Dataset of HOXB7, HOXB8 and HOXB9 basal 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 analyzing the expression of these genes in breast cancer cell lines representative of distinct molecular subtypes using a very sensitive quantification technique, the qPCR. The cell lines analyzed 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 Excel file, provided in the Raw data folder, to be analyzed 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 using the MCF10A cells as reference sample. P-values were considered statistically significant when P≤0.05. The obtained values are provided in Analyzed data folder. Data are presented as the mean ± SD of at least three independent experiments. When more than three experiments are available, we used all replicates to do the analysis or excluded discrepant results but always keeping at least three replicates. The analyzed results showed that HOXB7 tends to be upregulated in all breast cancer cell lines when compared to the normal cell model, while HOXB8 and HOXB9 are significantly upregulated in MCF7, BT474 and MDA231 cells with no significant differences in SKBR3 and MDA468 cells. All genes presented expression levels highly subtype-dependent among different breast cancer cell lines.

HOXB7、HOXB8与HOXB9基因在乳腺癌中的表达谱因疾病复杂性及技术层面的问题而存在争议。本数据集针对上述两个核心问题展开研究：选取代表不同分子亚型的乳腺癌细胞系，采用灵敏度极高的定量技术——实时定量聚合酶链反应（qPCR），分析这些基因的表达水平。本次分析的细胞系依次为MCF7、BT474、SKBR3、MDA231、MDA468与MCF10A，分别对应腔面A型（Luminal A）、腔面B型（Luminal B）、HER2过表达型（HER2+）、三阴性Claudin低表达型、三阴性基底型及正常乳腺对照模型。原始数据通过CFX Manager 3.1软件（Bio-Rad公司）获取，将阈值线设置于扩增曲线的指数扩增期，从而为每个样本生成循环阈值（Cycle Threshold，CT）值。将CT值导入Raw data文件夹中提供的Excel文件，采用下述公式进行分析：RATIO= E靶基因^ – (靶基因的CT样本值) / E参比基因^ – (参比基因的CT样本值)，其中“E”代表此前已计算得到的引物扩增效率，且以甘油醛-3-磷酸脱氢酶（GAPDH）作为参比基因。统计分析采用Prism 8软件完成，以MCF10A细胞作为参照样本，使用校正了Welch法的非配对t检验；当P值≤0.05时，判定差异具有统计学意义。分析得到的结果存储于Analyzed data文件夹中。数据以至少3次独立实验的平均值±标准差形式呈现。若可获取超过3次实验的数据，将纳入所有重复样本进行分析，或剔除异常结果，但始终保留至少3次重复实验。分析结果显示：与正常乳腺对照模型相比，HOXB7在所有乳腺癌细胞系中均呈上调趋势；而HOXB8与HOXB9在MCF7、BT474及MDA231细胞中显著上调，在SKBR3与MDA468细胞中则无显著差异。所有基因的表达水平均高度依赖于乳腺癌细胞的分子亚型。