Identification Of A Transcription Factor Able To Alter The Cellular Identity And The Methylation Landscape Of Breast Cancer

Nora FERNANDEZ-JIMENEZ, International Agency for Research on Cancer (IARC), France
CAHAIS V. 1 , SKLIAS A. 1 , ANCEY P. 1 , ECSEDI S. 1 , DEGLI ESPOSTI D. 1 , CROS M. 1 , CUENIN C. 1 , HERNANDEZ-VARGAS H. 1 , HERCEG Z. 1

1 Epigenetics Group, International Agency for Research on Cancer, Lyon, France

Purpose: despite the numerous advances, breast cancer (BC) is still the most common cancer affecting women. Lowly methylated regions (LMRs), non-CpG loci that contain specific transcription factor (TF) motifs, have been suggested to act as regulators that define cellular identity but have not been reported in BC. Here, we aimed to identify the key subtype-specific TFs that shape BC methylome.
Methods: we selected subtype-specific LMRs using whole bisulfitome data available at TCGA. Differentially methylated regions (DMRs) within these LMRs were selected by comparing tumors and normal tissues in a larger TCGA cohort assessed by arrays. Finally, we predicted the most relevant TFs able to bind these DMRs. Additionally, we decided to overexpress the main TF identified in basal BC in MCF7, a luminal (epithelial) cell line to see whether it could induce a basal-like (mesenchimal) phenotype and modulate the methylome in vitro.
Results: we found 1,185 hypomethylated DMRs for basal subtype in silico that were enriched in EBF1 motifs. The methylation levels of the EBF1 motif-containing regions showed a strong negative correlation with the expression of 719 genes, including BTS2, CD74 and SLPI, putative oncogenes known to be specific for basal and/or poor outcome BC. Finally, in vitro overexpression of EBF1 was able to induce an epithelial-to-mesenchimal transition-like phenotype in the MCF7 cells, and to modify the methylation of 1072 loci in vitro (with a significant overlap with those targets found in silico).
Conclusions: EBF1 is able to change the methylation levels in vitro and seems to affect the molecular identity of the cells, leading to a more mesenchimal phenotype that could be translated into a more aggressive presentation of the disease.
Funding source: IARC Postdoctoral Fellowship (FP7–People–COFUND) and Postdoctoral Fellowship - Education Department of the Basque Government to NF-J during the first and the second year, respectively.