Genome-wide analysis of genetic alterations in Barrett's adenocarcinoma using single nucleotide polymorphism arrays

Abstract

We performed genome-wide analysis of copy-number changes and loss of heterozygosity (LOH) in Barrett's esophageal adenocarcinoma by single nucleotide polymorphism (SNP) microarrays to identify associated genomic alterations. DNA from 27 esophageal adenocarcinomas and 14 matching normal tissues was subjected to SNP microarrays. The data were analyzed using dChipSNP software. Copy-number changes occurring in at least 25% of the cases and LOH occurring in at least 19% were regarded as relevant changes. As a validation, fluorescence in situ hybridization (FISH) of 8q24.21 (CMYC) and 8p23.1 (SOX7) was performed. Previously described genomic alterations in esophageal adenocarcinomas could be confirmed by SNP microarrays, such as amplification on 8q (CMYC, confirmed by FISH) and 20q13 or deletion/LOH on 3p (FHIT) and 9p (CDKN2A). Moreover, frequent gains were detected on 2p23.3, 7q11.22, 13q31.1, 14q32.31, 17q23.2 and 20q13.2 harboring several novel candidate genes. The highest copy numbers were seen on 8p23.1, the location of SOX7, which could be demonstrated to be involved in amplification by FISH. A nuclear overexpression of the transcription factor SOX7 could be detected by immunohistochemistry in two amplified tumors. Copy-number losses were seen on 18q21.32 and 20p11.21, harboring interesting candidate genes, such as CDH20 and CST4. Finally, a novel LOH region could be identified on 6p in at least 19% of the cases. In conclusion, SNP microarrays are a valuable tool to detect DNA copynumber changes and LOH at a high resolution. Using this technique, we identified several novel genes and DNA regions associated with esophageal adenocarcinoma. KEYWORDS: Barrett's adenocarcinoma; copy-number changes; esophageal carcinoma; LOH; mapping array; SNP array Genomic alterations, such as amplification, deletion, translocation and loss of heterozygosity (LOH) play an important role in the pathogenesis and progression of cancer due to the activation of oncogenes or inactivation of tumor suppressor genes. Apart from numeric aberrations, such as gene amplification or deletion, which are frequently detected in carcinomas, other genomic changes in carcinogenesis, such as LOH, do not necessarily lead to DNA copy-number gain or loss. Several causes of LOH have been described, including deletion, non-disjunction and reduplication, mitotic recombination and gene conversion. 1 The two-hit model describes a tumor suppressor gene inactivation due to a loss of one allele and mutation of the other allele, resulting in an LOH. 2 Besides detailed investigation of known oncogenes and tumor suppressor genes, screening for novel genomic alterations in different cancers and precursor lesions provides information of molecular mechanisms in carcinogenesis.The incidence of esophageal (Barrett's) adenocarcinoma, mostly arising within the precancerous Barrett's esophagus, with the normal esophageal squamous epithelium changed into intestinal metaplasia, has risen in the past decades in western countries. 3 Screening for chromosomal alterations has bee...

Early Diagnostic Biomarkers for Esophageal Adenocarcinoma—The Current State of Play

“…(177) (195) (Continued on the following page) decade, several studies conducted using advanced genomic techniques such as array-comparative genomic hybridization (aCGH) and SNP arrays confirmed previously reported copy number alterations and identified novel genomic loci undergoing changes during process of metaplasia-dysplasia-carcinoma development (54)(55)(56)(57)(58)(59)(60). It has been shown that as the disease progresses from early to late stages, SNP abnormalities increase from approximately 2% to 30% (54,57).…”

“…It has been shown that as the disease progresses from early to late stages, SNP abnormalities increase from approximately 2% to 30% (54,57). The total number of SNP alterations in tissue samples is tightly correlated with previously reported DNA abnormalities such as aneuploidy, copy number alterations, and LOH highlighting the application of SNP-based genotyping to assess genomic abnormalities (54)(55)(56)(57)(58)(59)(60). Thus, SNP-based genotyping provides an alternative way to assess genomic abnormalities during EAC pathogenesis.…”

EPHX1 polymorphisms do not modify esophageal carcinoma susceptibility in Dutch Caucasians

“…Consequently it is complicated to interpret the most recent results of Ihsan et al (15), since additionally the overall data report inconsistent findings regarding esophageal cancer risk. Moreover, three recently performed genome-wide association studies, using detection of SNPs or cDNA microarray techniques, did not identify the EPHX1 gene as a susceptibility locus for ESCC or EAC (26)(27)(28).…”

Gene amplification of ERBB2 and EGFR in adenocarcinoma in situ and intramucosal adenocarcinoma of Barrett's esophagus

“…Recently, array-based comparative genomic hybridization (aCGH) or single nucleotide polymorphism (SNP) array have detected novel candidate genes involved in development and progression of Barrett's carcinoma. Among them, SOX7 5 and SNRPN 6 were identified as the most frequently amplified genes by two groups respectively.…”