Integration of multidimensional splicing data and GWAS summary statistics for risk gene discovery

A common strategy for the functional interpretation of genome-wide association study (GWAS) findings has been the integrative analysis of GWAS and expression data. Using this strategy, many association methods (e.g., PrediXcan and FUSION) have been successful in identifying trait-associated genes via mediating effects on RNA expression. However, these approaches often ignore the effects of splicing, which can carry as much disease risk as expression. Compared to expression data, one challenge to detect associations using splicing data is the large multiple testing burden due to multidimensional splicing events within genes. Here, we introduce a multidimensional splicing gene (MSG) approach, which consists of two stages: 1) we use sparse canonical correlation analysis (sCCA) to construct latent canonical vectors (CVs) by identifying sparse linear combinations of genetic variants and splicing events that are maximally correlated with each other; and 2) we test for the association between the genetically regulated splicing CVs and the trait of interest using GWAS summary statistics. Simulations show that MSG has proper type I error control and substantial power gains over existing multidimensional expression analysis methods (i.e., S-MultiXcan, UTMOST, and sCCA+ACAT) under diverse scenarios. When applied to the Genotype-Tissue Expression Project data and GWAS summary statistics of 14 complex human traits, MSG identified on average 83%, 115%, and 223% more significant genes than sCCA+ACAT, S-MultiXcan, and UTMOST, respectively. We highlight MSG’s applications to Alzheimer’s disease, low-density lipoprotein cholesterol, and schizophrenia, and found that the majority of MSG-identified genes would have been missed from expression-based analyses. Our results demonstrate that aggregating splicing data through MSG can improve power in identifying gene-trait associations and help better understand the genetic risk of complex traits.     

食管组织和外周血中代谢和DNA修复相关基因的表达谱分析

目的:研究代谢酶和DNA修复相关基因在食管组织和外周血中的表达谱.方法:收集93例淮安地区食管癌病例的食管癌旁正常组织和外周血,采用实时荧光定量RT-PCR方法定量分析食管正常组织和外周血中的代谢酶和修复酶共计11个基因的mRNA水平.结果:11个代谢酶和修复酶基因在食管组织和外周血的表达水平有明显差异,食管组织中GSTPI＞NQOI、MGMT＞hMLH1、hMSH2、hOGG1、XRCC1、XPD,XPA、CYP2E1＞MTHFR;在外周血中GSTP1＞hMLH1、hMSH2、XPA、MGMT＞hOGG1、NQO1、CYP2E1、XRCC1、XPD＞MTHFR.食管组织基因表达水平与外周血相应基因的表达之间未发现有统计学意义的直线相关关系.结论:代谢酶和修复酶基因在食管组织和外周血的表达谱相似,但基因表达水平有差异,本分析为这些基因的研究提供了基础数据的支持.外周血和食管组织在肿瘤易感性和肿瘤发生相关的生物标志物研究中具有不同的应用价值.     

氧化应激对腺病毒E1A蛋白活化NF-κB转录活性的影响及其机制研究

目的:探讨腺病毒E1A蛋白对细胞内抗氧化物质谷胱甘肽(GSH)水平的影响及氧化应激对腺病毒E1A蛋白介导的核因子-κB(NF-κB)转录活化的影响。方法:构建稳定表达E1A蛋白的大鼠肺泡上皮细胞(E1A组)及对照质粒转染细胞(对照组),每组5×105个细胞,试验重复3次。采用H2O2刺激细胞,检测细胞内GSH水平。脂多糖(LPS)和肿瘤坏死因子-α(TNF-α)进行刺激,丁胱亚磺酰亚胺(BSO)进行干预,Western blot法检测NF-κB和AP-1蛋白的表达。结果:E1A+细胞内GSH基础水平与E1A-比较无显著差异,但在H2O2作用后没有诱导出GSH含量的上升,表现为下降而低平的趋势,去除氧化剂后,仍低于正常水平。E1A-细胞在氧化剂的作用后呈明显的上升趋势,去除氧化剂后仍高于基础水平。细胞内NF-κB蛋白表达(积分吸光度值):刺激前E1A+细胞分别为79.3±4.6和80.3±3.8,在LPS和TNF-α刺激后分别为81.8±3.9～89.9±1.6和94.1±1.9～99.8±1.6,均明显高于对照组(刺激前分别为68.3±3.8和69.4±4.3,刺激后分别为70.1±2.8～80.8±3.6和73.4±4.9～83.2±6.7)。给予BSO预处理后再用LPS和TNF-α刺激,E1A-细胞NF-κB蛋白表达的积分吸光度值(1.22±0.16和1.75±0.13)与LPS或TNF-α单独作用组(1.25±0.18和1.69±0.19)无明显差别;E1A+细胞NF-κB蛋白表达的积分吸光度值(1.75±0.10和2.26±0.21)明显高于LPS或TNF-α单独作用组(1.35±0.12和1.80±0.14)。结论:腺病毒潜伏感染持续表达E1A蛋白可以影响细胞GSH,降低细胞对氧化应激的耐受性,并可能通过此机制造成NF-κB异常转录活化,而GSH的降低又进一步放大了E1A介导的NF-κB转录活化作用。     

