Construction of monocyte-related prognosis model based on comprehensive analysis of bulk RNA-seq and single-cell RNA-seq in high-grade serous ovarian cancer

Abstract

High-grade serous ovarian cancer (HGSOC) is a common subtype of ovarian cancer with high mortality. Finding a new biomarker is useful for the diagnosis and treatment of HGSOC. The scRNA and bulk RNA data were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The monocyte-related clusters were identified and annotated by Seruat and SingleR package. The Kaplan–Meier and receiver operating characteristic curve was used to determine the prognosis. The differentially expressed genes were determined by limma. The single sample Gene Set Enrichment Analysis, Gene Set Enrichment Analysis, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes were used for the enrichment function. The correlation between drug activity and gene expression was assessed by rcellminer and rcellminer Data package. We identified 9 cell types and obtained 37 differentially expressed marker genes of monocyte. A2M, CD163, and FPR1 were screened out as hub genes and used to construct risk model in HGSOC through univariate and multivariate cox analysis. Single sample Gene Set Enrichment Analysis showed risk score was related to B cell and T cell signal pathways, and further analysis showed most immune checkpoint genes expressions were upregulated in high-risk score group. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis exhibited that hub gene related genes were involved in signal receptor binding and cytokine-cytokine interaction. Low A2M expression and high expression of CD163 and FPR1 were associated with poor prognosis. Gene Set Enrichment Analysis revealed that A2M promoted tumor development through enhancing immune cell related signal pathways, while CD163 and FPR1 inhibited tumor development through activated carcinogenic signal pathways. Drug sensitivity analysis revealed that these hub genes could be potential therapeutic targets for the treatment of HGSOC. We constructed a risk model for the overall survival and explored the potential mechanism of monocyte in HGSOC.