胆囊癌组织中IL-8表达及TAM计数的临床病理意义

目的:检测胆囊腺癌组织中白细胞介素-8(IL-8)mRNA的表达、肿瘤相关巨噬细胞(TAM)计数并探讨其临床病理意义。方法:收集中南大学湘雅二医院及湖南省人民医院近五年胆囊腺癌手术切除标本36例及慢性胆囊炎手术切除标本10例,采用原位分子杂交方法检测IL-8表达,ABC免疫组化法进行TAM计数。比较胆囊腺癌和慢性胆囊炎标本组织中IL-8 mRNA表达和TAM计数的差异,并分析其与胆囊腺癌临床病理特征之间的关系。结果:胆囊腺癌组织中IL-8 mRNA表达阳性率及其评分均明显高于慢性胆囊炎(P0.01),IL-8 mRNA表达阳性率及其评分与其侵犯胆总管及发生淋巴结转移显著相关(P0.05)。胆囊腺癌组织中TAM计数(24.89±0.84)明显高于慢性胆囊炎组织(16.19±0.66),差异有统计学意义(P0.01);侵犯胆总管、肝脏及发生淋巴结转移的胆囊腺癌组织中TAM计数高于未侵犯胆总管、肝脏及发生淋巴结转移的胆囊腺癌组织TAM计数,其中侵犯胆总管和发生淋巴结转移之间差异显著(P0.01)。IL-8 mRNA阳性病例的TAM计数均明显高于阴性病例(P0.01),TAM计数与IL-8 mRNA评分间也存在显著正相关(r=0.748,P0.001)。结论:IL-8和TAM计数与胆囊癌的发生和发展密切相关,IL-8可能在促进TAM向胆囊癌组织迁移浸润中起作用。     

基于网络的肾癌随访系统的建立与应用

目的:肾癌是泌尿系常见肿瘤,需长期随访,传统统计及随访方式已逐渐不能适应现代临床及科研需求,我们尝试建立基于网络的肾癌随访系统,满足临床实际工作和科研需求。方法:以Microsoft Office Access 2007软件构建数据库管理系统,分为资料录入模块、检索分析模块、网络随访模块,选取我院2008.5至2012.12收治的132例肾癌患者,将资料录入已建成的数据库,利用网络随访辅助传统随访方式进行随访。结果:构建的肾癌随访数据库,能够实现授权账户登录,检索、分析、肿瘤自动评级等功能,可根据不同检索条件筛选出适合病历,在传统随访方式的基础上联合应用网络随访方式可提高随访效率及随访率,并能获得更详实的随访资料。结论:基于网络的肾癌随访系统操作简便,能够实现无纸化管理,数据详实,检索便捷,为科学制定治疗方案提供帮助,可一定程度上提高随访率及随访效率,降低失访率和患者就医成本。     

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome‐scale metabolic modeling

Genome‐scale metabolic models (GEMs) have proven useful as scaffolds for the integration of omics data for understanding the genotype–phenotype relationship in a mechanistic manner. Here, we evaluated the presence/absence of proteins encoded by 15,841 genes in 27 hepatocellular carcinoma (HCC) patients using immunohistochemistry. We used this information to reconstruct personalized GEMs for six HCC patients based on the proteomics data, HMR 2.0, and a task‐driven model reconstruction algorithm (tINIT). The personalized GEMs were employed to identify anticancer drugs using the concept of antimetabolites; i.e., drugs that are structural analogs to metabolites. The toxicity of each antimetabolite was predicted by assessing the in silico functionality of 83 healthy cell type‐specific GEMs, which were also reconstructed with the tINIT algorithm. We predicted 101 antimetabolites that could be effective in preventing tumor growth in all HCC patients, and 46 antimetabolites which were specific to individual patients. Twenty‐two of the 101 predicted antimetabolites have already been used in different cancer treatment strategies, while the remaining antimetabolites represent new potential drugs. Finally, one of the identified targets was validated experimentally, and it was confirmed to attenuate growth of the HepG2 cell line.     

