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。     

肠道病毒71型感染机制研究进展

重症手足口病及其死亡病例多由肠道病毒71型(Enterovirus A71,EV-A71)感染引起,且近年来在亚太地区广泛流行。由于EV-A71具有严格的宿主细胞寄生性,需依赖细胞的能量和代谢系统完成其复制过程。因此研究该病毒在进入、脱衣壳等感染早期过程中病毒与宿主相互作用的机制,不仅有助于理解其致病机理,同时可为建立相应预防和治疗的策略提供科学依据。为此,就EV-A71感染早期的致病机制的研究进展进行了综述。     

人免疫球蛋白中肠道病毒71型中和抗体效价的测定

采用经典微量细胞病变法,应用近两年分离自中国手足口病(HFMD)高发区的3株肠道病毒71型(EV71)病毒株,对中国不同血液制品厂家生产的35批人免疫球蛋白制品进行抗-EV71中和效价检测。结果显示,3株不同EV71病毒株间的抗-EV71中和效价差异均在4倍以内,差异无显著的统计学意义(F=2.323,P0.05)。根据这3株毒株检测结果判定,35批人免疫球蛋白的抗-EV71均为阳性,肌肉注射用免疫球蛋白(简称肌丙)的抗-EV71-GMTs(525.9)显著高于静脉注射用免疫球蛋白(简称静丙)的GMTs(252.3,F=66.518,P0.01)。30批静丙的抗-EV71-GMTs中和效价分布在128.0~384.0之间。应开展原料血浆中抗-EV71中和效价的筛选,研制高效价的EV71特异性免疫球蛋白制品,用于HFMD的治疗和预防。     

2008～2011年贵州省肠道病毒71型分子流行特征分析

为研究贵州省肠道病毒71型(EV71)的基因型和分子流行特征,监测了全省报告的手足口病病例,选择2008年以来贵州全省部分EV71阳性标本进行病毒分离及VP1全基因测序(含重症病例、死亡病例和轻症病例),与国内外近年流行毒株及各亚型代表株进行基因比对,分析同源性及基因亚型。2008年、2009年及2011年贵州省流行的主要病原为EV71,获得109株参比序列毒株的同源性为95.3%～99.7%,贵州省毒株与邻省及山东省、上海市、南京市、吉林省和宁波市代表株的同源性最高,轻症与重死病例的核苷酸及氨基酸序列无明显的特征性差异,未出现不同基因亚型病毒的输入或改变,仍属C4a亚型。同地区、同年度内的核苷酸序列差异小于跨地区、跨年度差异。     

肠道病毒71型研究进展

肠道病毒71型是一种具有较强致病性的肠道病毒,主要引起患者手足口病(Hand,foot and mouth disease,HFMD)。已在世界多个地区爆发和流行,主要症状是手、足、口、臀等部位皮疹或疱疹,少数患儿可以并发无菌性脑膜炎、脑炎、急性弛缓性麻痹等严重神经系统并发症,呼吸道感染和心肌炎等,可致残、致死。2007—2008年中国多个地区均有较大规模流行,危害十分严重。近四十年的多次流行中,EV71病毒的基因不断进化,研究其基因变化特点对早期诊断、分型以及了解基因与流行、致病的关系等有着重要的意义。对EV71感染尚缺乏有效的抗病毒药物,研制有效的预防性疫苗迫在眉睫,目前有灭活疫苗、减毒疫苗、多肽或蛋白疫苗、DNA疫苗等多种尝试,但至今尚无EV71疫苗上市。本文对EV71基因、实验室诊断和疫苗方面的研究进展进行了综述。     

