CpG基元的免疫学进展及基因治疗策略

CpG诱发免疫反应的能力对免疫预防是一大优点,但在基因治疗中,质粒中所含的CpG基元能够阻止基因转移或导致巨大副作用（炎症和毒性）,本文简单综述了CpG基元的免疫学活性,主要作用和信号转导通路,并且针对它在基因治疗中存在的问题及可能的解决办法进行探讨。     

增加CpG基元的汉坦病毒核蛋白基因疫苗的免疫作用

以往的研究表明非甲基化胞嘧啶鸟嘌呤二核苷酸为基元构成的特定结构是一种很有希望的候选疫苗佐剂。为了研究增加CpG基元的汉坦病毒核蛋白基因疫苗的免疫作用,在本实验中,将重组真核表达质粒 pcDNA3.1 S(ISS)直接肌注免疫BALB/c 小鼠,分别用ELISA法检测血清特异性抗体的变化,MTT法检测 T细胞增殖反应,以及用ELISA kit检测免疫鼠脾细胞上清液中细胞因子IL 4和IFN γ的动态变化,从而了解免疫鼠的体液免疫反应和细胞免疫反应。结果显示 pcDNA3.1 S(ISS)接种组的小鼠血清抗体水平、T细胞增殖反应以及细胞因子IFN γ的产生水平较对照组 pcDNA3.1 S和空载体 pcDNA3.1 接种组的要高。而细胞因子 IL 4 较对照组却无明显变化。由此可见,增加CpG基元的质粒能够增强其所诱导的免疫反应,可用于那些需要借助强有力细胞免疫来清除病原体的疫苗研制中。     

增加CpG基元的汉坦病毒核蛋白基因疫苗的免疫作用

以往的研究表明非甲基化胞嘧啶鸟嘌呤二核苷酸为基元构成的特定结构是一种很有希望的候选疫苗佐剂.为了研究增加CpG基元的汉坦病毒核蛋白基因疫苗的免疫作用,在本实验中,将重组真核表达质粒pcDNA3.1+S(ISS)直接肌注免疫BALB/c小鼠,分别用ELISA法检测血清特异性抗体的变化,MTT法检测T细胞增殖反应,以及用ELISA kt检测免疫鼠脾细胞上清液中细胞因子IL-4和IFN-γ的动态变化,从而了解免疫鼠的体液免疫反应和细胞免疫反应.结果显示pcDNA3.1+S(ISS)接种组的小鼠血清抗体水平、T细胞增殖反应以及细胞因子IFN-γ的产生水平较对照组pcDNA3.1+S和空载体pcDNA3.1+接种组的要高.而细胞因子IL-4较对照组却无明显变化.由此可见,增加CpG基元的质粒能够增强其所诱导的免疫反应,可用于那些需要借助强有力细胞免疫来清除病原体的疫苗研制中.     

CpG甲基化与基因调控

CpG双核苷酸中的胞嘧啶甲基化和去甲基化在哺乳动物的基因表达中有重要的调控作用.哺乳动物基因组中有两类启动子:CpG岛启动子和CpG缺乏启动子.两种蛋白质因子通过与甲基化CpG的相互作用影响基因表达,CpG岛在基因组分析中也有广泛的用途.     

人类基因组上CpG岛的定位和系统分析

为了研究CpG岛产生和消失机制以及位于基因启动子区域外的CpG岛保守性等问题,我们通过序列比对和进化保守性分析等方法,分析在人类和小鼠中保守的基因上的CpG岛。结果显示已有保守序列的突变以及序列插入删除是CpG岛产生和消失的主要原因,进一步分析发现52%的在小鼠基因组上保守序列完全缺失的CpG岛位于两个转座子之间,提示转座子所介导的序列插入是CpG岛形成和消失的重要原因。人类基因组上在启动子区域外的CpG岛中约有79%为新产生的CpG岛,显著高于启动子区域内新产生的CpG岛比例(41%)。GO分析表明与这些CpG岛相关的部分基因与神经系统发育显著相关,提示新产生的CpG岛参与神经发育过程。     

微环DNA研究进展

质粒载体在基因治疗中占据重要地位.传统质粒DNA在真核生物中可能会引起严重的炎症反应,未甲基化的CpG序列可能抑制基因的表达,最好的解决办法是在生产质粒载体过程中将细菌调控序列整体消除.微环DNA是一种新颖的小环超螺旋表达框,它是传统质粒在大肠杆菌体内通过位点特异性重组得到的.微环DNA缺乏抗性标记基因、复制原点等细菌...     

