与其他组织学类型乳腺癌的特异性基因特征谱则未发现此类一致性。本研究数据证实了单碱基突变可诱导细胞发生广泛重塑，使其朝向特定癌症表型转变。本批样本采用全外显子测序（whole exome sequencing）技术，以解析MCF-10A与MCF-10A-H1047R敲入细胞系之间的遗传变异。