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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: 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.This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

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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Normalized protein level measurement of VEGFR1, VEGFR2 and VEGFR3 to GAPDH on HUVEC and MEC in (A) and (B), respectively.
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pone-0110871-g005: Normalized protein level measurement of VEGFR1, VEGFR2 and VEGFR3 to GAPDH on HUVEC and MEC in (A) and (B), respectively.

Mentions: We plotted the ratio of measured protein levels of VEGFR1, VEGFR2 and VEGFR3 to the GAPDH in HUVEC and MEC in Figure 5 (A) and (B), respectively, normalized to the first time point. We observed that VEGFR1 and VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. Interestingly, VEGFR1 and VEGFR2 were restored to the initial protein level after the mid-time point of VEGF treatment, suggesting that some downstream signaling of VEGF pathway may induce VEGFR1 and VEGFR2 expression. Figure 5 (B) shows that VEGFR1 drops after VEGF treatment in MEC, showing its minimum level at 3 hr, then, VEGFR1 recovers continuously. Similarly, VEGFR2 shows minimum level at 6 hr, and recovered after that time point. This “drop and recovery” pattern is not shown in VEGFR3. There might indicate different regulation mechanisms for VEGFR1/2 and VEGFR3 in endothelial cells.


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)

Normalized protein level measurement of VEGFR1, VEGFR2 and VEGFR3 to GAPDH on HUVEC and MEC in (A) and (B), respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110871-g005: Normalized protein level measurement of VEGFR1, VEGFR2 and VEGFR3 to GAPDH on HUVEC and MEC in (A) and (B), respectively.
Mentions: We plotted the ratio of measured protein levels of VEGFR1, VEGFR2 and VEGFR3 to the GAPDH in HUVEC and MEC in Figure 5 (A) and (B), respectively, normalized to the first time point. We observed that VEGFR1 and VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. Interestingly, VEGFR1 and VEGFR2 were restored to the initial protein level after the mid-time point of VEGF treatment, suggesting that some downstream signaling of VEGF pathway may induce VEGFR1 and VEGFR2 expression. Figure 5 (B) shows that VEGFR1 drops after VEGF treatment in MEC, showing its minimum level at 3 hr, then, VEGFR1 recovers continuously. Similarly, VEGFR2 shows minimum level at 6 hr, and recovered after that time point. This “drop and recovery” pattern is not shown in VEGFR3. There might indicate different regulation mechanisms for VEGFR1/2 and VEGFR3 in endothelial cells.

Bottom Line: 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.This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

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
Related in: MedlinePlus