Digestive Diseases and Sciences

, Volume 56, Issue 2, pp 387–396 | Cite as

DNA Methylation in the Rectal Mucosa Is Associated with Crypt Proliferation and Fecal Short-Chain Fatty Acids

  • Daniel L. Worthley
  • Vicki L. J. Whitehall
  • Richard K. Le Leu
  • Natsumi Irahara
  • Ronald L. Buttenshaw
  • Kylie-Ann Mallitt
  • Sonia A. Greco
  • Ingunn Ramsnes
  • Jean Winter
  • Ying Hu
  • Shuji Ogino
  • Graeme P. Young
  • Barbara A. Leggett
Original Article



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.


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.


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.


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 NH3 concentrations (P = 0.003).


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.


DNA methylation Epigenetics Colorectal cancer Carcinogenesis 



CpG island methylator phenotype


Chromosomal instability


Colorectal cancer


Percent of methylated reference



Thank you to the volunteers that took part in this study. This study was part funded by a National Health and Medical Research Council project grant (442965), National Starch Food Innovation support, a Gastroenterological Society of Australia post-graduate medical scholarship (D.L.W.), the Royal Australasian College of Physicians Cottrell Fellowship (D.L.W.), a Royal Brisbane and Women’s Hospital Foundation Research Grant (V.L.W, D.L.W, B.A.L) and a Queensland Smart State PhD award (D.L.W). This study was funded by a National Health and Medical Research Council project grant (442965), a Gastroenterological Society of Australia post-graduate medical scholarship (D.L.W), the Royal Australasian College of Physicians Cottrell Fellowship (D.L.W.), a Queensland Smart State PhD award (D.L.W), and the Royal Brisbane and Women’s Hospital Foundation.

Conflict of interest statement


Supplementary material

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Daniel L. Worthley
    • 1
    • 2
  • Vicki L. J. Whitehall
    • 1
    • 2
  • Richard K. Le Leu
    • 3
  • Natsumi Irahara
    • 4
  • Ronald L. Buttenshaw
    • 1
    • 2
  • Kylie-Ann Mallitt
    • 5
  • Sonia A. Greco
    • 1
    • 2
  • Ingunn Ramsnes
    • 1
    • 2
  • Jean Winter
    • 3
  • Ying Hu
    • 3
  • Shuji Ogino
    • 4
    • 6
  • Graeme P. Young
    • 3
  • Barbara A. Leggett
    • 1
    • 2
  1. 1.Conjoint Gastroenterology LaboratoryRoyal Brisbane and Women’s Hospital Research Foundation Clinical Research CentreBrisbaneAustralia
  2. 2.Queensland Institute of Medical ResearchThe Bancroft CentreBrisbane, HerstonAustralia
  3. 3.Flinders Centre for Cancer Prevention and ControlFlinders University of South AustraliaAdelaideAustralia
  4. 4.Department of Medical OncologyDana-Farber Cancer InstituteBostonUSA
  5. 5.Statistics UnitQueensland Institute of Medical ResearchBrisbaneAustralia
  6. 6.Department of PathologyBrigham and Women’s Hospital and Harvard Medical SchoolBostonUSA

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