Gene co-expression network analysis revealed novel biomarkers for ovarian cancer

Abstract

Ovarian cancer is the second most common gynecologic cancer and remains the leading cause of death of all gynecologic oncologic disease. Therefore, understanding the molecular mechanisms underlying the disease, and the identification of effective and predictive biomarkers are invaluable for the development of diagnostic and treatment strategies. In the present study, a differential co-expression network analysis was performed via meta-analysis of three transcriptome datasets of serous ovarian adenocarcinoma to identify novel candidate biomarker signatures, i.e. genes and miRNAs. We identified 439 common differentially expressed genes (DEGs), and reconstructed differential co-expression networks using common DEGs and considering two conditions, i.e. healthy ovarian surface epithelia samples and serous ovarian adenocarcinoma epithelia samples. The modular analyses of the constructed networks indicated a co-expressed gene module consisting of 17 genes. A total of 11 biomarker candidates were determined through receiver operating characteristic (ROC) curves of gene expression of module genes, and miRNAs targeting these genes were identified. As a result, six genes (CDT1, CNIH4, CRLS1, LIMCH1, POC1A, and SNX13), and two miRNAs (mir-147a, and mir-103a-3p) were suggested as novel candidate prognostic biomarkers for ovarian cancer. Further experimental and clinical validation of the proposed biomarkers could help future development of potential diagnostic and therapeutic innovations in ovarian cancer.

Comprehensive analysis of clinical prognosis and biological significance of CNIH4 in cervical cancer

“…3,4 Multiple studies show that CNIH4 is expressed in many malignant tumors and participates in their development, invasion, and metastasis. [5][6][7][8] Therefore, CNIH4 may function as an oncogene. Mishra et al reported that TMED9 protein inhibits the enhancing effect of TMED3-WNT-TCF on colon cancer cell metastasis by promoting the CNIH4/TGF-α/GLI cascade.…”

“…It is located on the long arm of Chromosome 1, Region 4, Band 2, and sub‐band 3,4 . Multiple studies show that CNIH4 is expressed in many malignant tumors and participates in their development, invasion, and metastasis 5–8 . Therefore, CNIH4 may function as an oncogene.…”

Upregulation of POC1A in lung adenocarcinoma promotes tumour progression and predicts poor prognosis

“…suggests that POC1A may influence tumour progression and represent a potential therapeutic target for cancer 12 . Investigations by Ceyda Kasavi indicate that POC1A exhibits superior diagnostic capability for ovarian cancer and could serve as a candidate factor for diagnosis and treatment 13 . Yuma Wada et al.…”

Noncoding RNA-associated competing endogenous RNA networks in trastuzumab-induced cardiotoxicity

“…The co-expression network of ncRNAs refers to the network of non-protein-coding RNA molecules involved in the regulation of gene expression in cells, reflecting the interaction and regulatory relationship between these ncRNA molecules, and their expression levels also show a certain correlation. Differential co-expression networks have been widely used to discover gene modules and hub genes in various cancers, such as ovarian cancer [ 19 ], retinoblastoma [ 20 ], and cervical cancer [ 21 ].…”