问号钩体趋化相关基因特征分析

目的 预测问号钩体黄疸出血群赖型赖株的趋化信号传导途径，并深入分析趋化相关基因。方法 使用ProtParam tool，NCBI／Blastp进行蛋白参数分析和结构域分析，使用Clustalw软件进行多序列对比，与大肠埃希菌K-12趋化相关基因进行比较。结果 问号钩体趋化相关基因共30个，分为MCPs和che两组基因，功能与大肠埃希菌趋化相关基因相似，并预测出问号钩体趋化信号传导途径。结论 问号钩体趋化相关基因较大肠埃希菌、苍白密螺旋体和伯氏疏螺旋体多，提示其趋化传导途径更为复杂，适应宿主的能力也更强，可能是钩体的重要毒力因子之一。     

利用生物信息学分析幽门螺杆菌Lpp20蛋的化学和免疫学分子特征

目的分析幽门螺杆菌(Helicobacterpylori,Hp)郑州分离株MEL-HP27Lpp20蛋白的主要化学和免疫学分子特征,为Hp基因工程疫苗和诊断抗原的研究奠定基础。方法根据本研究室克隆的HpMEL-HP27lpp20基因的核苷酸序列推导出该基因表达产物(Lpp20)的氨基酸序列,应用生物信息学软件Omiga2.0、Anthepro4.5和GenBank数据库对Lpp20分子的主要化学特征和抗原活性进行分析。结果MEL-HP27Lpp20蛋白的氨基酸序列长度为175aa,Lpp20蛋白的分子量为19.122kDa,等电点为9.950,pH7.0时带电荷为9.035,280nm摩尔消光系数为12210,280nm吸光度为0.639,具有2个有抗原活性的结构域。结论MEL-HP27Lpp20蛋白分子具有典型抗原分子的结构特征,有希望成为新的Hp疫苗候选抗原。     

The protease allergen Der p 1 cleaves cell surface DC-SIGN and DC-SIGNR: experimental analysis of in silico substrate identification and implications in allergic responses

Background The cysteine protease Der p 1 from the house dust mite Dermatophagoides pteronyssinus is one of the most potent allergens known. An attractive mechanism for a component of Der p 1 allergenicity lies in its ability to cleave key regulatory molecules from leucocyte surfaces, subverting cellular function and driving abnormal immunoglobulin E (IgE) responses. Objective Although CD23, CD25 and CD40 have already been identified as major Der p 1 targets, other significant substrates may also exist. Methods To investigate this, knowledge of the proteolytic properties of Der p 1 was used to perform in silico digestion of human dendritic cell surface proteins, using the prediction of protease specificity (PoPS) bioinformatics tool, in conjunction with cellular in vitro analysis and cleavage site determination. Results Targets identified included DC‐SIGN and DC‐SIGNR, two C‐type lectins implicated mostly in pathogen trafficking. Treatment of positively expressing cells with Der p 1 led to loss of detectable surface DC‐SIGN and DC‐SIGNR. Digestion of purified soluble recombinant DC‐SIGN and DC‐SIGNR, followed by N‐terminal sequencing and MALDI mass spectrometry, indicated in each case one major cleavage site and several minor sites, the former correlating well with Der p 1 enzymology and the folded state of the substrate proteins. Loss of DC‐SIGN from the cell surface led to reduced binding of intracellular adhesion molecule‐3, an endogenous DC‐SIGN ligand expressed on naïve T cells which is thought to be involved in T‐helper type 1 cytokine signalling. Conclusion These data provide evidence of lectin involvement in the initiation of the allergic response and the value of using genome‐wide in silico digestion tools.     

Comprehensive analysis of lncRNA-associated ceRNA network reveals the novel potential of lncRNA,miRNA and mRNA biomarkers in human rectosigmoid junction cancer

