Abstract 4274: Identifying the regulatory network structure of the genes involved in signaling pathways underlying ER-PR-HER2+ breast cancer using Bayesian modeling of genome-wide NRF1 DNA motif sequence-enriched genes
Authors: Jairo D. Ramos, Jayanta Das, Changwon Yoo, Deoudutta Roy
Journal: Cancer Research (2018)

Abstract Nuclear respiratory factor 1 (NRF1) [alpha-palindromic binding protein (α-PAL)] is a redox-sensitive transcription factor. NRF1 localizes to several thousand sites in the genome. Role of NRF1 has remained largely unexplored in breast cancer (BCa). We have recently shown that reactive oxygen species (ROS) contribute to estrogen-induced growth of BCa cells through an NRF1 signaling pathway. In this study, we used a systematic approach integrating ChIP DNA-seq computational analysis, NRF1 protein-DNA motif binding analysis, breast cancer signaling pathway analysis, and Bayesian modeling to discover genes involved in HER2+ (HER2+ER−PR−) breast cancer. First, we used ChIP-seq of normal human mammary epithelial cells (HMEC) and three breast cancer cell lines, HCC1954, MCF7 and T47D, to identify NRF1 regulated genes in breast cancer. We then identified the genome-wide NRF1-enriched DNA regions in estrogen- and progesterone receptors-negative and amplified HER2 (ER-/PR-/HER2+) - HCC1954 breast cancer cell line compared to normal human mammary epithelial cells (HMEC) to discover the NRF1 regulatory network. Analysis of NRF1 binding activity in breast cancer cell line HCC1954 compared to normal mammary epithelial cells (HMEC) shows that more than 7,000 genes have NRF1 binding activity in the region located +/- 2,000 bp from TSS and the top 2,000 correlated with breast cancer showed a significant difference in the average amount of binding protein. The majority (83%) of NRF1 target genes that may participate in the process of cells acquiring characteristics of malignancy present NRF1 binding sites in the regulatory region located +/- 2,000 bp from TSS. Finally we used RNA microarray data from TCGA to detect changes in NRF1 expression levels and to develop a probabilistic graphic model using Bayesian network analysis to investigate how the putative causal genes may interact in breast cancer. NRF1 expression was significantly higher in HER+ breast cancer samples compared to normal breast tissues. This is consistent with our experimental data, which also showed higher expression of NRF1 in HER2+ breast cancer brain metastasis samples. NRF1 binding sites are present in the regulatory region located +/- 2,000 bp from TSS in the majority of target genes (83%). NRF1 binding activity in the region located +/- 2,000 bp from TSS significantly correlated with breast cancer. Bayesian structural modeling revealed 27 NRF1 target genes are part of the hallmarks of breast cancer. NRF1 is a parent of GADD45A, WNT9A and SHC2. Likewise, SHC2 is parent of CDK4, which in turn is parent of BRCA1. In summary, these findings revealed novel roles of NRF1 and its regulatory network presumably involved in the development of HER2+ER−PR− breast tumor, one of the two most aggressive breast cancer subtypes with poor prognosis. Citation Format: Jairo D. Ramos, Jayanta Das, Changwon Yoo, Deoudutta Roy. Identifying the regulatory network structure of the genes involved in signaling pathways underlying ER-PR-HER2+ breast cancer using Bayesian modeling of genome-wide NRF1 DNA motif sequence-enriched genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4274.