小鼠骨髓细胞中p16和Ralb基因启动区CpG岛的甲基化位点分析

抑癌基因p16和白血病致癌因子Ralb与白血病的发生密切相关,其启动子区CpG岛的甲基化对基因表达具有重要作用.本文旨在分析p16、Ralb基因启动子区CpG岛甲基化位点信息,并比较这两个基因在小鼠骨髓细胞和原代培养的骨髓细胞中甲基化状态的差异.运用"MethPrimer"软件预测p16、Ralb基因启动子区的CpG岛,设计甲基化特异性引物.利用重亚硫酸盐测序法(BSP)检测甲基化位点信息.结果显示,p16有1个CpG岛,岛上21个CpG位点全部未发生甲基化;Ralb有2个CpG岛,CpG岛1上的5个CpG位点全部呈甲基化状态,而CpG岛2上的17个CpG位点全部呈非甲基化状态,且小鼠骨髓细胞和体外原代培养的骨髓细胞中两基因的甲基化状态一致.表明p16、Ralb基因甲基化状态未受外界培养条件的影响而改变,提示在与两基因甲基化相关的研究中体外试验可替代体内试验.     

预测DNA序列中短CpG岛新方法

在基因表达调控中,长度在200~500bp之间的短CpG岛具有非常重要的作用,然而目前并没有一种非常好的方法寻找短CpG岛。基于给定长度DNA片段上碱基随机分布的排列组合算法,我们定义了一种计算CpG观察预期比的新方法。结合DNA片段长度和GC含量这两个参数,该方法给出了人类21号和22号染色体上CpG岛分布的预测结果。根据CpG岛与基因功能区、Alu重复序列和UCSC的CpG岛对比分析,本研究给出了新的CpG岛判断准则:(1)CpG岛不小于200bp;(2)GC占比不小于50%;(3)CpG观察预期比不小于1.4。通过与Takai方法的对比分析显示,新方法能够显著地排除Alu重复序列对CpG岛预测的影响,并且能够准确预测具有更短长度的CpG岛在DNA片段上的分布。多基因转录起始位点基因分析结果表明,短CpG岛是UCSC的CpG岛的核心组成部分,短CpG岛是参与基因表达调控的核心元件。本研究为预测和分析短CpG岛在人类基因调控中的作用提供了必要的手段。     

果蝇启动子区域CpG岛和TATA框预测与分析

CpG岛和TATA框在基因表达调控方面具有重要的作用,本研究从EBI核酸数据库中下载经试验证实的果蝇启动子序列共计1 917条,对其中的CpG岛、GC碱基分布和TATA框进行了分析。预测果蝇启动子序列中CpG岛的最佳参数组合为:GC最低含量为0.44,CpG最低出现率为0.6,CpG岛最小长度为200 bp,在此条件下,发现有84.82%的果蝇启动子中含有1~2个独立的CpG岛。果蝇启动子序列的平均GC含量为39.83%,GC碱基在启动子中的分布表现出规律性变化。果蝇启动子中TATA框的分布比较广泛,有32.86%的启动子中含有1个TATA框;有18.73%的启动子中含有2个TATA框;另有13.88%的启动子中含有2个以上的TATA框;此外,有34.53%的启动子没有TATA框。表明果蝇启动子中有比较丰富的CpG岛和TATA框。     

人类全基因组范围的CpG岛的预测与分析

CpG岛的甲基化是表观遗传中基因表达调控的重要机制。虽然目前已存在几个从DNA序列判别CpG岛的标准,但如何在标准中选择合适的参数仍是研究的焦点。文章通过分析比较两种经典CpG岛判定标准与三种预测方法,提出了改进的CpG岛预测方法——CpGISeeker。应用该预测方法,结合判定标准中的三个基本参数组合出的13组组合参数,在人类全基因组范围内进行了CpG岛预测,并统计分析了CpG岛的重复序列组成以及相对于基因转录起始位点的位置分布情况。分析结果表明CpGISeeker具有更精确判定CpG岛的特性;同时还提示,随着判定标准严格性的增加,CpG岛的重复序列含量降低,与基因转录起始位点的相关性提高。将CpG岛最小尺寸为500bp、GC含量为60%、CpG出现率达到0.65的组合参数作为标准,是目前预测CpG岛的最佳方式。     

