Epigenomic program of Barrett's-associated neoplastic progression reveals possible involvement of insulin signaling pathways.

Although the molecular basis of esophageal adenocarcinoma (EAC) and its precursor, Barrett’s esophagus (BE), have been studied, further insights are needed into early premalignant events. In the current study, we comprehensively identified epigenetically altered genes at various time points during neoplastic progression in BE. We compared global DNA methylation profiles of two groups of BE patients: 1) patients who later progressed to high-grade dysplasia (HGD) or EAC, termed ‘progressors (P)’; and 2) those who did not progress to HGD or EAC, termed ‘nonprogressors (NPs)’. First, we conducted a comprehensive, genome-wide CpG island methylation analysis on a cohort of nine BE specimens. These specimens were obtained from two sets of Barrett’s metaplasia patients with known outcomes: five were from Ps and four were from NPs. All the tissue specimens used in this study were obtained from patients who provided informed written consent under an approved protocol by the Institutional Review Board at the University of Maryland, School of Medicine, the Baltimore Veterans Affairs Medical Center and the Johns Hopkins University School of Medicine. Ps were defined as patients with index (i.e. pre-progression experimental study) biopsies showing either no dysplasia, indefinite for dysplasia, or low-grade dysplasia (LGD) at endoscopy performed at least 6 months before the diagnosis of either HGD or EAC. NPs were defined as patients who had undergone at least three surveillance endoscopic examinations with index biopsies but did not progress beyond LGD. CpG island methylation analysis was conducted by combining two techniques: 1) methylated CpG island amplification (MCA) and 2) CpG island oligonucleotide microarrays. The MCA method was first used to enrich and amplify methylated DNA fragments (Toyota et al. 1999). These enriched methylated DNA fragments were then labeled and hybridized to 244K Human CpG Island microarrays (Agilent Technologies, Santa Clara, CA, USA). These