Dataset of HOXB7, HOXB8 and HOXB9 RNA expression in breast cancer cell lines

The HOXB7, HOXB8 and HOXB9 gene expression profiles in breast cancer are contradictory due to disease complexity and technical issues. The data presented here cover these two points by analysing the expression of these genes in breast cancer cell lines representative of distincts molecular subtypes using a very sensitive quantification technique, the qPCR. The cell lines analysed were MCF7, BT474, SKBR3, MDA231, MDA468 and MCF10A representative of Luminal A, Luminal B, HER2+, triple-negative claudin low, triple-negative basal and normal model, respectively. The raw data was accessed by CFX Manager 3.1 software (Bio-Rad) and a threshold line was put into the exponential phase of the amplification curve generating a Cycle Threshold (CT) number for each sample. The CT numbers were transferred to an Excell file to be analysed using the formula: RATIO= E target^ – (CT sample for the target gene) / E reference^ – (CT sample for the reference gene), in which “E” refers to primer efficiencies previously calculated and GAPDH is the reference gene. The statistical analyses were made with Prism 8 using the unpaired T test with Welch’s correction. P-values were considered statistically significant when P≤0.05. Data are presented as the mean ± SD of three independent experiments. The analyzed results, showed that HOXB7 tends to be overexpressed in all breast cancer cell lines when compared to the normal cell model, while HOXB8 and HOXB9 are significantly overexpressed only in MCF7, BT474 and MDA231 cells. All genes presented expression levels highly subtype-dependent among breast cancer cell lines.由于疾病本身的复杂性与实验技术局限，乳腺癌中HOXB7、HOXB8与HOXB9基因的表达谱研究结论存在矛盾。本数据集通过针对不同分子亚型乳腺癌细胞系中上述基因的表达分析，覆盖了上述两个矛盾来源，实验采用了灵敏度极高的定量技术qPCR（quantitative real-time PCR）。本次分析的细胞系依次为MCF7、BT474、SKBR3、MDA231、MDA468与MCF10A，分别对应Luminal A型、Luminal B型、HER2阳性型、三阴性Claudin低表达型、三阴性基底型乳腺癌细胞系以及正常乳腺细胞模型。原始数据通过Bio-Rad公司的CFX Manager 3.1软件获取，在扩增曲线的指数期绘制阈值线，从而得到每个样本的循环阈值（Cycle Threshold，简称CT）值。将CT值导入Excel文件，采用以下公式进行分析：RATIO = E靶基因^–(靶基因样本CT值) / E参比基因^–(参比基因样本CT值)，其中"E"为预先计算得到的引物扩增效率，GAPDH作为参比基因。统计分析采用Prism 8软件完成，使用带Welch校正的非配对t检验；当P值≤0.05时，认为差异具有统计学意义。实验数据以三次独立实验的均值±标准差（standard deviation，简称SD）形式呈现。分析结果显示：与正常乳腺细胞模型相比，HOXB7在所有乳腺癌细胞系中均呈过表达趋势；而HOXB8与HOXB9仅在MCF7、BT474及MDA231细胞系中出现显著过表达。所有靶基因的表达水平均与乳腺癌细胞系的分子亚型高度相关。