Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer

Abstract

Background The heterogeneous subtypes and stages of epithelial ovarian cancer (EOC) differ in their biological features, invasiveness, and response to chemotherapy, but the transcriptional regulators causing their differences remain nebulous. Methods In this study, we compared high-grade serous ovarian cancers (HGSOCs) to low malignant potential or serous borderline tumors (SBTs). Our aim was to discover new regulatory factors causing distinct biological properties of HGSOCs and SBTs. Results In a discovery dataset, we identified 11 differentially expressed genes (DEGs) between SBTs and HGSOCs. Their expression correctly classified 95% of 267 validation samples. Two of the DEGs, TMEM30B and TSPAN1, were significantly associated with worse overall survival in patients with HGSOC. We also identified 17 DEGs that distinguished stage II vs. III HGSOC. In these two DEG promoter sets, we identified significant enrichment of predicted transcription factor binding sites, including those of RARA, FOXF1, BHLHE41, and PITX1. Using published ChIP-seq data acquired from multiple non-ovarian cell types, we showed additional regulatory factors, including AP2-gamma/TFAP2C, FOXA1, and BHLHE40, bound at the majority of DEG promoters. Several of the factors are known to cooperate with and predict the presence of nuclear hormone receptor estrogen receptor alpha (ER-alpha). We experimentally confirmed ER-alpha and PITX1 presence at the DEGs by performing ChIP-seq analysis using the ovarian cancer cell line PEO4. Finally, RNA-seq analysis identified recurrent gene fusion events in our EOC tumor set. Some of these fusions were significantly associated with survival in HGSOC patients; however, the fusion genes are not regulated by the transcription factors identified for the DEGs. Conclusions These data implicate an estrogen-responsive regulatory network in the differential gene expression between ovarian cancer subtypes and stages, which includes PITX1. Importantly, the transcription factors associated with our DEG promoters are known to form the MegaTrans complex in breast cancer. This is the first study to implicate the MegaTrans complex in contributing to the distinct biological trajectories of malignant and indolent ovarian cancer subtypes.

PITX1 plays essential functions in cancer

“…Analogous to the observations in breast cancer, the interaction between PITX1 and ERa has been substantiated in ovarian cancer cell lines (72). While ERa's pivotal engagement in the PI3K/AKT and RAS/ERK signaling pathways within the context of ovarian cancer has undergone extensive elucidation, the present study refrained from delving into the specific functions of PITX1 and ERa in this ovarian cancer context (73).…”

ANS: Adjusted Neighborhood Scoring to improve assessment of gene signatures in single-cell RNA-seq data

“…Previous research on PITX1 in cancer has revealed cancer-type-specific effects. While upregulation of PITX1 has been shown to be associated with tumor progression in lung adenocarcinoma 31 , kidney renal clear cell carcinoma 32 , breast 33 , epithelial ovarian 34 , and prostate 35 cancer, interestingly, in other cancer types, such as melanoma 36 , ESCC 37 , osteosarcoma 38 and head and neck squamous cell carcinoma 39 , down-regulation of PITX1 has been found to enhance tumor progression. Other EMT-related genes exclusively present in our signature included two long-non-coding RNA genes: ABHD11-AS1 and BCYRN1 .…”

Molecular features as promising biomarkers in ovarian cancer

“…The PDGFC, SERPINE2, TSPAN1, ANK1, and SYNPO are involved in cell migration and cytoskeleton organization. 40…”