Department of Medicine, University of Verona, Verona, Italy.
PLoS One. 2012;7(2):e31015. doi: 10.1371/journal.pone.0031015. Epub 2012 Feb 15.
Acanthocytes, abnormal thorny red blood cells (RBC), are one of the biological hallmarks of neuroacanthocytosis syndromes (NA), a group of rare hereditary neurodegenerative disorders. Since RBCs are easily accessible, the study of acanthocytes in NA may provide insights into potential mechanisms of neurodegeneration. Previous studies have shown that changes in RBC membrane protein phosphorylation state affect RBC membrane mechanical stability and morphology. Here, we coupled tyrosine-phosphoproteomic analysis to topological network analysis. We aimed to predict signaling sub-networks possibly involved in the generation of acanthocytes in patients affected by the two core NA disorders, namely McLeod syndrome (MLS, XK-related, Xk protein) and chorea-acanthocytosis (ChAc, VPS13A-related, chorein protein). The experimentally determined phosphoproteomic data-sets allowed us to relate the subsequent network analysis to the pathogenetic background. To reduce the network complexity, we combined several algorithms of topological network analysis including cluster determination by shortest path analysis, protein categorization based on centrality indexes, along with annotation-based node filtering. We first identified XK- and VPS13A-related protein-protein interaction networks by identifying all the interactomic shortest paths linking Xk and chorein to the corresponding set of proteins whose tyrosine phosphorylation was altered in patients. These networks include the most likely paths of functional influence of Xk and chorein on phosphorylated proteins. We further refined the analysis by extracting restricted sets of highly interacting signaling proteins representing a common molecular background bridging the generation of acanthocytes in MLS and ChAc. The final analysis pointed to a novel, very restricted, signaling module of 14 highly interconnected kinases, whose alteration is possibly involved in generation of acanthocytes in MLS and ChAc.
棘形红细胞，一种异常的带刺状红细胞（RBC），是神经棘红细胞增多症（NA）综合征的生物学标志之一，这是一组罕见的遗传性神经退行性疾病。由于 RBC 很容易获取，因此对 NA 中的棘形红细胞的研究可能为神经退行性变的潜在机制提供了线索。先前的研究表明，RBC 膜蛋白磷酸化状态的变化会影响 RBC 膜的机械稳定性和形态。在这里，我们将酪氨酸磷酸化蛋白质组分析与拓扑网络分析相结合。我们旨在预测可能涉及两种核心 NA 疾病（即 McLeod 综合征（MLS，XK 相关，Xk 蛋白）和舞蹈棘红细胞增多症（ChAc，VPS13A 相关，chorein 蛋白）患者棘形红细胞生成的信号转导子网络。通过实验确定的磷酸蛋白质组数据集使我们能够将随后的网络分析与发病机制联系起来。为了降低网络的复杂性，我们结合了拓扑网络分析的几种算法，包括通过最短路径分析确定聚类、基于中心性指数的蛋白质分类，以及基于注释的节点过滤。我们首先通过识别将 Xk 和 chorein 与患者中酪氨酸磷酸化改变的相应蛋白质组连接起来的所有互作最短路径，鉴定出与 XK 和 VPS13A 相关的蛋白质-蛋白质相互作用网络。这些网络包括 Xk 和 chorein 对磷酸化蛋白质最有可能的功能影响途径。我们通过提取代表在 MLS 和 ChAc 中生成棘形红细胞的共同分子背景的高度相互作用的信号蛋白的受限集合，进一步细化了分析。最终分析指出了一个新的、非常受限的 14 个高度相互作用的激酶信号模块，其改变可能涉及 MLS 和 ChAc 中棘形红细胞的生成。
