The large non-coding RNA ANRIL, which is associated with atherosclerosis, periodontitis and several forms of cancer, regulates ADIPOR1, VAMP3 and C11ORF10

Hum Mol Genet. 2013 Nov 15;22(22):4516-27. doi: 10.1093/hmg/ddt299. Epub 2013 Jun 27.

Abstract

The long non-coding RNA ANRIL is the best replicated genetic risk locus of coronary artery disease (CAD) and periodontitis (PD), and is independently associated with a variety of other immune-mediated and metabolic disorders and several forms of cancer. Recent studies showed a correlation of decreased concentrations of proximal ANRIL transcripts with homozygous carriership of the CAD and PD main risk alleles. To elucidate the relation of these transcripts to disease manifestation, we constructed a short hairpin RNA in a stable inducible knock-down system of T-Rex 293 HEK cell lines, specifically targeting the proximal transcripts EU741058 and DQ485454. By genome-wide expression profiling using Affymetrix HG1.0 ST Arrays, we identified the transcription of ADIPOR1, VAMP3 and C11ORF10 to be correlated with decreased ANRIL expression in a time-dependent manner. We validated these findings on a transcriptional and translational level in different cell types. Exploration of the identified genes for the presence of disease associated variants, using Affymetrix 500K genotyping and Illumina custom genotyping arrays, highlighted a region upstream of VAMP3 within CAMTA1 to be associated with increased risk of CAD [rs10864294 P = 0.015, odds ratio (OR) = 1.30, 95% confidence interval (CI) = 1.1-1.6, 1471 cases, 2737 controls] and aggressive PD (AgP; P = 0.008, OR = 1.31, 95% CI = 1.1-1.6, 864 cases, 3664 controls). In silico replication in a meta-analysis of 14 genome-wide association studies of CAD of the CARDIoGRAM Consortium identified rs2301462, located on the same haplotype block, as associated with P = 0.001 upon adjustment for sex and age. Our results give evidence that specific isoforms of ANRIL regulate key genes of glucose and fatty acid metabolism.

MeSH terms

  • Atherosclerosis / genetics
  • Atherosclerosis / pathology
  • Coronary Artery Disease / genetics*
  • Coronary Artery Disease / pathology
  • Fatty Acids / metabolism
  • Gene Expression Regulation
  • Gene Knockdown Techniques
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study
  • Genotype
  • Glucose / metabolism
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Neoplasms / genetics*
  • Neoplasms / pathology
  • Oligonucleotide Array Sequence Analysis
  • Periodontitis / genetics*
  • Periodontitis / pathology
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / metabolism
  • Receptors, Adiponectin / genetics*
  • Time Factors
  • Transcription Factors / genetics*
  • Vesicle-Associated Membrane Protein 3 / genetics*

Substances

  • ADIPOR1 protein, human
  • ANRIL long non-coding RNA, human
  • Fatty Acids
  • Protein Isoforms
  • RASSF7 protein, human
  • RNA, Long Noncoding
  • Receptors, Adiponectin
  • Transcription Factors
  • VAMP3 protein, human
  • Vesicle-Associated Membrane Protein 3
  • Glucose