Effect of bone marrow–derived mesenchymal stromal cells on hepatoma

Background aimsThe aim of the study was to evaluate the effect of mesenchymal stromal cells (MSCs) on tumor cell growth in vitro and in vivo and to elucidate the apoptotic and anti-proliferative mechanisms of MSCs on a hepatocellular carcinoma (HCC) murine model.MethodsThe growth-inhibitory effect of MSCs on the Hepa 1–6 cell line was tested by means of methyl thiazolyl diphenyl-tetrazolium assay. Eighty female mice were randomized into four groups: group 1 consisted of 20 mice that received MSCs only by intrahepatic injection; group 2 consisted of 20 HCC mice induced by inoculation of Hepa 1–6 cells into livers without MSC treatment; group 3 consisted of 20 mice that received MSCs after induction of liver cancer; group 4 consisted of 20 mice that received MSCs after induction of liver cancer on top of induced biliary cirrhosis.ResultsMSCs exhibited a growth-inhibitory effect on Hepa 1–6 murine cell line in vitro. Concerning in vivo study, decreases of serum alanine transaminase, aspartate transaminase and albumin levels after MSC transplantation in groups 2 and 3 were found. Gene expression of α-fetoprotein was significantly downregulated after MSC injection in the HCC groups. We found that gene expression of caspase 3, P21 and P53 was significantly upregulated, whereas gene expression of Bcl-2 and survivin was downregulated in the HCC groups after MSC injection. Liver specimens of the HCC groups confirmed the presence of dysplasia. The histopathological picture was improved after administration of MSCs to groups 2 and 3.ConclusionsMSCs upregulated genes that help apoptosis and downregulated genes that reduce apoptosis. Therefore, MSCs could inhibit cell division of HCC and potentiate their death.     

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis

Background

In somatic cancer genomes, delineating genuine driver mutations against a background of multiple passenger events is a challenging task. The difficulty of determining function from sequence data and the low frequency of mutations are increasingly hindering the search for novel, less common cancer drivers. The accumulation of extensive amounts of data on somatic point and copy number alterations necessitates the development of systematic methods for driver mutation analysis.

Results

We introduce a framework for detecting driver mutations via functional network analysis, which is applied to individual genomes and does not require pooling multiple samples. It probabilistically evaluates 1) functional network links between different mutations in the same genome and 2) links between individual mutations and known cancer pathways. In addition, it can employ correlations of mutation patterns in pairs of genes. The method was used to analyze genomic alterations in two TCGA datasets, one for glioblastoma multiforme and another for ovarian carcinoma, which were generated using different approaches to mutation profiling. The proportions of drivers among the reported de novo point mutations in these cancers were estimated to be 57.8% and 16.8%, respectively. The both sets also included extended chromosomal regions with synchronous duplications or losses of multiple genes. We identified putative copy number driver events within many such segments. Finally, we summarized seemingly disparate mutations and discovered a functional network of collagen modifications in the glioblastoma. In order to select the most efficient network for use with this method, we used a novel, ROC curve-based procedure for benchmarking different network versions by their ability to recover pathway membership.

Conclusions

The results of our network-based procedure were in good agreement with published gold standard sets of cancer genes and were shown to complement and expand frequency-based driver analyses. On the other hand, three sequence-based methods applied to the same data yielded poor agreement with each other and with our results. We review the difference in driver proportions discovered by different sequencing approaches and discuss the functional roles of novel driver mutations. The software used in this work and the global network of functional couplings are publicly available at http://research.scilifelab.se/andrej_alexeyenko/downloads.html.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-308) contains supplementary material, which is available to authorized users.     

Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?

Background

Patient-derived tumor xenografts in mice are widely used in cancer research and have become important in developing personalized therapies. When these xenografts are subject to DNA sequencing, the samples could contain various amounts of mouse DNA. It has been unclear how the mouse reads would affect data analyses. We conducted comprehensive simulations to compare three alignment strategies at different mutation rates, read lengths, sequencing error rates, human-mouse mixing ratios and sequenced regions. We also sequenced a nasopharyngeal carcinoma xenograft and a cell line to test how the strategies work on real data.

