Integrated miRNomic and lipidomic analysis in mice for the identification of novel miRNAs involved in lipid metabolism

Abstract

Background and aims: The miRNomic and lipidomic profiles of mice with specific genotypes/phenotypes were integrated with a novel approach, with the aim of increasing our knowledge on the mutual interplay between miRNAs and lipids, and thus to discover previously uncharacterized miRNAs, potentially playing a role in lipid metabolism.
Methods: miRNomic and lipidomic analyses were performed in wild-type, Pcsk9 and Ldlr knockout mice fed normal laboratory diet or Western diet. Small RNA was extracted from liver, brain, duodenum, jejunum, ileum and abdominal white adipose tissue and quantified by RNAseq. Lipid species were quantified by high-throughput mass-spectrometry in liver, aorta and plasma. miRNA expression levels were tested for correlations with each lipid measurement in different samples. Highly correlated, uncharacterized miRNAs were subjected to testing in vitro in murine hepatoma Hepa1-6 cells. For each miRNA to be tested, cells were transfected with the miRNA mimic, the miRNA inhibitor and a non-target control. After 24-hours incubation, the cellular content of cholesterol and triglycerides was measured. For each miRNA, at least three independent experiments were carried out.
Results: Correlation analyses between miRNA expression levels and lipid concentrations in the different experimental conditions led to the selection of miRNAs potentially playing a major role in the regulation of lipid levels. Correlations mainly clustered in liver. Among selected miRNAs, some were already known to be related to lipid metabolism (miR-33, miR-210 and miR-21a) whereas others, including miR-431-5p, miR-434-3p, miR-434-5p and miR-677-5p had never been associated to lipid changes before. In vitro experiments allowed to highlight a potential role of miR-431-5p and miR-677-5p in the modulation of total cholesterol and triglyceride concentrations.
Conclusions: This study, bridging miRNomic and lipidomic data in well characterized mouse models, allowed to identify novel miRNAs potentially playing a role in the modulation of lipid levels.