RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma.
RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma.
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RNA-Seq 分析生成全面的转录组景观并揭示肝细胞癌中复杂的转录模式。
DOI：
10.1371/journal.pone.0026168
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Chen ZN
中科院分区：
文献类型：
--
作者：
Huang Q;Lin B;Liu H;Ma X;Mo F;Yu W;Li L;Li H;Tian T;Wu D;Shen F;Xing J;Chen ZN
RNA-seq是在基因和外显子水平上全面表征整个转录组的强大工具，并具有识别新剪接变体的独特能力。迄今为止，HBV相关肝细胞癌（HCC）的RNA-seq分析尚未报道。在这项研究中，我们在Solexa/Illumina GAII平台上对来自HCC患者的10对匹配的癌症和非癌组织进行了转录组分析。平均而言，每个泳道上测序的样品获得约2160万个测序读数和1060万个比对读数，这能够鉴定每个样品的所有注释基因的> 50%。此外，我们确定了1,378个显著差异表达基因（DEG）和24338个差异表达外显子（DEE）。全面的功能分析表明，细胞生长相关的，代谢相关的和免疫相关的途径是最显着的富集DEGs，指出一个复杂的机制，肝癌的癌变。位置基因富集分析表明，DEG在染色体8q21.3 - 24.3富集最显著。最有趣的发现来自外显子水平的分析，其中我们表征了基因和外显子水平之间的三种主要表达变化模式，这意味着HCC中转录物特异性差异表达的复杂景观。最后，我们发现了一个新的高度上调的ATAD 2基因外显子-外显子连接在肝癌组织。总的来说，据我们所知，我们的研究代表了HBV相关HCC转录组的最全面表征，包括外显子水平表达变化和新的剪接变体，这说明了RNA-seq的力量，并为在全系统水平上理解HCC发病的分子机制提供了重要线索。
RNA-seq is a powerful tool for comprehensive characterization of whole transcriptome at both gene and exon levels and with a unique ability of identifying novel splicing variants. To date, RNA-seq analysis of HBV-related hepatocellular carcinoma (HCC) has not been reported. In this study, we performed transcriptome analyses for 10 matched pairs of cancer and non-cancerous tissues from HCC patients on Solexa/Illumina GAII platform. On average, about 21.6 million sequencing reads and 10.6 million aligned reads were obtained for samples sequenced on each lane, which was able to identify >50% of all the annotated genes for each sample. Furthermore, we identified 1,378 significantly differently expressed genes (DEGs) and 24, 338 differentially expressed exons (DEEs). Comprehensive function analyses indicated that cell growth-related, metabolism-related and immune-related pathways were most significantly enriched by DEGs, pointing to a complex mechanism for HCC carcinogenesis. Positional gene enrichment analysis showed that DEGs were most significantly enriched at chromosome 8q21.3–24.3. The most interesting findings were from the analysis at exon levels where we characterized three major patterns of expression changes between gene and exon levels, implying a much complex landscape of transcript-specific differential expressions in HCC. Finally, we identified a novel highly up-regulated exon-exon junction in ATAD2 gene in HCC tissues. Overall, to our best knowledge, our study represents the most comprehensive characterization of HBV-related HCC transcriptome including exon level expression changes and novel splicing variants, which illustrated the power of RNA-seq and provided important clues for understanding the molecular mechanisms of HCC pathogenesis at system-wide levels.