Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE.
Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE.
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DOI：
10.1186/1755-8794-2-5
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发表时间：
2009-01-26
影响因子：
2.7
通讯作者：
Jin W
中科院分区：
文献类型：
--
作者：
Dong H;Ge X;Shen Y;Chen L;Kong Y;Zhang H;Man X;Tang L;Yuan H;Wang H;Zhao G;Jin W
肝细胞癌是世界上最常见的癌症之一，也是中国的第二大癌症杀手。癌症的启动和恶变是癌症相关基因序列或表达水平的基因变化积累的结果。在全球范围内确定癌症的基因表达谱尤为重要。Sage和LongSAGE就是为此目的而开发的。我们在正常肝脏和肝癌标本以及肝癌细胞系HepG2中进行了SAGE。同时，用LongSAGE同时对同一肝癌标本进行分析。对正常肝和肝细胞癌的差异表达基因进行了计算分析，并通过实时定量RT-PCR进行了进一步验证。对四个文库中的每一个都进行了大约50,000个标签的测序。对肝细胞癌技术副本的分析表明，剔除低丰度标签后，SAGE数据的重复性较高(R=0.97)。与正常肝组织的基因表达谱比较，发现224个与肝细胞的生物合成、细胞增殖、信号转导、细胞代谢和转运相关的基因在肝细胞癌中有差异表达。用实时定量RT-PCR方法验证SAGE数据中部分转录本的高表达。有趣的是，位于染色体7q21上的一对邻近基因--肌聚糖ε(Sgce)和父系表达基因(Peg10)在肝细胞癌中表现出相似的增强表达模式，提示这两个基因可能具有共同的去调控机制。我们的研究不受注释数据库的限制，在全基因组水平上描绘了肝癌的表达谱，并提供了可能与肝癌相关的新的候选基因。
Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and the second cancer killer in China. The initiation and malignant transformation of cancer result from accumulation of genetic changes in the sequences or expression level of cancer-related genes. It is of particular importance to determine gene expression profiles of cancers on a global scale. SAGE and LongSAGE have been developed for this purpose. We performed SAGE in normal liver and HCC samples as well as the liver cancer cell line HepG2. Meanwhile, the same HCC sample was simultaneously analyzed using LongSAGE. Computational analysis was carried out to identify differentially expressed genes between normal liver and HCC which were further validated by real-time quantitative RT-PCR. Approximately 50,000 tags were sequenced for each of the four libraries. Analysis of the technical replicates of HCC indicated that excluding the low abundance tags, the reproducibility of SAGE data is high (R = 0.97). Compared with the gene expression profile of normal liver, 224 genes related to biosynthesis, cell proliferation, signal transduction, cellular metabolism and transport were identified to be differentially expressed in HCC. Overexpression of some transcripts selected from SAGE data was validated by real-time quantitative RT-PCR. Interestingly, sarcoglycan-ε (SGCE) and paternally expressed gene (PEG10) which is a pair of close neighboring genes on chromosome 7q21, showed similar enhanced expression patterns in HCC, implicating that a common mechanism of deregulation may be shared by these two genes. Our study depicted the expression profile of HCC on a genome-wide scale without the restriction of annotation databases, and provided novel candidate genes that might be related to HCC.
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影响因子：
4.6
作者：
Romualdi, C;Bortoluzzi, S;Danieli, GA
通讯作者：
Danieli, GA
DOI：
10.1007/s00432-006-0094-8
发表时间：
2006-07-01
影响因子：
3.6
作者：
Iizuka, Norio;Tsunedomi, Ryouichi;Oka, Masaaki
通讯作者：
Oka, Masaaki
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3.3
作者：
Chen, X;Cheung, ST;Brown, PO
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Brown, PO
影响因子：
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作者：
Rashid, A;Wang, JS;Qian, GS;Lu, BX;Hamilton, SR;Groopman, JD
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Groopman, JD
影响因子：
46.9
作者：
Saha, S;Sparks, AB;Velculescu, VE
通讯作者：
Velculescu, VE