Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, Taipei 106, Taiwan.
Mol Cell Proteomics. 2013 May;12(5):1335-49. doi: 10.1074/mcp.O112.020404. Epub 2013 Feb 8.
Deciphering the network of signaling pathways in cancer via protein-protein interactions (PPIs) at the cellular level is a promising approach but remains incomplete. We used an in situ proximity ligation assay to identify and quantify 67 endogenous PPIs among 21 interlinked pathways in two hepatocellular carcinoma (HCC) cells, Huh7 (minimally migratory cells) and Mahlavu (highly migratory cells). We then applied a differential network biology analysis and determined that the novel interaction, CRKL-FLT1, has a high centrality ranking, and the expression of this interaction is strongly correlated with the migratory ability of HCC and other cancer cell lines. Knockdown of CRKL and FLT1 in HCC cells leads to a decrease in cell migration via ERK signaling and the epithelial-mesenchymal transition process. Our immunohistochemical analysis shows high expression levels of the CRKL and CRKL-FLT1 pair that strongly correlate with reduced disease-free and overall survival in HCC patient samples, and a multivariate analysis further established CRKL and the CRKL-FLT1 as novel prognosis markers. This study demonstrated that functional exploration of a disease network with interlinked pathways via PPIs can be used to discover novel biomarkers.
在细胞水平上通过蛋白质-蛋白质相互作用（PPIs）解析癌症信号通路网络是一种很有前途的方法，但仍不完整。我们使用原位邻近连接测定法在两种肝癌（HCC）细胞，Huh7（最小迁移细胞）和Mahlavu（高迁移细胞）中的 21 个相互关联的通路中鉴定和量化了 67 种内源性 PPIs。然后，我们应用差异网络生物学分析，确定了新的相互作用 CRKL-FLT1 具有较高的中心度排名，并且这种相互作用的表达与 HCC 和其他癌细胞系的迁移能力强烈相关。在 HCC 细胞中敲低 CRKL 和 FLT1 会通过 ERK 信号和上皮-间充质转化过程导致细胞迁移减少。我们的免疫组织化学分析显示，CRKL 和 CRKL-FLT1 对的表达水平较高，与 HCC 患者样本中无病生存率和总生存率降低强烈相关，多变量分析进一步确立了 CRKL 和 CRKL-FLT1 为新型预后标志物。这项研究表明，通过 PPIs 对相互关联的通路进行疾病网络的功能探索可用于发现新的生物标志物。
