Abstract 1189: Chromosomal aberrations reveal novel genes with prognostic significance in esophageal adenocarcinoma
Authors: Goh Xin Yi C. , Rees Jonathan RE , Chin Suet-Feung , Newman Scott , O'Donovan Maria , YIstra Bauke , Caldas Carlos , Edwards Paul AW , Fitzgerald Rebecca C. 
Published: February 2011

Abstract
INTRODUCTION: The incidence of esophageal adenocarcinoma (EAC) has increased 6-fold in the west over the last 30 years, with a dismal survival rate of about 10%. Understanding the genomic aberrations and molecular pathogenesis in this cancer may enhance disease interventions.
AIMS: To identify novel molecular targets with prognostic significance and to better characterize EAC by analyzing chromosomal aberrations across the whole genome.
METHODS: An in-house oligonucleotide array comparative genomic hybridization (CGH) was performed on 89 chemo-naive EAC resection samples with long-term clinical follow-up data to identify regions of copy number gains/losses: good quality data obtained for 56 samples. Illumina Human Cyto Single-nucleotide Polymorphism (SNP)-12 Beadarray was carried out to map genomic boundaries of regions with aberrations. Touch-imprinting fluorescence in situ hybridization (FISH) assays were carried out using bacterial artificial chromosome probes on interphase nuclei of frozen samples to confirm findings. Regions with potential homozygous deletions (HDs) were investigated by multiplex nested PCR using microdissected DNA of frozen samples. The degree and pattern of genomic gains were studied using different FISH probes.
RESULTS: 19 minimal regions with gains and 12 regions with losses (cut off=2 standard deviations (SD) above/below mean log2 ratios) were identified. Potential HDs (cut off=3 SD) were identified in 4 samples (7.1%) at 9p21. Nested multiplex PCR and FISH (quantitative: 100 nuclei per sample counted) confirmed a p16 deletion in all 4 samples. SNP analysis suggested another region of potential HD that involves a novel gene, ELAVL2. Amplifications (cut off=3 SD) in 6 samples (10.7%) at 8p23.1 were confirmed by analyses from the SNP array, which narrowed down the width of amplicon to 2 regions involving: (a) SOX7/PINX1 (5/6 samples) and (b) GATA4, NEIL2, FDFT1 and CTSB (4/6 samples). FISH assays confirmed amplifications of GATA4, NEIL2, FDFT1, CTSB, SOX7 (6 or more copies/centromere) and gains of PINX1 (3-6 copies/centromere). Unsupervised K means clustering (50 iterations) of the array CGH data generated 5 groups and survival analyses identified a group (32.1% of cohort) with significantly worse prognosis (median survival=500 days, p=0.0149). Modified T test with adjusted Bonferroni correction identified 17 clones with different log2 ratios (p&lt;0.05), implicating 4 regions of gains and including 6 novel genes, between this group and the other 4 combined. The only clinical difference between this group and the others was an increased male:female ratio (Fishers exact test; p=0.01).
CONCLUSIONS: 9p deletions and 8p amplifications are present in 7-11% of samples. The use of array CGH has identified copy number gains with prognostic significance in EAC. Further work is required to determine whether the genes involved have a causative role.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1189.