Study of transcriptional effects of drugs on SNU-423 hepatocellular carcinoma cell lines. Homo sapiens

Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death worldwide. Like in many cancers, tumor heterogeneity in HCC hampers the development of personalized therapies. Integrative genomics contributed to characterize HCC subtypes by identifying specific genetic alterations and molecular signatures, leading to targeted drug candidates. However, no consensus was achieved for genes and pathways recurrently altered in HCC. Here, a meta-analysis of 15 independent HCC datasets identifies a comprehensive signature consisting of 935 genes commonly deregulated in HCC as compared to the surrounding non-tumor tissue (P<0.01). The 935-gene HCC signature covers well-established cancer hallmarks (e.g. proliferation, metabolic reprogramming, microenvironment remodeling) together with specific hallmarks associated with protein turnover and epigenetics. Accordingly, the 935-gene HCC signature highlights relevant drugs for systemic therapies, including including two histone deacetylase (HDAC) inhibitors (trichostatin A and vorinostat), PI3K inhibitor LY294002, mTOR inhibitor sirolimus (also known as rapamycin), alpha-estradiol and resveratrol. The impact of these drugs as compared to sorafenib that is currently used for the treatment of advanced HCC was evaluated on the viability of 6 HCC-derived cell lines. We concluded that combined therapies targeting common and subtype-specific cancer networks may represent a relevant strategy to efficiently treat liver cancer. Overall design: SNU-423 cells (ATCC® CRL-2238™, grade III/IV) were grown in a RPMI-1640 medium supplemented with 100U/ml penicillin, 100μg/ml streptomycin and 10% fetal bovine serum. Cultures were performed at 37°C in a 5% CO2 atmosphere. Alpha-estradiol, LY294002, rapamycin, resveratrol, sorafenib and vorinostat were purchased from Santa Cruz Biotechnology (Heidelberg, Germany). Trichostatin A was purchased from Sigma-Aldrich (St. Louis, MO, USA). All molecules were solubilized in a dimethyl sulfoxide (DMSO) solution. For the microarray experiments the concentrations were optimized to induce 50% cell mortality after a 72h drug exposure, in order to allow the extraction of nucleic acids from the remaining viable cells. Experiments were performed in monoplicates.

肝细胞癌（Hepatocellular carcinoma, HCC）是全球范围内第二大与癌症相关的死亡原因。与多数癌症类似，肝细胞癌的肿瘤异质性阻碍了个性化治疗的开发进程。整合基因组学通过识别特异性遗传改变与分子特征，推动了肝细胞癌亚型的表征研究，并催生了靶向药物候选物。然而，学界目前尚未在肝细胞癌反复发生改变的基因与通路上达成共识。本研究对15个独立的肝细胞癌数据集开展荟萃分析，鉴定出一套包含935个基因的综合特征集：相较于癌旁非肿瘤组织，这些基因在肝细胞癌组织中普遍存在表达失调（P<0.01）。该935基因特征集覆盖了增殖、代谢重编程、微环境重塑等经典癌症特征，同时包含与蛋白质周转及表观遗传学相关的特异性特征。据此，该特征集筛选出了可用于系统治疗的相关药物，包括两种组蛋白去乙酰化酶（histone deacetylase, HDAC）抑制剂——曲古抑菌素A与伏立诺他、PI3K抑制剂LY294002、mTOR抑制剂西罗莫司（又名雷帕霉素）、α-雌二醇以及白藜芦醇。本研究以当前用于晚期肝细胞癌治疗的索拉非尼作为对照，评估了上述药物对6株肝细胞癌来源细胞系存活率的影响。研究结论显示，靶向常见癌症通路与亚型特异性癌症网络的联合治疗策略，或可成为高效治疗肝癌的有效方案。整体实验设计：将SNU-423细胞（ATCC® CRL-2238™，III/IV级）置于添加了100U/ml青霉素、100μg/ml链霉素及10%胎牛血清的RPMI-1640培养基中培养，培养条件为37℃、5%CO₂培养环境。α-雌二醇、LY294002、雷帕霉素、白藜芦醇、索拉非尼及伏立诺他均购自德国海德堡的Santa Cruz Biotechnology公司；曲古抑菌素A购自美国密苏里州圣路易斯的Sigma-Aldrich公司。所有药物均以二甲基亚砜（dimethyl sulfoxide, DMSO）溶解。为便于从剩余存活细胞中提取核酸，本研究针对芯片实验优化了药物浓度，使药物暴露72小时后可诱导50%的细胞死亡率。所有实验均以单重复形式开展。