The Long Noncoding RNA Expression Profile of Hepatocellular Carcinoma Identified by Microarray Analysis

Abstract

BackgroundThousands of long noncoding RNAs (lncRNAs) have been reported in mammalian genomes. These RNAs represent an important subset of pervasive genes involved in a broad range of biological functions. Aberrant expression of lncRNAs is associated with many types of cancers. Here, in order to explore the potential lncRNAs involved in hepatocellular carcinoma (HCC) oncogenesis, we performed lncRNA gene expression profile analysis in 3 pairs of human HCC and adjacent non-tumor (NT) tissues by microarray.MethodologyDifferentially expressed lncRNAs and mRNAs were detected by human lncRNA microarray containing 33,045 lncRNAs and 30,215 coding transcripts. Bioinformatic analyses (gene ontology, pathway and network analysis) were applied for further study of these differentially expressed mRNAs. By qRT-PCR analysis in nineteen pairs of HCC and adjacent normal tissues, we found that eight lncRNAs were aberrantly expressed in HCC compared with adjacent NT tissues, which is consistent with microarray data.ConclusionsWe identified 214 lncRNAs and 338 mRNAs abnormally expressed in all three HCC tissues (Fold Change ≥2.0, P<0.05 and FDR <0.05) with the genome-wide lncRNAs and mRNAs expression profile analysis. The lncRNA-mRNA co-expression network was constructed, which may be used for predicting target genes of lncRNAs. Furthermore, we demonstrated for the first time that BC017743, ENST00000395084, NR_026591, NR_015378 and NR_024284 were up-regulated, whereas NR_027151, AK056988 and uc003yqb.1 were down-regulated in nineteen pairs of HCC samples compared with adjacent NT samples. Expression of seven lncRNAs was significantly correlated to their nearby coding genes. In conclusion, our results indicated that the lncRNA expression profile in HCC was significantly changed, and we identified a series of new hepatocarcinoma associated lncRNAs. These results provide important insights about the lncRNAs in HCC pathogenesis.

Identification of novel long non-coding RNAs deregulated in hepatocellular carcinoma using RNA-sequencing

“…Finally, we observed different co-expression patterns in different genomic contexts, suggesting that while a common pattern of co-expression could not be revealed for lncRNAs, this seems to be highly loci-dependent. Contrary to previous studies aimed at the analysis of lncRNAs in HCC [28, 29], which were based on microarray platforms, we performed RNA-seq, which is not biased by probe selection. Moreover, these two previous studies analysed primarily HBV-associated HCCs, while our series contained mostly patients with HCV- or alcohol-associated HCCs.…”

“…The findings showed deregulation of hundreds of lncRNAs. One study was based on the analysis of five cases of HBV-associated HCC and the second one on the analysis of 3 cases [28, 29]. …”

Progress and Prospects of Long Noncoding RNAs (lncRNAs) in Hepatocellular Carcinoma

“…Generally, lncRNAs can influence almost every cellular behavior of the central dogma, from transcription to translation by diverse mechanisms including epigenetic alterations, lncRNA-miRNA/DNA interactions, protein-lncRNA interactions and genetic variations [44,[58][59][60][61] (Fig. 2).…”

Expression and Clinical Significance of the Novel Long Noncoding RNA ZNF674-AS1 in Human Hepatocellular Carcinoma

“…ZNF674 antisense RNA 1 (ZNF674-AS1, NR_015378), located at Xp11.23, is a novel lncRNA that was identified from a lncRNA microarray analysis [10]. Zhu et al demonstrated for the first time that ZNF674-AS1 was upregulated in 19 pairs of HCC samples compared with adjacent tumor samples [10].…”

“…Further, lncRNAs regulate gene expression at the epigenetic, transcriptional, posttranscriptional, and translational levels during cancer development [13, 18]. ZNF674 antisense RNA 1 (ZNF674-AS1, NR_015378) is an lncRNA that was first identified from the lncRNA expression profile of HCC identified by microarray analysis [10]. However, its association with HCC is unclear.…”