Proteomic Shifts in Embryonic Stem Cells with Gene Dose Modifications Suggest the Presence of Balancer Proteins in Protein Regulatory Networks

Large numbers of protein expression changes are usually observed in mouse models for neurodegenerative diseases, even when only a single gene was mutated in each case. To study the effect of gene dose alterations on the cellular proteome, we carried out a proteomic investigation on murine embryonic stem cells that either overexpressed individual genes or displayed aneuploidy over a genomic region encompassing 14 genes. The number of variant proteins detected per cell line ranged between 70 and 110, and did not correlate with the number of modified genes. In cell lines with single gene mutations, up and down-regulated proteins were always in balance in comparison to parental cell lines regarding number as well as concentration of differentially expressed proteins. In contrast, dose alteration of 14 genes resulted in an unequal number of up and down-regulated proteins, though the balance was kept at the level of protein concentration. We propose that the observed protein changes might partially be explained by a proteomic network response. Hence, we hypothesize the existence of a class of ��balancer�� proteins within the proteomic network, defined as proteins that buffer or cushion a system, and thus oppose multiple system disturbances. Through database queries and resilience analysis of the protein interaction network, we found that potential balancer proteins are of high cellular abundance, possess a low number of direct interaction partners, and show great allelic variation. Moreover, balancer proteins contribute more heavily to the network entropy, and thus are of high importance in terms of system resilience. We propose that the ��elasticity�� of the proteomic regulatory network mediated by balancer proteins may compensate for changes that occur under diseased conditions.

在神经退行性疾病的小鼠模型研究中，即便仅单个基因发生突变，通常也能观测到大量蛋白质表达出现改变。为探究基因剂量改变对细胞蛋白质组（proteome）的影响，我们对两类小鼠胚胎干细胞开展了蛋白质组学研究：一类为过表达单个基因的细胞系，另一类为在包含14个基因的基因组区域上存在非整倍性（aneuploidy）的细胞系。各细胞系中检测到的变异蛋白数量介于70至110之间，且与发生修饰的基因数量无显著相关性。在携带单个基因突变的细胞系中，与亲本细胞系相比，上调与下调的差异表达蛋白（differentially expressed proteins）在数量与浓度层面均保持平衡。与之相反，14个基因的剂量改变会导致上调与下调的蛋白质数量失衡，但在蛋白质浓度层面仍维持平衡。我们推测，本次观测到的蛋白质变化可部分通过蛋白质组网络应答机制予以解释。据此，我们提出蛋白质组网络中存在一类"平衡因子"蛋白（balancer proteins）：这类蛋白可对系统起到缓冲与稳定作用，进而对抗多种系统扰动。通过数据库检索与蛋白质相互作用网络（protein interaction network）的韧性分析，我们发现潜在的平衡因子蛋白具有以下特征：细胞丰度高、直接相互作用伴侣数量少，且存在显著的等位基因变异。此外，平衡因子蛋白对网络熵（network entropy）的贡献更大，因此在系统韧性（system resilience）层面具有重要意义。我们推测，由平衡因子蛋白介导的蛋白质组调控网络的"弹性"，可补偿疾病状态下发生的各类变化。