Induction of HOXA9 expression in three-dimensional organotypic culture of the Claudin-low breast cancer cells

Abstract

The gene expression signatures of the molecular intrinsic subtypes of breast cancer are regulated by epigenetic mechanisms such as methylation of CpG islands in gene promoters. Epigenetic codes can be regulated by the tumor microenvironment. The Claudin-low subtype is associated with triple-negative invasive ductal carcinomas in patients. Herein we explored epigenetic regulation of gene expression in the Claudin-low breast cancer cells by extracellular matrix (ECM), a key component of the tumor microenvironment. We modeled attachment to ECM using laminin rich ECM three-dimensional organotypic culture (lrECM 3D). In 2D and lrECM 3D cultures we examined expression of the homeobox (HOX) genes that epigenetically regulated in development and cancer. We demonstrated induction of the selected HOX genes in lrECM 3D culture of the Claudin-low breast cancer cells MDA-MB-231 and Hs578T. In particular activation of HOXA9 expression in lrECM 3D culture required binding of bromodomain containing 4 to the HOXA9 promoter and involved CpG hypomethylation. Our findings warrant further investigation of the ECM-regulated epigenetic coding of gene expression in the Claudin-low breast cancer.

Induction of a novel isoform of the lncRNA HOTAIR in Claudin‐low breast cancer cells attached to extracellular matrix

“…We chose Claudin‐low MDA‐MB‐231 and Hs578T cells because of their invasive and metastatic competence (Neve et al ., 2006; Prat et al ., 2010). We recently reported a widespread induction of the homeobox (HOX) genes in lrECM 3D culture over 2D culture of MDA‐MB‐231 cells and Hs578T cells (Li et al ., 2016). The HOXC cluster‐derived HOTAIR exhibited a robust increase in MDA‐MB‐231 cells from day 2 to day 10 (Fig.…”

“…Induction of HOTAIR correlated with invasive growth of MDA‐MB‐231 cells and Hs578T cells (Fig. 1C) (Li et al ., 2016). We previously reported invasive growth as evidenced by stellate morphology of MDA‐MB231 (Li et al ., 2016).…”

“…1C) (Li et al ., 2016). We previously reported invasive growth as evidenced by stellate morphology of MDA‐MB231 (Li et al ., 2016). Herein, we demonstrated similar stellate morphology of Hs578T cells in lrECM 3D culture using fluorescent staining for filamentous actin (Fig.…”

“…Chromatin immunoprecipitation (ChIP) was performed as previously described with minor modifications (Li et al ., 2016). Millipore (Darmstadt, Germany) provided EZ ChIP Kit (Cat #17–371).…”

“…Emerging evidence from lrECM 3D culture suggests epigenetic regulation of gene expression by the ECM signaling in cancer cells (Lelievre, 2010; Li et al ., 2016; Teoh‐Fitzgerald et al ., 2014). However, ECM‐regulated expression and functions of lncRNA have not been examined in Claudin‐low breast cancer cells.…”