title: Genome-wide analysis of DNA methylation in subjects with type 1 diabetes identifies epigenetic modifications associated with proliferative diabetic retinopathy.
abstract: BACKGROUND
  Epigenetic variation has been linked to several human diseases. Proliferative diabetic retinopathy (PDR) is a major cause of vision loss in subjects with diabetes. However, studies examining the association between PDR and the genome-wide DNA methylation pattern are lacking. Our aim was to identify epigenetic modifications that associate with and predict PDR in subjects with type 1 diabetes (T1D).
  
  
  METHODS
  DNA methylation was analyzed genome-wide in 485,577 sites in blood from cases with PDR (n = 28), controls (n = 30), and in a prospective cohort (n = 7). False discovery rate analysis was used to correct the data for multiple testing. Study participants with T1D diagnosed before 30 years of age and insulin treatment within 1 year from diagnosis were selected based on 1) subjects classified as having PDR (cases) and 2) subjects with T1D who had had diabetes for at least 10 years when blood DNA was sampled and classified as having no/mild diabetic retinopathy also after an 8.7-year follow-up (controls). DNA methylation was also analyzed in a prospective cohort including seven subjects with T1D who had no/mild diabetic retinopathy when blood samples were taken, but who developed PDR within 6.3 years (converters). The retinopathy level was classified by fundus photography.
  
  
  RESULTS
  We identified differential DNA methylation of 349 CpG sites representing 233 unique genes including TNF, CHI3L1 (also known as YKL-40), CHN2, GIPR, GLRA1, GPX1, AHRR, and BCOR in cases with PDR compared with controls. The majority of these sites (79 %) showed decreased DNA methylation in cases with PDR. The Natural Killer cell-mediated cytotoxicity pathway was found to be significantly (P = 0.006) enriched among differentially methylated genes in cases with PDR. We also identified differential DNA methylation of 28 CpG sites representing 17 genes (e.g. AHRR, GIPR, GLRA1, and BCOR) with P <0.05 in the prospective cohort, which is more than expected by chance (P = 0.0096).
  
  
  CONCLUSIONS
  Subjects with T1D and PDR exhibit altered DNA methylation patterns in blood. Some of these epigenetic changes may predict the development of PDR, suggesting that DNA methylation may be used as a prospective marker of PDR.
authors.affiliation: Department of Clinical Sciences, Ophthalmology, Lund University, Scania University Hospital, 205 02, Malmö, Sweden. elisabet.agardh@med.lu.se.
authors.forename: Elisabet
authors.initials: E
authors.lastname: Agardh
authors.affiliation: Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden. lundstig@telia.com.
authors.forename: Annika
authors.initials: A
authors.lastname: Lundstig
authors.affiliation: Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden. alexander.perfilyev@med.lu.se.
authors.forename: Alexander
authors.initials: A
authors.lastname: Perfilyev
authors.affiliation: Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden. petr.volkov@med.lu.se.
authors.forename: Petr
authors.initials: P
authors.lastname: Volkov
authors.affiliation: Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden. tovefreiburghaus@gmail.com.
authors.forename: Tove
authors.initials: T
authors.lastname: Freiburghaus
authors.affiliation: Department of Clinical Sciences, Endocrinology, Lund University, Scania University Hospital, 205 02, Malmö, Sweden. eero.lindholm@med.lu.se.
authors.forename: Eero
authors.initials: E
authors.lastname: Lindholm
authors.affiliation: Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden. tina.ronn@med.lu.se.
authors.forename: Tina
authors.initials: T
authors.lastname: Rönn
authors.affiliation: Department of Clinical Sciences, Endocrinology, Lund University, Scania University Hospital, 205 02, Malmö, Sweden. Carl-david.agardh@med.lu.se.
authors.forename: Carl-David
authors.initials: CD
authors.lastname: Agardh
authors.affiliation: Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden. charlotte.ling@med.lu.se.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Ling
mesh_terms: D000328:Adult; D015331:Cohort Studies; D019175:DNA Methylation / Q000235:genetics*; D003922:Diabetes Mellitus, Type 1 / Q000150:complications / Q000235:genetics*; D003930:Diabetic Retinopathy / Q000175:diagnosis / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006801:Humans; D008297:Male; D008875:Middle Aged; D011446:Prospective Studies