Novel Chromosomal Abnormalities in Barrett's Esophagus and Esophageal Adenocarcinoma Identified by Array Comparative Genomic Hybridization (CGH)
Atin Agarwal, Taylor Appleberry, Sushovan Guha, Jaffer Ajani, Wayne Hofstetter, Stephen Swisher, Patrick Lennon, Asif Rashid, Dipen Maru. The University of Texas M.D.Anderson Cancer Center, Houston; PerkinElmer, Inc, Waltham; Pathgroup, Nashville
Background: Prior genome wide studies using biopsy samples of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) have shown gains of chromosomes 1q, 7q, 8p and losses of chromosomes 3p, 9p, 16q, 17p, and 21q22. Present study performed array CGH on carefully macro dissected fresh frozen tissue samples of BE and EAC and found novel regions of chromosomal alterations.
Design: The study comprised of 14 patients (M:F;11:3, average age 68 years) with BE associated EAC who underwent esophagogastrectomy without preoperative chemoradiation. Tumor stage was T1aN0 in 4, T1bN0 in 6, T1bN1 in 1, T2No in 2 and T4N2 in 1. H&E section of fresh frozen samples from squamous mucosa, non-dysplastic BE and EAC from the resection specimens were reviewed and area with more than 80% of lesion was macrodissected from the frozen block followed by DNA extraction using TRIzol Reagent (Life Technologies, CA) with post-PCR purification. Microarray analysis was performed using bacterial artificial chromosome (BAC) DNA microarrays (Constitutional Chip 4.0, PerkinElmer, Finland). This microarray has over 5200 BAC clones, including targeted coverage in well-characterized chromosomal regions, subtelomeric regions, and pericentromeric regions, as well as backbone coverage of the genome with an average resolution of 0.5 Mb. DNA extracted from either BE or EAC tissue was analyzed using DNA from squamous mucosa from the same patient as a reference. Arrays were scanned at 10 microns using a ScanArray Gx scanner (PerkinElmer) and analyzed using GenePix Pro 6.1 (Molecular Devices, CA).
Results: In BE, gains of chromosomal loci 1p36.33, 1p36.32, 3q21.3, 9q34.2, 9q34.3, 12q24.31, 12q24.33, 16p13.3, 16q24.3, 20q13.3, 21q22.3, 22q13.32 were present in two (18%) samples and losses of loci 9p21.3 in two (18%) samples. The remaining eight BE samples showed no chromosomal gains or losses. All EAC samples showed chromosmal gains. Six (43%) EAC showed gain of chromosomal loci 8p23.1 and 20q13.33, and four (37%) of 7p12.3 and 8q24.3. Other chromosomal gains included 5p15.33, 7p12.3, 7p11.2, 7q11.21, 7q21.13, 7q21.2-21.3, and 8q24.13 in 3 or less tumors. Loss of chromosome Yq11.22 was seen in all EAC from men.
Conclusions: There is marked increase in gains at multiple chromosomes in EAC as compared to BE. Present study supports prior studies showing gains of chromosomal locus 8p23.1 and identifies gain of chromosomal locus 20q13.33 and loss of locus Yq11.22 as novel abnormalities in EAC.
Monday, March 19, 2012 1:00 PM
Poster Session II # 83, Monday Afternoon