Computational identification of phospho-tyrosine sub-networks related to acanthocyte generation in neuroacanthocytosis

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