Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression
Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression
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DOI：
10.1016/j.cels.2017.11.010
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发表时间：
2018-01-24
期刊：
影响因子：
9.3
通讯作者：
Klingmueller, Ursula
中科院分区：
文献类型：
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作者：
Lucarelli, Philippe;Schilling, Marcel;Klingmueller, Ursula
在用转化生长因子β（TGF-β）刺激细胞后，Smad蛋白形成三聚体复合物并激活广谱靶基因。目前还没有解决哪些可能的Smad复合物是在细胞环境中形成的，以及这些复合物如何促进基因表达。通过结合定量质谱与计算选择策略，我们预测并提供实验证据的三个最相关的Smad复合物在小鼠肝癌细胞系Hepa 1 -6。利用动态途径建模，我们指定的贡献，每个Smad复合物的代表性Smad靶基因的表达，并显示这些贡献是保守的人肝癌细胞系和原代肝细胞。我们预测，基于患者样本的基因表达数据，增加量的Smad 2/3/4蛋白和Smad 2磷酸化作为肝细胞癌的标志，并通过实验验证了这一预测。我们的研究结果表明，建模方法可以解开复杂的转录因子复合物的形成及其对基因表达的影响。
Upon stimulation of cells with transforming growth factor beta (TGF-beta), Smad proteins form trimeric complexes and activate a broad spectrum of target genes. It remains unresolved which of the possible Smad complexes are formed in cellular contexts and how these contribute to gene expression. By combining quantitative mass spectrometry with a computational selection strategy, we predict and provide experimental evidence for the three most relevant Smad complexes in the mouse hepatoma cell line Hepa1-6. Utilizing dynamic pathway modeling, we specify the contribution of each Smad complex to the expression of representative Smad target genes, and show that these contributions are conserved in human hepatoma cell lines and primary hepatocytes. We predict, based on gene expression data of patient samples, increased amounts of Smad2/3/4 proteins and Smad2 phosphorylation as hallmarks of hepatocellular carcinoma and experimentally verify this prediction. Our findings demonstrate that modeling approaches can disentangle the complexity of transcription factor complex formation and its impact on gene expression.