DNA methylation as an adjunct to histopathology to detect prevalent, inconspicuous dysplasia and early-stage neoplasia in Barrett's esophagus.

Alvi MA, Liu X, O'Donovan M, Newton R, Wernisch L, Shannon NB, Shariff K, Di Pietro M, Bergman JJ, Ragunath K, Fitzgerald RC.

Source

Hutchison/MRC Research Centre, University of Cambridge.

Abstract

PURPOSE:

Endoscopic surveillance of Barrett's esophagus (BE) is problematic because dysplasia/early-stage neoplasia are frequently invisible and likely to be missed due to sampling bias. Molecular abnormalities may be more diffuse than dysplasia. The aim was therefore to test whether DNA methylation; especially on imprinted and X-chromosome genes; is able to detect dysplasia/early-stage neoplasia. Experimental design: 27K methylation arrays were used to find genes best able to differentiate between 22 BE and 24 esophageal adenocarcinoma (EAC) samples. These were validated using pyrosequencing on a retrospective cohort (60 BE, 36 dysplastic and 90 EAC) and then in a prospective multicenter study (98 BE patients, including 28 dysplastic and 9 early EAC) designed to utilize biomarkers to stratify patients according to their prevalent dysplasia/EAC status.

RESULTS:

23% genes on the array, including 7% of X-linked and 69% of imprinted genes, demonstrated statistically significant changes in methylation in EAC vs. BE (Wilcoxon P<0 .05=".05" 2="2" 6="6" able="able" and="and" area="area" based="based" be="be" between="between" candidate="candidate" cohort.="cohort." cohort="cohort" curve="curve" distinguish="distinguish" dysplasia="dysplasia" earson="earson" externally="externally" four="four" from="from" genes="genes" gja12="gja12" greatest="greatest" groups="groups" high:="high:" in="in" intermediate:="intermediate:" internally="internally" into="into" low="low" methylated="methylated" methylation="methylation" number="number" of="of" on="on" p="p" panel="panel" patients="patients" pigr="pigr" prospective="prospective" retrospective="retrospective" rin2="rin2" risk:="risk:" risk="risk" s="s" selected="selected" showed="showed" stratify="stratify" successfully="successfully" the="the" this="this" three="three" to="to" under="under" validated="validated" was="was" were="were">2).

CONCLUSION:

Widespread DNA methylation changes were observed in Barrett's carcinogenesis including ≈70% of known imprinted genes. A four-gene methylation panel stratified BE patients into three risk groups with potential clinical utility.