Copy Number Gains at 8q24 and 20q11-q13 in Gastric Cancer Are More Common in Intestinal-Type than Diffuse-Type

The present study was aimed at discovering DNA copy number alterations (CNAs) involved in the carcinogenesis of stomach and at understanding their clinicopathological significances in the Korean population. DNA copy numbers were analyzed using Agilent 244K or 400K array comparative genomic hybridization (aCGH) in fresh-frozen tumor and matched normal tissues from 40 gastric cancer patients. Some of the detected CNA regions were validated using multiplex ligation-dependent probe amplification (MLPA) in six of the 40 patients and customized Agilent 60K aCGH in an independent set of 48 gastric cancers. The mRNA levels of genes at common CNA regions were analyzed using quantitative real-time PCR. Copy number gains were more common than losses across the entire genome in tumor tissues compared to matched normal tissues. The mean number of alterations per case was 64 for gains and 40 for losses, and the median aberration length was 44016 bp for gains and 4732 bp for losses. Copy number gains were frequently detected at 7p22.1 (20%), 8q24.21 (27%–30%), 8q24.3 (22%–48%), 13q34 (20%–31%), and 20q11-q13 (25%–30%), and losses at 3p14.2 (43%), 4q35.2 (27%), 6q26 (23%), and 17p13.3 (20%–23%). CNAs at 7p22.1, 13q34, and 17p13.3 have not been reported in other populations. Most of the copy number losses were associated with down-regulation of mRNA levels, but the correlation between copy number gains and mRNA expression levels varied in a gene-dependent manner. In addition, copy number gains tended to occur more commonly in intestinal-type cancers than in diffuse-type cancers. In conclusion, the present study suggests that copy number gains at 8q24 and 20q11-q13 and losses at 3p14.2 may be common events in gastric cancer but CNAs at 7p22.1, 13q34, and 17p13.3 may be Korean-specific.本研究旨在探寻参与胃癌发生过程中的DNA拷贝数变异（copy number alterations, CNAs），并阐明其在韩国人群中的临床病理意义。本研究对40名胃癌患者的新鲜冷冻肿瘤组织及配对正常组织，采用安捷伦（Agilent）244K或400K阵列比较基因组杂交（array comparative genomic hybridization, aCGH）技术分析DNA拷贝数。研究对部分检出的CNA区域进行了验证：对40例患者中的6例采用多重连接依赖性探针扩增（multiplex ligation-dependent probe amplification, MLPA）技术，对独立队列的48例胃癌样本采用定制化安捷伦（Agilent）60K aCGH技术。针对常见CNA区域内的基因，采用实时荧光定量PCR（quantitative real-time PCR）技术分析其mRNA表达水平。相较于配对正常组织，肿瘤组织全基因组范围内的拷贝数扩增（copy number gains）发生率高于拷贝数缺失（copy number losses）。每例样本的平均变异数目：扩增为64个，缺失为40个；变异片段的中位长度：扩增为44016 bp，缺失为4732 bp。拷贝数扩增高频检出区域包括7p22.1（20%）、8q24.21（27%~30%）、8q24.3（22%~48%）、13q34（20%~31%）及20q11-q13（25%~30%）；拷贝数缺失高频检出区域包括3p14.2（43%）、4q35.2（27%）、6q26（23%）及17p13.3（20%~23%）。7p22.1、13q34及17p13.3区域的CNAs尚未在其他人群中被报道。多数拷贝数缺失与mRNA表达水平下调相关，但拷贝数扩增与mRNA表达水平的关联则因基因而异。此外，相较于弥漫型胃癌，肠型胃癌中拷贝数扩增的发生率更高。综上，本研究表明，8q24及20q11-q13区域的拷贝数扩增与3p14.2区域的拷贝数缺失可能是胃癌发生的常见事件，而7p22.1、13q34及17p13.3区域的CNAs则可能为韩国人群特异性的变异。