基于节点-模块置信度及局部模块度双重约束挖掘前列腺癌候选疾病模块

前列腺癌病因及发病机理研究有助于前列腺癌预防和治疗.目前,前列腺癌生化试验研究方法成本高、耗时,而基于网络计算方法容易受基因表达谱数据不完整、噪声高及实验样本数量少等约束.为此,本文提出一种基于节点-模块置信度及局部模块度的双重约束算法(命名为NMCOM),挖掘前列腺癌候选疾病模块.NMCOM算法不依赖基因表达谱数据,采用候选基因与致病表型之间一致性得分,候选基因与致病基因之间语义相似性得分融合排序策略,选取起始节点,并基于节点-模块置信度及局部模块度双重约束挖掘前列腺癌候选疾病模块.通过对挖掘出的模块进行富集分析,最终得到18个有显著意义的候选疾病基因模块.与单一打分排序方法及随机游走重开始方法相比,NMCOM融合排序策略的平均排名比小、AUC值大,且挖掘出结果明显优于其他模块挖掘算法,模块生物学意义显著.NMCOM算法不仅能准确有效地挖掘前列腺癌候选疾病模块,且可扩展挖掘其他疾病候选模块.     

基于miRNA-mRNA联合分析的卵巢癌调控网络构建

研究表明微小RNA(microRNA,miRNA)通过影响转录后基因表达来调节机体功能,并与肿瘤的发生有密切关系。然而目前癌症致病过程的转录调控网络重构大多致力于转录层面的基因表达数据的处理和分析,如何整合转录及转录后不同类型的生物数据以挖掘它们的共调控机制是目前的研究热点之一。基于此,本研究利用联合非负矩阵分解算法融合卵巢癌miRNA数据和基因表达数据形成共模块,其次对特征模块中miRNA的靶基因进行预测分析,最后对mi RNA-mRNA共模块进行转录及转录后共调控网络构建。仿真结果及分子生物学分析表明,通过联合矩阵分析方法所提取的共模块显示出了与卵巢癌致病具有显著的生物相关性和潜在的联系,此外,GO生物过程分析也进一步的揭示了所提取的共模块中miRNA靶基因的生物学功能与卵巢癌致病密切相关。     

时间延迟基因调控网络重构的决策树方法研究

基因调控网络的重构是功能基因组中最具挑战性的课题之一. 针对基因间转录调控的时间延迟性, 提出了一种寻找时间延迟调控关系的方法: 多点延迟调控网络算法, 简称TdGRN (time-delayed gene regulatory networking). 该方法根据时间序列基因表达谱数据, 构建时间延迟基因表达矩阵, 利用有监督决策树分类器方法和随机重排技术挖掘基因之间的时间延迟调控关系, 从而构建时间延迟的基因调控网络. 该方法是一种不依赖模型的基因网络重建方法, 相对于目前采用的基于模型的网络重建方法有显著优势, 可直接利用连续的基因表达谱数据发现延迟任一时间单位差的基因表达调控关系, 并避免了目前一些研究方法中需要人为设定基因的最大调控子数目(k)的问题. 将该方法应用于酿酒酵母细胞周期的基因表达谱数据, 并构建时间延迟的基因调控网络, 结果发现多数时间延迟调控关系获得了已有知识的支持.     

基于人类信号网络和表达谱数据挖掘动脉粥样硬化相关模块

目的:动脉粥样硬化是一种高致死率的慢性炎症疾病,其发生和发展的机制尚不明确。本文基于人类信号网络和基因表达谱数据对动脉粥样硬化相关模块进行挖掘,以探究其在疾病发生发展中的作用机制。方法:结合人类信号网络和基因表达谱数据,设计显著差异模块筛选策略,通过功能分析,挖掘动脉粥样硬化相关模块,对动脉粥样硬化的致病机制进行研究。结果:基于网络模块的平均表达值改变量,采用两种随机方法,进行显著差异模块筛选,最终获得8个动脉粥样硬化相关的显著差异模块。结论:应用本文提出的整合筛选策略,能识别与动脉粥样硬化相关的模块,获得潜在的致病基因,并从外周血的基因表达改变来探究动脉粥样硬化致病机制,这对动脉粥样硬化的诊断、治疗以及发生发展机制的研究具有重要意义。     

