The purpose of this program is to significantly advance our understanding of mechanisms of HDL Dysfunction in (1) Familial Hypercholesterolemia and (2) Chronic Kidney Disease, as well as the impact of (3) Oxidative modifications to HDL. The proposed research strategies are highly cross disciplinary and require extensive next-generation RNA sequencing and transcriptome-scale analysis. An effective and dedicated non-coding RNA and bioinformatics core is essential for the success of the proposed studies. Specifically, the Non-Coding RNA and Bioinformatics Core is designed to handle the large volume of sequencing needs and data analysis for Projects 1, 2, and 3. We are highly trained, skilled, and published in smRNA-Seq. and RNA seq. Furthermore, we have developed in-house sequencing analysis pipelines that will be implemented by computational biologists and biostatisticians under the guidance of the Core Leader, Dr. Kasey C. Vickers. The purpose of the Non-Coding RNA and Bioinformatics Core is to use massive parallel DNA sequencing to analyze small and long RNA expression and abundance associated with HDL dysfunction in a timely and efficiently manner with high-quality data management and integration into complex bioinformatics systems.
The function of the Non-Coding RNA and Bioinformatics Core is critical to the goals of the proposed projects. Specifically, the Core will be dedicated to accurate sequencing-based profiling of smRNA (mlRNA), long non-coding RNA, and mRNA. Moreover, Core D is designed to seamlessly apply high-level pathway and systems bioinformatics, and biostatistical comparisons and correlation analyses with various HDL functions and parameters.
|Babaev, Vladimir R; Hebron, Katie E; Wiese, Carrie B et al. (2014) Macrophage deficiency of Akt2 reduces atherosclerosis in Ldlr null mice. J Lipid Res 55:2296-308|
|Vickers, Kasey C; Landstreet, Stuart R; Levin, Michael G et al. (2014) MicroRNA-223 coordinates cholesterol homeostasis. Proc Natl Acad Sci U S A 111:14518-23|
|Allen, Ryan M; Vickers, Kasey C (2014) Coenzyme Q10 increases cholesterol efflux and inhibits atherosclerosis through microRNAs. Arterioscler Thromb Vasc Biol 34:1795-7|