Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

Abstract

Background: High grade serous ovarian carcinoma (HGSOC) is the most common subtype of epithelial ovarian cancers (EOC) with poor prognosis. In most cases EOC is widely disseminated at the time of diagnosis. Despite the optimal cytoreductive surgery and chemotherapy most patients develop chemoresistance, and the 5-year overall survival being only 25-35%.

Methods: Here we analyzed the gene expression profiles of 10 primary HGSOC tumors and 10 related omental metastases using RNA sequencing and identified 100 differentially expressed genes.

Results: The differentially expressed genes were associated with decreased embryogenesis and vasculogenesis and increased cellular proliferation and organismal death. Top upstream regulators responsible for this gene signature were NR5A1, GATA4, FOXL2, TP53 and BMP7. A subset of these genes were highly expressed in the ovarian cancer among the cancer transcriptomes of The Cancer Genome Atlas. Importantly, the metastatic gene signature was suggestive of poor survival in TCGA data based on gene enrichment analysis.

Conclusion: By comparing the gene expression profiles of primary HGSOC tumors and their matched metastasis, we provide evidence that a signature of 100 genes is able to separate these two sample types and potentially predict patient survival. Our study identifies functional categories of genes and transcription factors that could play important roles in promoting metastases and serve as markers for cancer prognosis.

Keywords: HGSOC; Metastasis; Ovarian carcinoma; RNA sequencing; Transcriptome.

Fig. 1

a Hierarchical clustering of the 100 most differentially regulated genes between primary EOC samples and their matching omental metastases based on average correlation of the log2 expression values (rpkm). Red = primary tumor, blue = metastasis. The image was generated using Java Treeview 1.1.6r4 [17] b Volcano plot of log2 fold change and -log10 (FDR) of the differentially regulated genes demonstrated that majority of the genes are downregulated in the omental samples. c IPA® gene ontology analysis of the genes demonstrated that cellular functions related to embryonic development and vasculogenesis were decreased whereas those related to organismal survival, cellular maintenance and proliferation were increased. d IPA® analysis of upstream transcription regulators identified activation of the TP53 and inhibition of the BMP7 pathways. Blue color stands for predicted inhibition and orange for predicted activation. The tones of color indicate confidence level (light = low confidence; dark = high confidence).

Fig. 2

FOXL2, GATA4, NR5A1, AMHR2, MAL and WIPF3 were found highly expressed in ovarian cancers compared to many other cancers type in TCGA dataset. The figures were downloaded from cBioPortal [43, 44]

Fig. 3

a Survival analysis of our differentially regulated genes in TCGA patients using GSVA tool. Gene set enrichment analysis was limited to gene sets that were upregulated for upregulated metastasis genes and downregulated for downregulated metastasis genes. 29 samples enriched with our metastasis signature showed poorer survival b Genes AMHR2, FAM19A2, GATA4, MAL, PAX5, PCSK6 and SFRP2 from univariate cox proportional hazard regression (nominal P-value < 0.05 Walds test) are shown as Kaplan Meier curves.

Fig. 4

a Normalized and centered log2 expression values of primary tumors and metastasis of the upregulated genes of the cluster C1 [10] (blue = low expression, red = high expression, green = primary tumor, orange = metastasis) b The gene ontology analysis (DAVID) suggested that cellular functions related to extracellular matrix and cell cycle were activated in the genes that clustered into C1 group in Tothill et al study [10].