细胞焦亡在肠道病毒A71型感染中的作用

肠道病毒A组71型(Enterovirus A71,EV-A71)是引起手足口病(Hand,foot,and mouth disease,HFMD)最常见的病原体之一,而细胞焦亡是一种以细胞溶解及炎症反应为主要特征的细胞程序性死亡。目前细胞焦亡参与EV-A71致病的分子机制尚不清楚。本研究旨在探索EV-A71感染引起的焦亡与病毒感染之间的关系。EV-A71感染Vero细胞,6 h后检测caspase-1 mRNA和蛋白的表达水平,结果显示EV-A71感染促使caspase-1表达升高,表明EV-A71感染引起细胞焦亡;检测IL-1β和IL-18 mRNA和蛋白的表达水平,结果显示EV-A71感染促进IL-1β和IL-18的表达升高,表明EV-A71诱导的焦亡与炎症的产生有关。EV-A71感染后加入caspase-1抑制剂Ac-YVADCMK,在感染后6 h检测caspase-1和EV-A71的mRNA和蛋白的表达水平,结果显示加入Ac-YVAD-CMK可降低caspase-1和EV-A71的mRNA及蛋白水平,表明Ac-YVAD-CMK可抑制细胞焦亡和病毒的感染;检测IL-1β和IL-...     

肠道病毒71型(EV-A71)感染ICR小鼠模型的建立

为研究肠道病毒71型(Enterovirus 71,EV-A71)经不同攻毒方式感染不同日龄ICR乳鼠的感染情况,了解EV-A71在小鼠体内的动态分布和感染机制,为建立EV-A71感染动物模型,本研究采用分离自重症手足口患儿的EV-A71毒株,分别通过肌肉注射(Intramuscular injection,IM)、腹腔注射(Intraperitoneal injection,IP)以及脑内注射(Intracerebral injection,IC)的方式感染3日、5日和9日龄ICR乳鼠,感染后定期采集血液和各组织,通过Realtime PCR追踪各组织中病毒载量变化,并且通过切片制作和免疫组化对感染乳鼠进行病原学和病理学分析。结果显示:对于低日龄(≤5日龄)乳鼠,注射剂量在104.5 TCID50/g·体重时IM、IP及IC均为较好的感染方式,都会出现神经症状,且有极高的致死率。随着日龄增长,感染后症状有所减轻,但IM和IP感染途径对大日龄乳鼠仍具有良好的致病性,且IM和IP死亡率显著高于IC死亡率。经IM、IP和IC注射感染病毒的3日龄乳鼠在6dpi体重相对于各对照组分别下降了1.54g(31.43%)、1.31g(15.06%)和2.52g(44.28%),而经IM和IP感染的5日龄乳鼠6dpi体重相对于各对照组分别下降了0.605g(8.95%)、0.886g(15.51%),经IC感染的5日龄乳鼠6dpi体重相对于对照组上升了0.904g(14.70%),感染组体重均显著低于对应的同期对照组(P0.05)。经IM、IP和IC感染病毒的3日龄乳鼠9dpi均死亡,而5日龄乳鼠9dpi存活率分别为42.8%、25%和87.5,14dpi存活率分别为0%、0%和25%,9日龄乳鼠9dpi存活率分别为70%、84.62%和100%。病理学及免疫组化检查显示EV-A71病毒具有强烈的嗜神经性及嗜骨骼肌的特性,可导致病毒血症、脑神经元及骨骼肌坏死、心肌间质水肿及多脏器炎症反应。我们系统地研究了不同攻毒方式感染不同日龄的ICR乳鼠后的病毒动态分布及免疫病理损伤,发现经肌肉注射或腹腔注射5日龄乳鼠能够建立理想的EV-A71感染动物模型。     

肠道病毒71型SHZH03株VP1基因的进化分析

构建了肠道病毒71型（EV71）中国（深圳）分离株SHZH03全基因组的8个相互重叠的克隆,对其全基因组7406bp的核苷酸进行序列测定,利用DNA—Star软件分析外壳蛋白基因VP1的遗传进化。结果表明,SHZH03和SHZH98与亚洲流行株中的台湾1998年流行株、日本1999年流行株的遗传距离较近,而与新加坡2000年和2001年流行株的遗传距离较远;SHZH03株与一些欧洲流行株有较大的差异。以上结果说明我国深圳地区流行的肠道病毒71型有可能来源于台湾1998年的EV71大规模流行时的毒株。     

