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Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

Chu LH, Lee E, Bader JS, Popel AS - PLoS ONE (2014)

Bottom Line: Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome") could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention.We used the Short Time-series Expression Miner (STEM) to identify significant temporal gene expression profiles.The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.

ABSTRACT
Angiogenesis involves stimulation of endothelial cells (EC) by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome") could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A). We used the Short Time-series Expression Miner (STEM) to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME) show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC) and human microvascular EC (MEC). The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

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Activation pattern of receptor tyrosine kinases on 3D collagen I for TIME cells.
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pone-0110871-g003: Activation pattern of receptor tyrosine kinases on 3D collagen I for TIME cells.

Mentions: Since tyrosine kinase activity is of great interest in translational applications, we scrutinize the genes annotated as protein tyrosine kinase activity in the functional enrichment of positive regulation of angiogenesis in Table S3. The GO category “transmembrane receptor protein tyrosine kinase activity” (adjusted p-value = 1.64E-13) contains eighteen proteins ALK, EGFR, EPHA1, EPHB2, FGFR1, FGFR2, FGFR3, FGFR4, FGFRL1, FLT1 (VEGFR1), FLT4 (VEGFR3), IGF1R, KDR (VEGFR2), NRP1, NRP2, NTRK2, TEK and TIE1. We merge proteomic and genomic data based on the 2007 protocol [25] by Cytoscape [16]. The proteins with gene transcripts on 3D type I collagen for TIME cells in Figure 3 show that FLT1 is activated consistently after 6 h, KDR only activated at 24 h, and FLT4 decreased from 15 min to 9 hr then increased from 12 hr to 24 hr. The VEGF ligands family and their receptors play important roles in the development, maintenance, and remodeling of the vasculature [26], [27]. Thus, we select three VEGF receptor tyrosine kinases VEGFR1 (FLT1), VEGFR2 (KDR), and VEGFR3 (FLT4) to perform protein-level time series in vitro experiments.


Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

Chu LH, Lee E, Bader JS, Popel AS - PLoS ONE (2014)

Activation pattern of receptor tyrosine kinases on 3D collagen I for TIME cells.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199761&req=5

pone-0110871-g003: Activation pattern of receptor tyrosine kinases on 3D collagen I for TIME cells.
Mentions: Since tyrosine kinase activity is of great interest in translational applications, we scrutinize the genes annotated as protein tyrosine kinase activity in the functional enrichment of positive regulation of angiogenesis in Table S3. The GO category “transmembrane receptor protein tyrosine kinase activity” (adjusted p-value = 1.64E-13) contains eighteen proteins ALK, EGFR, EPHA1, EPHB2, FGFR1, FGFR2, FGFR3, FGFR4, FGFRL1, FLT1 (VEGFR1), FLT4 (VEGFR3), IGF1R, KDR (VEGFR2), NRP1, NRP2, NTRK2, TEK and TIE1. We merge proteomic and genomic data based on the 2007 protocol [25] by Cytoscape [16]. The proteins with gene transcripts on 3D type I collagen for TIME cells in Figure 3 show that FLT1 is activated consistently after 6 h, KDR only activated at 24 h, and FLT4 decreased from 15 min to 9 hr then increased from 12 hr to 24 hr. The VEGF ligands family and their receptors play important roles in the development, maintenance, and remodeling of the vasculature [26], [27]. Thus, we select three VEGF receptor tyrosine kinases VEGFR1 (FLT1), VEGFR2 (KDR), and VEGFR3 (FLT4) to perform protein-level time series in vitro experiments.

Bottom Line: Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome") could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention.We used the Short Time-series Expression Miner (STEM) to identify significant temporal gene expression profiles.The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.

ABSTRACT
Angiogenesis involves stimulation of endothelial cells (EC) by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome") could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A). We used the Short Time-series Expression Miner (STEM) to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME) show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC) and human microvascular EC (MEC). The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

Show MeSH