Identification of a novel peptide ligand of human vascular endothelia growth factor receptor 3 for targeted tumour diagnosis and therapy

Human vascular endothelia growth factor receptor 3 (VEGFR-3) is up-regulated in a variety of human cancers. It is a potentially rational target for drug delivery. To identify novel ligands with specific binding capabilities to VEGFR-3, we screened a phage display peptide library and found a consensus motif of the peptides which is displayed by the positive phages CSDxxHxWC (x is any amino acid). The phage displaying peptide CSDSWHYWC (designated as P1) exhibited the highest affinity to VEGFR-3 in phage ELISA and the chemically synthesized P1 could bind to VEGFR-3 specifically in a dose-dependent manner. In addition, the flow cytometry assay and immunofluorescence showed that the FITC labelled P1 could bind to VEGFR-3 positive carcinoma cells with specificity. Our study suggests that P1 may be a homing peptide for treatment of tumours.     

伪狂犬病毒跨突触示踪视觉系统神经网络的研究进展

伪狂犬病毒（PRV）作为一种亲神经性的病毒,它以其自我复制、跨突触、特异性传递的三大优势在揭示神经系统中功能性神经元之间的连接发挥着重大的作用。经基因重组后的伪狂犬病毒不但继承了原有病毒的优势,同时还延伸出其他特异性的功能,如重组后加入了荧光蛋白的伪狂犬病毒在视觉系统神经通路的研究中发挥了重要作用。本文就目前伪狂犬病毒跨突触示踪视觉系统神经网络中的研究做一综述。     

口服脊髓灰质炎减毒活疫苗(人二倍体细胞)的稳定性研究

目的评价细胞工厂工艺连续生产的口服脊髓灰质炎减毒活疫苗(人二倍体细胞)的稳定性。方法疫苗在-20℃放置24个月,检测病毒滴度、外观、抗生素残留量、无菌性,及对病毒血清型进行鉴别;2~8℃放置12个月检测疫苗稳定性;室温放置7周、37℃放置7 d检测加速热稳定性并冻融的稳定性。结果该疫苗-20℃可贮存24个月以上,2~8℃有效期可延长至12个月,且冻融不会影响疫苗的稳定性。结论疫苗质量稳定,各项检测结果均符合《中华人民共和国药典》三部(2010版)及企业《口服脊髓灰质炎减毒活疫苗(人二倍体细胞)注册标准》。     

有效抽提乙醇中螨标本的核DNA

对如何有效地从乙醇保存的叶螨中抽提核基因组DNA作了探讨。70％乙醇保存的叶螨标本,经过干燥,TEN洗涤,蛋白酶K消化,酚—氯仿抽提,2倍体积无水乙醇沉淀等步骤,得到叶螨核基因组DNA沉淀,再用TE或无菌水溶解后,以其为模板,进行随机引物PCR扩增。结果显示.该方法抽提的DNA无Taq酶抑制物,且其纯度达到进行PCR反应对模板要求的程度。这为采用AP-PCR技术研究螨的系统分类提供了便利。     

