Topological characterization of the Protein Interaction Network involved in neuronal polarity.

ZAMPONI N; QUASSOLLO G; TOUZ MC; CACERES A

Congreso; Congreso Argentino de Bioinformática y Biología Computacional. 4ta. Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (SolBio).; 2013

Even though neurons initially generate several equivalent neurites, only one of them becomes an axon, while the remaining others become dendrites (polarization). This early asymmetric neurite outgrowth (axon specification) is regulated by signalling molecules that have established roles in cytoskeletal rearrangements and protein trafficking. This cellular process depends on a balance of positive and negative signals, and results in the formation of a single axon. The currently accepted model proposes four stages in the development of polarity: stage 1) neurons form several thin filopodia; stage 2) neurons form a number of immature neurites (minor processes); stage 3) one of these minor processes rapidly begins to extend, becoming much longer than the other neurites (axon); stage 4) after one week of culture the rest of the processes differentiate into dendrites. Neurite extension is driven by four main steps: an increase in the amount of plasma membrane by vesicle recruitment and fusion; the local concentration and activation of signalling molecules (such as Rho GTPase and phosphatidylinositol 3-kinase (PI3K)), an increase in actin dynamics; and an increase in microtubule formation. After extension, some signalling molecules counteract the positive regulation, induce microtubule catastrophe, decrease actin dynamics and decrease the amount of plasma membrane by endocytosis and by preventing vesicle fusion. When positive signals overcome negative signals, the autoactivation of receptors or adhesion molecules and the recruitment of signalling molecules cause one neurite to elongate rapidly. Continuous elongation is supported by a positive feedback loop and sustains the activation cycle. The inhibitory signals that mutually antagonize neurite extension (negative feedback) are progressively generated at the growing axon more than at the other neurites, and interfere with their specification into axons. We wanted to characterize the large scale topological structure of the molecular system associated with neuron polarization. For that matter, the protein interaction network of neuron polarity was constructed, using as a starting point a set of proteins with known and proven function in the axonal specification, such as: Rac1, Rho A, Cdc42, PI3K, Rap1B, TIAM1 and TIAM2, among others. The resulting network consists of 7213 nodes and 40795 interactions, and serves as a framework to understand neuron polarization at the larger scale, and to search for novel functional candidates. We performed topological and functional enrichment analysis on the network obtained, and we classified relevant nodes using topological indices. These analyses revealed, for example, that the PAR3/6 complex, Cdc42 and RAC1 are hubs, and that GSK3 beta, 14-3-3 and PKC alpha proteins have the highest bottlenecks indexes.