Dataset of HOXB7, HOXB8 and HOXB9 expression profiles in cell lines representative of the breast cancer molecular subtypes Luminal a (MCF7), Luminal b (BT474), HER2+ (SKBR3) and triple-negative (MDA231, MDA468), compared to a model of normal cells (MCF10A)

Abstract

Alterations in HOXB genes expression in breast cancer have been described and related to therapy response and disease progression. However, due to breast cancer complexity and heterogeneity, added to the use of different technical approaches, the observed expression profiles are sometimes contradictory. Here, we provided the analyses of HOXB7, HOXB8 and HOXB9 expression profiles in cell lines extensively used in the literature addressing the putative role of HOXB genes in breast cancer (MCF7, BT474, SKBR3, MDA231 and MDA468) and representative of the clinical breast cancer molecular subtypes (Luminal A, Luminal B, HER2+ and Triple-negatives Claudin-low/Basal), compared to a normal breast model (MCF10A), using quantitative-PCR (qPCR). This technique allows a very sensitive quantification of gene expression and was performed using the fluorophore SYBR Green in order to obtain the expression levels relative to a reference gene, GAPDH in this case. We showed that HOXB7 is upregulated in all breast cancer cells analyzed, while HOXB8 and HOXB9 are significantly upregulated in MCF7 (Luminal A), BT474 (Luminal B) and MDA231 cells (Triple-negative Claudin-low). In addition, we found that the magnitude of the upregulation is highly subtype-specific, being the HER2+ cells the model with lowest HOXB7 upregulation, presenting very low or even null expression for HOXB8 and HOXB9, respectively. These results are analyzed in more detail in "HOX genes function in Breast Cancer development" [1] and are potentially relevant for a better understanding of the molecular heterogeneity of breast cancer, in addition to be a valuable tool assisting researchers in the choice of the most suitable cell models to perform functional assays concerning HOXB7, HOXB8 and HOXB9 genes.

Keywords: Breast cancer; Cell lines; HOXB genes; Molecular classification; qPCR.

Fig. 1

HOXB7, HOXB8 and HOXB9 basal mRNA expression levels analyzed by qPCR in five breast cancer cell lines representing distinct molecular subtypes (blue bars), in comparison with normal breast cells (MCF10A, purple bars). Statistical analyses by unpaired T test with Welch's correction. Y-axis depicts the ratios of HOXB expression relative to GAPDH expression. *p-value<0.05, **p-value<0.01 and ***p-value <0.001 (A) HOXB7 is significantly upregulated in all breast cancer cell lines analyzed. (B) Higher magnification evidencing HOXB7 upregulation in SKBR3 cells. (C) HOXB8 is significantly upregulated in MCF7, BT474 and MDA231 cells. (D) xHOXB9 is significantly upregulated in MCF7, BT474 and MDA231 cells and silenced in SKBR3 cells.