Affymetrix SNP array data for hepatocellular carcinoma and their adjacent liver tissue samples. Homo sapiens

Chromosomal DNA copy number alterations are a hallmark of human malignancies, including hepatocellular carcinoma (HCC). However, which oncogenes or tumor suppressors located on regions with DNA copy number aberration may contribute to HCC initiation and progression still remain obscure. Here we performed a genome-wide DNA copy number analysis on human HCC samples to identify novel potential oncogenes or tumor suppressors with DNA copy number aberrations. Genome-wide DNA copy numbers analysis was performed with single nucleotide polymorphism micoarray. RT-PCR and immunohistochemical staining were employed to evaluate the NOXIN expression in HCC samples. Colony formation, cell cycle analysis and tumor xenograft assays were performed to assess the role of NOXIN in HCC cells. Reciprocal co-immunoprecipitation experiments were used to detect the interaction between NOXIN and DNA polymerase a primase. Genome-wide DNA copy number analysis on 43 paired HCC samples indentified the smallest DNA amplification region containing NOXIN, along with the elevated transcript. NOXIN overexpression was significantly associated with HCC tumor stage. Enforced NOXIN promoted cellular proliferation, colony formation, cell migration and in vivo tumorigenicity, whereas RNA interference against NOXIN can attenuate these effects. Interestingly, NOXIN overexpression can accelerate the G1-S transition of cell cycle progression through enhancing DNA synthesis in HCC cells, as indicated by bromodeoxyuridine incorporation. Furthermore, NOXIN can interact with DNA polymerase a, implying that NOXIN may promote de novo DNA synthesis via affiliating formation of DNA polymerase-primase complex. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from hepatocellular carcinoma and adjacent liver tissue samples. Overall design: Copy number analysis of Affymetrix 500K SNP arrays was performed for 43 hepatocellular carcinoma tissue samples, which their adjacent liver tissues were used as references for copy number inference.

染色体DNA拷贝数变异是包括肝细胞癌（hepatocellular carcinoma, HCC）在内的人类恶性肿瘤的标志性特征。然而，位于DNA拷贝数异常区域的致癌基因与抑癌基因中，究竟哪些可推动肝细胞癌的发生与进展，目前仍尚不明确。本研究针对人类肝细胞癌样本开展全基因组DNA拷贝数分析，以期筛选出携带DNA拷贝数异常的新型潜在致癌基因与抑癌基因。本研究采用单核苷酸多态性微阵列（single nucleotide polymorphism microarray）完成全基因组DNA拷贝数分析。采用逆转录聚合酶链式反应（reverse transcription polymerase chain reaction, RT-PCR）与免疫组织化学染色技术，检测肝细胞癌样本中NOXIN的表达水平。通过集落形成实验、细胞周期分析与异种移植瘤实验，评估NOXIN在肝细胞癌细胞中的功能作用。采用双向免疫共沉淀实验，检测NOXIN与DNA聚合酶α引物酶（DNA polymerase α primase）之间的相互作用。对43例配对肝细胞癌样本的全基因组DNA拷贝数分析，鉴定出了包含NOXIN的最小DNA扩增区域，同时发现该区域的转录本表达水平显著上调。NOXIN过表达与肝细胞癌的肿瘤分期呈显著相关。强制过表达NOXIN可促进细胞增殖、集落形成与细胞迁移，并增强体内致瘤能力；而针对NOXIN的RNA干扰可削弱上述效应。有趣的是，经溴脱氧尿苷（bromodeoxyuridine, BrdU）掺入实验证实，NOXIN过表达可通过增强肝细胞癌细胞的DNA合成速率，加速细胞周期的G1-S期转换。此外，NOXIN可与DNA聚合酶α（DNA polymerase α）相互结合，这提示NOXIN可能通过参与DNA聚合酶-引物酶复合物的组装，促进新生DNA合成。本研究按照制造商提供的操作指南，对从肝细胞癌及癌旁肝组织样本中提取的DNA开展Affymetrix SNP芯片实验。实验整体设计：对43例肝细胞癌组织样本开展Affymetrix 500K SNP芯片的拷贝数分析，以其对应的癌旁肝组织作为拷贝数推断的参照样本。