基于加权基因共表达网络分析构建胃癌转移预测模型

背景与目的：通过对高通量功能基因组数据库（Gene Expression Omnibus,GEO）中一组含有转移和非转移性胃癌以及癌旁组织的基因芯片进行加权基因共表达网络分析（weighted gene co-expression network analysis,WGCNA）,筛选出与胃癌发生和转移显著相关的分子,为胃癌的治疗和生存期延长的研究提供参考。方法：采用WGCNA方法对19例胃癌患者基因表达进行差异分析;结合临床数据,选取与临床信息高度相关的基因模块构建网络。结果：利用WGCNA我们筛选出了Lightsteelblue模块与胃癌转移明确相关,同时对模块中的基因进一步进行分析,筛选出4个基因：C5AR1、AP3M2、TYMP、ANXA2P1作为核心靶基因。通过表达分析和受试者工作特征（receiver operating characteristic,ROC）曲线分析验证上述基因与胃癌发生、转移明确相关。同时,通过外部ONCOMINE和Kaplan-Meier plot数据库验证上述基因在胃癌中高表达,高表达这些基因的患者有着更差的预后。并利用GSE14210数据集构建基于这些基因的预测患者预后和疾病进展模型。结果提示我们所筛选的4个基因具有成为潜在胃癌转移和治疗生物标志物的可能。结论：鉴定筛选出与胃癌发生和转移相关的4个基因,可为胃癌发生、转移和治疗的研究提供参考。     

Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis

AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis (WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study. METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus (GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes. The function of the genes were annotated by gene ontology (GO). RESULTS: In this study, we identified four co-expression modules significantly correlated with clinic traits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location (sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter (LTD). Additionally, we identified the hug gene (top connectivity with other genes) in each module. The hub gene RPS15A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma. CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.     

Effects of heme precursors on CYP1A2 and POR expression in the baculovirus/Spodoptera frugiperda system

Objective: CYP1A2 and NADPH-CYP450 oxidoreductase (POR) were expressed in the baculovirus/Spodoptera frugiperda (sf9) system. The aim of this study was to investigate the effects of heme precursors on the expression of CYP1A2 and POR. Methods: The heme precursors [δ-Aminolaevulinic Acid (5-ALA), Fe3+ and hemin] were introduced into the system to evaluate their effects on the expression of CYP1A2, POR and their co-expression. All the proteins were identified using immunoblotting, CO-difference spectroscopy, or cytochrome c assay. Results: In the present study, functional CYP1A2 and POR were successfully expressed in the baculovirus/sf9 system, and both of them showed high activities. Co-addition of 5-ALA and Fe3+ significantly improved expression of CYP1A2 by about 50% compared with the addition of 5-ALA, Fe3+ or hemin alone. Either co-addition of 5-ALA and Fe3+ or addition of 5-ALA or Fe3+ alone improved the POR expression level 2 fold and its activity 7-10 fold compared with control (no addition). However, unlike CYP1A2, there was no difference between the co-addition and addition of these heme precursors alone. Different ratios of BvCYP1A2 to BvPOR also affected the co-expression of CYP1A2 and POR, with a 3:1 ratio of BvCYP1A2 / BvPOR significantly increasing their co-expression. Surprisingly, the addition of 0.1 mM 5-ALA or Fe3+ alone, but not their co-addition, could significantly improve the CYP1A2 and POR co-expression (P < 0.05). Conclusion: 5-ALA and Fe3+ increased the expression of CYP1A2 and POR in a baculovirus/sf9 system, but the pattern of their expression was different between their expression alone and co-expression.     

Muscle fibre type adaptation in the elderly human muscle

This short review discusses changes in the fibre type distribution, myosin heavy chain isoform composition and histological appearance of the very elderly human skeletal muscle. Point of origin of the discussion comes from data that we have obtained from muscle biopsies from the vastus lateralis muscle of a group of frail very elderly subjects (age: 88 +/- 3 years, range 85-97). Myosin heavy chain composition of muscle homogenates and single fibres, fibre type distribution, fibre size and capillary density were examined and compared with muscle biopsies from the young vastus lateralis muscle. Histological preparations of the muscle biopsies from our elderly subjects showed extended "grouping" (Nygaard & Sanchez, Anat Rec 1992: 202: 451-459) of the fibre types as well as significant changes in the appearance and size of the individual muscle fibres. On average, the fibre type composition of our very elderly subjects do not seem to be different to what is observed in a corresponding young group when examined with ATPase histochemistry. Likewise, the MHC composition of the muscle homogenates is comparable to what is observed in young subjects. Nevertheless, a detailed examination of the MHC composition of single fibres from the old subjects revealed that the most prominent phenotype was fibres co-expressing MHC I and MHC IIA. This is very different from what is observed in the young muscle. Detailed investigation of longitudinally cut fibres indicated that some fibres in the very old muscle, in contrast to the young muscle, switch fibre type along the length of the fibre or contain areas or nuclear domains in which the MHC expression is different from the remaining part of the fibre.     

