title: Genome-wide analysis of DNA methylation differences in muscle and fat from monozygotic twins discordant for type 2 diabetes.
abstract: BACKGROUND
  Monozygotic twins discordant for type 2 diabetes constitute an ideal model to study environmental contributions to type 2 diabetic traits. We aimed to examine whether global DNA methylation differences exist in major glucose metabolic tissues from these twins.
  
  
  RESULTS
  Skeletal muscle (n = 11 pairs) and subcutaneous adipose tissue (n = 5 pairs) biopsies were collected from 53-80 year-old monozygotic twin pairs discordant for type 2 diabetes. DNA methylation was measured by microarrays at 26,850 cytosine-guanine dinucleotide (CpG) sites in the promoters of 14,279 genes. Bisulfite sequencing was applied to validate array data and to quantify methylation of intergenic repetitive DNA sequences. The overall intra-pair variation in DNA methylation was large in repetitive (LINE1, D4Z4 and NBL2) regions compared to gene promoters (standard deviation of intra-pair differences: 10% points vs. 4% points, P<0.001). Increased variation of LINE1 sequence methylation was associated with more phenotypic dissimilarity measured as body mass index (r = 0.77, P = 0.007) and 2-hour plasma glucose (r = 0.66, P = 0.03) whereas the variation in promoter methylation did not associate with phenotypic differences. Validated methylation changes were identified in the promoters of known type 2 diabetes-related genes, including PPARGC1A in muscle (13.9±6.2% vs. 9.0±4.5%, P = 0.03) and HNF4A in adipose tissue (75.2±3.8% vs. 70.5±3.7%, P<0.001) which had increased methylation in type 2 diabetic individuals. A hypothesis-free genome-wide exploration of differential methylation without correction for multiple testing identified 789 and 1,458 CpG sites in skeletal muscle and adipose tissue, respectively. These methylation changes only reached some percentage points, and few sites passed correction for multiple testing.
  
  
  CONCLUSIONS
  Our study suggests that likely acquired DNA methylation changes in skeletal muscle or adipose tissue gene promoters are quantitatively small between type 2 diabetic and non-diabetic twins. The importance of methylation changes in candidate genes such as PPARGC1A and HNF4A should be examined further by replication in larger samples.
authors.affiliation: Steno Diabetes Center, Gentofte, Denmark. rrm@sund.ku.dk
authors.forename: Rasmus
authors.initials: R
authors.lastname: Ribel-Madsen
authors.forename: Mario F
authors.initials: MF
authors.lastname: Fraga
authors.forename: Stine
authors.initials: S
authors.lastname: Jacobsen
authors.forename: Jette
authors.initials: J
authors.lastname: Bork-Jensen
authors.forename: Ester
authors.initials: E
authors.lastname: Lara
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Calvanese
authors.forename: Agustin F
authors.initials: AF
authors.lastname: Fernandez
authors.forename: Martin
authors.initials: M
authors.lastname: Friedrichsen
authors.forename: Birgitte F
authors.initials: BF
authors.lastname: Vind
authors.forename: Kurt
authors.initials: K
authors.lastname: Højlund
authors.forename: Henning
authors.initials: H
authors.lastname: Beck-Nielsen
authors.forename: Manel
authors.initials: M
authors.lastname: Esteller
authors.forename: Allan
authors.initials: A
authors.lastname: Vaag
authors.forename: Pernille
authors.initials: P
authors.lastname: Poulsen
mesh_terms: D000273:Adipose Tissue / Q000378:metabolism*; D019175:DNA Methylation; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics / Q000378:metabolism*; D055106:Genome-Wide Association Study; D006801:Humans; D018482:Muscle, Skeletal / Q000378:metabolism*; D014430:Twins, Monozygotic