title: DNA methylation in ductal carcinoma in situ related with future development of invasive breast cancer.
abstract: BACKGROUND
  Ductal carcinoma in situ (DCIS) is a heterogeneous, pre-invasive lesion associated with an increased risk for future invasive ductal carcinoma. However, accurate risk stratification for development of invasive disease and appropriate treatment decisions remain clinical challenges. DNA methylation alterations are early events in the progression of cancer and represent emerging molecular markers that may predict invasive recurrence more accurately than traditional measures of DCIS prognosis.
  
  
  RESULTS
  We measured DNA methylation using the Illumina HumanMethylation450K array of estrogen-receptor positive DCIS (n = 40) and adjacent-normal (n = 15) tissues from subjects in the New Hampshire Mammography Network longitudinal breast imaging registry. We identified locus-specific methylation differences between DCIS and matched adjacent-normal tissue (95,609 CpGs, Q < 0.05). Among 40 DCIS cases, 13 later developed invasive disease and we identified 641 CpG sites that exhibited differential DNA methylation (P < 0.01 and median |∆β| > 0.1) in these cases compared with age-matched subjects without invasive disease. The set of differentially methylated CpG loci associated with disease progression was enriched in homeobox-containing genes (P = 1.3E-09) and genes involved with limb morphogenesis (P = 1.0E-05). In an independent cohort, a subset of genes with progression-related differential methylation between DCIS and invasive breast cancer were confirmed. Further, the functional relevance of these genes' regulation by methylation was demonstrated in early stage breast cancers from The Cancer Genome Atlas database.
  
  
  CONCLUSIONS
  This work contributes to the understanding of epigenetic alterations that occur in DCIS and illustrates the potential of DNA methylation as markers of DCIS progression.
authors.affiliation: Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA.
authors.forename: Kevin C
authors.initials: KC
authors.lastname: Johnson
authors.affiliation: Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS USA.
authors.forename: Devin C
authors.initials: DC
authors.lastname: Koestler
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway ; The K.G. Jebsen Center for Breast Cancer, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
authors.forename: Thomas
authors.initials: T
authors.lastname: Fleischer
authors.affiliation: Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA.
authors.forename: Panpan
authors.initials: P
authors.lastname: Chen
authors.affiliation: Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA.
authors.forename: Erik G
authors.initials: EG
authors.lastname: Jenson
authors.affiliation: Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Marotti
authors.affiliation: Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA ; The Dartmouth Institute, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766 USA.
authors.forename: Tracy
authors.initials: T
authors.lastname: Onega
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway ; The K.G. Jebsen Center for Breast Cancer, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway ; Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus Hospital, Lørenskog, Norway.
authors.forename: Vessela N
authors.initials: VN
authors.lastname: Kristensen
authors.affiliation: Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA.
authors.forename: Brock C
authors.initials: BC
authors.lastname: Christensen
keywords: Array; Breast; Cancer; DCIS; Methylation; TCGA