Understanding proteome remodeling in aneuploidy

摘要 染色体含量不平衡，即所谓的非整倍性，是许多人类遗传疾病的标志， 癌的非整倍体不仅导致非整倍体上编码基因的表达改变， 染色体，但也影响基因表达全基因组。对于许多非整倍体相关疾病， 目前尚不清楚哪些基因或基因组是疾病病理学的关键驱动因素。分子研究 非整倍性的结果可以为“基因型-表型”关联提供宝贵的线索，从而导致 更好地了解疾病的发展机制。由于已知的大量转录后 蛋白质组学测量是非整倍体条件下的过程和蛋白质的功能重要性的一部分， 这对于鉴定在蛋白质水平上剂量不平衡的基因是必不可少的。然而，生物学和 技术挑战，如个体基因组的变异性，有限的定量再现性， 测量的准确性，以及缺乏识别间接机制的战略，阻碍了 对非整倍体进行高效的蛋白质组学检查。我们假设非整倍体细胞会利用其特有的 蛋白质稳态和细胞信号传导途径来处理大规模蛋白质剂量失衡， 在非整倍性胁迫下新获得或改变的蛋白质-蛋白质相互作用在以下方面发挥重要作用： 调节分子网络和细胞适应性。在这个提议中，我们将使用来自人类的等基因细胞模型， 和小鼠非整倍体病例。我们将进一步发展和应用基于定量质量的技术 光谱和新的分析策略的基础上，蛋白质的背景分析，以发现直接和 非整倍体模型中的间接蛋白质组学效应。这项建议的结果极为重要。第一、 以蛋白质组学为中心多层次数据集将描述当几种蛋白质 数以百计的基因获得或丢失，破译通常激活的信号转导过程， 非整倍体模型，并提供机会来预测特定基因拷贝数的细胞影响 变更（CNA）。第二，蛋白质背景分析技术将是一个非常宝贵的工具，用于识别疾病。 在非整倍体和其他疾病条件下的新蛋白功能和关联。第三，重要的 逃避内稳态控制或与信号中枢紧密相互作用的蛋白质将提供一个重要的 在非整倍体病例中进一步功能研究的蛋白靶点，如肺鳞状细胞癌和 与所研究的细胞模型相关的三体性疾病。

ABSTRACT Unbalanced chromosome content, so-called aneuploidy, is a hallmark of many human genetic diseases and cancers. Aneuploidy not only results in the altered expression of the genes encoded on the aneuploid chromosome, but also affects gene expression genome-wide. For many aneuploidy related diseases, it is still not clear which gene or gene sets are the key drivers of disease pathology. Research on molecular consequences of aneuploidy could shed invaluable light on “genotype-phenotype” association, thus leading to a better understanding of disease development mechanisms. Due to the known substantial post-transcriptional processes in aneuploidy condition and the functional importance of proteins, proteomic measurement is indispensable to identify genes that are dosage-imbalanced at the protein level. However, biological and technical challenges such as the variability of the individual genome, the limited quantitative reproducibility and accuracy of the measurement, and the lack of strategies for identifying indirect mechanisms have hindered efficient proteomic scrutiny on aneuploidy. We hypothesize that the aneuploid cells would employ characteristic proteostasis and cell signaling pathways to deal with the large-scale protein dosage imbalance, and that the newly acquired or altered protein-protein interactions under aneuploidy stress play an important role in regulating molecular network and cellular fitness. In this proposal, we will use isogenic cell models from human and mouse aneuploidy cases. We will further develop and apply the techniques based on quantitative mass spectrometry and new analytical strategies based on protein- context profiling to discover the direct and indirect proteomic effects in the aneuploidy models. Results from this proposal are extremely important. First, the proteomic- centric, multilayered dataset will describe how protein homeostasis is maintained when several hundreds of genes that are gained or lost, decipher commonly activated signaling processes across aneuploidy models, and provide opportunities to predict the cellular impact of specific gene copy number alteration (CNA). Second, the protein-context profiling technique will be an invaluable tool for identifying de novo protein functions and associations in aneuploidy and other disease conditions. Third, those significant proteins escaping the homeostasis control or tightly interacting to signaling hubs will provide a list of important protein targets for further functional studies in aneuploidy cases, such as lung squamous cell carcinomas and trisomy disorders that are relevant to the studied cell models.