title: Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases.
abstract: BACKGROUND
  Crohn's disease (CD) and ulcerative colitis (UC) are common forms of inflammatory bowel disease (IBD). Monozygotic (MZ) twin discordance rates and epidemiologic data implicate that environmental changes and epigenetic factors may play a pathogenic role in IBD. DNA methylation (the methylation of cytosines within CpG dinucleotides) is an epigenetic modification, which can respond to environmental influences. We investigated whether DNA methylation might be connected with IBD in peripheral blood leukocyte (PBL) DNA by utilizing genome-wide microarrays.
  
  
  METHODS
  Two different high-throughput microarray-based methods for genome-wide DNA methylation analysis were employed. First, DNA isolated from MZ twin pairs concordant (CD: 4; UC: 3) and discordant (CD: 4; UC: 7) for IBD was interrogated by a custom-made methylation-specific amplification microarray (MSAM). Second, the recently developed Illumina Infinium HumanMethylation450 BeadChip arrays were used on 48 samples of PBL DNA from discordant MZ twin pairs (CD: 3; UC: 3) and treatment-naive pediatric cases of IBD (CD: 14; UC: 8), as well as controls (n = 14). The microarrays were validated with bisulfite pyrosequencing.
  
  
  RESULTS
  The MSAMs did not yield significant IBD associations. The Methylation BeadChip approach identified a single DNA methylation association of IBD at TEPP (testis, prostate and placenta-expressed protein) when DNA isolated selectively from peripheral blood mononuclear cells was analyzed (8.6% increase in methylation between CD and control, FDR = 0.0065).
  
  
  CONCLUSIONS
  Microarray interrogation of IBD-dependent DNA methylation from PBLs appears to have limited ability to detect significant disease associations. More detailed and/or selective approaches may be useful for the elucidation of connections between the DNA methylome and IBD in the future.
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: R Alan
authors.initials: RA
authors.lastname: Harris
authors.forename: Dorottya
authors.initials: D
authors.lastname: Nagy-Szakal
authors.forename: Natalia
authors.initials: N
authors.lastname: Pedersen
authors.forename: Antone
authors.initials: A
authors.lastname: Opekun
authors.forename: Jiri
authors.initials: J
authors.lastname: Bronsky
authors.forename: Pia
authors.initials: P
authors.lastname: Munkholm
authors.forename: Cathrine
authors.initials: C
authors.lastname: Jespersgaard
authors.forename: PaalSkytt
authors.initials: P
authors.lastname: Andersen
authors.forename: Bela
authors.initials: B
authors.lastname: Melegh
authors.forename: George
authors.initials: G
authors.lastname: Ferry
authors.forename: Tine
authors.initials: T
authors.lastname: Jess
authors.forename: Richard
authors.initials: R
authors.lastname: Kellermayer
mesh_terms: D000328:Adult; D019175:DNA Methylation / Q000235:genetics*; D004200:Diseases in Twins / Q000235:genetics; D005260:Female; D055106:Genome-Wide Association Study / Q000379:methods; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000235:genetics*; D007963:Leukocytes, Mononuclear / Q000378:metabolism*; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D014430:Twins, Monozygotic / Q000235:genetics; D055815:Young Adult