Limits...
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

Phosphorylation site clusters displayed as a co-clustered correlation networks (CCCNs).RTK, SFK and PAG1 phosphorylation sites were selected from the co-cluster correlation network shown in S11 Fig, where edges represent Spearman correlations greater than 0.5 from phosphorylation sites that co-clustered from t-SNE embeddings. Edge line thickness is proportional to correlation and the number of cases in which phosphorylation sites co-clustered from different embeddings. Two separate groups containing the most highly phosphorylated RTK and SFK sites are shown. Heat maps (right) show the primary data for phosphorylation on specific sites. (A) The network containing phosphorylation sites ALK 1507 (the most highly phosphorylated site on ALK), FYN 420, PDGFRA 762 and LYN 508 was extended to include other PNCP phosphorylation sites that co-clustered with positive Spearman correlation; no PAG1 phosphorylation sites co-clustered with this group. (B) Five highly phosphorylated PAG1 sites co-clustered with phosphorylation sites on IGF1R, DDR2, EGFR, and FGFR1. Note that the conserved peptide sequence for FYN 531; SRC 530; YES1 537 was inclusively summed to both FYN 531; YES1 537 and SRC 530 in the phosphorylation site network, but exclusively summed to FYN_i in the total protein phosphorylation networks based on the presence of other FYN phosphopeptides in the same samples. By the exclusive criteria, FYN 420; LCK 394; SRC 419; YES1 426 in (A) most likely represents FYN activation; FYN 531; YES1 537 most likely represents FYN inhibitory phosphorylation; and the inclusive summing method likely over-represents the amounts of SRC inhibitory phosphorylation in (B).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4401789&req=5

pcbi.1004130.g008: Phosphorylation site clusters displayed as a co-clustered correlation networks (CCCNs).RTK, SFK and PAG1 phosphorylation sites were selected from the co-cluster correlation network shown in S11 Fig, where edges represent Spearman correlations greater than 0.5 from phosphorylation sites that co-clustered from t-SNE embeddings. Edge line thickness is proportional to correlation and the number of cases in which phosphorylation sites co-clustered from different embeddings. Two separate groups containing the most highly phosphorylated RTK and SFK sites are shown. Heat maps (right) show the primary data for phosphorylation on specific sites. (A) The network containing phosphorylation sites ALK 1507 (the most highly phosphorylated site on ALK), FYN 420, PDGFRA 762 and LYN 508 was extended to include other PNCP phosphorylation sites that co-clustered with positive Spearman correlation; no PAG1 phosphorylation sites co-clustered with this group. (B) Five highly phosphorylated PAG1 sites co-clustered with phosphorylation sites on IGF1R, DDR2, EGFR, and FGFR1. Note that the conserved peptide sequence for FYN 531; SRC 530; YES1 537 was inclusively summed to both FYN 531; YES1 537 and SRC 530 in the phosphorylation site network, but exclusively summed to FYN_i in the total protein phosphorylation networks based on the presence of other FYN phosphopeptides in the same samples. By the exclusive criteria, FYN 420; LCK 394; SRC 419; YES1 426 in (A) most likely represents FYN activation; FYN 531; YES1 537 most likely represents FYN inhibitory phosphorylation; and the inclusive summing method likely over-represents the amounts of SRC inhibitory phosphorylation in (B).

Mentions: These data motivated further higher resolution interrogation of the relationships between individual protein phosphorylation events. We investigated the relationships among phosphorylation sites by clustering phosphorylation sites (summed from homologous phosphopeptides) and visualizing data structure as a co-cluster correlation network (CCCN). The edge-weighted, spring-embedded layout of this network showed several distinct groups of sites with statistical relationships to other groups (S11 Fig). The data were interrogated with a focus on the most highly phosphorylated sites on RTKs, SFKs, and PAG1 to ask if phosphorylation sites cluster together. Two distinct clusters are shown in Fig 8. ALK was detected in 22 distinct phosphopeptides in neuroblastoma samples, which could be collapsed into 13 distinct phosphorylation sites based on sequence homology. Fig 8A shows that the ALK phosphorylation site, ALK 1507, which was most frequently seen in neuroblastoma samples, was associated with inhibited LYN (LYN 508), and activated FYN (FYN 420; LCK 394; SRC 419; YES1 426; this site was assigned to FYN in total phosphorylation calculations because other FYN phosphopeptides were detected in the same samples; see Materials and Methods). Co-clustered phosphorylation sites on several other proteins in this cluster resemble the cluster in Fig 1A. Fig 8B shows that other ALK phosphorylation sites (ALK 1096 and 1604) clustered with the most prominently detected phosphorylation site on DDR2 (DDR2 481), along with activated LYN (LYN 411), and inhibited FYN and SRC (FYN 531; YES1 537 and SRC 530). Also co-clustered with the group in Fig 8B were phosphorylation sites from other RTKs represented in the cluster in Fig 1B.


