Comprehensive analysis of long non-coding RNA expression profiles in hepatitis B virus-related hepatocellular carcinoma

Abstract

Hepatocellular carcinoma (HCC) is one of the most common kinds of malignancies and is closely correlated with hepatitis B virus (HBV) infection. Recent evidence has proved that long non-coding RNAs (lncRNAs) are implicated in development and progression of cancer. However, the contributions of lncRNAs to HBV-related HCC remain largely unknown. Here, we comprehensively investigated lncRNA expression profiles in HBV-related HCC by annotating and analyzing microarray datasets. By analyzing 42 HCC tissue samples with different etiology (HBV-related, alcohol-related, and primary HCC) and 15 normal liver tissues, we identified 182 lncRNAs that were specifically differentially expressed in HBV-related HCC, namely HBV-related HCC specific lncRNAs(HH-lncRNAs). Using an online function annotation tool, we found these HH-lncRNAs were associated many oncogenes and immunity related biological processes. 6 candidate HH-lncRNAs were selected and further validated by quantitative real-time PCR analysis in a cohort of HCC tissue samples. Function of a candidate HH-lncRNAs, BAIAP2-AS1, was further predicted by co-expression network and gene set enrichment analysis. These findings provide insights into HH-lncRNAs and offer resource for further search of biomarkers and therapeutic targets of HBV-related HCC.

Transcriptomic profiling of long non-coding RNAs in hepatitis B virus-related hepatocellular carcinoma

“…We compared the differentially expressed mRNA and lncRNA with previous studies. For example, BAIAP2-AS1 [ 24 ], THBS4 [ 25 ] are also over-expressed in our samples, which supports the reliability of our study. Although the difference of BAIAP2-AS1expression did not reach statistical significance, which may be due to the small number of samples analyzed.…”

“…Pan et al and Yu et al analyzed the lncRNA expression profiles between HBV-related HCC tissues and corresponding normal liver tissues using microarrays without characterizing the function of a specific lncRNA, respectively [ 22 , 23 ]. Gong et al investigated lncRNA expression profiles in HBV-related HCC by annotating and analyzing microarray datasets and identified 182 lncRNAs that were specifically differentially expressed in HBV-related HCC [ 24 ]. A recent study reported the expression profile on lncRNA among 5 male HBV-induced HCC cases by using microarray analysis [ 25 ].…”

Porcine endemic diarrhea virus infection regulates long noncoding RNA expression

“…Due to the lack of translated proteins, lncRNAs were considered "transcription noise" or "junk RNA". However, lncRNAs have already been shown to be a key factor in the regulation of gene expression, especially in cancer research (Gong et al, 2016;Huang et al, 2016;Jiang et al, 2016;Zhang et al, 2015). Recent studies demonstrated that viral infection can alter host lncRNA expression profile.…”

Long non-coding RNA HOTTIP promotes hepatocellular carcinoma tumorigenesis and development: A comprehensive investigation based on bioinformatics, qRT-PCR and meta-analysis of 393 cases

“…Hepatocellular carcinoma (HCC) is known as the most common liver malignancy worldwide, with extremely high incidence and mortality rate ( 1 – 5 ). In China, HCC frequently occurs owing to chronic infection of hepatitis B virus (HBV) ( 6 – 9 ). Other conditions, such as alcoholic hepatitis, non-alcoholic fatty liver disease, hemochromatosis and diabetes, also contribute to the development of HCC ( 10 – 12 ).…”