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ceRNA Network and WGCNA Analyses of Differentially Expressed Genes in Cervical Cancer Tissues for Association with Survival of Patients

  • General Gynecology: Original Article
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Abstract

The study aims to search and identify differentially expressed genes (DEGs) in cervical cancer tissues as novel biomarkers to predict cervical cancer prognosis. The Cancer Genome Atlas (TCGA) data on gene expression profiles in cervical cancer were downloaded and analyzed using R software to identify DEGs in cervical cancer tissues. miRNAs targeted by differentially expressed long non-coding RNAs (DElncRNAs) and mRNAs targeted by microRNAs (miRNAs) were identified using the online miRcode, miRTarBase, TargetScan, and miRDB tools. The ceRNA network and lncRNA expression modules in cervical cancer tissues were constructed using weighted gene co-expression network analysis (WGCNA) and analyzed bioinformatically. The Kaplan–Meier analysis was performed to confirm these DEGs as prognostic markers. Immunohistochemical (IHC) analysis was used to verify expression of the hub genes in 10 paired cervical cancer and normal tissues. A total of 1914 DEmRNAs, 210 DElncRNAs, and 67 DEmiRNAs were identified in cervical cancer samples. There were 39 lncRNAs, 19 miRNAs, and 87 mRNAs involved in the ceRNA network and 25 DElncRNAs, three DEmiRNAs, and four mRNAs involved in the ceRNA sub-network. CACNA1C-AS1 was associated with the yellow and blue modules in the ceRNA sub-network, and LIFR-AS1 was associated with the blue module. The DEmRNAs were involved in cancer-related pathways, and three hub genes (i.e., E2F1, CCNB1, and CCNE1) were highly expressed in cervical squamous cell carcinoma and adenocarcinoma tissues and associated with the prognosis of patients. The ceRNA network and WGCNA analyses are useful to identify novel DEGs that can serve as prognostic markers in cervical cancer. The DEGs will be validated in future studies.

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Funding

This study was supported in part by grants from the National Natural Science Foundation of China (#81660434) and the Natural Science Foundation of Guangxi (#2018GXNSFAA050098).

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Authors and Affiliations

  1. Department of Gynecology, Nanning Second People’s Hospital, Nanning, 530021, Guangxi, China

    Yongjin Luo

  2. Jinan University, Guangzhou, 510632, Guangdong, China

    Zhen Liu

  3. Department of Gynecology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, Guangxi, China

    Zhen Liu & Xiaoxia Hu

Authors
  1. Yongjin Luo
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  2. Zhen Liu
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  3. Xiaoxia Hu
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Contributions

Xiaoxia Hu and Yongjin Luo conceived and designed the experiments; Zhen Liu and Xiaoxia Hu prepared the manuscript; Yongjin Luo analyzed the data.

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Correspondence to Xiaoxia Hu.

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Luo, Y., Liu, Z. & Hu, X. ceRNA Network and WGCNA Analyses of Differentially Expressed Genes in Cervical Cancer Tissues for Association with Survival of Patients. Reprod. Sci. (2024). https://doi.org/10.1007/s43032-024-01477-z

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