Genome-wide identification of binding sites of GRHL2 in luminal-like and basal A subtypes of breast cancer

Abstract

Grainyhead like 2 (GRHL2) is one of three mammalian homologues of the grainyhead (GRH) gene. It suppresses the oncogenic epithelial-mesenchymal transition (EMT), acting as a tumor suppressor. On the other hand, GHRL2 promotes cell proliferation by increasing human telomerase reverse transcriptase (hTERT) activity, serving as a tumor promoter. According to gene expression profiling, breast cancer can be divided into basal-like (basal A and basal B), luminal-like, HER2 enriched, claudin-low and normal-like subtypes. To identify common and subtype-specific genomic binding sites of GRHL2 in breast cancer, GRHL2 ChIP-seq was performed in three luminal-like and three basal A human breast cancer cell lines. Most binding sites of GRHL2 were found in intergenic and intron regions. 13,351 common binding sites were identified in basal A cells, which included 551 binding sites in gene promoter regions. For luminal-like cells, 6,527 common binding sites were identified, of which 208 binding sites were found in gene promoter regions. Basal A and luminal-like breast cancer cells shared 4711 GRHL2 binding sites, of which 171 binding sites were found in gene promoter regions. The identified GRHL2-binding motifs are all identical to a motif reported for human ovarian cancer, indicating conserved GRHL2 DNA-binding among human cancer cells. Notably, no binding sites of GRHL2 were detected in the promoter regions of several established EMT-related genes, including CDH1, ZEB1, ZEB2 and CDH2 genes. Collectively, this study provides a comprehensive overview of interactions of GRHL2 with DNA and lays the foundation for further understanding of common and subtype-specific signaling pathways regulated by GRHL2 in breast cancer.