Results

We found the "filtering" and "combined reference" strategies performed better than aligning reads directly to human reference in terms of alignment and variant calling accuracies. The combined reference strategy was particularly good at reducing false negative variants calls without significantly increasing the false positive rate. In some scenarios the performance gain of these two special handling strategies was too small for special handling to be cost-effective, but it was found crucial when false non-synonymous SNVs should be minimized, especially in exome sequencing.

Conclusions

Our study systematically analyzes the effects of mouse contamination in the sequencing data of human-in-mouse xenografts. Our findings provide information for designing data analysis pipelines for these data.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1172) contains supplementary material, which is available to authorized users.     

上皮组织特异性表达N-LMP1和CR2转基因猪胚胎成纤维细胞的构建与鉴定

目的 构建上皮组织特异性表达鼻咽癌来源潜伏膜蛋白1（N-LMP1）和人补体受体2（CR2）真核表达载体,转染猪胚胎成纤维细胞并筛选整合有N-LMP1和CR2基因的细胞克隆,为构建与EBV感染相关的猪鼻咽癌模型奠定基础.方法 通过直接合成ED-L2启动子和N-LMP1,从人B淋巴细胞中的RNA经RT-PCR扩增出CR2,将上述3个片段逐个连接到真核表达载体pN1上,构建上皮组织特异性表达N-LMP1和CR2的载体pN1-ED-L2-N-LMP1-CR2;用脂质体转染猪胚胎成纤维细胞,经药物G418 筛选和PCR鉴定阳性克隆.结果 成功构建上皮组织特异性表达N-LMP1和CR2的真核表达载体pN1-ED-L2-N-LMP1-CR2,并成功整合到猪胚胎成纤维细胞的基因组中,获得了整合有目的 基因N-LMP1和CR2的猪胚胎成纤维细胞克隆.结论 获得了上皮组织特异性表达N-LMP1和CR2 的猪胚胎成纤维细胞克隆,为通过细胞核移植方法获得表达N-LMP1和CR2转基因猪提供了供体细胞.     

P13K／AKT信号转导通路与人舌鳞癌细胞TCA8113顺铂耐药的相关性研究

目的：探讨P13K特异性抑制剂LY294002逆转顺铂耐药口腔鳞癌细胞TCA8113／CDDP的可行性。方法：采用间歇性加药,逐步递增CDDP药量,体外连续诱导培养TCA8113／CDDP细胞;用不同浓度的LY294002和顺铂处理TCA8113和TCA8113／CDDP细胞;MTT法观察对细胞增殖的影响,Western印迹分析LY294002作用前后p-Akt、Akt、P13K蛋白的表达。结果：建立了舌鳞癌耐药细胞TCA8113／CDDP,耐药指数为7．7;MTT实验显示LY294002对TCA8113和TCA8113／CDDP细胞的抑制作用与浓度及作用时间呈正相关;LY294002联合顺铂对2种细胞的抑制作用比单用顺铂效果好;P13K、Akt、P—AKT蛋白表达明显降低,其中TCA8113／CDDP细胞中P13K、AKT、p-AKT蛋白的表达比TCA8113细胞明显增多（P〈0．05）。结论：LY294002能增加耐药口腔鳞癌顺铂化疗的敏感性。     

Honokiol Suppresses Renal Cancer Cells’ Metastasis via Dual-Blocking Epithelial-Mesenchymal Transition and Cancer Stem Cell Properties through Modulating miR-141/ZEB2 Signaling

Renal cell carcinoma (RCC) is associated with a high frequency of metastasis and only few therapies substantially prolong survival. Honokiol, isolated from Magnolia spp. bark, has been shown to exhibit pleiotropic anticancer effects in many cancer types. However, whether honokiol could suppress RCC metastasis has not been fully elucidated. In the present study, we found that honokiol suppressed renal cancer cells’ metastasis via dual-blocking epithelial-mesenchymal transition (EMT) and cancer stem cell (CSC) properties. In addition, honokiol inhibited tumor growth in vivo. It was found that honokiol could up-regulate miR-141, which targeted ZEB2 and modulated ZEB2 expression. Honokiol reversed EMT and suppressed CSC properties partly through the miR-141/ZEB2 axis. Our study suggested that honokiol may be a suitable therapeutic strategy for RCC treatment.