虫媒黄病毒亚基因组RNA

黄病毒是一大科人类致病性的单股正链RNA病毒。黄病毒包括登革病毒、西尼罗脑炎病毒及日本脑炎病毒等成员,主要径通过节肢动物的叮咬进行传播,即为虫媒黄病毒。研究发现,在虫媒黄病毒复制过程中,除病毒基因组正链RNA、互补的负链RNA及两者的杂合RNA分子外,在病毒感染细胞后还能产生一种病毒亚基因组RNA(subgenomic RNA,sgRNA)。近年对这种sgRNA展开了比较多的研究,结果表明,其产生机制与已知的其他病毒sgRNA产生机制并不相同。该sgRNA的产生与虫媒黄病毒基因组3’非编码区所形成的保守二级结构有关,同时宿主核酸酶对其的不完全降解亦有重要作用。虫媒黄病毒基因组3’非编码区中带有多个与病毒复制相关的RNA元件,而sgRNA的发现有助于全面地认识病毒RNA与宿主RNA代谢途径间的相互作用,为最终阐明病毒的致病机制奠定基础。     

Characterization of the genetic components of Streptomyces lividans linear plasmid SLP2 for replication in circular and linear modes

The nucleotide sequence of Streptomyces lividans linear plasmid SLP2 consists of 50,410 bp (C. H. Huang, C. Y. Chen, H. H. Tsai, C. Chen, Y. S. Lin, and C. W. Chen, Mol. Microbiol. 47:1563-1576, 2003). Here we report that the basic SLP2 locus for plasmid replication in circular mode resembles that of Streptomyces linear plasmids pSLA2 and SCP1 and comprises iterons(SLP2) and the adjacent rep(SLP2) gene. More efficient replication additionally required the 47-bp sequence between bp 581 and 628 upstream of the iterons. Replacement of either the iterons or the rep gene of SLP2 by the corresponding genes of pSLA2 or SCP1 still allows propagation in Streptomyces, although the transformation frequencies were 3 orders of magnitude lower than the original plasmids, suggesting that these plasmids share similar replication mechanisms. To replicate SLP2 in linear mode, additional SLP2 loci--either mtap(SLP2)/tpg(SLP2) or mtap(SLP2)/ilrA(SLP2)--were required. IlrA(SLP2) protein binds specifically to the iterons(SLP2) in vitro. Interactions were detected between these SLP2-borne replication proteins (Mtap(SLP2), Tpg(SLP2), and IlrA(SLP2)) and the telomeric replication proteins (TpgL, TapL, and TpgL) of the S. lividans chromosome, respectively, but the SLP2 proteins failed to interact. These results suggest that SLP2 recruits chromosomally encoded replication proteins for its telomere replication.     

丙型肝炎病毒功能基因在CHO细胞中的表达研究

丙型肝炎病毒(HCV)与宿主细胞因子的相互作用已经成为国内外研究的热点和难点。近期研究已经证实HCV的感染对宿主多种途径中基因的转录均能产生影响。为了进一步研究究竟是HCV中的哪些功能基因在与特定细胞因子的相互作用中起主导作用,构建了分别含有HCV Core、E1、E2、p7、NS2、NS3、NS4A、NS4B、NS5A和NS5B基因的真核表达质粒,分别转入宿主细胞CHO-K1中,在G418的选择压力下筛选获得稳定表达HCV单个蛋白的细胞系(10株)。PCR和RT-PCR可分别从稳定细胞系中检测到相应的HCV基因的DNA和mRNA,冻存和复苏不会造成HCV基因的丢失。Western-blot检测到稳定细胞系中表达E1,E2和NS5B蛋白,说明HCV基因在CHO-K1中已经形成稳定表达。薄层层析(TLC)结果显示,含有不同HCV基因的稳定传代细胞系中,UDP-葡萄糖神经酰胺葡萄糖基转移酶(UGCG)活性均发生了不同程度的变化,其中E2和p7的表达使胞内UGCG的活性提高了约1倍,NS2和NS5A则使UGCG的酶活提高了约0.6倍。该稳定细胞系的建立为研究病毒与宿主因子的相互作用及药物筛选奠定了基础。