Integrated Analysis of Copy Number Variation and Genome-Wide Expression Profiling in Colorectal Cancer Tissues

Integrative analyses of multiple genomic datasets for selected samples can provide better insight into the overall data and can enhance our knowledge of cancer. The objective of this study was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues. Sixty-four paired CRC samples from the same patients were subjected to CNV profiling using the Illumina HumanOmni1-Quad assay, and validation was performed using multiplex ligation probe amplification method. Genome-wide expression profiling was performed on 15 paired samples from the same group of patients using the Affymetrix Human Gene 1.0 ST array. Significant genes obtained from both array results were then overlapped. To identify molecular pathways, the data were mapped to the KEGG database. Whole genome CNV analysis that compared primary tumor and non-cancerous epithelium revealed gains in 1638 genes and losses in 36 genes. Significant gains were mostly found in chromosome 20 at position 20q12 with a frequency of 45.31% in tumor samples. Examples of genes that were associated at this cytoband were PTPRT, EMILIN3 and CHD6. The highest number of losses was detected at chromosome 8, position 8p23.2 with 17.19% occurrence in all tumor samples. Among the genes found at this cytoband were CSMD1 and DLC1. Genome-wide expression profiling showed 709 genes to be up-regulated and 699 genes to be down-regulated in CRC compared to non-cancerous samples. Integration of these two datasets identified 56 overlapping genes, which were located in chromosomes 8, 20 and 22. MLPA confirmed that the CRC samples had the highest gains in chromosome 20 compared to the reference samples. Interpretation of the CNV data in the context of the transcriptome via integrative analyses may provide more in-depth knowledge of the genomic landscape of CRC.对选定样本的多组基因组数据集开展整合分析，可更全面地解析整体数据特征，深化我们对癌症的认知。本研究旨在阐明结直肠癌（colorectal cancer, CRC）样本及其对应癌旁正常组织中拷贝数变异（copy number variation, CNV）与基因表达的关联。研究纳入64例来自同一患者的配对CRC样本，采用Illumina HumanOmni1-Quad基因分型芯片进行CNV谱分析，并通过多重连接依赖探针扩增方法完成验证。针对同批次患者中的15例配对样本，采用Affymetrix Human Gene 1.0 ST基因表达芯片开展全基因组表达谱分析，随后对两种芯片实验得到的显著差异基因进行取交集分析。为识别分子通路，将数据映射至京都基因与基因组百科全书（KEGG）数据库。对比原发性肿瘤与癌旁正常上皮组织的全基因组CNV分析结果显示，肿瘤样本中存在1638个基因的拷贝数扩增、36个基因的拷贝数缺失。显著扩增区域主要集中于20号染色体20q12细胞带，在肿瘤样本中的发生频率达45.31%，该细胞带内的相关基因包括PTPRT、EMILIN3及CHD6。拷贝数缺失最显著的区域位于8号染色体8p23.2细胞带，在所有肿瘤样本中的发生频率为17.19%，该区域内的相关基因包括CSMD1与DLC1。全基因组表达谱分析结果显示，相较于癌旁正常样本，CRC组织中共709个基因上调表达、699个基因下调表达。对上述两组数据集进行整合分析后，共得到56个交集基因，这些基因分布于8号、20号及22号染色体。MLPA验证结果证实，相较于对照样本，CRC样本的20号染色体存在最高频率的拷贝数扩增。通过整合分析从转录组层面解析CNV数据，可为结直肠癌的基因组特征研究提供更深入的认知。