A speedy method to detect inserted DNA fragment in cell lines transfected with retroviral vectors

Cells transfected by retroviral vectors are brought in agene of particular interest and are very useful in avariety of experiments. It is essential to testify that theDNA fragment was successfully introduced into the cellstogether with the retroviral vectors. Polymerase chainreaction is believed to be a fast and convenient method forthis purpose when using primers flanking the cloning siteof the inserted DNA. Unfortunately, a single PCR reactionoften fails to amplify the targeted fragment because of theexistence of endogenous virus DNA in cell genome. However,in this study we conducted a procedure for a single PCR,using vector-specific primers as well as a nested PCR, andsuccessfully detected the DNA fragments cloned in MFGretroviral vectors in 22 transfected cell lines. We alsoproved that real time quantitative PCR in combination withMFG-specific primer is useful to determine copy number ofthe retroviral vector in murine producer cell lines.     

Multiple displacement amplification enables large-scale clonal analysis following retroviral gene therapy

Analysis of the fate of retrovirally transduced cells after transplantation is often hampered by the scarcity of available DNA. We evaluated a promising method for whole-genome amplification, called multiple displacement amplification (MDA), with respect to even and accurate representation of retrovirally transduced genomic DNA. We proved that MDA is a suitable method to subsequently quantify engraftment efficiencies by quantitative real-time PCR by analyzing retrovirally transduced DNA in a background of untransduced DNA and retroviral integrations found in primary material from a retroviral transplantation model. The portion of these retroviral integrations in the amplified samples was 1.02-fold (range 0.2, to 2.1-fold) the portion determined in the original genomic DNA. Integration site analysis by ligation-mediated PCR (LM-PCR) is essential for the detection of retroviral integrations. The combination of MDA and LM-PCR showed an increase in the sensitivity of integration site analysis, as a specific integration site could be detected in a background of untransduced DNA, while the transduced DNA made up only 0.001%. These results show for the first time that MDA enables large-scale sensitive detection and reliable quantification of retrovirally transduced human genomic DNA and therefore facilitates follow-up analysis in gene therapy studies even from the smallest amounts of starting material.     

白细胞介素6重组逆转录病毒载体的构建及鉴定

目的 构建特异性过表达大鼠IL-6基因的重组逆转录病毒载体,并在大鼠嗜铬细胞瘤PC12细胞和人胚肾HEK293细胞中检测IL-6的表达。方法以大鼠骨髓间充质干细胞mRNA为模板,经PCR获得目的基因IL-6,将其定向克隆到逆转录病毒载体pSEB-3H中,构建重组逆转录病毒质粒pSEB—IL-6,经脂质体分别转染到PC12细胞和HEK293细胞中,应用Real—timePCR和ELISA的方法在mRNA和蛋白质水平检测IL-6的表达变化。继而用HEK293细胞中包装获得的含有pSEB—IL-6的病毒颗粒进一步感染PC12细胞,Real—timePCR检测,IL-6mRNA的表达水平变化。结果PCR电泳及酶切鉴定证实目的基因正确克隆至逆转录病毒载体中,其基因序列与Genbank报道一致;Real—timePCR和ELISA结果均显示,逆转录病毒质粒pSEB—IL-6转染PC12细胞和HEK293细胞后,IL-6的表达水平较对照组显著上调;经pSEB—IL-6逆转录病毒颗粒感染的PC12细胞中,IL-6mRNA表达水平较对照组提高4倍。结论成功构建了特异性表达大鼠儿-6基因的重组逆转录病毒载体pSEB—IL-6,并获得了具有感染能力的逆转录病毒颗粒,感染真核细胞后可高表达IL-6,为进一步研究IL-6的功能及其在多种疾病中的免疫调节机制提供重要的分子手段。     

Identification and classification of endogenous retroviruses in cattle

The aim of this study was to identify the endogenous retrovirus (ERV) sequences in a bovine genome. We subjected bovine genomic DNA to PCR with degenerate or ovine ERV (OERV) family-specific primers that aimed to amplify the retroviral pro/pol region. Sequence analysis of 113 clones obtained by PCR revealed that 69 were of retroviral origin. On the basis of the OERV classification system, these clones from degenerate PCR could be divided into the beta3, gamma4, and gamma9 families. PCR with OERV family-specific primers revealed an additional ERV that was classified into the bovine endogenous retrovirus (BERV) gamma7 family. In conclusion, here we report the results of a genome scale study of the BERV. Our study shows that the ERV family expansion in cattle may be somewhat limited, while more diverse family members of ERVs have been reported from other artiodactyls, such as pigs and sheep.     

