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Neuroblastoma tyrosine kinase signaling networks involve FYN and LYN in endosomes and lipid rafts.

Palacios-Moreno J, Foltz L, Guo A, Stokes MP, Kuehn ED, George L, Comb M, Grimes ML - PLoS Comput. Biol. (2015)

Bottom Line: Clusters of proteins in these networks are indicative of functional signaling pathways.The analysis indicates that receptor tyrosine kinases are functionally compartmentalized into distinct collaborative groups distinguished by activation and intracellular localization of SRC-family kinases, especially FYN and LYN.Changes in intracellular localization of activated FYN and LYN were observed in response to stimulation of the receptor tyrosine kinases, ALK and KIT.

View Article: PubMed Central - PubMed

Affiliation: Division of Biological Sciences, Center for Structural and Functional Neuroscience, University of Montana, Missoula, Montana, United States of America.

ABSTRACT
Protein phosphorylation plays a central role in creating a highly dynamic network of interacting proteins that reads and responds to signals from growth factors in the cellular microenvironment. Cells of the neural crest employ multiple signaling mechanisms to control migration and differentiation during development. It is known that defects in these mechanisms cause neuroblastoma, but how multiple signaling pathways interact to govern cell behavior is unknown. In a phosphoproteomic study of neuroblastoma cell lines and cell fractions, including endosomes and detergent-resistant membranes, 1622 phosphorylated proteins were detected, including more than half of the receptor tyrosine kinases in the human genome. Data were analyzed using a combination of graph theory and pattern recognition techniques that resolve data structure into networks that incorporate statistical relationships and protein-protein interaction data. Clusters of proteins in these networks are indicative of functional signaling pathways. The analysis indicates that receptor tyrosine kinases are functionally compartmentalized into distinct collaborative groups distinguished by activation and intracellular localization of SRC-family kinases, especially FYN and LYN. Changes in intracellular localization of activated FYN and LYN were observed in response to stimulation of the receptor tyrosine kinases, ALK and KIT. The results suggest a mechanism to distinguish signaling responses to activation of different receptors, or combinations of receptors, that govern the behavior of the neural crest, which gives rise to neuroblastoma.

No MeSH data available.


Related in: MedlinePlus

Proteins that cluster with RTKs.Proteins with tyrosine kinase, tyrosine phosphatase, SH2, and/or SH3 domains (PNCPs) that co-clustered with ALK (A), IGF1R (B), and EGFR (C) by t-SNE using both Spearman and Euclidean dissimilarity representations (“hard” filter), graphed as networks with PPI edges (left) and heat maps (right). The size and color of nodes is scaled to graph total phosphopeptides detected for each protein; blue represents phosphorylation on inhibitory sites (e.g., SFKs labelled “SFK_i”), yellow, all other sites. Heat maps (right) display the relative total phosphopeptide amounts for each protein on a blue-yellow scale (black represents NA; key, bottom right), sorted most to least left to right and top to bottom for samples and proteins, respectively, in each cluster.
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pcbi.1004130.g001: Proteins that cluster with RTKs.Proteins with tyrosine kinase, tyrosine phosphatase, SH2, and/or SH3 domains (PNCPs) that co-clustered with ALK (A), IGF1R (B), and EGFR (C) by t-SNE using both Spearman and Euclidean dissimilarity representations (“hard” filter), graphed as networks with PPI edges (left) and heat maps (right). The size and color of nodes is scaled to graph total phosphopeptides detected for each protein; blue represents phosphorylation on inhibitory sites (e.g., SFKs labelled “SFK_i”), yellow, all other sites. Heat maps (right) display the relative total phosphopeptide amounts for each protein on a blue-yellow scale (black represents NA; key, bottom right), sorted most to least left to right and top to bottom for samples and proteins, respectively, in each cluster.

Mentions: For the first, exclusive cluster analysis, we focused on PNCPs and proteins whose phosphorylation pattern was statistically most similar determined by both Euclidean distance and Spearman correlation (Figs 1 and S6). Heat maps (Fig 1 and S6, right) indicate that the phosphorylation patterns in the primary data are reasonably consistent within each cluster. The RTK, ALK, clustered with two other RTKs (FGFR1, PDGFRA), activated FYN, and LYN phosphorylated on the C-terminal inhibitory site (LYN_i; Fig 1A). The tyrosine kinase, FAK (PTK2), and the adaptor molecules BCAR1, SHC1 and CBLB were included in this group of PNCPs. We also noted other clusters that suggest interactions among phosphorylated tyrosine kinases: IGF1R with LYN, FER, the phosphatase PTPN11/SHP-2, and the tyrosine kinase TNK2, whose interactions with other proteins in this group have not been previously characterized (Fig 1B). In addition, we found that EGFR and EPHB3 clustered with inhibited FYN and SRC as well as the SH3, SH2 containing tyrosine kinase, ABL1, and MPP5, a protein with PDZ, SH3, and guanylate kinase domains whose interactions are not characterized (Fig 1C). Examples of other clusters identified using this hard filter are shown in S6 Fig. These clusters define phosphorylated proteins most commonly phosphorylated together in the same samples in this data set, which suggests possible interactions among signaling proteins that were previously unknown. Assignment of proteins to one cluster should not be viewed as evidence for excluding it from participating in a signaling pathway identified in another cluster, however [34].


