Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation

Comander, Jason; Natarajan, Sripriya; Gimbrone, Michael A.; García‐Cardeña, Guillermo

doi:10.1186/1471-2164-5-17

Cited by 18 publications

(10 citation statements)

References 41 publications

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“…Differences were considered significant at P<0.05. For microarray data, gene regulation differences of p<0.001 were considered significant as determined using Z-pool statistical methodology as described previously [16]. …”

Section: Methodsmentioning

confidence: 99%

Defining the regulation of KLF4 expression and its downstream transcriptional targets in vascular endothelial cells

Villarreal

Zhang

Larman

et al. 2010

Biochemical and Biophysical Research Communications

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149

119

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The Kruppel-like factor 2 (KLF2) and Kruppel-like factor 4 (KLF4) transcription factors have recently been shown to act as critical regulators of endothelial homeostasis. While several insights have been made into the signaling mechanisms orchestrating endothelial KLF2 expression, those governing the expression of KLF4 in the vascular endothelium remain largely unknown. Here, we show that diverse vasoprotective stimuli including an atheroprotective shear stress waveform, simvastatin, and resveratrol induce the expression of KLF4 in cultured human endothelial cells. We further demonstrate that the induction of KLF4 by resveratrol and atheroprotective shear stress occurs via a MEK5/MEF2-dependent signaling pathway. Since MEK5 activation is also critical for the expression of KLF2, we assessed the individual contribution of KLF4 and KLF2 to the global transcriptional activity triggered by MEK5 activation. Genome-wide transcriptional profiling of endothelial cells overexpressing KLF4, KLF2, or constitutively active MEK5 revealed that 59.2% of the genes regulated by the activation of MEK5 were similarly controlled by either KLF2 or KLF4. Collectively, our data identify a significant degree of mechanistic and functional conservation between KLF2 and KLF4, and importantly, provide further insights into the complex regulatory networks governing endothelial vasoprotection.

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Section: Methodsmentioning

confidence: 99%

Defining the regulation of KLF4 expression and its downstream transcriptional targets in vascular endothelial cells

Villarreal

Zhang

Larman

et al. 2010

Biochemical and Biophysical Research Communications

Self Cite

149

119

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“…In order to create this integrated experimental strategy, our laboratory first established platforms to perform genome-wide transcriptional profiling using microarrays coupled with several bioinformatics tools used for the systematic analyses of the resultant large datasets [29–31]. An in vitro model system was then created in which cultured human endothelial cells can be exposed to well-defined shear stress waveforms that accurately simulate those present in vivo [32].…”

Section: Atheroprone Vs Atheroprotective Endothelial Phenotypesmentioning

confidence: 99%

Vascular endothelium, hemodynamics, and the pathobiology of atherosclerosis

Gimbrone

García‐Cardeña

2013

Cardiovascular Pathology

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The localization of atherosclerotic lesion formation to regions of disturbed blood flow associated with certain arterial geometries, in humans and experimental animals, suggests an important role for hemodynamic forces in the pathobiology of atherosclerosis. There is increasing evidence that the vascular endothelium, which is directly exposed to various fluid mechanical forces generated by pulsatile blood flow, can discriminate among these different biomechanical stimuli and transduce them into genetic regulatory programs that modulate endothelial function. In this brief review, we discuss how biomechanical stimuli generated by blood flow can influence endothelial functional phenotypes, and explore the working hypothesis of “atheroprone” hemodynamic environments as “local risk factors” in atherogenesis. In addition, we consider the therapeutic implications of the activation of “atheroprotective genes” and their role as “critical regulatory nodes” in vascular homeostasis.

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“…In total, 681 genes were found to have statistically significant regulation, as determined by Z statistics (32) (Fig. 2A).…”

Section: Hemodynamic Simulation Of Coronary Collateral Shearmentioning

confidence: 99%

“…A, application of the simulated coronary collateral waveforms to cultured human EC resulted in genome-wide differences in endothelial transcriptional profiles. Significant differences across three independent samples were determined statistically for p Ͻ 0.001, using a z-statistic method of pooled variances (32). Normalizing ACC gene expression to NCC yielded 267 significantly up-regulated genes (red) and 414 significantly down-regulated genes (blue).…”

Section: Hemodynamic Simulation Of Coronary Collateral Shearmentioning

confidence: 99%

Biomechanical Regulation of Endothelium-dependent Events Critical for Adaptive Remodeling

Mack

Zhang

Chung

et al. 2009

Journal of Biological Chemistry

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Alterations in hemodynamic shear stress acting on the vascular endothelium are critical for adaptive arterial remodeling. The molecular mechanisms regulating this process, however, remain largely uncharacterized. Here, we sought to define the responses evoked in endothelial cells exposed to shear stress waveforms characteristic of coronary collateral vessels and the subsequent paracrine effects on smooth muscle cells. A lumped parameter model of the human coronary collateral circulation was used to simulate normal and adaptive remodeling coronary collateral shear stress waveforms. These waveforms were then applied to cultured human endothelial cells (EC), and the resulting differences in EC gene expression were assessed by genome-wide transcriptional profiling to identify genes distinctly regulated by collateral flow. Analysis of these transcriptional programs identified several genes to be differentially regulated by collateral flow, including genes important for endothelium-smooth muscle interactions. In particular, the transcription factor KLF2 was up-regulated by the adaptive remodeling coronary collateral waveform, and several of its downstream targets displayed the expected modulation, including the down-regulation of connective tissue growth factor. To assess the effect of endothelial KLF2 expression on smooth muscle cell migration, a three-dimensional microfluidic assay was developed. Using this three-dimensional system, we showed that KLF2-expressing EC co-cultured with SMC significantly reduce SMC migration compared with control EC and that this reduction can be rescued by the addition of exogenous connective tissue growth factor. Collectively, these results demonstrate that collateral flow evokes distinct EC gene expression profiles and functional phenotypes that subsequently influence vascular events important for adaptive remodeling.Coronary collateralization or arteriogenesis is a vascular adaptive remodeling process that occurs in the context of arterial occlusion when preexisting collateral arterioles remodel to form larger diameter bypass arteries. The current arteriogenesis paradigm implicates local hemodynamics, recruitment/activation of monocytes, and structural remodeling of the vascular wall as key steps in collateralization (1). Two primary stages of collateralization have been described based predominantly on observations from femoral artery ligation models that induce collateral remodeling via an instantaneous increase in collateral flow. The initial stage of collateralization is characterized by a wave of monocyte-driven inflammation and rapid vasodilation, an immediate compensatory response to increased collateral flow. In the second phase of collateralization, the initial inflammatory response is resolved, and the newly formed conductance artery wall is stabilized (2). To date, considerable attention has been dedicated to investigating the inflammatory regulation of this process (i.e. MCP-1 and GM-CSF), but despite evidence on the importance of the endothelium and endothelium-derived ...

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Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation

Cited by 18 publications

References 41 publications

Defining the regulation of KLF4 expression and its downstream transcriptional targets in vascular endothelial cells

Defining the regulation of KLF4 expression and its downstream transcriptional targets in vascular endothelial cells

Vascular endothelium, hemodynamics, and the pathobiology of atherosclerosis

Biomechanical Regulation of Endothelium-dependent Events Critical for Adaptive Remodeling

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