Integrated analysis of long noncoding RNA expression profiles in lymph node metastasis of hepatocellular carcinoma

Abstract

BackgroundHepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and metastasis of HCC is the leading cause of poor prognosis. Among all the extrahepatic metastases, lymph node metastasis (LNM) is common, second only to lung metastasis. However, the pathogenesis of HCC LNM remains largely unknown. MethodsMicroarray was performed to investigate the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in serum samples from HCC LNM patients (N = 4) and HCC non-LNM controls (N = 5). Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was applied to validate the expression levels of randomly selected differential lncRNAs and mRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were employed to explore the potential functions of differentially expressed mRNAs. Co-expression networks were further constructed to elucidate the interactions of the differential genes and to speculate on the potential functions of the dominant lncRNAs. In this research, we attempted to illuminate the correlations between lncRNA and HCC LNM. ResultsCompared with the non-LNM group, a total of 234 lncRNAs and 58 mRNAs were obtained as significantly dysregulated genes in LNM group (p < 0.05, fold change ≥ 2). Functional enrichment analyses showed that upregulated mRNAs are mostly enriched for glucose-6-phosphate dehydrogenase activity, biotin binding and AP-3 adaptor complex, while the downregulated mRNAs are enriched for macrophage colony-stimulating factor receptor binding, succinate-CoA ligase activity and palmitoyltransferase activity. In addition, coexpression network revealed that the dominant lncRNAs are potential participants of protein metabolic process, integral component of membrane, RNA binding, Golgi apparatus, as well as focal adhesion pathway. ConclusionThis study first revealed the expression profiles and potential functions of dysregulated lncRNAs and mRNAs in HCC LNM, which may provide novel clues for further studies on HCC LNM.