Plasmid DNA induces increased lymphocyte trafficking: a specific role for CpG motifs

Bacterial DNA, primarily through immunostimulatory cytosine-guanine (CpG) motifs, induces the secretion of cytokines and activates a variety of effector cells. We investigated the possibility that CpG motifs might also modulate immunosurveillance by altering cell trafficking through a regional lymph node. Intradermal injection of plasmid DNA induced rapid and prolonged increases in the number of lymphocytes collected in efferent lymph. This effect on cell trafficking was not dependent on the expression of an encoded reporter gene but varied with plasmid construct and required a circular form. Injection of synthetic oligodeoxyribonucleotides containing CpG motifs did not alter lymphocyte trafficking but CpG-enhanced plasmid induced a dose-dependent increase in cell trafficking. Phenotypic analyses revealed that the increase in cell trafficking involved all lymphocyte subpopulations and represented a mass movement of cells. These observations reveal that bacterial DNA, through immunostimulatory CpG motifs, alters immunosurveillance by increasing cell recruitment to a regional lymph node.     

Plasmid DNA activates murine macrophages to induce inflammatory cytokines in a CpG motif-independent manner by complex formation with cationic liposomes

Plasmid DNA (pDNA) is very important in non-viral gene therapy and DNA vaccination. Unmethylated CpG motifs in bacterial DNA, but not in vertebrate DNA, are known to trigger an inflammatory response, which inhibits gene expression while improving immunological consequences. In this report, we investigated the cytokine secretion induced by pDNA/cationic liposome complexes using murine macrophages. Naked CpG DNA induced tumor necrosis factor-alpha (TNF-alpha) secretion from the macrophages, but DNA without CpG motif did not, demonstrating that the cytokine induction was mediated by CpG motifs. pDNA complexed with cationic liposomes, but not the cationic liposomes alone, produced a significant amount of TNF-alpha from the macrophages. Surprisingly, methylated pDNA and calf thymus DNA complexed with the cationic liposomes were also able to induce TNF-alpha production, indicating that these responses were not dependent on CpG motifs. Taken together, the present study demonstrated that for the first time DNA can stimulate murine macrophages in a CpG motif-independent manner when it is complexed with the cationic liposomes.     

The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes

We used the 4C-Seq technique to characterize the genome-wide patterns of spatial contacts of several CpG islands located on chromosome 14 in cultured chicken lymphoid and erythroid cells. We observed a clear tendency for the spatial clustering of CpG islands present on the same and different chromosomes, regardless of the presence or absence of promoters within these CpG islands. Accordingly, we observed preferential spatial contacts between Sp1 binding motifs and other GC-rich genomic elements, including the DNA sequence motifs capable of forming G-quadruplexes. However, an anchor placed in a gene/CpG island-poor area formed spatial contacts with other gene/CpG island-poor areas on chromosome 14 and other chromosomes. These results corroborate the two-compartment model of the spatial organization of interphase chromosomes and suggest that the clustering of CpG islands constitutes an important determinant of the 3D organization of the eukaryotic genome in the cell nucleus. Using the ChIP-Seq technique, we mapped the genome-wide CTCF deposition sites in the chicken lymphoid and erythroid cells that were used for the 4C analysis. We observed a good correlation between the density of CTCF deposition sites and the level of 4C signals for the anchors located in CpG islands but not for an anchor located in a gene desert. It is thus possible that CTCF contributes to the clustering of CpG islands observed in our experiments.     

The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes

We used the 4C-Seq technique to characterize the genome-wide patterns of spatial contacts of several CpG islands located on chromosome 14 in cultured chicken lymphoid and erythroid cells. We observed a clear tendency for the spatial clustering of CpG islands present on the same and different chromosomes, regardless of the presence or absence of promoters within these CpG islands. Accordingly, we observed preferential spatial contacts between Sp1 binding motifs and other GC-rich genomic elements, including the DNA sequence motifs capable of forming G-quadruplexes. However, an anchor placed in a gene/CpG island-poor area formed spatial contacts with other gene/CpG island-poor areas on chromosome 14 and other chromosomes. These results corroborate the two-compartment model of the spatial organization of interphase chromosomes and suggest that the clustering of CpG islands constitutes an important determinant of the 3D organization of the eukaryotic genome in the cell nucleus. Using the ChIP-Seq technique, we mapped the genome-wide CTCF deposition sites in the chicken lymphoid and erythroid cells that were used for the 4C analysis. We observed a good correlation between the density of CTCF deposition sites and the level of 4C signals for the anchors located in CpG islands but not for an anchor located in a gene desert. It is thus possible that CTCF contributes to the clustering of CpG islands observed in our experiments.     

