induction of the long noncoding RNA ... MeXis in response to LXR activation amplifies LXR-dependent Abca1 transcription in macrophages

Activation of ligand-dependent liver X receptors (LXRs) promotes cholesterol transport in macrophages through the induction of genes such as Abca1, which encodes a cholesterol efflux transporter crucial for the generation of HDL. A new study now shows that induction of the long noncoding RNA (lncRNA) MeXis in response to LXR activation amplifies LXR-dependent Abca1 transcription in macrophages. This finding provides new insights into the molecular mechanisms controlling cellular cholesterol homeostasis and the pathogenesis of atherosclerosis, and expands our understanding of the cell-type-selective response of LXR.

“We wondered why Abca1 is very robustly induced with LXR activation in macrophages, but minimally induced in the liver,” says study investigator Tamer Sallam. To study the mechanisms regulating LXR-dependent transcription, the researchers first performed genome-wide transcriptional profiling of mouse peritoneal macrophages treated with or without the LXR agonist GW3965. In addition to inducing well-known LXR target genes, LXR activation induced genes encoding lncRNAs. One of the most strongly induced was a gene localized close to Abca1, which the investigators named MeXis (for macrophage-expressed LXR-induced sequence).

Credit: V. Summersby/Macmillan Publishers Limited

Next, Sallam and colleagues showed that MeXis regulates Abca1 expression and function. In vitro, siRNA-mediated MeXis knockdown or use of an antisense oligonucleotide targeting MeXis led to a reduction in Abca1 expression in mouse peritoneal macrophages. MeXis overexpression increased Abca1 levels and cholesterol efflux capacity. Consistent with these findings, mice with MeXis deficiency fed a Western diet had lower Abca1 expression than wild-type mice. Loss of MeXis altered Abca1 expression in a tissue-specific manner: Abca1 expression was lower in the heart, kidney, and macrophages of MeXis-deficient mice compared with wild-type mice, but liver Abca1 levels were similar in both groups. Peritoneal macrophages from MeXis-deficient mice fed a Western diet had higher cholesterol levels than those in wild-type mice, with no differences in plasma lipid levels between the groups.

To assess the role of MeXis in atherosclerosis, the investigators reconstituted the bone marrow of irradiated Ldlr−/− mice with wild-type or MeXis−/− bone marrow cells and analysed the atherosclerotic plaques after 17 weeks of Western diet feeding. Loss of MeXis in bone marrow cells was associated with a significant increase in atherosclerosis burden, with increased macrophage numbers in the plaques and decreased Abca1 expression in plaque macrophages.

MeXis modulates Abca1 transcription by altering chromosome architecture at the Abca1 gene locus. An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) in peritoneal macrophages showed that MeXis deficiency led to blunted accessibility at multiple sites in the Abca1 gene locus. Further studies revealed that MeXis interacts with and guides binding of DDX17, a nuclear receptor coactivator, to LXR binding sites in Abca1 enhancer regions.

Finally, Sallam and colleagues assessed the relevance of these findings in humans and found that the genomic region surrounding the MeXis–Abca1 locus had a degree of conservation between human and mouse genomes. The investigators identified a noncoding RNA induced in response to LXR activation in a human macrophage cell line. Antisense oligonucleotide targeting of this RNA transcript reduced ABCA1 levels, whereas lentiviral transduction of MeXis increased ABCA1 expression. A genome-wide association study identified a moderately significant association between a single nucleotide polymorphism in this RNA transcript and coronary artery disease.

“We do not think that MeXis entirely explains why LXRs differentially regulate Abca1,” points out Sallam, “but our results suggest that lncRNAs play important roles in the context-specific effects of nuclear receptors. We still have a long way to go but, based on the proposed function of MeXis, it is conceivable that figuring out ways to boost MeXis levels within lesions may reduce heart disease burden,” concludes Sallam.