基于SNP共表达网络肝癌分子分型及预后分析

基于SNP突变数据与mRNA表达谱关联分析,构建一种肝癌分子分型方法并对比不同分型预后的差异,并对不同分型肝癌的发生发展机制进一步研究。首先通过TCGA数据库收集359例肝细胞癌患者的SNP突变数据和mRNA表达数据,采用Wilcoxon秩和检验,筛选突变后差异表达基因,并通过生物信息学工具String和Cytoscape 构建差异表达基因的蛋白互作网络,筛选连接度最高的10个Hub基因。利用Consensus Cluster Plus软件包,基于Hub基因mRNA表达水平构建NMF分子分型模型,再结合生存数据评估各分型患者的预后。最后利用加权基因共表达网络分析(WGCNA),识别与肝癌分子分型相关的模块,并针对关键模块的基因进行通路富集,从而对不同分型肝癌的基因表达谱进行比较。结果:NMF模型将肝癌分为高危、低危2个分型,其中CDKN2A和FOXO1基因对分型贡献度高。生存分析显示低危组患者的生存情况显著优于高危组,高危组富集多个与肿瘤细胞侵蚀、转移、复发过程相关的信号通路,低危组则与细胞周期和胰液分泌相关。本研究在无先验性信息的前提下,基于突变后显著差异表达的Hub基因表达水平构建的肝癌分子分型对肝癌患者预后评估具有一定的指导意义,其中CDKN2A和FOXO1突变是肝癌患者的不良预后因素,针对二者的靶向药研发,可能为肝癌患者提供新的治疗策略。     

伴HBV感染性肝癌调控枢纽基因筛选与初步鉴定

慢性乙型肝炎病毒(Hepatitis B virus,HBV)感染引起的原发性肝癌涉及多种基因、转录本和蛋白质的相互作用及调控。从单个基因的角度来看,某个基因的表达量的改变只能对肝癌发生发展的局部作出解释而无法从整体行为进行深入和全面的探索,无法满足高度复杂性的调控研究需要。筛选乙肝相关性肝癌的基因芯片数据获取差异表达基因后,应用加权基因共表达网络分析算法构建基因共表达网络,识别与肝癌发生相关的模块,利用可视化筛选枢纽基因,并针对枢纽基因进行基因本体富集分析和初步验证。富集分析和文献挖掘一致发现,某些枢纽基因确实与多种癌症的发生与发展存在显著的关联。权重基因共表达网络分析方法被证明是一个高效的系统生物学方法,应用该方法发现了新的HBV相关性肝癌枢纽基因。经实验验证,发现枢纽基因SHARPIN促进细胞迁移。该研究对肝癌发生的调控机制以及发现HBV慢性感染导致肝癌的新型诊断标志物和(或)药物作用靶点提供了新的视野。     

基于分子生态学网络探究西藏草地放牧对土壤微生物群落的影响

【目的】揭示西藏地区放牧对在功能基因层面上的微生物相互作用的影响。【方法】利用最近发明的网络工具(基于随机矩阵理论的分子生态学网络)分别在对照和放牧条件下分析基因芯片中碳循环和氮循环基因。【结果】碳和氮循环基因网络在对照和放牧条件下都具有无标度、小世界、模块性和层次性的拓扑学特征。放牧条件下的网络关键基因(模块枢纽和连通者)与对照显著不同。放牧导致网络变得小而紧密,暗示环境压力的存在。地上植物生物量与微生物基因网络显著相关(P=0.001),证实了研究样地地上植物与地下微生物紧密相连。【结论】放牧显著改变了西藏草地在功能基因层面上的微生物相互作用关系。     

活血化瘀方抗糖尿病心肌病的药理调控机制研究

目的:从基因表达谱的角度探究活血化瘀方抗糖尿病心肌病的药理调控机制。方法:采用链脲霉素建立糖尿病心肌病大鼠模型后,随机分组并对其中一组给予活血化瘀方灌胃,检测生理数据,并取样进行基因表达水平检测。针对芯片数据,初处理后依次进行:基因表达差异分析、基因表达与性状相关性分析、基因连接性差异分析和加权的基因共表达网络分析,最后整合上述多种分析结果,寻找关键基因。结果:成功建立糖尿病心肌病大鼠模型,并得到一系列从不同角度分析的结果:一千多个差异表达基因,五千多个差异连接性基因,鉴定出三个共表达网络中的关键模块以及三个关键基因。结论:活血化瘀方通过调节与糖尿病心肌病或者糖尿病密切相关的生物分子及其活动,同时综合作用于多种基础的细胞生理活动,从而影响糖尿病心肌病的发展。     

