Highly expressed genes in pancreatic ductal adenocarcinomas: a comprehensive characterization and comparison of the transcription profiles obtained from three major technologies.
Highly expressed genes in pancreatic ductal adenocarcinomas: a comprehensive characterization and comparison of the transcription profiles obtained from three major technologies.
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发表时间：
2003-12
期刊：
影响因子：
11.2
通讯作者：
C. Iacobuzio-Donahue;R. Ashfaq;A. Maitra;N. Adsay;G. Shen-Ong;K. Berg;M. Hollingsworth;J. Cameron;C. Yeo;S. Kern;M. Goggins;R. Hruban
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作者：
C. Iacobuzio-Donahue;R. Ashfaq;A. Maitra;N. Adsay;G. Shen-Ong;K. Berg;M. Hollingsworth;J. Cameron;C. Yeo;S. Kern;M. Goggins;R. Hruban
当使用基因表达谱来了解人类肿瘤时，人们经常面临一长串需要进一步分类成有意义数据的基因。我们对从胰腺癌中获得的基因表达谱进行了全面的评估和比较，以确定那些表达差异最大的基因，从而最有希望转化为临床有用的靶标。从50个正常胰腺或十二指肠粘膜组织样本、7个慢性胰腺炎样本和39个胰腺癌组织或癌细胞样本中制备cDNA，并将其杂交到完整的Affymetrix Human Genome U133 GeneChip（阵列为U133A和U133B），同时分析45,000个片段，对应3.3万个已知基因和6000个表达序列标签。与非肿瘤组织相比，胰腺癌中的基因表达水平至少高出3倍。与非肿瘤组织相比，377个Affymetrix片段在胰腺癌标本中的表达水平为bb0或= 3倍，对应234个已知基因。通过对两种正常胰腺导管细胞（HX和H126）的基因表达文库（http://www.ncbi.nlm.nih.gov/SAGE/）的连续分析，排除了17个在正常胰腺导管上皮中高表达的基因（多于5个标签/文库）。在剩下的217个已知基因中，有75个已经被报道在胰腺癌中高表达，而剩下的142个基因是新发现的。我们使用主成分分析（PCA）来鉴定这217个被鉴定为胰腺癌组织或细胞系中表达差异最大和特异性最强的基因。PCA鉴定的差异表达最多的基因有间皮素（Mesothelin）、Muc4、Muc5A/C、Kallikrein 10、转谷氨酰胺酶2、fastin、TMPRSS3和stratifin。PCA鉴定出的这些基因的差异表达表明，它们是新的治疗靶点、肿瘤标志物或筛选胰腺癌样本以获取肿瘤分类或潜在治疗反应信息的更有吸引力的靶点之一。我们的发现还与先前报道的其他胰腺癌全基因表达研究中高表达基因的发现进行了详细比较。我们发现基因表达的强劲变化通常由多个基因表达平台确定。40个基因通过多种方法（U133寡核苷酸序列、cDNA序列或基因表达序列分析）鉴定，其中6个基因通过三种方法均鉴定。我们的研究结果确定了一组在胰腺癌中高表达的新基因，验证了先前报道的基因的差异表达，并为那些差异表达最多的基因转化为临床有用的靶标提供了额外的支持。
When using gene expression profiling to understand human tumors, one is often confronted with long lists of genes that need to be further categorized into meaningful data. We performed a comprehensive evaluation and comparison of gene expression profiles obtained from pancreatic cancers to determine those genes most differentially expressed and thus with the most promise for translation into clinically useful targets. cDNA was prepared from 50 samples of normal pancreas or duodenal mucosal tissues, 7 samples of chronic pancreatitis, and 39 samples of pancreas cancer tissues or cancer cell lines and hybridized to the complete Affymetrix Human Genome U133 GeneChip set (arrays U133A and U133B) for simultaneous analysis of 45,000 fragments corresponding to 33,000 known genes and 6,000 expressed sequence tags. Genes expressed at levels at least 3-fold greater in the pancreatic cancers as compared with nonneoplastic tissues were identified. Three hundred seventy-seven Affymetrix fragments were identified as having > or = 3-fold expression levels in pancreas cancer specimens as compared with nonneoplastic tissues, corresponding to 234 known genes. Serial analysis of gene expression libraries (http://www.ncbi.nlm.nih.gov/SAGE/) of two normal pancreatic ductal cell cultures (HX and H126) were used to exclude 17 genes with high expression levels in the normal duct epithelium (more than five tags/library). Of the remaining 217 known genes, 75 have been previously reported as highly expressed in pancreatic cancers, while the remaining 142 genes are novel. We used principal components analysis (PCA) to identify the genes among these 217 identified as the most differentially expressed and specific to pancreatic cancer tissues or cell lines. Among the most differentially expressed genes identified by PCA were Mesothelin, Muc4, Muc5A/C, Kallikrein 10, Transglutaminase 2, Fascin, TMPRSS3 and stratifin. The differential expression identified by PCA for these genes indicates they are among the more attractive targets for novel therapeutic targets, tumor markers, or as a means of screening pancreatic cancer samples for information regarding tumor classification or potential therapeutic responses. Our findings were also compared in detail to the previously reported findings of highly expressed genes in other studies of global gene expression in pancreatic cancers. We found that robust changes in gene expression were most often identified by more than one gene expression platform. Forty genes were identified by more than one method (U133 oligonucleotide arrays, cDNA arrays or serial analysis of gene expression), and 6 of these genes were identified by all three methods. Our findings identify a novel set of genes as highly expressed in pancreatic cancer, validate the differential expression of previously reported genes, and provide additional support for those genes most differentially expressed to be translated into clinically useful targets.