TLR3和TLR4基因多态性与EV71感染手足口病严重性及易感性的关系研究

手足口病(Hand-foot-and-mouth disease,HFMD)是5岁以下婴幼儿常见的病毒性肠道传染病,该病主要由人肠道病毒71型(Enterovirus 71,EV71)型及柯萨奇A组16型(Coxsackievirus A16,CV-A16)引起,但关于TLR3、TLR4基因多态性与EV71感染手足口病的报道较少。为探讨EV71感染手足口病患儿TLR3和TLR4基因多态性与EV71感染手足口病严重性及易感性的关系,本研究选择2016年8月至2017年8月就诊于安徽医科大学第一附属医院的EV71感染手足口病患儿166例,其中重症组76例,轻症组90例,并选择同期来院体检的健康者120例作为对照组。收集患者入院时的年龄、性别、发热天数等基线资料,采集血液检测白细胞计数(White blood cell count,WBC)、丙氨酸转氨酶(Alanine aminotransferase,ALT)、谷草转氨酶(Glutamate transaminase,AST)、酶联免疫吸附试验(Enzyme-linked immunosorbent assay,ELISA)检测血清C反应蛋白(C reactive protein,CRP)、干扰素-γ(Interferon-γ,IFN-γ)水平;分离外周血单个核细胞提取DNA,琼脂糖凝胶电泳检测DNA情况;聚合酶链反应(Polymerase chain reaction,PCR)扩增TLR3c.1377C/T和TLR4-896A/G,限制性内切酶Tap I(TthHB8 I)、Nco I分别酶切TLR3、TLR4 PCR扩增产物,凝胶成像系统记录实验结果,对扩增产物进行测序,分析其基因多态性结果。结果显示,对照组与EV71感染组TLR3c.1377C/T位点的基因型分布与C、T等位基因频率均无显著统计学意义(P0.05);EV71感染组中重症组TT基因型较轻症组显著升高(P0.05);重症组T等位基因频率显著高于轻症组(P0.05),C等位基因频率显著低于轻症组(P0.05);EV71感染组中,TLR3c.1377C/T位点不同基因型患儿在年龄、性别及ALT、AST、CKMB水平上无显著差异(P0.05);TLR3c.1377C/T位点TT型患儿的发热时间及WBC、CRP水平显著高于CT和CC型,CT型患儿的发热时间及WBC、CRP水平显著高于CC型(P0.05);CC型患儿的IFN-γ水平显著高于CT和TT型(P0.05);TLR4-896A/G基因电泳条带为140bp的特异性扩增产物,为野生型Asp/Asp基因型,对照组和EV71感染组均未出现A→G的突变。本研究得出结论,TLR3c.1377C/T位点有CC、TT、CT三个基因型,且携带T等位基因EV71感染手足口病患儿进展为重症的风险较高;TLR4-896A/G基因无突变,与EV71感染手足口病患儿疾病严重性和易感性无关。     

肠道病毒71型分子流行病学研究进展

肠道病毒71型(Enterovirus type71,EV71),自1974年首次报道以来,在世界范围内引起多次爆发与流行[1].EV71感染主要引起患者手足口病(hand,foot and mouth disease,HFMD),在临床上与柯萨奇病毒A16(Coxsakie A16,CA16)感染所引起的手足口病难以区别,但EV71还能够引起多种与神经系统相关的疾病[2].近年来,EV71病毒的流行在亚太地区呈上升趋势[3～5],其中最令人关注的是在该地区的EV71感染引起越来越严重的中枢神经系统症状.     

Identification of hub genes in colorectal cancer based on weighted gene co-expression network analysis and clinical data from The Cancer Genome Atlas

Colorectal cancer (CRC) is one of the most common tumors worldwide and is associated with high mortality. Here we performed bioinformatics analysis, which we validated using immunohistochemistry in order to search for hub genes that might serve as biomarkers or therapeutic targets in CRC. Based on data from The Cancer Genome Atlas (TCGA), we identified 4832 genes differentially expressed between CRC and normal samples (1562 up-regulated and 3270 down-regulated in CRC). Gene ontology (GO) analysis showed that up-regulated genes were enriched mainly in organelle fission, cell cycle regulation, and DNA replication; down-regulated genes were enriched primarily in the regulation of ion transmembrane transport and ion homeostasis. Weighted gene co-expression network analysis (WGCNA) identified eight gene modules that were associated with clinical characteristics of CRC patients, including brown and blue modules that were associated with cancer onset. Analysis of the latter two hub modules revealed the following six hub genes: adhesion G protein-coupled receptor B3 (BAI3, also known as ADGRB3), cyclin F (CCNF), cytoskeleton-associated protein 2 like (CKAP2L), diaphanous-related formin 3 (DIAPH3), oxysterol binding protein-like 3 (OSBPL3), and RERG-like protein (RERGL). Expression levels of these hub genes were associated with prognosis, based on Kaplan–Meier survival analysis of data from the Gene Expression Profiling Interactive Analysis database. Immunohistochemistry of CRC tumor tissues confirmed that OSBPL3 is up-regulated in CRC. Our findings suggest that CCNF, DIAPH3, OSBPL3, and RERGL may be useful as therapeutic targets against CRC. BAI3 and CKAP2L may be novel biomarkers of the disease.     

