Pan-Cancer Analyses Reveal Genomic Features of FOXM1 Overexpression in Cancer

Abstract

FOXM1 is frequently overexpressed in cancer, but this has not been studied in a comprehensive manner. We utilized genotype-tissue expression (GTEx) normal and The Cancer Genome Atlas (TCGA) tumor data to define FOXM1 expression, including its isoforms, and to determine the genetic alterations that promote FOXM1 expression in cancer. Additionally, we used human fallopian tube epithelial (FTE) cells to dissect the role of Retinoblastoma (Rb)-E2F and Cyclin E1 in FOXM1 regulation, and a novel human embryonic kidney cell (HEK293T) CRISPR FOXM1 knockout model to define isoform-specific transcriptional programs. FOXM1 expression, at the mRNA and protein level, was significantly elevated in tumors with FOXM1 amplification, p53 inactivation, and Rb-E2F deregulation. FOXM1 expression was remarkably high in testicular germ cell tumors (TGCT), high-grade serous ovarian cancer (HGSC), and basal breast cancer (BBC). FOXM1 expression in cancer was associated with genomic instability, as measured using aneuploidy signatures. FTE models confirmed a role for Rb-E2F signaling in FOXM1 regulation and in particular identified Cyclin E1 as a novel inducer of FOXM1 expression. Among the three FOXM1 isoforms, FOXM1c showed the highest expression in normal and tumor tissues and cancer cell lines. The CRISPR knockout model demonstrated that FOXM1b and FOXM1c are transcriptionally active, while FOXM1a is not. Finally, we were unable to confirm the existence of a FOXM1 auto-regulatory loop. This study provides significant and novel information regarding the frequency, causes, and consequences of elevated FOXM1 expression in human cancer.

Co-regulation and functional cooperativity of FOXM1 and RHNO1 bidirectional genes in ovarian cancer

“…BDPs are often enriched with specific histone modifications H3K4me3, H3K9ac, H3K27ac, and H3K4me2 (Bornelov et al, 2015) and, in agreement, ENCODE data revealed that H3K4me3 and H3K27Ac are enriched in bimodal peaks at the F/R-BDP, suggesting correlated transcriptional activity in both directions ( Figure S3). ENCODE data also revealed an E2F1 peak, consistent with E2F's known involvement in BDP regulation and prior data identifying E2F1 as a regulator of FOXM1 expression ( Figure S3) (Barger et al, 2019;Barger et al, 2015;Chen et al, 2014;Millour et al, 2011).…”

“…The FOXM1/RHNO1 BDP (F/R-BDP) region contains a CpG island (CGI), a common feature of BDPs ( Figure S3) (Antequera, 2003;Takai and Jones, 2004;Wakano et al, 2012).BDPs are often enriched with specific histone modifications H3K4me3, H3K9ac, H3K27ac, and H3K4me2 (Bornelov et al, 2015) and, in agreement, ENCODE data revealed that H3K4me3 and H3K27Ac are enriched in bimodal peaks at the F/R-BDP, suggesting correlated transcriptional activity in both directions ( Figure S3). ENCODE data also revealed an E2F1 peak, consistent with E2F's known involvement in BDP regulation and prior data identifying E2F1 as a regulator of FOXM1 expression ( Figure S3) (Barger et al, 2019;Barger et al, 2015;Chen et al, 2014;Millour et al, 2011).The data presented above suggested that FOXM1 and RHNO1 are co-regulated. In agreement, we observed highly significant correlation of FOXM1 and RHNO1 expression in normal and cancer tissues, and in both mouse and human samples ( Figure 1B).…”

“…The 12p13.33 amplicon contains FOXM1 and RHNO1, co-expressed bidirectional genes FOXM1 is located at 12p13.33, a region with frequent copy number gains in HGSC and several other cancers (Barger et al, 2019;Barger et al, 2015). 12p13.33 amplification was associated with reduced overall survival in HGSC but, unexpectedly, FOXM1 mRNA expression did not (Barger et al, 2015).…”

“…FOXM1 also promotes HR (Khongkow et al, 2014;Maachani et al, 2016;Monteiro et al, 2013;Park et al, 2012) and chemoresistance (Carr et al, 2010;Fang et al, 2018;Kwok et al, 2010;Tassi et al, 2017;Zhao et al, 2014). Pan-cancer analyses have demonstrated increased FOXM1 expression across a variety of cancers and a robust connection to genomic instability and poor prognosis (Barger et al, 2019;Carter et al, 2006;Gentles et al, 2015;Jiang et al, 2015;Li et al, 2017).…”

BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation

“…The iBRD4 plasmids were constructed using the pCW57-GFP-2A-MCS backbone (Addgene, 71783), which was a gift from Adam Karpf and previously described 83 .…”