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

Abstract

We report that the oncogenic transcription factor FOXM1 is arranged in a head-to-head configuration with RHNO1, a gene involved in the ATR/CHK1-dependent DNA replication stress (DRS) response. FOXM1 and RHNO1 are both amplified and upregulated in high-grade serous ovarian cancer (HGSC). FOXM1 and RHNO1 expression are closely associated in normal and cancer tissues, including single cells, and a bidirectional promoter (F/R-BDP) mediates balanced expression. Targeting of FOXM1 and RHNO1 in HGSC cells using shRNA, CRISPR mutagenesis, or CRISPR interference directed to the F/R-BDP reduced DNA homologous recombination repair (HR) capacity, increased DNA damage, reduced clonogenic survival, and sensitized HGSC cells to the poly-ADP ribosylase inhibitor (PARPi) olaparib. Thus, there is functional cooperativity between FOXM1 and RHNO1 in cancer cells, and combinatorial targeting of this bidirectional gene pair may be a novel cancer therapeutic strategy. More broadly, our data provide evidence that bidirectional gene units function in human cancer.Here, we show that FOXM1 and RHNO1 are co-amplified and co-expressed in HGSC, and that their expression in controlled by a bidirectional promoter (named the F/R-BDP). We additionally show that FOXM1 and RHNO1 they cooperatively promote HR, cell survival, and PARPi resistance. Co-regulation and functional cooperativity between FOXM1 and RHNO1 suggests that this bidirectional gene unit is a potential therapeutic target in HGSC and/or other cancers. More generally, our data provide evidence that cooperative bidirectional gene units functionally contribute to cancer. ResultsThe 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). The 12p13.33 amplicon includes 33 genes (Figure S1). To identify genes at 12p13.33 that might functionally cooperate with FOXM1, we performed expression correlation analyses. FOXM1 expression showed the strongest correlation with RHNO1 expression in HGSC (Figure 1A), pan-cancer (data not shown), and normal human tissues ( Figure S2). In addition, RHNO1 mRNA expression correlated with reduced HGSC survival (data not shown). Genomic analyses of FOXM1 and RHNO1 revealed a head-to-head arrangement with an intervening putative bidirectional promoter (BDP) ( Figure S3). Approximately 10% of human genes are arranged in this manner, and the gene pairs are frequently co-regulated and can function in similar biochemical pathways (Trinklein et al., 2004;Wakano et al., 2012;. 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., 20...

Pan-Cancer Analysis of Head-to-Head Gene Pairs in Terms of Transcriptional Activity, Co-expression and Regulation

“…In another study, co-regulation and functional co-operativity of a H2H pair, FOXM1 and RHNO1 , was also proved in ovarian cancer. FOXM1-RHNO1 cooperatively promoted high-grade serous ovarian cancer (HGSC) cell growth, and knockdown of the two genes sensitized HGSC cells to the PARPi olaparib and mitigates acquired olaparib resistance ( Barger et al, 2019 ). Here is a very recent report that PLAGL2-POFUT1 were proved to synergistically promote colorectal tumorigenesis by maintaining stemness of colorectal cancer stem cells, and modifying or editing transcriptional binding sites in their bidirectional promoter simultaneously suppressed both PLAGL2 and POFUT1 expression, which could offer promising therapeutic approaches ( Li et al, 2019 ).…”

Identification of candidate genes on the basis of SNP by time-lagged heat stress interactions for milk production traits in German Holstein cattle

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