Systems genetics identifies a co-regulated module of liver microRNAs associated with plasma LDL cholesterol in murine diet-induced dyslipidemia

Abstract

Chronically altered levels of circulating lipids, termed dyslipidemia, is a significant risk factor for a number of metabolic and cardiovascular morbidities. MicroRNAs (miRNAs) have emerged as important regulators of lipid balance, have been implicated in dyslipidemia, and have been proposed as candidate therapeutic targets in lipid-related disorders including atherosclerosis. A major limitation of most murine studies of miRNAs in lipid metabolic disorders is that they have been performed in just one (or very few) inbred strains, such as C57BL/6. Moreover, although individual miRNAs have been associated with lipid phenotypes, it is well understood that miRNAs likely work together in functional modules. To address these limitations, we implemented a systems genetics strategy using the Diversity Outbred (DO) mouse population. Specifically, we performed gene and miRNA expression profiling in the livers from ~300 genetically distinct DO mice after 18 wk on either a high-fat/high-cholesterol diet or a high-protein diet. Large-scale correlative analysis of these data with a wide range of cardio-metabolic end points revealed a co-regulated module of miRNAs significantly associated with circulating low-density lipoprotein cholesterol (LDL-C) levels. The hubs of this module were identified as miR-199a, miR-181b, miR-27a, miR-21_-_1, and miR-24. In sum, we demonstrate that a high-fat/high-cholesterol diet robustly rewires the miRNA regulatory network, and we identify a small group of co-regulated miRNAs that may exert coordinated effects to control circulating LDL-C.

RETRACTED: Genetic Architecture Modulates Diet-Induced Hepatic mRNA and miRNA Expression Profiles in Diversity Outbred Mice

“…We have previously reported that diet significantly affects miRNA and mRNA expression in the DO population ( Coffey et al 2017 ). Moreover, having identified relationships between expression and genetic architecture, we sought to explore the effect of diet by comparing the cis and trans architecture of eQTL from separate genome scans of HFCA-fed mice ( n = 134) and HP-fed mice ( n = 114).…”

“…Given our previous reports of diet effects on hepatic gene expression ( Coffey et al 2017 , 2019 ) and our observation of differing correlative structures between homologous GWAS candidate genes and traits in the DO population, we hypothesized that diet could affect the overall structure of eQTL and mirQTL. Thus, we performed eQTL and mirQTL analysis with diet as an interactive covariate and identified 6155 significant eQTL and 23 mirQTL (Figure S6, A and B), after completing individual permutation thresholds ( Table 1 ).…”

“…Details of the mouse experiments have been reported previously ( Smallwood et al 2014 ; Coffey et al 2017 , 2019 ). In brief, 292 female DO mice (J:DO, Jackson Laboratory stock number 009376, outbreeding generation 11) were obtained from the Jackson Laboratory (Bar Harbor, ME) as 146 full sibling pairs at 4 weeks of age.…”

“…To determine the effect of diet on hepatic mRNA and miRNA, we performed differential gene expression analysis. Transcripts with a robust multiarray average value of four or greater in at least 25% of samples were included ( Coffey et al 2017 ), which resulted in 11,377 transcripts and 246 miRNA. The Wilcoxon rank-sum test was performed for both miRNA and mRNA data and P -values were corrected using the BH method.…”

Adropin: An endocrine link between the biological clock and cholesterol homeostasis

“…The third experiment examined the effect of dietary cholesterol on Enho expression in liver of mice from DO mouse population developed from eight inbred strains of mice [31] . Full details on animal handling, feeding, measurement of phenotypes, and microarray analysis were previously published [32] , [33] . Briefly, a cohort of 288 DO mice were fed either an atherogenic high-fat, high-cholesterol diet with cholic acid (HFCA, n = 144) or a calorie-matched non-atherogenic high protein (HP, n = 144) diet for 18 wk.…”