title: Altered DNA methylation landscapes of polycomb-repressed loci are associated with prostate cancer progression and ERG oncogene expression in prostate cancer.
abstract: OBJECTIVE
  To assess differentially methylated "landscapes" according to prostate cancer Gleason score (GS) and ERG oncogene expression status, and to determine the extent of polycomb group (PcG) target gene involvement, we sought to assess the genome-wide DNA methylation profile of prostate cancer according to Gleason score and ERG expression.
  
  
  METHODS
  Genomic DNA from 39 prostate cancer specimens was hybridized to CpG island microarrays through differential methylation hybridization. We compared methylation profiles between Gleason score and ERG expression status as well as Gleason score stratified by ERG expression status. In addition, we compared results from our dataset to publicly available datasets of histone modifications in benign prostate cells.
  
  
  RESULTS
  We discovered hundreds of distinct differentially methylated regions (DMR) associated with increasing Gleason score and ERG. Furthermore, the number of DMRs associated with Gleason score was greatly expanded by stratifying samples into ERG-positive versus ERG-negative, with ERG-positive/GS-associated DMRs being primarily hypermethylated as opposed to hypomethylated. Finally, we found that there was a significant overlap between either Gleason score-related or ERG-hypermethylated DMRs and distinct regions in benign epithelial cells that have PcG signatures (H3K27me3, SUZ12) and lack active gene expression signatures (H3K4me3, RNA pol II).
  
  
  CONCLUSIONS
  This work defines methylation landscapes of prostate cancer according to Gleason score, and suggests that initiating genetic events may influence the prostate cancer epigenome, which is further perturbed as prostate cancer progresses. Moreover, CpG islands with silent chromatin signatures in benign cells are particularly susceptible to prostate cancer-related hypermethylation.
authors.affiliation: Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
authors.forename: Ken
authors.initials: K
authors.lastname: Kron
authors.forename: Dominique
authors.initials: D
authors.lastname: Trudel
authors.forename: Vaijayanti
authors.initials: V
authors.lastname: Pethe
authors.forename: Laurent
authors.initials: L
authors.lastname: Briollais
authors.forename: Neil
authors.initials: N
authors.lastname: Fleshner
authors.forename: Theodorus
authors.initials: T
authors.lastname: van der Kwast
authors.forename: Bharati
authors.initials: B
authors.lastname: Bapat
mesh_terms: D016000:Cluster Analysis; D019175:DNA Methylation; D018450:Disease Progression; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D056426:Genetic Loci; D006801:Humans; D008297:Male; D058977:Molecular Sequence Annotation; D060787:Neoplasm Grading; D063146:Polycomb-Group Proteins / Q000378:metabolism*; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D015534:Trans-Activators / Q000235:genetics*; D000071230:Transcriptional Regulator ERG
chemical_list: C072312:ERG protein, human; D063146:Polycomb-Group Proteins; D015534:Trans-Activators; D000071230:Transcriptional Regulator ERG