Supplementary Material for: Differential Gene Expression Profiles of Metastases in Paired Primary and Metastatic Colorectal Carcinomas

Background and Methods: Despite the overwhelming clinical significance of metastases, the cellular and molecular mechanisms involved are largely unknown. In order to define significant differences between primary colon carcinomas and their metastases, we analyzed gene expression profiles of 12 sets of triple-paired tissues using 19 K human oligonucleotide microarrays. A total of 36 microarray experiments were analyzed by unsupervised two-way hierarchical clustering and multi-dimensional scaling (MDS). Results: Both methods completely distinguished normal mucosa from carcinoma, but failed to demonstrate a complete classification of primary and metastatic carcinomas. We found a separable tendency to be classified into the primary and metastatic colon carcinomas by MDS. In supervised hierarchical clustering, we identified 80 genes that were differentially expressed between paired primary and metastatic colon carcinomas. The 80 identified genes also successfully distinguished three validation sets of primary and lung-metastatic colon carcinomas. A specific set of genes was identified that distinguished the metastasis from the corresponding primary tumor in nearly half of the metastases analyzed. Conclusions: We suggest that a more accurate model of the metastatic potential is based on a global tumor expression pattern along with the appearance of distinct metastatic variants. This molecular profiling may be useful for the future study of colon cancer metastasis.

背景与方法：尽管转移瘤具有极高的临床意义，但其涉及的细胞与分子机制仍未完全阐明。为明确结直肠癌原发灶与其转移瘤之间的显著差异，本研究采用19K人类寡核苷酸微阵列芯片，对12组三重配对组织样本的基因表达谱展开分析。本研究对共计36项微阵列实验数据，通过无监督双向层次聚类与多维标度分析（Multi-dimensional Scaling, MDS）进行处理。结果：两种分析方法均可完全区分正常黏膜与癌组织，但均无法实现结直肠癌原发灶与转移灶的完全分类。通过MDS分析，我们发现结直肠癌原发灶与转移灶存在可区分的聚类趋势。在监督层次聚类分析中，我们鉴定出80个在配对结直肠癌原发灶与转移灶间差异表达的基因。该80个差异基因亦可有效区分3组验证集的结直肠癌原发灶与肺转移灶样本。本研究还鉴定出一组特异性基因，可在近半数纳入分析的转移灶样本中，实现转移瘤与其对应原发灶的有效区分。结论：本研究认为，更精准的转移潜能预测模型应基于全局肿瘤表达谱，并结合特异性转移变异亚型的出现特征。该分子特征谱可为未来结直肠癌转移的相关研究提供参考价值。