利用恒河婴猴模型对肠道病毒71型传播感染特征的生物学分析

本文在前期工作基础上,进一步对肠道病毒71型(EV71)从恒河婴猴的感染个体向其他未感染个体传播的可能性及相关生物学特性做了初步分析.通过喷雾形式经呼吸道感染1~2月龄恒河婴猴(A组);在观察临床症状同时,于感染后第7天,取该组动物粪便处理后,将上清液以喷雾形式经呼吸道感染新的婴猴个体(B组),随后对该次代感染个体进行...     

2009年云南省2株肠道病毒71型分离株全基因组序列遗传特性分析

对2009年云南省肠道病毒71型分离株KMM09和KM186-09进行全基因组序列测序,并与我国及其它国家流行的EV71基因型进行比较和进化分析。KMM09和KM186-09基因组长为7 409bp,编码2 193个氨基酸,VP1系统进化分析显示2009年云南分离株属于C4基因型的C4a亚型。在结构区,与其它基因型相比较,C基因型之间的核苷酸和氨基酸的同源性高于其它基因型;而在非结构区,C4与B基因型和CA16原型株G10同源性高于其它C基因亚型。通过RDP3重组软件和blast比对分析,发现EV71C4基因型与B3基因型,与CA16原型株G10的基因组在非结构区存在重组。EV71全基因组序列的比较和分析,对了解引起我国手足口病暴发或流行C4基因亚型EV71毒株的遗传特性具有重要意义。     

Genetic analysis of the VP1 region of human enterovirus 71 strains isolated in Fuyang,China, during 2008

Enterovirus 71 (EV71) is a common cause of Hand, foot, and mouth disease (HFMD) and may also cause severe neurological diseases, such as encephalitis and poliomyelitis-like paralysis. To examine the genetic diversity of EV71, we determined and analyzed the complete VP1 sequences (891 nucleotides) from nine EV71 strains isolated in Fuyang, China. We found that nine EV71 strains isolated were over 98% homologous at the nucleotide level and 93%-100% homologous to members of the C4 subgenogroup. At the amino acid level, these Fuyang strains were 99% -100% homologous to one another, 97%-100% homologous to members of the C4 subgenogroup, and the histidine(H) at amino acid position 22 was conserved among the Fuyang strains. The results indicate that Fuyang isolates belong to genotype C4, and an H at position 22 appears to be a marker for the Fuyang strains.     

2008～2010年河南省人肠道病毒71型基因特征和重组分析

对河南省2008～2010年河南省人肠道病毒71型进行基因特征及重组特点研究。对河南省2008～2010年分离的5株肠道病毒EV71型构建VP1序列系统进化树并分析其全基因组序列的重组特点。VP1序列系统进化分析显示2008～2010年河南株均属于C4基因型的C4a亚群,Bootscan分析和5’NCR、P1、P2、P3区的进化树证实C4基因型在2A～2B处存在EV71的B基因型和C基因型的型内重组及在3B～3C处存在EV71的B基因型和CA16/G-10间的型间重组。2008～2010年河南EV71分离株为C4基因型的C4a亚群,与2004年以来的中国大陆优势株流行趋势完全一致,EV71C4基因型存在基因型内和型间双重组现象。     

The essential role of clathrin-mediated endocytosis in the infectious entry of human enterovirus 71