Unmethylated CpG motifs mimicking bacterial DNA triggers the local and systemic innate immune parameters and expression of immune-relevant genes in gilthead seabream

Unmethylated CpG motifs present in bacterial DNA are recognized by leucocyte receptors triggering an immune response. We have evaluated herein the immunomodulatory actions of a CpG motif in an important commercial fish, the gilthead seabream. Thus, 1, 3 and 7days after intraperitoneal injection of the CpG motif the seabream immune parameters and gene expression profile were evaluated. Firstly, humoral innate immune responses were unaffected by CpG ODN 1668. On the other hand, ODN injection significantly enhanced the number of peritoneal leucocytes (PELs) 1day after injection and increased the main innate immune parameters of PELs and HKLs (head-kidney leucocytes). Thus, injection of ODN 1668 significantly increased respiratory burst, peroxidase, cytotoxic and phagocytic activities, with variations in increment and time. The cytotoxic activity of HKLs was the most increased (up to 4.2-fold). Moreover, the expression profile of immune-relevant genes in head-kidney was affected, with substantial up-regulation of TLR9, IL-1beta, Mx, TGFbeta and Gal8 gene expression. These results demonstrate that unmethylated CpG motifs prime the fish immune response with promising applications for aquaculture.     

CpG oligodeoxynucleotides as vaccine adjuvants in primates

Synthetic oligodeoxynucleotides (ODN) containing unmethylated CpG motifs act as immune adjuvants in mice, boosting the humoral and cellular response to coadministered Ags. CpG ODN that stimulate human PBMC are only weakly active in mice. Thus, alternative animal models are needed to monitor the activity and safety of "human" CpG ODN in vivo. This work demonstrates that rhesus macaques recognize and respond to the same CpG motifs that trigger human immune cells. Coadministering CpG ODN with heat-killed Leishmania vaccine provided significantly increased protection of macaques against cutaneous Leishmania infection. These findings indicate that rhesus macaques provide a useful model for studying the in vivo activity of human CpG motifs, and that ODN expressing these motifs act as strong immune adjuvants.     

CpG序列的免疫激活机理及应用

ＣｐＧ序列是一些在动物体内具有强烈的免疫激活功能的寡聚脱氧核苷酸。本文探讨了ＣｐＧ 序列在动物体内激活免疫反应的作用机理,概述了ＣｐＧ应用研究的进展,展望了ＣｐＧ 序列的应用前景     

Comparative proteomics study reveals that bacterial CpG motifs induce tumor cell autophagy in vitro and in vivo

Unmethylated CpG dinucleotides, present in bacterial DNA, are recognized in vertebrates via the Toll-like receptor 9 (TLR9) and are known to act as an anticancer agent by stimulating immune cells to induce a proinflammatory response. Although the effects of CpG-oligodeoxynucleotides (CpG-ODNs) in immune cells have been widely studied, little is known regarding their molecular effects in TLR9-positive tumor cells. To better understand the role of these bacterial motifs in cancer cells, we analyzed proteome modifications induced in TLR9-positive tumor cells in vitro and in vivo after CpG-ODN treatment in a rat colon carcinoma model. Proteomics analysis of tumor cells by two-dimensional gel electrophoresis followed by mass spectrometry identified several proteins modulated by bacterial CpG motifs. Among them, several are related to autophagy including potential autophagic substrates. In addition, we observed an increased glyceraldehyde-3-phosphate dehydrogenase expression, which has been shown to be sufficient to trigger an autophagic process. Autophagy is a self-digestion pathway whereby cytoplasmic material is sequestered by a structure termed the autophagosome for subsequent degradation and recycling. As bacteria are known to trigger autophagy, we assessed whether bacterial CpG motifs might induce autophagy in TLR9-positive tumor cells. We showed that CpG-ODN can induce autophagy in rodent and human tumor cell lines and was TLR9-dependent. In addition, an increase in the number of autophagosomes can also be observed in vivo after CpG motif intratumoral injection. Our findings bring new insights on the effect of bacterial CpG motifs in tumor cells and may be relevant for cancer treatment and more generally for gene therapy approaches in TLR9-positive tissues.