title: DNA methylation in the rectal mucosa is associated with crypt proliferation and fecal short-chain fatty acids.
abstract: BACKGROUND
  DNA methylation varies throughout the normal colorectal mucosa and DNA methylation in normal appearing mucosa is associated with serrated and adenomatous neoplasia elsewhere within the colorectum.
  
  
  OBJECTIVE
  The purpose of this study was to measure luminal chemistry, rectal proliferation and mucosal DNA methylation and thus determine whether regional and pathological patterns of DNA methylation could be explained by luminal and epithelial factors.
  
  
  METHODS
  Twenty healthy subjects had normal rectal mucosal biopsies and a 24-h fecal collection. Rectal biopsies were analyzed for epithelial proliferation (Ki67 immunohistochemistry) and DNA methylation at 17 different markers, including "type A" markers (ESR1, GATA5, HIC1, HPP1, SFRP1), "type C" markers (MGMT, MLH1, CDKN2A, MINT1, MINT2, MINT31, IGF2, CACNA1G, NEUROG1, SOCS1, RUNX3), and LINE-1. Fecal analysis included short-chain fatty acids (SCFA), pH and ammonia. Mean "type A" and CIMP panel methylation Z-scores were calculated.
  
  
  RESULTS
  Rectal proliferation was significantly correlated with methylation at ESR1 (ρ = 0.81, P = 0.003) and GATA5 (ρ = 0.78, P = 0.012). LINE-1 methylation was 71.7 vs. 74.1%, in patients with "low" and "high" fecal total SCFA concentration (defined by the median value), respectively (P = 0.0019). On multivariate linear regression "type A" methylation was independently associated with rectal proliferation (P = 0.001). LINE-1 methylation was directly associated with rectal proliferation (P = 0.038) and total fecal SCFA concentration (P = 0.002), and inversely associated with fecal NH(3) concentrations (P = 0.003).
  
  
  CONCLUSIONS
  DNA methylation in normal rectal mucosa is associated with crypt proliferation and fecal SCFA concentration. These associations may help to explain regional differences in DNA methylation as well as providing a possible link between the colorectal lumen and carcinogenesis.
authors.affiliation: Conjoint Gastroenterology Laboratory, Royal Brisbane and Women's Hospital Research Foundation Clinical Research Centre, Brisbane, QLD, Australia. daniel.worthley@uqconnect.edu.au
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Worthley
authors.forename: Vicki L J
authors.initials: VL
authors.lastname: Whitehall
authors.forename: Richard K
authors.initials: RK
authors.lastname: Le Leu
authors.forename: Natsumi
authors.initials: N
authors.lastname: Irahara
authors.forename: Ronald L
authors.initials: RL
authors.lastname: Buttenshaw
authors.forename: Kylie-Ann
authors.initials: KA
authors.lastname: Mallitt
authors.forename: Sonia A
authors.initials: SA
authors.lastname: Greco
authors.forename: Ingunn
authors.initials: I
authors.lastname: Ramsnes
authors.forename: Jean
authors.initials: J
authors.lastname: Winter
authors.forename: Ying
authors.initials: Y
authors.lastname: Hu
authors.forename: Shuji
authors.initials: S
authors.lastname: Ogino
authors.forename: Graeme P
authors.initials: GP
authors.lastname: Young
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Leggett
mesh_terms: D058739:Aberrant Crypt Foci / Q000378:metabolism / Q000473:pathology; D000328:Adult; D000368:Aged; D000641:Ammonia / Q000032:analysis; D015415:Biomarkers; D015179:Colorectal Neoplasms / Q000378:metabolism / Q000473:pathology; D019175:DNA Methylation / Q000502:physiology*; D005232:Fatty Acids, Volatile / Q000032:analysis*; D005243:Feces / Q000737:chemistry*; D005260:Female; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D012007:Rectum / Q000378:metabolism* / Q000473:pathology
chemical_list: D015415:Biomarkers; D005232:Fatty Acids, Volatile; D000641:Ammonia