基于hMeDIP-seq分析肝癌小鼠癌组织中肝癌相关信号分子基因的羟甲基化

本研究通过hMeDIP-Seq技术和生物信息学分析,从肝细胞癌模型小鼠肝癌组织和肝组织基因组羟甲基化的角度研究肝癌相关信号通路,以期探讨肝癌相关信号分子基因的羟甲基化分布及其与基因表达的关系。研究结果表明,肝癌组织中共有52个具有显著统计学意义的肝癌相关信号分子基因发生了羟(FDR0.05),而肝组织的则没有出现有统计学意义的相关羟甲基化信号分子基因。而且,这些信号分子基因的羟甲基化位点全部分布在基因表达的调控区域(外显子外),包括启动子-转录启始位点区、内含子区和基因间区。由于DNA羟甲基化是激活基因表达的重要手段,因此,这些区域的羟甲基化表明这些基因在肝癌组织中处于激活状态,并得到了RT-q PCR实验的抽样证明。由此可见,肝癌组织基因组上发生的羟甲基化与肝癌相关;它们通过激活大量的信号分子基因引起肝癌相关信号通路的异常活化,从而引起肝癌的发生或迁移。     

Identification of SLITRK6 as a Novel Biomarker in hepatocellular carcinoma by comprehensive bioinformatic analysis

Hepatocellular carcinoma (HCC) is the most common primary malignancy of the adult liver and morbidity are increasing in recent years, however, there is still no effective strategy to prevent and diagnose HCC. Therefore, it is urgent to research the effective biomarker to predict clinical outcomes of HCC tumorigenesis. In the current study, differentially expressed genes in HCC and normal tissues were investigated using the Gene Expression Omnibus (GEO) dataset GSE144269 and The Cancer Genome Atlas (TCGA). Gene differential expression analysis and weighted correlation network analysis (WGCNA) methods were used to identify nine and 16 key gene modules from the GEO dataset and TCGA dataset, respectively, in which the green module in the GEO dataset and magenta module in TCGA were significantly correlated with HCC occurrence. Third, the enrichment score of gene function annotation results showed that these two key modules focus on the positive regulation of inflammatory response and cell differentiation, etc. Besides, PPI network analysis, mutation analysis, and survival analysis found that SLITRK6 had high connectivity, and its mutation significantly impacted overall survival. In addition, SLITRK6 was found to be low expressed in tumor cells. To summarize, SLITRK6 mutation was found to significantly affect the occurrence and prognosis of HCC. SLITRK6 was confirmed as a new potential gene target for HCC, which may provide a new theoretical basis for personalized diagnosis and chemotherapy of HCC in the future.     

Genome-wide integrative analysis revealed a correlation between lengths of copy number segments and corresponding gene expression profile

Microarray analysis has been applied to comprehensively reveal the abnormalities of DNA copy number (CN) and gene expression in human cancer research during the last decade. These analyses have individually contributed to identify the genes associated with carcinogenesis, progression, metastasis of tumor cells and poor prognosis of cancer patients. However, it is known that the correlation between profiles of CN and gene expression does not highly correlate. Factors which determine the degree of correlation remain largely unexplained. To investigate one such factor, we performed trend analyses between the lengths of CN segments and corresponding gene expression profiles from microarray data in hepatocellular carcinoma (HCC) and colorectal carcinoma (CRC). Significant correlations were observed in CN gain of HCC and CRC (p<0.05). The trend of the CN loss showed a significant correlation in HCC although there was no correlation between the length of CN loss segments and gene expression in CRC. Our findings suggest that the influence of CN on gene expression highly depends on the length of CN region, especially in the case of CN gain. To the best of our knowledge, this is the first study describing the correlation between lengths of CNA segments and expression profiles of corresponding genes.     

Altered transferrin gene expression in preneoplastic and neoplastic liver lesions induced in rats with N-nitrosomorpholine

The expression of the gene for the iron transport protein transferrin was found to be altered in preneoplastic and neoplastic lesions induced in the rat liver by N-nitrosomorpholine. The total RNA of ten hepatocellular carcinomas (HCC) was investigated by Northern blot analysis using a cDNA-probe comprising 150 bp of the 3′ region and compared with the total hepatic RNA in untreated rats. Seven hepatocellular carcinomas showed slight or pronounced reduction in transferrin expression. In situ hybridization of two additional hepatocellular carcinomas revealed marked reduction in the mRNA level for the transferrin gene compared with the surrounding tissue. In contrast, the majority of early preneoplastic lesions storing excess glycogen and tigroid cell foci expressed increased levels of transferrin mRNA. The loss of glycogen in mixed cell foci, which represent a later stage of hepatocarcinogenesis, was usually accompanied by a decrease in transferrin mRNA suggesting a close relationship between this change in gene expression and cellular dedifferentiation emerging during hepatocarcinogenesis.     

