title: Genome-wide DNA methylation profiling of peripheral blood mononuclear cells in irritable bowel syndrome.
abstract: BACKGROUND
  Irritable bowel syndrome (IBS) is a stress-sensitive disorder. Environmental factors including stress can trigger epigenetic changes, which have not been well-studied in IBS. We performed a pilot study investigating genome-wide DNA methylation of IBS patients and healthy controls (HCs) to identify potential epigenetic markers and associated pathways. Additionally, we investigated relationships of epigenetic changes in selected genes with clinical traits.
  
  
  METHODS
  Twenty-seven IBS patients (59% women; 10 IBS-diarrhea, 8 IBS-constipation, 9 IBS-mixed) and 23 age- and sex-matched HCs were examined. DNA methylation from peripheral blood mononuclear cells (PBMCs) was measured using HM450 BeadChip, and representative methylation differences were confirmed by bisulphite sequencing. Gene expression was measured using quantitative PCR. Gastrointestinal (GI) and non-GI symptoms were measured using validated questionnaires. Associations were tested using non-parametric methods.
  
  
  RESULTS
  Genome-wide DNA methylation profiling of IBS patients compared with HCs identified 133 differentially methylated positions (DMPs) (mean difference ≥10%; p < 0.05). These genes were associated with gene ontology terms including glutathione metabolism related to oxidative stress and neuropeptide hormone activity. Validation by sequencing confirmed differential methylation of subcommissural organ (SCO)-Spondin (SSPO), glutathione-S-transferases mu 5 (GSTM5), and tubulin polymerization promoting protein genes. Methylation of two promoter CpGs in GSTM5 was associated with epigenetic silencing. Epigenetic changes in SSPO gene were positively correlated with hospital anxiety and depression scores in IBS patients (r > 0.4 and false discovery rate <0.05).
  
  
  CONCLUSIONS
  This study is the first to comprehensively explore the methylome of IBS patients. We identified DMPs in novel candidate genes which could provide new insights into disease mechanisms; however, these preliminary findings warrant confirmation in larger, independent studies.
authors.affiliation: Oppenheimer Center for Neurobiology of Stress at UCLA, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
authors.forename: S
authors.initials: S
authors.lastname: Mahurkar
authors.affiliation: Center for Systems Biomedicine, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
authors.forename: C
authors.initials: C
authors.lastname: Polytarchou
authors.affiliation: Center for Systems Biomedicine, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
authors.forename: D
authors.initials: D
authors.lastname: Iliopoulos
authors.affiliation: Department of Medicine, Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
authors.forename: C
authors.initials: C
authors.lastname: Pothoulakis
authors.affiliation: Oppenheimer Center for Neurobiology of Stress at UCLA, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
authors.forename: E A
authors.initials: EA
authors.lastname: Mayer
authors.affiliation: Oppenheimer Center for Neurobiology of Stress at UCLA, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
authors.forename: L
authors.initials: L
authors.lastname: Chang
mesh_terms: D000328:Adult; D019175:DNA Methylation; D005260:Female; D055106:Genome-Wide Association Study; D006801:Humans; D043183:Irritable Bowel Syndrome / Q000235:genetics*; D007963:Leukocytes, Mononuclear / Q000378:metabolism*; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D010865:Pilot Projects; D016133:Polymerase Chain Reaction; D013312:Stress, Physiological / Q000235:genetics*
keywords: DNA methylation; bisulphite sequencing; human methylation 450 array; irritable bowel syndrome; oxidative stress