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Comprehensive Analysis of circRNA, lncRNA, miRNA and mRNA Expression Profiles and Their Competing Endogenous RNA Networks in Hepatitis B Virus-Related Hepatocellular Carcinoma

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Abstract

Pursuing knowledge about circular RNA (circRNA), long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) expression profiles and their competing endogenous RNA (ceRNA) networks in hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC) was the focus of this research. Expression patterns of circRNAs, lncRNAs, miRNAs, and mRNAs were searched for in relation to HBV-related HCC using whole-transcriptome sequencing. The expression levels of chosen circRNA, lncRNA, miRNA, and mRNA were analyzed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The potential connections and roles of ceRNA were deduced via bioinformatics research. The sum of 284 circRNAs, 2,927 lncRNAs, 693 miRNAs, and 5566 mRNAs were discovered to be expressed at considerably different levels in HBV-related HCC tissue and adjacent normal tissue. And the most significantly up- and down-regulated circRNAs, lncRNAs, miRNAs, and mRNAs were verified in HBV-related HCC by qRT-PCR. The circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA networks of HBV-related HCC were established, and the ceRNA regulatory networks revealed the gene expression mechanisms controlled by ncRNAs. Collectively, we revealed the contribution of various circRNA, lncRNA, miRNA, and mRNA expression profiles and identified their ceRNA regulatory networks in HBV-related HCC, providing a theoretical basis for further exploration.

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Funding

This work was supported by the National Natural Science Foundation of China (82060446), the Province Natural Science Foundation of Jiangxi Province (20212BAB206036), the Province Natural Science Foundation of Jiangxi Province (20232BAB216067), the Outstanding Young Scholars Fund Project of Jiangxi Natural Science Foundation (20212ACB216006), and the High-end Talents Project of Jiangxi “Double Thousand Plan” Science and Technology Innovation (jxsq2019201094).

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Authors and Affiliations

  1. Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China

    Shaoying Yan, Peng Fu, Huiming Li & Zikun Huang

  2. Nanchang Key Laboratory of Diagnosis of Infectious Diseases, Nanchang, Jiangxi, China

    Shaoying Yan & Zikun Huang

  3. Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China

    Renfeng Shan

  4. Department of Urology, The First Affiliated Hospital of Nanchang University, No.17, Yongwaizheng Street, Nanchang, 330006, Jiangxi, China

    Binbin Gong

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  1. Shaoying Yan
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Correspondence to Renfeng Shan or Binbin Gong.

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Yan, S., Fu, P., Li, H. et al. Comprehensive Analysis of circRNA, lncRNA, miRNA and mRNA Expression Profiles and Their Competing Endogenous RNA Networks in Hepatitis B Virus-Related Hepatocellular Carcinoma. Mol Biotechnol (2024). https://doi.org/10.1007/s12033-024-01056-2

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