DLC-1与肝癌关系研究

DLC-1基因是一种肿瘤抑制基因,位于人类染色体8p21．3-22。它是RhoA特异性GTP酶的激动蛋白,与调控细胞增殖和粘附的信号传导通路关系密切,在人类多种肿瘤中呈低表达或表达缺失。研究发现DLC-1基因在原发性肝癌(HCC)及肝癌细胞系中表达缺失,提示该基因在原发性肝癌中抑制了肝癌细胞的增殖。DLC-1表达的恢复引起了caspase-3介导的细胞凋亡,抑制肝癌细胞的生长和癌细胞的浸润,从而在肝细胞癌的转移、侵袭及肿瘤细胞的生物特性方面发挥作用。因其与肝癌发生,转移乃至复发关系密切,使其在肝癌早期发现,早期预测肝癌的转移复发及肝癌的预后方面发挥重要角色。     

Altered transferrin gene expression in preneoplastic and neoplastic liver lesions induced in rats with N-nitrosomorpholine.

The expression of the gene for the iron transport protein transferrin was found to be altered in preneoplastic and neoplastic lesions induced in the rat liver by N-nitrosomorpholine. The total RNA of ten hepatocellular carcinomas (HCC) was investigated by Northern blot analysis using a cDNA-probe comprising 150 bp of the 3' region and compared with the total hepatic RNA in untreated rats. Seven hepatocellular carcinomas showed slight or pronounced reduction in transferrin expression. In situ hybridization of two additional hepatocellular carcinomas revealed marked reduction in the mRNA level for the transferrin gene compared with the surrounding tissue. In contrast, the majority of early preneoplastic lesions storing excess glycogen and tigroid cell foci expressed increased levels of transferrin mRNA. The loss of glycogen in mixed cell foci, which represent a later stage of hepatocarcinogenesis, was usually accompanied by a decrease in transferrin mRNA suggesting a close relationship between this change in gene expression and cellular dedifferentiation emerging during hepatocarcinogenesis.     

硫氧还蛋白-1减弱脂连蛋白对小鼠移植性肝癌生长的抑制作用

硫氧还蛋白-1 (thioredoxin 1, Trx1)是机体氧化还原调控的重要蛋白质。脂连蛋白(adiponectin, APN)是一种由脂肪组织分泌的细胞因子。二者在癌症特别是肝癌的发展中具有重要调控作用,但其在调控肝癌的进程中是否存在相关性,且改变这种相关性是否直接影响肝癌的发生发展,目前尚未见报道。本文通过分析癌症和肿瘤基因图谱 (The Cancer Genome Atlas, TCGA) 数据库中大量肝癌患者组织样本数据后,首次发现Trx1与APN在肝癌的进程中存在显著负相关表达。在荷瘤鼠中分别过量表达Trx1、APN和Trx1,采用Western 印迹、免疫组织化学染色及TUNEL等方法检测发现,过量表达的Trx1,缓解了APN引起的瘤内Trx1蛋白水平下降,减弱APN对肿瘤的抑制作用,同时增加Ki67阳性细胞数目,减少细胞凋亡和p-JNK阳性细胞数目。上述结果表明,改变Trx1与APN的负相关性后,APN对肝癌细胞成瘤的抑制作用明显减弱。提示在抑制肝癌细胞生长及肝癌治疗的过程中,调控Trx1及APN的相关性可能起到十分重要的作用,这为临床肝癌的治疗提供更为全面有效的理论机制。     

Loss of the orphan nuclear receptor SHP is more pronounced in fibrolamellar carcinoma than in typical hepatocellular carcinoma

Hepatocellular carcinoma (HCC) remains a major problem in oncology. The molecular mechanisms which underlie its pathogenesis are poorly understood. Recently the Small Heterodimer Partner (SHP), an orphan nuclear receptor, was suggested to be involved as a tumor suppressor in hepatocellular carcinoma development. To date, there are no such studies regarding fibrolamellar carcinoma, a less common variant of HCC, which usually affects young people and displays distinct morphological features. The aim of our project was to evaluate the SHP levels in typical and fibrolamellar hepatocellular carcinoma with respect to the levels of one of the cell cycle regulators, cyclin D1. We assessed the immunoreactivity levels of SHP and cyclin D1 in 48 typical hepatocellular carcinomas, 9 tumors representing the fibrolamellar variant, 29 non malignant liver tissues and 7 macroregenerative nodules. We detected significantly lower SHP immunoreactivity in hepatocellular carcinoma when compared to non malignant liver tissue. Moreover, we found that SHP immunoreactivity is reduced in fibrolamellar carcinoma when compared to typical hepatocellular carcinoma. We also found that SHP is more commonly lost in HCC which arises in the liver with steatosis. The comparison between the cyclin D1 and SHP expression revealed the negative correlation between these proteins in the high grade HCC. Our results indicate that the impact of loss of SHP protein may be even more pronounced in fibrolamellar carcinoma than in a typical form of HCC. Further investigation of mechanisms through which the loss of SHP function may influence HCC formation may provide important information in order to design more effective HCC therapy.