Ogy. Author manuscript; readily available in PMC 2014 May 01.Published in final edited
Ogy. Author manuscript; obtainable in PMC 2014 May perhaps 01.Published in final edited form as: Gastroenterology. 2013 May ; 144(five): 95666.e4. doi:ten.1053j.gastro.2013.01.019.NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptHypomethylation of Noncoding DNA Regions and Overexpression with the Extended Noncoding RNA, AFAP1-AS1, in Barrett’s Esophagus and Esophageal AdenocarcinomaWenjing Wu1,two,, Tushar D. Bhagat3,, Xue Yang2, Jee Hoon Song2, Yulan Cheng2, Rachana Agarwal2, John M. Abraham2, Sariat Ibrahim2, Matthias Bartenstein3, Zulfiqar Hussain3, Masako Suzuki3, Yiting Yu3, Wei Chen1, Charis Eng4, John Greally3, Amit Verma3, and Stephen J. Meltzer2 for Laboratory Medicine, The initial Affiliated Hospital, KDM5 review School of Medicine, Xi’an Jiaotong University, Xi’an, China 2Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Complete Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 3Albert Einstein College of Medicine, Bronx, New York 4Cleveland Clinic, Cleveland, Ohio1CenterAbstractBACKGROUND AIMS–Alterations in methylation of protein-coding genes are associated with Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC). Dys-regulation of noncoding RNAs occurs throughout carcinogen-esis but has never ever been studied in BE or EAC. We applied high-resolution methylome evaluation to recognize adjustments at genomic regions that encode noncoding RNAs in BE and EAC. METHODS–We analyzed methylation of 1.8 million CpG web sites utilizing massively parallel sequencing-based Assistance tagging in matched EAC, BE, and typical esophageal tissues. We also analyzed human EAC (OE33, SKGT4, and FLO-1) and typical (HEEpic) esophageal cells. RESULTS–BE and EAC exhibited genome-wide hypomethylation, drastically affecting intragenic and repetitive genomic components too as noncoding regions. These methylation alterations targeted small and lengthy noncoding regions, discriminating typical from matched BE or EAC tissues. A single long noncoding RNA, AFAP1-AS1, was particularly hypomethylated and overexpressed in BE and EAC tissues and EAC cells. Its silencing by little interfering RNA inhibited proliferation and colony-forming ability, induced apoptosis, and lowered EAC cell migration and invasion without having altering the expression of its protein-coding counterpart, AFAP1.2013 by the AGA InstituteReprint requests, Address requests for reprints to: Stephen J. Meltzer, MD, The Johns Hopkins University College of Medicine, 1503 East Jefferson Street, Space 112, Baltimore, Maryland 21287; smeltzerjhmi.edu. (410) 502-1329; or Amit Verma, MB, BS, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Chanin Developing, Area 302B, Bronx, New York 10461. amit.vermaeinstein.yu.edu. Authors share co-first authorship. Conflicts of interest The authors disclose no conflicts.Supplementary Material Note: To access the supplementary material accompanying this article, take a look at the on the web version of Gastroenterology at gastrojournal.org, and at http:dx.doi.org10.1053j.gastro.2013.01.019.Wu et al.PageCONCLUSIONS–BE and EAC exhibit lowered methylation that incorporates noncoding regions. Methylation from the extended noncoding RNA AFAP1-AS1 is reduced in BE and EAC, and its expression CLK Biological Activity inhibits cancer-related biologic functions of EAC cells. Keywords Esophageal Cancer Progression; Tumor Improvement; Gene Regulation; Noncoding RNA Esophageal adenocarcinoma (EAC) is one of the fastest-growing cancers within the Western planet. Ninety-five percent of EA.
