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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

PNCP enrichment in endosomes and DRM fractions.(A) The most highly phosphorylated PNCPs that were present in endosome fractions from two or more cell lines, graphed as in Fig 1 except node size and color intensity represents total phosphorylation in endosome fractions. (B) Enrichment of proteins in endosome and DRM fractions was calculated as the ratio of amounts in endosomes or DRMs vs. the average in all other fractions and samples from that cell line, graphed as a heat map. (C) SFK and PAG1 phosphorylation site enrichment in LAN-6 cells (left) and SK-N-BE(2) cells (right).
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pcbi.1004130.g005: PNCP enrichment in endosomes and DRM fractions.(A) The most highly phosphorylated PNCPs that were present in endosome fractions from two or more cell lines, graphed as in Fig 1 except node size and color intensity represents total phosphorylation in endosome fractions. (B) Enrichment of proteins in endosome and DRM fractions was calculated as the ratio of amounts in endosomes or DRMs vs. the average in all other fractions and samples from that cell line, graphed as a heat map. (C) SFK and PAG1 phosphorylation site enrichment in LAN-6 cells (left) and SK-N-BE(2) cells (right).

Mentions: Endosomes from three neuroblastoma cell lines were characterized by phosphoproteomic analysis. In all endosome fractions from three cell lines (LAN-6, SMS-KCN, SK-N-BE(2)), 908 proteins were detected, including 22 RTKs, 10 tyrosine phosphatases; 30 SH2- and 44 SH3-domain-containing proteins. The most highly phosphorylated RTKs in neuroblastoma were those identified in Fig 5A by large yellow nodes that indicates large amounts detected in endosome fractions (e.g., DDR2, ALK, KIT, RET, EGFR, PDGFA, FGFR1). FYN and LYN containing both activating and inhibiting phosphorylations were also prominent in endosomes, along with PAG1, inhibited SRC (SRC_i), the SH3 adaptor protein BCAR1, several other adaptor proteins, two tyrosine phosphatases (PTPN11/SHP-2 and PTPRN), and PLCG1/PLCĪ³1, which was found previously in endosomes in PC12 cells [53]. Notably, 26 out of the 55 SH3-domain-containing proteins in the human genome that were predicted to have a function in endocytosis based on orthologous interactions in C. elegans were found in neuroblastoma endosome fractions, and 2 of the 55 were detected in lysosome fractions [24].


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)

PNCP enrichment in endosomes and DRM fractions.(A) The most highly phosphorylated PNCPs that were present in endosome fractions from two or more cell lines, graphed as in Fig 1 except node size and color intensity represents total phosphorylation in endosome fractions. (B) Enrichment of proteins in endosome and DRM fractions was calculated as the ratio of amounts in endosomes or DRMs vs. the average in all other fractions and samples from that cell line, graphed as a heat map. (C) SFK and PAG1 phosphorylation site enrichment in LAN-6 cells (left) and SK-N-BE(2) cells (right).
© Copyright Policy
Related In: Results  -  Collection

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

pcbi.1004130.g005: PNCP enrichment in endosomes and DRM fractions.(A) The most highly phosphorylated PNCPs that were present in endosome fractions from two or more cell lines, graphed as in Fig 1 except node size and color intensity represents total phosphorylation in endosome fractions. (B) Enrichment of proteins in endosome and DRM fractions was calculated as the ratio of amounts in endosomes or DRMs vs. the average in all other fractions and samples from that cell line, graphed as a heat map. (C) SFK and PAG1 phosphorylation site enrichment in LAN-6 cells (left) and SK-N-BE(2) cells (right).
Mentions: Endosomes from three neuroblastoma cell lines were characterized by phosphoproteomic analysis. In all endosome fractions from three cell lines (LAN-6, SMS-KCN, SK-N-BE(2)), 908 proteins were detected, including 22 RTKs, 10 tyrosine phosphatases; 30 SH2- and 44 SH3-domain-containing proteins. The most highly phosphorylated RTKs in neuroblastoma were those identified in Fig 5A by large yellow nodes that indicates large amounts detected in endosome fractions (e.g., DDR2, ALK, KIT, RET, EGFR, PDGFA, FGFR1). FYN and LYN containing both activating and inhibiting phosphorylations were also prominent in endosomes, along with PAG1, inhibited SRC (SRC_i), the SH3 adaptor protein BCAR1, several other adaptor proteins, two tyrosine phosphatases (PTPN11/SHP-2 and PTPRN), and PLCG1/PLCĪ³1, which was found previously in endosomes in PC12 cells [53]. Notably, 26 out of the 55 SH3-domain-containing proteins in the human genome that were predicted to have a function in endocytosis based on orthologous interactions in C. elegans were found in neuroblastoma endosome fractions, and 2 of the 55 were detected in lysosome fractions [24].

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