Core B: Proteomics Core.

项目摘要 许多致命的癌症表现出由细胞周期蛋白D、CDK4或CDK6的形式驱动的路径突变，这些细胞周期蛋白D、CDK4或CDK6是它们的抑制因子 蛋白质、RB视网膜母细胞瘤蛋白和E2F转录因子。其中包括乳腺癌， 黑色素瘤、头颈癌、食道癌和垂体癌。我们知道Rb抑制E2F 转录因子控制细胞增殖的关键基因，但Rb也有转录非依赖性 影响细胞分裂和存活的活动。相当大的兴趣是由该药的临床疗效驱动的 Cyclin D/CDK4抑制剂Palbociclib，提示该途径的其他成分可能是 抑制物，或者新的靶点可能驻留在该途径中。尽管蛋白质组学工作确定了 与Rb途径和蛋白质的关键分子效应器和调节因子--途径组分有关 调节这些因素的翻译后修饰(PTM)仍不清楚。在这里，我们将首先关注 系统鉴定(1)在G1/S进程中观察到的蛋白质、PTM和信号依赖关系； (2)用鸟枪法和磷酸化蛋白质组学鉴定哪些通路成分对帕波西利有反应； 确定Cyclin D-CDK4/6和Rb/E2F组分的核质调节复合体；(4) 建立蛋白质相互作用网络，将PTMS与蛋白质相互作用和活性联系起来；(5)确定 CDK4/6、Cyclin D1/2/3、Rb和E2F组分的平行图之间相互作用的特异性；以及(6) 识别在这一途径的组成部分中发现的TCGA癌病变。这些测量和 蛋白质组学核心进行的干扰将组装成PTM和蛋白质-蛋白质的网络 相互作用(PPI)，推动了这一关键癌症途径的新假说。

Project Summary Many deadly cancers show mutations in a pathway driven by forms of cyclin D, Cdk4 or Cdk6, their inhibitory proteins, the Rb retinoblastoma protein, and the E2F transcription factors. These include breast cancer, melanoma, head and neck cancer, esophageal and pituitary cancers. We know that Rb suppresses E2F transcription factors to control genes critical for cell proliferation, but Rb also has transcription-independent activities that impact cell division and survival. Considerable interest is driven by the clinical efficacy of the cyclin D/Cdk4 inhibitor palbociclib, suggesting that additional components of this pathway may be targets of the inhibitor, or that new targets may reside within the pathway. Despite proteomic work identifying proteins that associate with pathway components, the key molecular effectors and regulators of the Rb pathway and protein post-translational modifications (PTMs) that regulate these factors remain unclear. Here we will focus first on systematically identifying (1) the proteins, PTMs, and signal dependencies observed during G1/S progression; (2) identifying which pathway components respond to Palbociclib by shotgun and phosphoproteomics; (3) defining nuclear and cytoplasmic regulated complexes for Cyclin D-Cdk4/6 and Rb/E2F components; (4) building protein interaction networks to link PTMs to protein interactions and activity; (5) determining the specificity of interactions among paralogs of the Cdk4/6, Cyclin D1/2/3, Rb and E2F components; and (6) identifying TCGA cancer lesions found within components of this pathway. These measurements and perturbations performed by the Proteomics Core will be assembled into a network of PTMs and protein-protein interactions (PPIs), driving new hypotheses for this critical cancer pathway.