Research Article: Identification of coordinately regulated microRNA-gene networks that differ in baboons discordant for LDL-cholesterol

Date Published: March 15, 2019

Publisher: Public Library of Science

Author(s): Genesio M. Karere, Jeremy P. Glenn, Shifra Birnbaum, Roy Garcia, John L. VandeBerg, Laura A. Cox, Peng Yu.


Plasma low-density lipoprotein cholesterol (plasma LDL-C), vascular endothelial cells and peripheral blood mononuclear cells (PBMCs), particularly monocytes, play key roles in initiating atherosclerosis, the primary cause of cardiovascular disease (CVD). Although the mechanisms underlying development of atherosclerosis are not well understood, LDL-C is known to influence expression of endothelial microRNAs (miRNAs) and gene-targets of miRNAs to promote cell senescence. However, the impact of LDL-C on expression of PBMC miRNAs and miRNA targeted genes in response to an atherogenic diet is not known. In this study, we used unbiased methods to identify coordinately responsive PBMC miRNA- gene networks that differ between low and high LDL-C baboons when fed a high-cholesterol, high-fat (HCHF) diet.

Using RNA Seq, we quantified PBMC mRNAs and miRNAs from half-sib baboons discordant for LDL-C plasma concentrations (low LDL-C, n = 3; high LDL-C, n = 3) before and after a 7-week HCHF diet challenge. For low LDL-C baboons, 626 genes exhibited significant change in expression (255 down-regulated, 371 up-regulated) in response to the HCHF diet, and for high LDL-C baboons 379 genes exhibited significant change in expression (162 down-regulated, 217 up-regulated) in response to the HCHF diet. We identified 494 miRNAs identical to human miRNAs and 47 novel miRNAs. Fifty miRNAs were differentially expressed in low LDL-C baboons (21 up- and 29 down-regulated) and 20 in high LDL-C baboons (11 up- and 9 down-regulated) in response to the HCHF diet. Among the differentially expressed miRNAs were miR-221/222 and miR-34a-3p, which were down-regulated, and miR-148a/b-5p, which was up-regulated. In addition, gene-targets of these miRNAs, VEGFA, MAML3, SPARC, and DMGDH, were inversely expressed and are central hub genes in networks and signaling pathways that differ between low and high LDL-C baboon HCHF diet response.

We have identified coordinately regulated HCHF diet-responsive PBMC miRNA-gene networks that differ between baboons discordant for LDL-C concentrations. Our findings provide potential insights into molecular mechanisms underlying initiation of atherosclerosis where LDL-C concentrations influence expression of specific miRNAs, which in turn regulate expression of genes that play roles in initiation of lesions.

Partial Text

Cardiovascular disease (CVD), the leading cause of morbidity and mortality in developed countries [1,2], is commonly associated with development of atherosclerosis. The pathophysiological characteristics of atherosclerosis are a consequence of interactions between genetic and environmental factors including diet. Clinical and epidemiological studies indicate that atherosclerotic burden is positively correlated with plasma LDL-C concentrations [3–6], and high LDL-C concentration is a major risk factor or atherosclerosis [7].

Plasma high LDL-C concentration is a major risk factor for atherosclerosis, the leading cause of CVD. LDL-C contributes greatly to the development and progression of atherosclerosis by inducing the expression of EC adhesion molecules and ameliorating endothelial cell apoptosis. Various studies have shown that LDL-C particles, particularly when oxidized, induce EC apoptosis by altering the expression of miRNAs or miRNA target genes in vitro [11, 12]. In addition, PBMCs, particularly monocytes play a key role during initiation of atherogenesis, where they infiltrate vascular intima and differentiate to macrophages, triggering a cascade of inflammatory signals. Further, recent studies have demonstrated that monocyte-derived exosomes transport miRNAs that activate adhesion molecules of EC in vitro [22, 23]. Previously, we showed that LDL-C concentrations influence the expression of hepatic miRNAs in response to a HCHF diet [13]. In the current study, we aimed to assess differential expression of PBMC miRNAs and miRNA gene-targets in baboons differing in LDL-C response to a HFHC diet, together with identification of coordinately expressed miRNAs and miRNA gene-targets using unbiased methods. To address these aims we combined high throughput RNA sequencing together with bioinformatics, including TargetScan software embedded in IPA, EM algorithm in Partek package, GO and KEGG pathway analysis. To our knowledge this is the first study to interrogate the expression of miRNAs and miRNA targets in PBMCs in response to a HCHF diet challenge in nonhuman primates discordant forLDL-C response to a dietary challenge.




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