Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells

Abstract

Increased physiological levels of oxysterols are major risk factors for developing atherosclerosis and cardiovascular disease. Lipid-loaded macrophages, termed foam cells, are important during the early development of atherosclerotic plaques. To pursue the hypothesis that ligand-based modulation of the nuclear receptor LXRα is crucial for cell homeostasis during atherosclerotic processes, we analysed genome-wide the action of LXRα in foam cells and macrophages. By integrating chromatin immunoprecipitation-sequencing (ChIP-seq) and gene expression profile analyses, we generated a highly stringent set of 186 LXRα target genes. Treatment with the nanomolar-binding ligand T0901317 and subsequent auto-regulatory LXRα activation resulted in sequence-dependent sharpening of the genome-binding patterns of LXRα. LXRα-binding loci that correlated with differential gene expression revealed 32 novel target genes with potential beneficial effects, which in part explained the implications of disease-associated genetic variation data. These observations identified highly integrated LXRα ligand-dependent transcriptional networks, including the APOE/C1/C4/C2-gene cluster, which contribute to the reversal of cholesterol efflux and the dampening of inflammation processes in foam cells to prevent atherogenesis.

Liver X Receptor Activation Promotes Polyunsaturated Fatty Acid Synthesis in Macrophages

“…27 Interestingly, a recent Chip-sequencing survey performed in human macrophages showed a potential LXR binding site in ELOVL5 gene ≈10 000 bp upstream from the transcription start site. 28 To address the functionality of this potential LXRE in the ELOVL5 gene, the corresponding element (DR4 element: GGGTAAttccCGGGCA) was cloned upstream of a thymidine kinase promoter-luciferase vector or added to the proximal ELOVL5 promoter (−1000 bp) cloned into a pGL3 luciferase reporter vector. In both cases the activity of the promoters was significantly increased in HEK293T (human embryonic kidney 293) cells cotransfected with LXRα and RXRα expression vectors and treated with T0901317 ( Figure 2C).…”

“…23 We showed here that ELOVL5 is also a direct LXR target gene in human macrophages and that a potential LXRE identified previously by Chip-sequencing is fully functional. 28 In contrast to ACSLs and elongases, no redundancy exists for the ∆5 and ∆6 desaturases (FADS1 and FADS2), which are unique in the human genome and are absolutely required for PUFA synthesis. 34 Moreover, ∆6 desaturation has been described as the limiting step for long chain PUFA synthesis.…”

Network analysis: a new approach to study endocrine disorders

“…A recent study has used integrative genomic analysis to understand LXRa-dependent functional characteristics and transcriptional regulation pathways (Feldmann et al 2013). Several SNPs within LXRa-dependent binding sites were found to have differentially expressed target genes involved in the biological processes linked to inflammation, cell growth and apoptosis.…”

“…To analyse the role of LXRa modulation in atherosclerosis and related diseases, a human macrophage and foam cell network model was used to investigate the actions of a synthetic LXR agonist -T0901317, which has a potential atheroprotective role. By using transcriptional network analysis, highly integrated LXRa ligand-dependent transcriptional clusters were detected which contribute to the reversal of cholesterol efflux and the dampening of inflammation processes in the foam cells (Feldmann et al 2013). An important implication of these data is that network analysis in this field is helping the understanding of molecular mechanisms governing atherogenesis, which has relevance to therapeutic strategies to prevent atherosclerosis.…”

Protein set analyses: how could this impact the clinic?

“…Nevertheless, recent genome-wide association studies (GWAS) revealed that for many multifactorial diseases, the disease phenotypes cannot be mono-causally derived from the action of individual genes or proteins [2]. These genetic and other functional analyses not surprisingly indicated that (slowly developing) complex diseases such as atherosclerosis are rather the result of the rising deregulation of interconnected genes or the dysfunction of molecular pathways [3]. In this context, cellular clusters of chemically modifiable proteins exert many important biological functions, closely at the solubility equilibrium in the cell.…”