Core B: Proteomics Core.

项目摘要 许多致命的癌症显示出由细胞周期蛋白D、Cdk 4或Cdk 6形式驱动的途径中的突变，其抑制性 蛋白、Rb视网膜母细胞瘤蛋白和E2 F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E2 F 转录因子来控制对细胞增殖至关重要的基因，但Rb也具有转录非依赖性， 影响细胞分裂和存活的活动。相当大的兴趣是由本发明的临床功效驱动的。 细胞周期蛋白D/Cdk 4抑制剂palbociclib，这表明该途径的其他成分可能是细胞周期蛋白的靶点。 抑制剂，或者新靶可能存在于途径内。尽管蛋白质组学工作确定了 与途径组分、Rb途径的关键分子效应物和调节物和蛋白质相关 调节这些因子的翻译后修饰（PTM）仍不清楚。在这里，我们将首先关注 系统地鉴定（1）在G1/S进展期间观察到的蛋白质、PTM和信号依赖性; (2)通过鸟枪法和磷酸化蛋白质组学鉴定哪些途径组分对Palbociclib有反应;（3） 确定细胞周期蛋白D-Cdk 4/6和Rb/E2 F组分的细胞核和细胞质调节复合物;（4） 构建蛋白质相互作用网络以将PTM与蛋白质相互作用和活性联系起来;（5）确定 Cdk 4/6、细胞周期蛋白D1/2/3、Rb和E2 F组分的旁系同源物之间相互作用的特异性;以及（6） 识别在该途径的组分内发现的TCGA癌症病变。这些测量和 由蛋白质组学核心进行的扰动将组装成PTM和蛋白质-蛋白质网络 相互作用（PPI），推动这一关键癌症途径的新假设。

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.