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)

Phosphorylation site clusters displayed as a co-clustered correlation networks (CCCNs).RTK, SFK and PAG1 phosphorylation sites were selected from the co-cluster correlation network shown in S11 Fig, where edges represent Spearman correlations greater than 0.5 from phosphorylation sites that co-clustered from t-SNE embeddings. Edge line thickness is proportional to correlation and the number of cases in which phosphorylation sites co-clustered from different embeddings. Two separate groups containing the most highly phosphorylated RTK and SFK sites are shown. Heat maps (right) show the primary data for phosphorylation on specific sites. (A) The network containing phosphorylation sites ALK 1507 (the most highly phosphorylated site on ALK), FYN 420, PDGFRA 762 and LYN 508 was extended to include other PNCP phosphorylation sites that co-clustered with positive Spearman correlation; no PAG1 phosphorylation sites co-clustered with this group. (B) Five highly phosphorylated PAG1 sites co-clustered with phosphorylation sites on IGF1R, DDR2, EGFR, and FGFR1. Note that the conserved peptide sequence for FYN 531; SRC 530; YES1 537 was inclusively summed to both FYN 531; YES1 537 and SRC 530 in the phosphorylation site network, but exclusively summed to FYN_i in the total protein phosphorylation networks based on the presence of other FYN phosphopeptides in the same samples. By the exclusive criteria, FYN 420; LCK 394; SRC 419; YES1 426 in (A) most likely represents FYN activation; FYN 531; YES1 537 most likely represents FYN inhibitory phosphorylation; and the inclusive summing method likely over-represents the amounts of SRC inhibitory phosphorylation in (B).
© Copyright Policy
Related In: Results  -  Collection

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

pcbi.1004130.g008: Phosphorylation site clusters displayed as a co-clustered correlation networks (CCCNs).RTK, SFK and PAG1 phosphorylation sites were selected from the co-cluster correlation network shown in S11 Fig, where edges represent Spearman correlations greater than 0.5 from phosphorylation sites that co-clustered from t-SNE embeddings. Edge line thickness is proportional to correlation and the number of cases in which phosphorylation sites co-clustered from different embeddings. Two separate groups containing the most highly phosphorylated RTK and SFK sites are shown. Heat maps (right) show the primary data for phosphorylation on specific sites. (A) The network containing phosphorylation sites ALK 1507 (the most highly phosphorylated site on ALK), FYN 420, PDGFRA 762 and LYN 508 was extended to include other PNCP phosphorylation sites that co-clustered with positive Spearman correlation; no PAG1 phosphorylation sites co-clustered with this group. (B) Five highly phosphorylated PAG1 sites co-clustered with phosphorylation sites on IGF1R, DDR2, EGFR, and FGFR1. Note that the conserved peptide sequence for FYN 531; SRC 530; YES1 537 was inclusively summed to both FYN 531; YES1 537 and SRC 530 in the phosphorylation site network, but exclusively summed to FYN_i in the total protein phosphorylation networks based on the presence of other FYN phosphopeptides in the same samples. By the exclusive criteria, FYN 420; LCK 394; SRC 419; YES1 426 in (A) most likely represents FYN activation; FYN 531; YES1 537 most likely represents FYN inhibitory phosphorylation; and the inclusive summing method likely over-represents the amounts of SRC inhibitory phosphorylation in (B).
Mentions: These data motivated further higher resolution interrogation of the relationships between individual protein phosphorylation events. We investigated the relationships among phosphorylation sites by clustering phosphorylation sites (summed from homologous phosphopeptides) and visualizing data structure as a co-cluster correlation network (CCCN). The edge-weighted, spring-embedded layout of this network showed several distinct groups of sites with statistical relationships to other groups (S11 Fig). The data were interrogated with a focus on the most highly phosphorylated sites on RTKs, SFKs, and PAG1 to ask if phosphorylation sites cluster together. Two distinct clusters are shown in Fig 8. ALK was detected in 22 distinct phosphopeptides in neuroblastoma samples, which could be collapsed into 13 distinct phosphorylation sites based on sequence homology. Fig 8A shows that the ALK phosphorylation site, ALK 1507, which was most frequently seen in neuroblastoma samples, was associated with inhibited LYN (LYN 508), and activated FYN (FYN 420; LCK 394; SRC 419; YES1 426; this site was assigned to FYN in total phosphorylation calculations because other FYN phosphopeptides were detected in the same samples; see Materials and Methods). Co-clustered phosphorylation sites on several other proteins in this cluster resemble the cluster in Fig 1A. Fig 8B shows that other ALK phosphorylation sites (ALK 1096 and 1604) clustered with the most prominently detected phosphorylation site on DDR2 (DDR2 481), along with activated LYN (LYN 411), and inhibited FYN and SRC (FYN 531; YES1 537 and SRC 530). Also co-clustered with the group in Fig 8B were phosphorylation sites from other RTKs represented in the cluster in Fig 1B.

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