Next-generation sequencing of endoscopic biopsies identifies ARID1A as a tumor-suppressor gene in Barrett's esophagus.

The incidence of Barrett's esophagus (BE)-associated esophageal adenocarcinoma (EAC) is increasing. Next-generation sequencing (NGS) provides an unprecedented opportunity to uncover genomic alterations during BE pathogenesis and progression to EAC, but treatment-naive surgical specimens are scarce. The objective of this study was to establish the feasibility of using widely available endoscopic mucosal biopsies for successful NGS, using samples obtained from a BE 'progressor'. Paired-end whole-genome NGS was performed on the Illumina platform using libraries generated from mucosal biopsies of normal squamous epithelium (NSE), BE and EAC obtained from a patient who progressed to adenocarcinoma during endoscopic surveillance. Selective validation studies, including Sanger sequencing, immunohistochemistry and functional assays, were performed to confirm the NGS findings. NGS identified somatic nonsense mutations of AT-rich interactive domain 1A (SWI like) (ARID1A) and PPIE and an additional 37 missense mutations in BE and/or EAC, which were confirmed by Sanger sequencing. ARID1A mutations were detected in 15% (3/20) high-grade dysplasia (HGD)/EAC patients. Immunohistochemistry performed on an independent archival cohort demonstrated ARID1A protein loss in 0% (0/76), 4.9% (2/40), 14.3% (4/28), 16.0% (8/50) and 12.2% (12/98) of NSE, BE, low-grade dysplasia, HGD and EAC tissues, respectively, and was inversely associated with nuclear p53 accumulation (P=0.028). Enhanced cell growth, proliferation and invasion were observed on ARID1A knockdown in EAC cells. In addition, genes downstream of ARID1A that potentially contribute to the ARID1A knockdown phenotype were identified. Our studies establish the feasibility of using mucosal biopsies for NGS, which should enable the comparative analysis of larger 'progressor' versus 'non-progressor' cohorts. Further, we identify ARID1A as a novel tumor-suppressor gene in BE pathogenesis, reiterating the importance of aberrant chromatin in the metaplasia-dysplasia sequence.

New advances in the pathogenesis and progression of barrett's esophagus.

Barrett's esophagus (BE) is a premalignant condition in the esophagus, with a rising incidence rate among Caucasians, and an established risk factor for the subsequent progression to esophageal adenocarcinoma (EAC). In contrast to the stratified squamous epithelium that normally lines the distal esophagus, BE is characterized by columnar epithelium that to some extent resembles the mucosa of the lower intestinal tract. The mechanism of intestinalization of the esophagus is still uncertain. For many years, it was postulated that either abnormal differentiation of resident progenitor cells in the esophagus, or transdifferentiation of mature esophageal keratinocytes provoked by reflux-induced genetic alterations, resulted in the BE phenotype. However, more recent studies suggest that indigenous progenitor cells at the gastro-esophageal junction might, under unfavorable conditions such as TP63 loss or an activated inflammatory response, migrate to the esophagus and initiate columnar cell differentiation. In this review, we discuss the competing theories of the origins of BE, as well as the role of developmental signaling pathways such as Notch, Hedgehog, and Wnt/ß-catenin signaling that have been implicated in the molecular pathogenesis of BE and EAC. Additionally, we provide an overview of the mutational landscapes of BE and EAC, derived from the results of recently published next generation sequencing (NGS) studies. Future research should elucidate whether NGS on endoscopic mucosal biopsies can help in identifying BE patients at highest risk for EAC development, and whether some of the prevalent mutations are "actionable", leading to improvements in current therapeutic strategies for BE and EAC.

Squamous cell carcinoma in Barrett's esophagus: field effect versus metastasis.

Barrett's esophagus (BE) is a premalignant condition with an increased risk of developing esophageal adenocarcinoma (EAC). Risk factors for EAC overlap with those for esophageal squamous cell carcinoma (ESCC), but ESCC is surprisingly rare in BE. We report two cases of ESCC directly surrounded by BE. Both patients had a previous medical history of cancers, i.e., head and neck squamous cell carcinomas, and were using alcohol and smoking tobacco. Using immunohistochemistry for p63, CK5, CK7, and CDX2, it was confirmed that these carcinomas were pure squamous cell carcinomas, and not EACs or esophageal adenosquamous carcinomas arising from BE. Using TP53 mutation and loss of heterozygosity analysis, we established that the ESCCs in BE were not metastases of the previously diagnosed head and neck squamous cell carcinomas but de novo primary ESCCs. This study shows the strength of molecular analysis as an adjunct to the histopathologic diagnosis for distinguishing between metastases of prior cancers and primary cancers. Furthermore, these cases imply that presence of BE is not protective with regards to developing ESCC in the lower one third of the esophagus. We suggest that their ESCCs arose from islets of squamous epithelium in BE.