DNA methylation in the rectal mucosa is associated with crypt proliferation and fecal short-chain fatty acids.
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.
Worthley
Daniel L
DL
Conjoint Gastroenterology Laboratory, Royal Brisbane and Women's Hospital Research Foundation Clinical Research Centre, Brisbane, QLD, Australia. daniel.worthley@uqconnect.edu.au
Whitehall
Vicki L J
VL
Le Leu
Richard K
RK
Irahara
Natsumi
N
Buttenshaw
Ronald L
RL
Mallitt
Kylie-Ann
KA
Greco
Sonia A
SA
Ramsnes
Ingunn
I
Winter
Jean
J
Hu
Ying
Y
Ogino
Shuji
S
Young
Graeme P
GP
Leggett
Barbara A
BA
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
D015415:Biomarkers; D005232:Fatty Acids, Volatile; D000641:Ammonia