Genome-Wide Analysis of Long Noncoding RNA (lncRNA) Expression in Hepatoblastoma Tissues

Long noncoding RNAs (lncRNAs) have crucial roles in cancer biology. We performed a genome-wide analysis of lncRNA expression in hepatoblastoma tissues to identify novel targets for further study of hepatoblastoma. Hepatoblastoma and normal liver tissue samples were obtained from hepatoblastoma patients. The genome-wide analysis of lncRNA expression in these tissues was performed using a 4×180 K lncRNA microarray and Sureprint G3 Human lncRNA Chips. Quantitative RT-PCR (qRT-PCR) was performed to confirm these results. The differential expressions of lncRNAs and mRNAs were identified through fold-change filtering. Gene Ontology (GO) and pathway analyses were performed using the standard enrichment computation method. Associations between lncRNAs and adjacent protein-coding genes were determined through complex transcriptional loci analysis. We found that 2736 lncRNAs were differentially expressed in hepatoblastoma tissues. Among these, 1757 lncRNAs were upregulated more than two-fold relative to normal tissues and 979 lncRNAs were downregulated. Moreover, in hepatoblastoma there were 420 matched lncRNA-mRNA pairs for 120 differentially expressed lncRNAs, and 167 differentially expressed mRNAs. The co-expression network analysis predicted 252 network nodes and 420 connections between 120 lncRNAs and 132 coding genes. Within this co-expression network, 369 pairs were positive, and 51 pairs were negative. Lastly, qRT-PCR data verified six upregulated and downregulated lncRNAs in hepatoblastoma, plus endothelial cell-specific molecule 1 (ESM1) mRNA. Our results demonstrated that expression of these aberrant lncRNAs could respond to hepatoblastoma development. Further study of these lncRNAs could provide useful insight into hepatoblastoma biology.长链非编码RNA（long noncoding RNAs，lncRNAs）在癌症生物学领域发挥关键调控作用。本研究针对肝母细胞瘤组织中的长链非编码RNA表达开展全基因组分析，以期筛选出可用于肝母细胞瘤后续研究的新型潜在靶点。本研究从肝母细胞瘤患者群体中采集了肝母细胞瘤组织与配对正常肝组织样本，采用4×180K长链非编码RNA微阵列与Sureprint G3 Human lncRNA Chips芯片，对上述样本中的长链非编码RNA表达谱进行全基因组检测。通过定量逆转录聚合酶链反应（quantitative reverse transcription polymerase chain reaction，qRT-PCR）对芯片分析结果进行实验验证。通过倍数变化过滤法筛选得到差异表达的长链非编码RNA与信使RNA（messenger RNA，mRNA），并采用标准富集分析计算方法开展基因本体论（Gene Ontology，GO）功能富集与通路富集分析。通过复杂转录位点分析，明确长链非编码RNA与其邻近蛋白编码基因之间的表达关联。本研究结果显示，肝母细胞瘤组织中共鉴定出2736个差异表达的长链非编码RNA：其中1757个长链非编码RNA的表达水平较正常组织上调超过2倍，剩余979个则呈现表达下调。此外，在肝母细胞瘤样本中，针对120个差异表达的长链非编码RNA与167个差异表达的信使RNA，共获得420个匹配的长链非编码RNA-信使RNA调控对。共表达网络分析预测得到252个网络节点，以及120个长链非编码RNA与132个蛋白编码基因之间的420条连接边；其中369对连接为正相关，51对为负相关。最后，通过qRT-PCR实验验证了肝母细胞瘤中6个差异表达的长链非编码RNA，以及内皮细胞特异性分子1（endothelial cell-specific molecule 1，ESM1）信使RNA的表达异常。本研究证实，这些异常表达的长链非编码RNA可能参与肝母细胞瘤的发生发展进程；对上述长链非编码RNA开展进一步研究，可为阐明肝母细胞瘤的生物学机制提供全新的研究视角与理论参考。