Gene Expression Profiling Reveals a Massive, Aneuploidy-Dependent Transcriptional Deregulation and Distinct Differences between Lymph Node–Negative and Lymph Node–Positive Colon Carcinomas

To characterize patterns of global transcriptional deregulation in primary colon carcinomas, we did gene expression profiling of 73 tumors [Unio Internationale Contra Cancrum stage II (n = 33) and stage III (n = 40)] using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared with those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P < 1e-7). A significant proportion of these genes mapped to chromosome 20 (P = 0.01). Seventeen genes had a >5-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node-negative and lymph node-positive tumors (P < 0.001), the functional annotation of which revealed a preponderance of genes that play a role in cellular immune response and surveillance. The microarray-derived gene expression levels of 20 deregulated genes were validated using quantitative real-time reverse transcription-PCR in >40 tumor and normal mucosa samples with good concor- dance between the techniques. Finally, we established a relationship between specific genomic imbalances, which were mapped for 32 of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a signif- icant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/B-catenin signaling cascade, suggesting similar pathogenic pathways. [Cancer Res 2007;67(1):41-56] Samples of tumor and/or mucosa from a total of 65 colon cancer patients, i.e. 103 arrays

为阐明原发性结肠癌的全局转录失调模式，我们采用寡核苷酸微阵列（oligonucleotide microarrays）对73例肿瘤样本[国际抗癌联盟（Unio Internationale Contra Cancrum）II期（n=33）及III期（n=40）]开展基因表达谱分析。其中30例肿瘤的表达谱与配对正常黏膜样本进行了对比。我们鉴定出1950个在肿瘤与黏膜样本间存在极显著转录失调的基因（P < 1e-7），其中相当比例的基因定位于20号染色体（P = 0.01）。17个基因在正常结肠黏膜与癌组织间的平均表达差异超过5倍，包括MYC及推定癌基因HMGA1的上调。
此外，我们还鉴定出68个在淋巴结阴性与淋巴结阳性肿瘤间存在显著差异表达的基因（P < 0.001），对其进行功能注释后发现，这类基因大多参与细胞免疫应答与免疫监视过程。我们采用实时定量反转录聚合酶链反应（quantitative real-time reverse transcription-PCR）验证了20个失调基因的微阵列表达结果，在40余例肿瘤及正常黏膜样本中验证时，两种技术的结果一致性良好。
最终，我们建立了特定基因组失衡与全局转录活性改变之间的关联；其中32例分析过的结肠癌样本的基因组失衡通过比较基因组杂交（comparative genomic hybridization, CGH）技术完成定位。此前我们曾针对原发性直肠癌开展过类似分析。对结肠癌与直肠癌的系统性对比显示，二者在基因组失衡与转录失调方面存在显著重叠，包括Wnt/β-连环蛋白（Wnt/β-catenin）信号级联反应的激活，提示二者具有相似的致病通路。[Cancer Res 2007;67(1):41-56]
本研究共纳入65名结肠癌患者的肿瘤和/或黏膜样本，共计103张微阵列芯片。