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Transcriptomic profiling of long non-coding RNAs in non-virus associated hepatocellular carcinoma

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Abstract

Due to falling prevalence of viral hepatitis (VH), obesity, alcoholism and related liver diseases have become increasingly frequent and important as causes of hepatocellular carcinoma (HCC). However, mechanisms underlying hepatocarcinogenesis and tumor progression in VH-negative HCC remain poorly understood. Long non-coding RNAs (lncRNAs) have been implicated in pathogenesis of human diseases, including HCC. Here, by analyzing 20 clinical samples’ RNA-sequencing data generated from 8 VH-negative and 2 VH-positive HCC patients, we have identified and characterized 1,514 candidate lncRNAs. For differentially expressed genes (DEGs) between tumor tissues and adjacent non-tumor tissues (P < 0.05, |FC| > 2), the upregulated genes were mainly involved in the cell proliferation, and the downregulated genes mediated the metabolic processes and responses to oxidative stress, inflammation and toxic substances. Furthermore, the lncRNA-mRNA co-expression network was constructed, by which two genetic aberrations with high frequency in HCC, SPATA46 and TMEM78, were identified. In addition, we identified 16 DEGs between tumor issues from VH-negative and VH-positive HCC patients with aim to explore gene expression differences that could be involved in the pathogenesis of HCC with varying etiology. In conclusion, we performed the comprehensive analysis of lncRNA and mRNA expression profiles, which could provide valuable insights into the underlying genetic alteration in non-virus associated HCC.

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Acknowledgements

We gratefully thank Lijun Wang for PCR analysis. This study was supported by Shenzhen Foundation of Science and Technology (JCYJ20180305123929814, JCYJ20170307094549868 and JCYJ20160425103911638), Science and Technology Bureau of Baoan (2018JD124 and 2019JD031) and Funds for Young Scholar of Shenzhen Baoan People’s Hospital (2018A003).

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Authors and Affiliations

  1. Department of Gastroenterology, Center For Digestive Diseases, People’s Hospital of Baoan District, The 8th People’s Hospital of Shenzhen, Shenzhen, 518101, Guangdong, China

    Lu Liu, Ganlu Wang, Zhiwu Lv & Jintao Liu

  2. Department of Ophthalmology, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, Guangdong, China

    Chen He

  3. Department of Central Laboratory, People’s Hospital of Baoan District, The 8th People’s Hospital of Shenzhen, Shenzhen, 518101, Guangdong, China

    Haosheng Liu

  4. Hepatological Surgery Department, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, Guangdong, China

    Yong Ni & Yongqiang Zhan

  5. Shenzhen Xenotransplantation Medical Engineering Research and Development Center‚ Institute of Translational Medicine, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China

    Lisha Mou

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  1. Lu Liu
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Liu, L., He, C., Liu, H. et al. Transcriptomic profiling of long non-coding RNAs in non-virus associated hepatocellular carcinoma. Cell Biochem Biophys 78, 465–474 (2020). https://doi.org/10.1007/s12013-020-00915-4

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  • DOI: https://doi.org/10.1007/s12013-020-00915-4

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