Genome-wide identification of microRNA involved in the regulation of cholesterol metabolism and atherosclerosis development

Background. MicroRNAs (miRNAs), a recently discovered class of noncoding RNAs, are involved in the post-transcriptional regulation of genes belonging to different biological processes, including cholesterol homeostasis. Despite the recent advances in the characterization of these molecular switches, our understanding of the role of miRNAs in regulating lipid metabolism and atherosclerosis is still limited. Technological advances facilitate the genome-wide identification and quantification of miRNAs, as well as the identification of differentially expressed (DE) miRNAs. Aim. To identify DE miRNAs involved in either the regulation of cholesterol metabolism or atherosclerosis development. Methods. Six weeks old C57BL/6J mice as controls, hyperlipidemic/atherosclerosis-prone LdlrKO and hypolipidemic/atherosclerosis-resistant Pcsk9KO mice were fed either standard (CHOW) or Western-type (WD) diet for 16 weeks. At sacrifice, aorta, liver, small intestine, white adipose tissue, heart and brain were harvested. Small RNA was extracted from all tissues, sequenced with an Illumina Genome Analyzer IIx and analyzed with up to date bioinformatics and statistical approaches. Results. Analyses revealed more DE miRNAs in organs of LdlrKO mice vs Pcsk9KO and C57BL/6J than in Pcsk9KO vs C57BL/6J. As expected, Pcsk9KO vs C57BL/6J comparison yielded fewer DE miRNAs in all organs and dietary treatments. WD increased the number of DE miRNAs in all genotypes. Interestingly, liver and brain showed the highest number of DE miRNAs. Conclusions. We correctly identified DE miRNAs already known to play a role in cholesterol metabolism, such as miR-33a/b, miR143/145, mir27a/b, miR-155, miR-128 and miR-370. Other DE miRNAs showing similar expression pattern have predicted targets among the cholesterol metabolism related genes, but no target genes have been validated so far. DE miRNAs amongst samples are commented and reviewed, and predicted potential gene targets candidates are discussed.