Co-Expression of ErbB-Family Members in Human Breast Cancer: Her-2/neu is the Preferred Dimerization Candidate in Nodal-positive Tumors

Over-expression of members of the ErbB-receptor family has been associated with malignant transformation. The amplification of Her-2/neu in tumor tissue is now an established prognostic factor in breast cancer. In order to initiate signal transduction, ErbB-receptor monomers need to form homo- or heterodimers. The composition of these dimers is thought to influence both quality and quantity of downstream signaling pathways, and to determine the biological response. We have investigated the protein expression pattern of the four ErbB-receptors EGFR, Her-2/neu, Her-3 and Her-4, and correlated it with their putative ligands EGF, TGF- and HRG in 74 women with invasive breast cancer. Using western blot-analysis on cell membrane isolates, we detected the co-expression of all four ErbB-family members in 79.7% of cases, and of all of the three investigated ligands in 82.4%. We did not observe a correlation between EGFR and Her-2/neu or Her-4 protein expression, EGFR and Her-3 (p = 0.005), and Her-3 and Her-4 (p = 0.05) were clearly co-expressed. The strongest overall correlation, was found between Her-2/neu and Her-3 (p < 0.001) and between Her-2/neu and Her-4 (p = 0.001). This was particularly true in nodal-positive tumors (p <0.001 and p = 0.002) whereas in nodal-negative tumors the co-expression was either less significant (Her-2/neu and Her-3; p = 0.01) or not significant (Her-2/neu and Her-4). The co-expression of EGFR/Her-3 was associated with the expression of all ligands, whereas the Her-2/neu/Her-3 was correlated with HRG (p = 0.002), thereby indicating a functional relation between specific receptor-dimer combinations and putative ligands. Taken together, we have performed the first comprehensive survey of ErbB-system expression in breast cancer, and have demonstrated the presence of a co-regulated receptor/ligand system in vivo. We have further shown that Her-2/neu is the preferred co-expression partner in nodal-positive tumors and thus the most likely dimerization candidate in malignant breast tumors.     

反义TR和p21双基因共表达对人主动脉平滑肌细胞增殖与凋亡的作用

目的观察携带反义凝血酶受体(ATR)或/和p21的单、双基因重组腺病毒伴随病毒(rAAV)载体对人主动脉平滑肌细胞(ASMC)增殖与凋亡的影响。方法以携带ATR或/和p21的单、双基因rAAV感染人ASMC。半定量RT-PCR检测各基因的整合与表达;MTT法测定感染不同时间点的细胞存活率;流式细胞术检测细胞周期与凋亡细胞数目的变化;吖啶橙/溴化乙锭(AO/EB)染色检测凋亡细胞的比率。结果单、双基因在ASMC中均获得整合,且双基因发生了共表达;病毒感染4d时,ATR组、p21组和AP双基因组的细胞存活率与对照组相比分别降低了16.7%、21.6%和29.4%;三组的G0/G1期细胞数分别为(61.8±2.9)%、(82.5±4.0)%和(80.4±6.1)%;凋亡细胞数为(4.8±0.5)%、(5.7±0.1)%和(9.2±0.9)%;AO/EB染色显示的凋亡细胞比率分别为:对照组(1.5±0.8)%、ATR组(7.2±3.3)%、p21组(10.7±5.6)%、AP组(18.3±2.7)%。结论(1)双基因共表达对抑制细胞增殖和诱导凋亡的作用均较单基因具有较强的生物学效应。(2)为再狭窄的基因治疗提示了更优化的途径。     

