Transcriptome Profiling in Systems Vascular Medicine

Abstract

In the post-genomic, big data era, our understanding of vascular diseases has been deepened by multiple state-of-the-art “–omics” approaches, including genomics, epigenomics, transcriptomics, proteomics, lipidomics and metabolomics. Genome-wide transcriptomic profiling, such as gene microarray and RNA-sequencing, emerges as powerful research tools in systems medicine and revolutionizes transcriptomic analysis of the pathological mechanisms and therapeutics of vascular diseases. In this article, I will highlight the workflow of transcriptomic profiling, outline basic bioinformatics analysis, and summarize recent gene profiling studies performed in vascular cells as well as in human and mice diseased samples. Further mining of these public repository datasets will shed new light on our understanding of the cellular basis of vascular diseases and offer novel potential targets for therapeutic intervention.

Salvia miltiorrhizaBurge (Danshen): a golden herbal medicine in cardiovascular therapeutics

“…The possible therapeutic role of Danshen components for the treatment of chronic heart diseases related to cardiac remodeling must be further elucidated. Future directions of cardiovascular research involving Danshen include the following: (1) use of the total synthesis of bioactive components of Danshen for the purpose of cardiovascular therapeutics as an alternative to obtaining purified compounds from the medicinal plant, such as the recently described synthesis of tanshinone I [308] ; (2) use of a systems biology approach, such as RNA-sequencing [309] , or networkbased pharmacological research [310] to understand the gene regulation profile of each individual compound at the genomewide level; and (3) elucidation of the therapeutic effects of Danshen components in cardiovascular aging, which is a common basis for all major cardiovascular and metabolic diseases. Overall, Danshen and its bioactive constituents represent an invaluable source for small-molecule cardiovascular drug discovery.…”

Flow-dependent epigenetic regulation of IGFBP5 expression by H3K27me3 contributes to endothelial anti-inflammatory effects

“…RNA sequencing (RNA-seq) is a useful approach for probing the pathological mechanisms of vascular diseases 58 . RNA-seq was performed at the University of Rochester Genomics Research Center (URGRC) as previously described 57 .…”

Targeting Foam Cell Formation in Atherosclerosis: Therapeutic Potential of Natural Products

“…Therefore, it is important to further understand the regulatory mechanisms of foam cell formation by new biotechnologies. The widespread use of RNA-sequencing and lncRNA arrays (Xu, 2017) has empowered the discovery of new epigenetic regulators (such as lncRNAs) that are associated with or regulate foam cell formation, atherosclerosis, and related vascular diseases. Further elucidation of the role of these new regulators will provide us a clear picture of how foam cell formation is regulated and can be therapeutically targeted.…”