title: Methylation and expression of the tumour suppressor, PRDM5, in colorectal cancer and polyp subgroups.
abstract: BACKGROUND
  PRDM5 is an epigenetic regulator that has been recognized as an important tumour suppressor gene. Silencing of PRDM5 by promoter hypermethylation has been demonstrated in several cancer types and PRDM5 loss results in upregulation of the Wnt pathway and increased cellular proliferation. PRDM5 has not been extensively investigated in specific subtypes of colorectal cancers. We hypothesized it would be more commonly methylated and inactivated in serrated pathway colorectal cancers that are hallmarked by a BRAF V600E mutation and a methylator phenotype, compared to traditional pathway cancers that are BRAF wild type.
  
  
  METHODS
  Cancer (214 BRAF mutant, 122 BRAF wild type) and polyp (59 serrated polyps, 40 conventional adenomas) cohorts were analysed for PRDM5 promoter methylation using MethyLight technology. PRDM5 protein expression was assessed by immunohistochemistry in cancers and polyps. Mutation of PRDM5 was analysed using cBioPortal's publicly available database.
  
  
  RESULTS
  BRAF mutant cancers had significantly more frequent PRDM5 promoter methylation than BRAF wild type cancers (77/214,36% vs 4/122,3%; p<0.0001). Serrated type polyps had a lower methylation rate than cancers but were more commonly methylated than conventional adenomas (6/59,10% vs 0/40,0%). PRDM5 methylation was associated with advanced stages of presentation (p<0.05) and the methylator phenotype (p=0.03). PRDM5 protein expression was substantially down-regulated in both BRAF mutant and wild type cancer cohorts (92/97,95% and 39/44,89%). The polyp subgroups showed less silencing than the cancers, but similar rates were found between the serrated and conventional polyp cohorts (29/59, 49%; 23/40, 58% respectively). Of 295 colorectal cancers, PRDM5 was mutated in only 6 (2%) cancers which were all BRAF wild type.
  
  
  CONCLUSIONS
  Serrated pathway colorectal cancers demonstrated early and progressive PRDM5 methylation with advancing disease. Interestingly, PRDM5 protein expression was substantially reduced in all polyp types and more so in cancers which also indicates early and increasing PRDM5 down-regulation with disease progression. Methylation may be contributing to gene silencing in a proportion of BRAF mutant cancers, but the large extent of absent protein expression indicates other mechanisms are also responsible for this. These data suggest that PRDM5 is a relevant tumour suppressor gene that is frequently targeted in colorectal tumourigenesis.
authors.affiliation: Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. Catherine.Bond@qimrberghofer.edu.au.|School of Medicine, University of Queensland, Brisbane, Queensland, Australia. Catherine.Bond@qimrberghofer.edu.au.
authors.forename: Catherine E
authors.initials: CE
authors.lastname: Bond
authors.affiliation: Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. Mark.Bettington@qimrberghofer.edu.au.|School of Medicine, University of Queensland, Brisbane, Queensland, Australia. Mark.Bettington@qimrberghofer.edu.au.|Envoi Specialist Pathologists, Brisbane, Queensland, Australia. Mark.Bettington@qimrberghofer.edu.au.
authors.forename: Mark L
authors.initials: ML
authors.lastname: Bettington
authors.affiliation: Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. Sally.Pearson@qimrberghofer.edu.au.
authors.forename: Sally-Ann
authors.initials: SA
authors.lastname: Pearson
authors.affiliation: Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. Diane.McKeone@qimrberghofer.edu.au.
authors.forename: Diane M
authors.initials: DM
authors.lastname: McKeone
authors.affiliation: Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. Barbara.Leggett@health.qld.gov.au.|School of Medicine, University of Queensland, Brisbane, Queensland, Australia. Barbara.Leggett@health.qld.gov.au.|Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia. Barbara.Leggett@health.qld.gov.au.
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Leggett
authors.affiliation: Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. Vicki.Whitehall@qimrberghofer.edu.au.|School of Medicine, University of Queensland, Brisbane, Queensland, Australia. Vicki.Whitehall@qimrberghofer.edu.au.|Pathology Queensland, Brisbane, Queensland, Australia. Vicki.Whitehall@qimrberghofer.edu.au.
authors.forename: Vicki L J
authors.initials: VL
authors.lastname: Whitehall
mesh_terms: D000368:Aged; D014408:Biomarkers, Tumor / Q000096:biosynthesis* / Q000235:genetics; D045744:Cell Line, Tumor; D003111:Colonic Polyps / Q000235:genetics / Q000473:pathology; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D018899:CpG Islands; D019175:DNA Methylation / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000096:biosynthesis* / Q000235:genetics; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D016147:Genes, Tumor Suppressor; D006801:Humans; D008297:Male; D008875:Middle Aged; D009367:Neoplasm Staging; D011401:Promoter Regions, Genetic; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis; D014157:Transcription Factors / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; D004268:DNA-Binding Proteins; C487762:PRDM5 protein, human; D012333:RNA, Messenger; D014157:Transcription Factors; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf