Abstract 1813: FOXM1 target genes associated with cell cycle regulation predict breast cancer metastatic outcome.
Authors: Yau Christina , Meyer Laurence , Benz Stephen , Vaske Charles , Scott Gary , Egan Brian , Labhart Paul , Mitchell Elizabeth , Pourmand Nader , Benz Christopher 
Published: August 2014

Abstract
FOXM1 is a key transcription factor regulating both cell proliferation and DNA damage checkpoint responses; and previous studies have demonstrated that higher breast cancer FOXM1 expression is associated with worse patient survival. Despite its functional and prognostic significance, the FOXM1 cistrome remains largely uncharacterized. Thus, in this study we utilized chromatin immune-precipitation sequencing (CHIPseq, GenPathway) and paired-end RNA-sequencing (RNAseq, UCSC) to comprehensively characterize the direct FOXM1 target genes associated with transcriptomic differences between actively proliferating and non-proliferating (confluent) ER+ MCF-7 cells. CHIPseq analysis identified ∼2.5K peaks with differential FOXM1 binding (MACS, p &lt; 10−7). Peaks located within 5kb (-4.5kb to +0.5kb) of a transcription start site were assigned to genes, yielding 429 differentially bound genes. ∼5.1K genes were found to be differentially expressed (DESeq, BH-FDR corrected p &lt; 0.05, fold change &gt; 1.5). Of these, 145 were differentially bound by FOXM1 and referred to as direct target genes. These direct targets were enriched in 43 functional categories (GO biological processes, KEGG, Reactome or BioCarta pathways; Benjamini-corrected EASE score &lt; 0.05) predominantly related to cell cycle and chromatin assembly. The remaining ∼4.9K differentially expressed proliferation associated genes with unaltered FOXM1 DNA binding, referred to as indirect targets and including FOXM1 itself, were enriched in a far more diverse group of 46 functional categories including processes related to cell cycle, DNA repair and DNA damage response. The average expression levels of FOXM1 direct and indirect target genes were computed in a pooled set of 683 node-negative adjuvant chemotherapy-naïve breast cancers from four public sources (GSE2034, GSE5327, GSE7390, NKI-295) annotated for distant metastasis-free survival (DMFS). Higher average expression of FOXM1 direct and indirect target genes were associated with worse DMFS (log rank p value &lt; 0.00001 for cohorts dichotomized at median average expression). When the dichotomized cohorts were further stratified by ER status, significant DMFS associations were only observed within the ER+, but not the ER-, subsets. However, in the latter subset there was a trend for worse prognosis associated with high expression of FOXM1 direct targets (HR = 1.6, log rank p=0.08), but not with FOXM1 indirect gene targets (HR=1.0, log rank p = 0.88). Altogether, these findings demonstrate that following induction of breast cancer cell proliferation, FOXM1 direct target genes are primarily associated with cell cycle regulation and appear to be better biomarkers of breast cancer metastatic outcome than proliferation associated indirect gene targets not associated with FOXM1 binding changes.
Citation Format: Christina Yau, Laurence Meyer, Stephen Benz, Charles Vaske, Gary Scott, Brian Egan, Paul Labhart, Elizabeth Mitchell, Nader Pourmand, Christopher Benz. FOXM1 target genes associated with cell cycle regulation predict breast cancer metastatic outcome. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1813. doi:10.1158/1538-7445.AM2013-1813