Although accumulating evidence has confirmed the potential biological functions of long non-coding RNAs (lncRNAs) as competitive endogenous RNAs (ceRNAs) in colorectal tumorigenesis and progression, few studies have focused on rectosigmoid junction cancer. In the present study, a comprehensive analysis was conducted to explore lncRNA-mediated ceRNA implications and their potential value for prognosis. lncRNA, microRNA (miR/miRNA) and mRNA expression profiles were downloaded from The Cancer Genome Atlas database. Subsequently, a lncRNA-miRNA-mRNA regulatory network was constructed to evaluate the functions of these differentially expressed genes on overall survival (OS) for rectosigmoid junction cancer. As a result, a rectosigmoid junction cancer-specific ceRNA network was successfully constructed with 7 differentially expressed (DE)lncRNAs, 16 DEmiRNAs and 71 DEmRNAs. Among the network, one DElncRNA (small nucleolar RNA host gene 20) and three mRNAs (sodium- and chloride-dependent taurine transporter, fibroblast growth factor 13 and tubulin polyglutamylase TTLL7) were significantly associated with OS (P<0.05). Additionally, two lncRNAs (KCNQ1OT1 and MIR17HG) interacted with most of the DEmiRNAs. Notably, two top-ranked miRNAs (hsa-miR-374a-5p and hsa-miR-374b-5p) associated networks were identified to be markedly associated with the pathogenesis. Furthermore, four DEmRNAs (caveolin-1, MET, filamin-A and AKT3) were enriched in the Kyoto Encylopedia of Gene and Genomes pathway analysis, as well as being included in the ceRNA network. In summary, the present results revealed that a specific lncRNA-miRNA-mRNA network was associated with rectosigmoid junction cancer, providing several molecules that may be used as novel prognostic biomarkers and therapeutic targets.     

The roles of the cell division cycle-associated gene family in hepatocellular carcinoma

BackgroundThe members of the cell division cycle-associated (CDCA) gene family are significant regulators of cell proliferation known to play key roles in various cancers. However, the function of CDCA genes in hepatocellular carcinoma (HCC) is unclear. The aim of this research was to clarify the roles of CDCA family members in HCC using bioinformatics analysis tools.MethodsWe studied data on the mRNA and protein expression of CDCA genes and survival in patients with HCC using the Oncomine, UALCAN, HPA, CCLE, LinkedOmics, cBioPortal, and Metascape databases.ResultsSignificant overexpression of all CDCA members was found in HCC tissues. The expression levels of CDCAs were related to the tumor stage, and high expression levels were correlated with a low survival rate in patients with HCC. Also, we observed a high mutation rate (45%) of CDCAs in the HCC samples, which manifested as deep deletion, amplification, or increased mRNA expression. In the correlation analysis, we found that any 2 CDCA members were significantly positively correlated with each other. Cycle-related genes including AHCTF1, AKT1, BIRC5, CENPF, CENPL, and CENPQ were closely associated with CDCA gene alterations.ConclusionsThe findings of this study indicate that CDCAs may be potential therapeutic targets and prognostic indicators for patients with HCC.     

基于TCGA数据库分析肝细胞肝癌组织中HMMR表达与患者临床特征及预后的相关性

目的:研究透明质酸介导的运动受体（hyaluronan-mediated motility receptor,HMMR）的表达与肝细胞肝癌（hepatocellular carcinoma,HCC）的发生发展以及预后的关系。方法:在本研究中,我们通过从癌症基因组图谱(the cancer genome atlas,TCGA)数据库中下载HCC有关的数据进行生物信息学分析,探讨HMMR表达在HCC发生、发展和预后中的价值。根据HMMR mRNA表达的中位值将患者分为两组(HMMR高表达组和HMMR低表达组),应用Kruskal-Wallis检验和Logistic回归分析HMMR表达与患者临床特征之间的关系,利用Kaplan-Meier和Cox分析观察HMMR表达对HCC患者生存的影响,并进行PPI蛋白互作网络、GO富集和KEGG通路分析。最后通过实时荧光定量PCR(quantitative real-time PCR,qRT-PCR)验证HMMR mRNA在HCC组织样本中的表达。结果:HCC组织中HMMR的高表达与组织学分级(G3 vs G1,OR=2.675)、癌组织阶段(Ⅲ vs Ⅰ,OR=2.509）、T分期(T4 vs T1,OR=3.568)相关(P均<0.05)。Kaplan-Meier生存分析显示,HMMR高表达的HCC预后比HMMR低表达的患者差(P=6.858E-05)。Cox分析显示HMMR高表达是总体生存（overall survival,OS）的危险因素（HR:1.166,95%CI:1.027~1.324,P=0.018）。PPI蛋白互作、GO富集和KEGG通路分析鉴定了与HMMR存在相互作用的10个基因,分别为:FAM83D、CD44、TPX2、PLK4、AURKA、PLK1、NEK2、CDK1、BUB1及DLGAP5,它们主要富集在有丝分裂细胞周期相变的调控、细胞周期过程、ECM-受体相互作用、FoxO信号通路、EB病毒感染等。qRT-PCR结果显示,HMMR mRNA在HCC癌组织中高表达（P＜0.05）。结论:HMMR mRNA的高表达与HCC的发生发展密切相关,是HCC预后不良的独立危险因素。     

