Examination of the transcriptional regulation of inflammatory and thrombotic gene expressions by oxidized phospholipids in the human artic endothelial cells.

Under hyperlipidemic environment, the oxidized phospholipids accumulate in large vascular wall and activate vascular endothelial cells for the expression of inflammatory and thrombotic genes. The inflammatory cytokines induce recruitment of monocytes into the vessel wall, which eventually become macrophage foam cells. Thrombotic genes induce thrombolism and embolism under plaque rupture conditions that may cause occlusion of blood stream. These events are major causes for causes for fatal cardiovascular symptoms like heart attacks and strokes. Our lab specifically focuses on the initial step of the expression of inflammatory and thrombotic gene expressions in the endothelial cells by the oxidized phospholipids. We mainly adopt primary culture of human aortic endothelial cells and lab-prepared oxidized phospholipids for study. Technically, we use microarray, RNA-, and ChIP-seq analyses. In this project, we are interested in the role of bromodomain containing 4 (BRD4), a cofactor for gene transcriptional regulation. We confirmed that a list of BRD4 chemical inhibitors efficiently and selectively suppressed inflammatory and thrombotic gene expressions induced by oxidized phospholipids in the human aortic endothelial cells. BRD4 reversibly interacts specific histone acetyl modifications. In addition, BRD4 also physically interacts other transcriptional factors like p65 (RelA) for gene transcriptional regulation. A key question is what is the correlation of the genome interaction of BRD4 with inflammatory and thromobotic gene transcription profile regulated by oxidized phospholipids. Using HPC, we calculate lab-produced and public RNA- and ChIP-Seq datasets to find the answer using systems genetics and epigenetics analysis. Because of the size of the datasets of sequence reads, we need use of high performance computing capacity.

Computational Method:

UNIX-based RNA- and ChIP-Seq data analyzing tools, which are publically available.

Software:

RNA- and ChIP Sequence data processing and normalization.
RNA and ChIP-seq data mapping (STAR, bowtie, bowtie2, BWA and quantification HOMER)
Peak calling tools (MACS, MACS2, HOMER)
Promoter and Super-enhancer profiling (HOMER, ROSE)
Motif enrichment (HOMER)

Personnel involved in project and use of HPC:

Sangderk Lee, PI
Examination of the role of bromodomain-containing 4 (BRD4) in the proinflammatory and prothrombotic gene expressions induced by oxidized phospholipids in the human aortic endothelial cells.
Postdoctoral fellow in the lab: TBA

PI Publications related with current HPC application:

Lee S, Birukov KG, Romanoski CE, Springstead JR, Lusis AJ, Berliner JA. Role of phospholipid oxidation products in atherosclerosis. Circ Res. 2012 Aug 31;111(6):778-99. doi: 10.1161/CIRCRESAHA.111.256859. Review.
Romanoski CE, Lee S, Kim MJ, Ingram-Drake L, Plaisier CL, Yordanova R, Tilford C, Guan B, He A, Gargalovic PS, Kirchgessner TG, Berliner JA, Lusis AJ. Systems genetics analysis of gene-by-environment interactions in human cells. Am J Hum Genet. 2010 Mar 12;86(3):399-410. doi: 10.1016/j.ajhg.2010.02.002. Epub 2010 Feb 18.
Romanoski CE, Che N, Yin F, Mai N, Pouldar D, Civelek M, Pan C, Lee S, Vakili L, Yang WP, Kayne P, Mungrue IN, Araujo JA, Berliner JA, Lusis AJ. Network for activation of human endothelial cells by oxidized phospholipids: a critical role of heme oxygenase Circ Res. 2011 Aug 19;109(5):e27-41. doi: 10.1161/CIRCRESAHA.111.241869. Epub 2011 Jul 7.

Grants

Lee, Sangderk, 17GRNT33700302, Deciphering the regulatory mechanism of hepatic VLDL production by heparin binding EGF-like growth factor (HB-EGF), American Heart Association, 7/01/2017 - 6/30/2019