Transcriptomic profiling of long non-coding RNAs in non-virus associated hepatocellular carcinoma
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ORIGINAL PAPER
Transcriptomic profiling of long non-coding RNAs in non-virus associated hepatocellular carcinoma Lu Liu1 Chen He2 Haosheng Liu3 Ganlu Wang1 Zhiwu Lv1 Yong Ni4 Lisha Mou5 Yongqiang Zhan4 Jintao Liu1 ●
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Received: 14 May 2019 / Accepted: 29 April 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
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’ RNAsequencing 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. Keywords Hepatocellular carcinoma Long non-coding RNAs Non-viral factors Molecular mechanism ●
Introduction Hepatocellular carcinoma (HCC) is the most common form of liver cancer, and has high morbidity and mortality rate,
Supplementary information The online version of this article (https:// doi.org/10.1007/s12013-020-00915-4) contains supplementary material, which is available to authorized users. * Yongqiang Zhan [email protected] * Jintao Liu [email protected] 1
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Department of Gastroenterology, Center For Digestive Diseases, People’s Hospital of Baoan District, The 8th People’s Hospital of Shenzhen, Shenzhen 518101 Guangdong, China Department of Ophthalmology, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035 Guangdong, China
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particularly in Asia and Africa [1, 2]. HCC typically arises in the setting of chronic liver diseases at a rate dependent on complex interplay between host, disease and environmental factors. Chronic infections with hepatitis B virus (HBV), hepatitis C virus (HCV) and hepatitis D virus (HDV) account for over 80% of HCC cases. The number of viral hepatitis-related HCC case
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