基于数据挖掘分析SLC7家族在肺鳞状细胞癌组织中的表达及其临床价值

目的:探索氨基酸转运蛋白家族（SLC7）基因在肺鳞状细胞癌（lung squamous cell carcinoma,LUSC）组织中的表达及其临床价值。方法:利用GEPIA、cBioportal等生物信息学在线分析和可视化网站,分析公共数据库TCGA中的LUSC组织中SLC7家族基因表达和变异情况;通过Kaplan-Meier Plotter分析SLC7家族对LUSC的预后价值;通过STRING在线工具获得SLC7家族潜在的互作蛋白,并利用GO和KEGG对其进行功能和通路的富集分析,探索SLC7家族在LUSC中可能的调控机制。结果:SLC7A1、SLC7A5、SLC7A8和SLC7A11在LUSC组织中表达显著升高,SLC7A2、SLC7A6和SLC7A7在LUSC组织中表达降低;癌症基因组学分析显示,469例LUSC样本中SLC7基因家族总变异率为53.73%,主要以扩增为主（占32.2%）。SLC7家族的表达与预后关系分析结果显示,SLC7A2低表达和SLC7A5高表达的LUSC患者总体生存率降低,暗示SLC7A2和SLC7A5可能可以作为预后标志物。GO和KEGG分析发现SLC7家族蛋白及其潜在互作蛋白显著富集于蛋白消化吸收、癌症中心碳代谢和铁死亡相关通路。结论:SLC7A2和SLC7A5可能是LUSC潜在的预后标志物。     

基于生物信息学分析ASPH在预测肺腺癌预后中的价值及机制研究

目的:探讨天冬氨酸β-羟化酶(ASPH)在肺腺癌中的表达情况、预后价值和在癌症中的作用机制。方法:使用Oncomine、GEPIA和TIMER数据库分析ASPH在肿瘤组织和正常组织中的表达差异,并用HPA数据库在蛋白水平验证,推测其临床意义。应用Kaplan-Meier plotter及GEPIA探讨ASPH表达水平与肺腺癌患者总生存时间的关系,提取Oncomine数据库中患者的生存信息加以整理分析,绘制生存曲线,研究ASPH表达水平与预后的关系。绘制ASPH蛋白互作网络,并进行功能富集分析,研究其作用机制。结果:来自Oncomine、GEPIA和TIMER数据库的数据均表示ASPH在肺腺癌组织中显著高表达(P＜0.05),GEPIA数据库还证明了ASPH与肺腺癌患者病理分期显著相关。分析Oncomine数据表明,ASPH表达升高肺腺癌患者的生存时间更短(HR=0.39,95%CI:0.17~0.88,P=0.024 0),GEPIA及Kaplan-Meier plotter分析结果均支持ASPH高表达预示着肺腺癌患者预后更差(P=2.4E-08)。ASPH及相关基因功能涉及钙离子调控及缺氧反应,并参与Notch、mTOR信号通路,影响肿瘤的发生与发展。ASPH还与免疫细胞浸润及相关标志物呈现弱相关性。结论:ASPH在肺腺癌组织中表达明显升高,预示着患者预后不良,且参与多条与癌症相关的信号通路,与免疫细胞浸润呈现弱相关性,ASPH可能是肺腺癌新的预后和潜在治疗标志物。     

基于生物信息学的结直肠癌生物标志物的筛选与分析

目的:采用生物信息学方法分析结直肠癌（colorectal cancer,CRC）在转录组中的差异基因,建立基因互作网络,以期筛选出关键基因并探索其发病机制。方法:从TCGA数据库下载CRC转录组数据集,采用edgeR包筛选其差异基因。使用DAVID数据库对差异基因进行GO功能和KEGG通路富集分析。通过STRING数据库分析蛋白质互作网络,运用Cytoscape进行关键子网提取并构建KEGG通路-基因互作网络,最后结合生存分析等筛选并验证CRC潜在生物标志物。结果:对转录组数据集分析筛选出5 037个差异基因,其中上调基因1 571个、下调基因3 466个,从5 037个差异基因中提取到1 781个lncRNA。GO富集分析表明CRC的差异基因主要富集在钙离子结合、受体结合及结构分子活性等功能。KEGG富集分析表明其主要参与神经活性配体-受体相互作用和药物代谢-细胞色素p450等通路。使用Cytoscape软件提取出6个关键子网,通过各互作网络共筛选出288个关键基因,结合Kaplan Meier预后分析最终筛选发现67个CRC潜在调控基因（其中已有报道证实22个mRNA和7个lncRNA）具有预后价值,并采用ONCOMINE数据库进行了CRC临床样本验证。结论:本研究筛选出的67个潜在调控基因可作为CRC潜在生物标志物,为研究者创新CRC药物及治疗方案提供了新思路。