Molecular characterization of gastrointestinal cancer through serial analysis of gene expression and GICHIP and its diagnostic implication

基因表达序列分析(SAGE)是一种强大的技术，可以在不预先知道基因序列的情况下，以定量的方式对基因表达进行全基因组分析。我们对5个不同组织学和不同分期的胃癌标本进行了实验，建立了世界上最大的SAGE文库，共包含137,706个表达标签，其中包括唯一的38,903个标签(GEO登录号为GSE 545)。通过比较胃癌和正常胃粘膜的基因表达谱，结合定量RT-PCR，发现APOC1、CEACAM6和YF13H12在胃癌中经常过表达，FUS、CDH17、COL1A1、COL1A2和APOE与肿瘤的进展有关。我们挑选了在我们的胃癌文库中检测到的候选基因，但在各种正常组织的文库中没有检测到，特别是重要或关键的器官。通过定量RT-PCR检测这些基因在胃癌和正常组织中的表达，发现至少有8个基因在胃癌中特异表达。我们已经开发了定制的寡核苷酸微阵列，称为Ex-STOMACHIP，包含475个cDNA，包括我们的SAGE分析确定的特定基因，与癌症发生和进展相关的已知基因，以及化疗敏感性的标记基因。通过检测20例胃癌的基因表达谱，我们确定了可以区分肿瘤分期和组织学的基因簇。对于肿瘤相关基因的遗传多态性与胃癌的关系，我们对大约500名受试者进行了病例对照和病例-病例研究，发现HER2和MMP1的SNPs与胃癌有显著的相关性。CLDN18基因5‘端非编码区SNP(G/A)是一种新发现的胃癌下调基因，与胃癌发病风险相关(OR-5.17，95%CI：2.01-13.3)。

Serial analysis of gene expression (SAGE) is a powerful technique to allow genome-wide analysis of gene expression in a quantitative manner without a prior knowledge of the sequence of the gene. We performed on 5 samples of gastric cancer with different histology and stages, and created the largest SAGE libraries in the world, containing a total of 137,706 expressed tags including unique 38,903 tags (GEO accession number GSE 545). By comparing gene expression profiles between gastric cancer and normal gastric mucosa in combination with quantitative RT-PCR,APOC1,CEACAM6, and YF13H12 were found to be frequently overexpressed in gastric cancer, and FUS,CDH17,COL1A1,COL1A2, and APOE were associated with tumor progression. We picked up candidate genes that were detected in our gastric cancer libraries but not in the libraries from various normal tissues, especially important or crucial organs. The expression of these genes was examined in gastric cancers and normal human tissues by quantitative RT-PCR and found that at least 8 genes were specifically expressed in gastric cancers. We have developed custom-made oligo-DNA microarray, called Ex-STOMACHIP, with 475 cDNAs including specific genes identified by our SAGE analysis, known genes related to development and progression of cancer, and marker genes for chemosensitivity. By examining gene expression profiles of 20 gastric cancers, we identified gene clusters which can differentiate tumor stage and histology. Regarding the relation between genetic polymorphism of tumor-related genes and gastric cancer, we have performed case-control and case-case studied using about 500 subjects, and found a significant association with SNPs of HER2 and MMP-1. SNP (G/A) in 5'UTR of the CLDN18, newly identified as down-regulated gene in gastric cancer, was found to affect gastric cancer risk (OR-5.17,95%CI:2.01-13.3).