Little is currently known about the infectious entry process of human enterovirus 71 (HEV71) into host cells, which may represent potential anti-viral targeting sites. In this study a targeted small-interfering RNA (siRNA) screening platform assay was established and validated to identify and profile key cellular genes involved in processes of endocytosis, cytoskeletal dynamics, and endosomal trafficking essential for HEV71 infection. Screen evaluation was conducted via the expression of well characterized dominant-negative mutants, bioimaging studies (double-labeled immunofluorescence assays, transmission electron microscopy analysis), secondary siRNA-based dosage dependence studies, and drug inhibition assays. The infectious entry of HEV71 into rhabdomyosarcoma cells was shown to be significantly inhibited by siRNAs targeting genes associated with clathrin-mediated endocytosis (CME) that include AP2A1, ARRB1, CLTC, CLTCL1, SYNJ1, ARPC5, PAK1, ROCK1, and WASF1. The functional role of CME was verified by the observation of strong co-localization between HEV71 particles and clathrin as well as dose-dependent inhibition of HEV71 infection upon siRNA knockdown of CME-associated genes. HEV71 entry by CME was further confirmed via inhibition by dominant-negative EPS15 mutants and treatment of CME drug inhibitors, with more than 80% inhibition observed at 20 μm chlorpromazine. Furthermore, HEV71 infection was shown to be sensitive to the disruption of human genes in regulating early to late endosomal trafficking as well as endosomal acidic pH. The identification of clathrin-mediated endocytosis as the entry pathway for HEV71 infection of susceptible host cells contributes to a better understanding of HEV71 pathogenesis and enables future development of anti-viral strategies against HEV71 infection.     

Key genes and functional coexpression modules involved in the pathogenesis of systemic lupus erythematosus

We performed a systematic review of genome‐wide gene expression datasets to identify key genes and functional modules involved in the pathogenesis of systemic lupus erythematosus (SLE) at a systems level. Genome‐wide gene expression datasets involving SLE patients were searched in Gene Expression Omnibus and ArrayExpress databases. Robust rank aggregation (RRA) analysis was used to integrate those public datasets and identify key genes associated with SLE. The weighted gene coexpression network analysis (WGCNA) was adapted to identify functional modules involved in SLE pathogenesis, and the gene ontology enrichment analysis was utilized to explore their functions. The aberrant expressions of several randomly selected key genes were further validated in SLE patients through quantitative real‐time polymerase chain reaction. Fifteen genome‐wide gene expression datasets were finally included, which involved a total of 1,778 SLE patients and 408 healthy controls. A large number of significantly upregulated or downregulated genes were identified through RRA analysis, and some of those genes were novel SLE gene signatures and their molecular roles in etiology of SLE remained vague. WGCNA further successfully identified six main functional modules involved in the pathogenesis of SLE. The most important functional module involved in SLE included 182 genes and mainly enriched in biological processes, including defense response to virus, interferon signaling pathway, and cytokine‐mediated signaling pathway. This study identifies a number of key genes and functional coexpression modules involved in SLE, which provides deepening insights into the molecular mechanism of SLE at a systems level and also provides some promising therapeutic targets.     

Identification of gene coexpression modules,hub genes,and pathways related to spinal cord injury using integrated bioinformatics methods

Spinal cord injury (SCI) is characterized by dramatic neurons loss and axonal regeneration suppression. The underlying mechanism associated with SCI-induced immune suppression is still unclear. Weighted gene coexpression network analysis (WGCNA) is now widely applied for the identification of the coexpressed modules, hub genes, and pathways associated with clinic traits of diseases. We performed this study to identify hub genes associated with SCI development. Gene Expression Omnibus (GEO) data sets GSE45006 and GSE20907 were downloaded and the significant correlativity and connectivity between them were detected using WGCNA. Three significant consensus modules, including 567 eigengenes, were identified from the master GSE45006 data following the preconditions of approximate scale-free topology for WGCNA. Further bioinformatics analysis showed these eigengenes were involved in inflammatory and immune responses in SCI. Three hub genes Rac2, Itgb2, and Tyrobp and one pathway “natural killer cell-mediated cytotoxicity” were identified following short time-series expression miner, protein-protein interaction network, and functional enrichment analysis. Gradually upregulated expression patterns of Rac2, Itgb2, and Tyrobp genes at 0, 3, 7, and 14 days after SCI were confirmed based on GSE45006 and GSE20907 data set. Finally, we found that Rac2, Itgb2, and Tyrobp genes might take crucial roles in SCI development through the “natural killer cell–mediated cytotoxicity” pathway.