加权基因共表达网络分析挖掘老鸦瓣芽茎发育关键基因

目的 利用老鸦瓣Amana edulis各部位及芽茎不同发育时期RNA-Seq及基因表达量数据,挖掘老鸦瓣芽茎发育过程关键基因。方法 通过加权基因共表达网络分析（weighted gene co-expression network analysis,WGCNA）法构建网络,根据模块功能富集分析及基因表达模式进行共表达模块和核心基因的筛选。结果 通过基因表达量相关性进一步将网络划分为15个模块,将共表达模块与老鸦瓣芽茎3个发育时期相关联,鉴定到与芽茎发生高度相关的3个模块,即T1MEplum1模块、T2 MEdarkturquoise模块和T3 MElightcyan模块。对3个模块内的基因进行动态基因本体（gene ontology,GO）和京都基因与基因组百科全书（Kyoto encyclopedia of genes and genomes,KEGG）功能富集分析并绘制网络关系图,挖掘出4个与芽茎发育过程相关核心基因（Te＿c1647、Te＿c3695、Te＿c23305、Te＿c52282）,涉及蛋白质合成、次生代谢产物的糖基化修饰、植物激素调节等。结论 挖掘出的3个共表达模块...     

基于生物信息学的补气活血通络方对特发性肺间质纤维化的作用机制研究

目的 基于临床大样本基因芯片数据,确定补气活血通络方对特发性肺间质纤维化作用靶点和机制.方法 基于TCMSP数据库确定补气活血通络方的有效成分及作用靶点.利用Gene Expression Omnibusl(GEO)数据库的肺纤维化基因表达谱数据,构建加权基因共表达网络,确定肺纤维化发病的相关基因.将补气活血通络方的靶...     

Identification and in vitro validation of diagnostic and prognostic biomarkers for lung squamous cell carcinoma

BackgroundThe aim of the present study was to find diagnostic and prognostic biomarkers for lung squamous cell carcinoma (LUSC) and to validate key biomarkers in vitro.MethodsRNA sequencing was used to identify differentially expressed mRNAs (DEmRNAs) and differentially expressed long non-coding RNAs (DElncRNAs) in LUSC tissues. RNA sequencing results were validated using a published dataset. Diagnostic and prognostic values of candidate genes were evaluated by receiver-operating characteristic (ROC) curve analysis and survival analysis, respectively. To determine the effect of MIR205HG in LUSC, MIR205HG expression was knocked down in NCI-H520 cells. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and Transwell assay were used to respectively detect the effect of MIR205HG on cell proliferation and migration.ResultsIn total, 1,946 DEmRNAs and 428 DElncRNAs were identified in LUSC compared with normal tissues. A total of 851 DElncRNA-DEmRNA co-expression pairs were obtained. With the exception of NEAT1, MCM2, SERPINB5, ITGB8, CASC19, and MIR205HG were upregulated in LUSC. ROC curve analysis indicated that MCM2, SERPINB5, ITGB8, CASC19, and MIR205HG could predict LUSC. Survival analysis suggested that SERPINB5, NEAT1, and MIR205HG had potential prognostic value for LUSC. MIR205HG knockdown inhibited cell proliferation and migration, and significantly reduced the expression of ITGB8.ConclusionsThe findings of the present study could help determine the pathogenesis of LUSC and provide new and accurate therapeutic targets for its treatment.     

利用共表达网络分析寻找肝细胞肿瘤术后复发分子标记物

目的 结合肝细胞肿瘤（hepatocellular carcinoma,HCC）患者的表达谱数据和基因共表达网络分析,寻找HCC术后复发相关的分子标记物.方法 筛选35/41例术后复发/未复发患者的表达谱数据的差异表达基因,然后建立基因共表达网络;利用MCODE软件寻找网络中基因共表达模块以及核心基因;最后,利用三种交叉验证方法[留一交叉验证（LOOCV）、十折交叉验证（10 fold CV）以及蒙特卡罗交叉验证（MCCV）]证明核心基因的分类能力.结果 差异表达基因筛选得到316个差异基因,共表达网络分析得到了包括84个基因的网络,MCODE软件分析得到两个基因模块及其核心基因：RACGAP1和ETS2.三种交叉验证实验发现,这两个基因对HCC样本的分类结果,LOOCV：87％（86％ ～ 89％）、10 fold CV：88％（87％ ～89％）,MCCV：85％（85％ ～86％）.结论 以上结果提示,RACGAP1和ETS2基因可作为HCC术后复发的分子标记物.