Neuroblastoma tyrosine kinase signaling networks involve FYN and LYN in endosomes and lipid rafts.

Palacios-Moreno J, Foltz L, Guo A, Stokes MP, Kuehn ED, George L, Comb M, Grimes ML - PLoS Comput. Biol. (2015)

Proteins that cluster with RTKs.Proteins with tyrosine kinase, tyrosine phosphatase, SH2, and/or SH3 domains (PNCPs) that co-clustered with ALK (A), IGF1R (B), and EGFR (C) by t-SNE using both Spearman and Euclidean dissimilarity representations (“hard” filter), graphed as networks with PPI edges (left) and heat maps (right). The size and color of nodes is scaled to graph total phosphopeptides detected for each protein; blue represents phosphorylation on inhibitory sites (e.g., SFKs labelled “SFK_i”), yellow, all other sites. Heat maps (right) display the relative total phosphopeptide amounts for each protein on a blue-yellow scale (black represents NA; key, bottom right), sorted most to least left to right and top to bottom for samples and proteins, respectively, in each cluster.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401789&req=5

pcbi.1004130.g001: Proteins that cluster with RTKs.Proteins with tyrosine kinase, tyrosine phosphatase, SH2, and/or SH3 domains (PNCPs) that co-clustered with ALK (A), IGF1R (B), and EGFR (C) by t-SNE using both Spearman and Euclidean dissimilarity representations (“hard” filter), graphed as networks with PPI edges (left) and heat maps (right). The size and color of nodes is scaled to graph total phosphopeptides detected for each protein; blue represents phosphorylation on inhibitory sites (e.g., SFKs labelled “SFK_i”), yellow, all other sites. Heat maps (right) display the relative total phosphopeptide amounts for each protein on a blue-yellow scale (black represents NA; key, bottom right), sorted most to least left to right and top to bottom for samples and proteins, respectively, in each cluster.
Mentions: For the first, exclusive cluster analysis, we focused on PNCPs and proteins whose phosphorylation pattern was statistically most similar determined by both Euclidean distance and Spearman correlation (Figs 1 and S6). Heat maps (Fig 1 and S6, right) indicate that the phosphorylation patterns in the primary data are reasonably consistent within each cluster. The RTK, ALK, clustered with two other RTKs (FGFR1, PDGFRA), activated FYN, and LYN phosphorylated on the C-terminal inhibitory site (LYN_i; Fig 1A). The tyrosine kinase, FAK (PTK2), and the adaptor molecules BCAR1, SHC1 and CBLB were included in this group of PNCPs. We also noted other clusters that suggest interactions among phosphorylated tyrosine kinases: IGF1R with LYN, FER, the phosphatase PTPN11/SHP-2, and the tyrosine kinase TNK2, whose interactions with other proteins in this group have not been previously characterized (Fig 1B). In addition, we found that EGFR and EPHB3 clustered with inhibited FYN and SRC as well as the SH3, SH2 containing tyrosine kinase, ABL1, and MPP5, a protein with PDZ, SH3, and guanylate kinase domains whose interactions are not characterized (Fig 1C). Examples of other clusters identified using this hard filter are shown in S6 Fig. These clusters define phosphorylated proteins most commonly phosphorylated together in the same samples in this data set, which suggests possible interactions among signaling proteins that were previously unknown. Assignment of proteins to one cluster should not be viewed as evidence for excluding it from participating in a signaling pathway identified in another cluster, however [34].

Bottom Line: Clusters of proteins in these networks are indicative of functional signaling pathways.The analysis indicates that receptor tyrosine kinases are functionally compartmentalized into distinct collaborative groups distinguished by activation and intracellular localization of SRC-family kinases, especially FYN and LYN.Changes in intracellular localization of activated FYN and LYN were observed in response to stimulation of the receptor tyrosine kinases, ALK and KIT.

View Article: PubMed Central - PubMed

Affiliation: Division of Biological Sciences, Center for Structural and Functional Neuroscience, University of Montana, Missoula, Montana, United States of America.

ABSTRACT
Protein phosphorylation plays a central role in creating a highly dynamic network of interacting proteins that reads and responds to signals from growth factors in the cellular microenvironment. Cells of the neural crest employ multiple signaling mechanisms to control migration and differentiation during development. It is known that defects in these mechanisms cause neuroblastoma, but how multiple signaling pathways interact to govern cell behavior is unknown. In a phosphoproteomic study of neuroblastoma cell lines and cell fractions, including endosomes and detergent-resistant membranes, 1622 phosphorylated proteins were detected, including more than half of the receptor tyrosine kinases in the human genome. Data were analyzed using a combination of graph theory and pattern recognition techniques that resolve data structure into networks that incorporate statistical relationships and protein-protein interaction data. Clusters of proteins in these networks are indicative of functional signaling pathways. The analysis indicates that receptor tyrosine kinases are functionally compartmentalized into distinct collaborative groups distinguished by activation and intracellular localization of SRC-family kinases, especially FYN and LYN. Changes in intracellular localization of activated FYN and LYN were observed in response to stimulation of the receptor tyrosine kinases, ALK and KIT. The results suggest a mechanism to distinguish signaling responses to activation of different receptors, or combinations of receptors, that govern the behavior of the neural crest, which gives rise to neuroblastoma.

No MeSH data available.


Related in: MedlinePlus