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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

Enrichment of RTKs in endosomes and DRM fractions.Enrichment was graphed in PPI networks as big yellow nodes for positive enrichment and small blue nodes for de-enrichment. Green nodes of intermediate size indicate equal amounts in all fractions. PNCPs from LAN-6 endosomes (A) and DRMs (B); SK-N-BE(2) expressing TrkA (NTRK1) endosomes (C) and DRMs (D).
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pcbi.1004130.g006: Enrichment of RTKs in endosomes and DRM fractions.Enrichment was graphed in PPI networks as big yellow nodes for positive enrichment and small blue nodes for de-enrichment. Green nodes of intermediate size indicate equal amounts in all fractions. PNCPs from LAN-6 endosomes (A) and DRMs (B); SK-N-BE(2) expressing TrkA (NTRK1) endosomes (C) and DRMs (D).

Mentions: We asked whether particular phosphorylated proteins were enriched in endosomes and DRMs by calculating the ratio between amounts in those fractions compared to proteins in all other samples from the same cell line. ALK, FGFR1, RET, PDGFRA, DDR2, EGFR, and IGF1R were enriched in endosomes from two or more neuroblastoma cell lines, but there were profound differences among cell lines (Fig 5B). In Fig 6, enrichment was graphed in PPI networks as big yellow nodes for positive enrichment and small blue nodes for de-enrichment (defined as lower amounts in that fraction compared to elsewhere). In LAN-6 cells, most RTKs were enriched in endosomes, except EPHA2 and ROR1, which were enriched in DRMs (Fig 6A and 6B). In SK-N-BE(2) cells made to over-express NTRK1/TrkA, this receptor was enriched in endosomes and de-enriched in DRMs, whereas its related receptor, NTRK2/TrkB, had the opposite pattern, being enriched in DRMs and de-enriched in endosomes (Fig 6C and 6D). The SFKs, FYN and LYN were localized differently, with LYN (and LYN_i) being enriched in DRMs in LAN-6 and SK-N-BE(2) cells, and FYN (and FYN_i) being enriched in endosomes in LAN-6 cells, but not in SK-N-BE(2) cells (Fig 6). PAG1 was enriched in endosomes in LAN-6 cells (Fig 6A) and, in contrast, in DRMs in SK-N-BE(2) cells (Fig 6D).


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)

Enrichment of RTKs in endosomes and DRM fractions.Enrichment was graphed in PPI networks as big yellow nodes for positive enrichment and small blue nodes for de-enrichment. Green nodes of intermediate size indicate equal amounts in all fractions. PNCPs from LAN-6 endosomes (A) and DRMs (B); SK-N-BE(2) expressing TrkA (NTRK1) endosomes (C) and DRMs (D).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4401789&req=5

pcbi.1004130.g006: Enrichment of RTKs in endosomes and DRM fractions.Enrichment was graphed in PPI networks as big yellow nodes for positive enrichment and small blue nodes for de-enrichment. Green nodes of intermediate size indicate equal amounts in all fractions. PNCPs from LAN-6 endosomes (A) and DRMs (B); SK-N-BE(2) expressing TrkA (NTRK1) endosomes (C) and DRMs (D).
Mentions: We asked whether particular phosphorylated proteins were enriched in endosomes and DRMs by calculating the ratio between amounts in those fractions compared to proteins in all other samples from the same cell line. ALK, FGFR1, RET, PDGFRA, DDR2, EGFR, and IGF1R were enriched in endosomes from two or more neuroblastoma cell lines, but there were profound differences among cell lines (Fig 5B). In Fig 6, enrichment was graphed in PPI networks as big yellow nodes for positive enrichment and small blue nodes for de-enrichment (defined as lower amounts in that fraction compared to elsewhere). In LAN-6 cells, most RTKs were enriched in endosomes, except EPHA2 and ROR1, which were enriched in DRMs (Fig 6A and 6B). In SK-N-BE(2) cells made to over-express NTRK1/TrkA, this receptor was enriched in endosomes and de-enriched in DRMs, whereas its related receptor, NTRK2/TrkB, had the opposite pattern, being enriched in DRMs and de-enriched in endosomes (Fig 6C and 6D). The SFKs, FYN and LYN were localized differently, with LYN (and LYN_i) being enriched in DRMs in LAN-6 and SK-N-BE(2) cells, and FYN (and FYN_i) being enriched in endosomes in LAN-6 cells, but not in SK-N-BE(2) cells (Fig 6). PAG1 was enriched in endosomes in LAN-6 cells (Fig 6A) and, in contrast, in DRMs in SK-N-BE(2) cells (Fig 6D).

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