HSV-tk基因逆转录病毒重组体的构建与DNA序列分析

目的　构建含有单纯疱疹病毒Ⅰ型胸苷激酶 (HSV1 tk)基因的逆转录病毒重组载体pLXSN TK。方法设计一对寡核苷酸引物 ,用PCR方法从质粒pHSV10 6中特异扩增HSV tk基因片段 ( 1168bp) ,分别用BamHI和Eco RI酶切后 ,定向连接到质粒pLXSN中 ,转化宿主菌TG1,分别用上述内切酶 ,PCR和DNA测序鉴定重组质粒。结果　酶切鉴定所切下的片段和PCR扩增的片段大小均与预计相符 ,测序结果与文献报道序列及预计结果一致 ,证实符合表达框架。结论　成功构建了HSV tk嵌合重组质粒pLXSN TK。     

Isolation and analysis of retroviral integration targets by solo long terminal repeat inverse PCR

Upon retroviral infection, the genomic RNA is reverse transcribed to make proviral DNA, which is then integrated into the host chromosome. Although the viral elements required for successful integration have been extensively characterized, little is known about the host DNA structure constituting preferred targets for proviral integration. In order to elucidate the mechanism for the target selection, comparison of host DNA sequences at proviral integration sites may be useful. To achieve simultaneous analysis of the upstream and downstream host DNA sequences flanking each proviral integration site, a Moloney murine leukemia virus-based retroviral vector was designed so that its integrated provirus could be removed by Cre-loxP homologous recombination, leaving a solo long terminal repeat (LTR). Taking advantage of the solo LTR, inverse PCR was carried out to amplify both the upstream and downstream cellular flanking DNA. The method called solo LTR inverse PCR, or SLIP, proved useful for simultaneously cloning the upstream and downstream flanking sequences of individual proviral integration sites from the polyclonal population of cells harboring provirus at different chromosomal sites. By the SLIP method, nucleotide sequences corresponding to 38 independent proviral integration targets were determined and, interestingly, atypical virus-host DNA junction structures were found in more than 20% of the cases. Characterization of retroviral integration sites using the SLIP method may provide useful insights into the mechanism for proviral integration and its target selection.     

Trim22对脂多糖诱导的巨噬样细胞促炎细胞因子的负向调节作用

目的: 构建人Trim22的重组逆转录病毒载体,观察过表达Trim22对脂多糖(LPS)诱导的巨噬样细胞促炎细胞因子产生的影响。方法: 经PCR法扩增,把Trim22克隆入逆转录病毒载体MSCV2.2 IRES-GFP(MSCV),并对重组载体进行菌落PCR、双酶切及测序鉴定。用Lipofectamine将MSCV、GAG-POL、VSV-G载体共转染至293T包装细胞。用病毒上清感染U937细胞,通过流式细胞仪分选GFP阳性细胞。用佛波酯诱导U937细胞分化为巨噬样细胞,LPS刺激后观察过表达Trim22对促炎细胞因子表达的影响。结果: 经测序等鉴定,成功构建MSCV-Trim22逆转录病毒表达载体。病毒上清感染U937细胞后,经流式细胞仪分选获得稳定表达Trim22的U937细胞。LPS刺激巨噬样细胞后,Trim22过表达组TNFα和IL6的表达水平显著小于对照组(P<0.05)。结论: 成功构建人Trim22的逆转录病毒表达载体,Trim22能抑制LPS诱导的巨噬样细胞TNFα和IL6的产生。     

大肠埃希菌嘌呤核苷磷酸化酶基因载体的构建及对胰腺癌细胞的作用

目的构建大肠埃希菌（Escherichia coli）嘌呤核苷磷酸化酶（purine nucleoside phosphorylase,PNP）基因表达载体,研究其生物活性,为肿瘤的基因治疗奠定基础。方法PCR扩增大肠埃希菌K12的PNP基因,T4连接酶将PNP连接人pMSCV逆转录病毒载体,构建重组逆转录病毒载体pMSCV／PNP。pM—SCV／PNP转化感受态大肠埃希菌XLI-Blue,提取pMSCV／PNP,酶切、PCR和测序鉴定。病毒包装细胞293产生重组逆转录病毒pMSCV／PNP,流式细胞仪测病毒滴度。pMSCV／PNP转染胰腺癌细胞BXPC-3,倒置荧光显微镜观察,FACS分离转染阳性细胞（GFP阳性）。RT—PCR检测PNPmRNA在胰腺癌细胞BXPC-3细胞中的表达,MTT法检测PNP基因的生物活性。结果PCR扩增出大肠埃希菌PNP基因（738bp）,酶切和PCR的电泳条带显示pMSCV／PNP,测序结果正常。293包装细胞产生高滴度（3．6×10^7U／m1）重组逆转录病毒pMSCV／PNP。RT—PCR实验结果表明,pMSCV／PNP转染的胰腺癌细胞BXPC-3表达PNPmRNA。前药6-甲基嘌呤-2’-脱氧核苷（MePdR）作用72h浓度达1．00mg／L,BXPC-3／PNP细胞存活率为10．09％,随着MePdR浓度加大,BXPC-3／PNP细胞存活率继续下降直至为0。结论构建了pMSCV／PNP载体,获得了表达大肠埃希菌PNP基因的BXPC-3细胞克隆,PNP／MePdR自杀基因系统对胰腺癌细胞BXPC-3有较强的抑杀作用。     

The rat interleukin-5 gene: characterization and expression by retroviral gene transfer and polymerase chain reaction.

The rat interleukin-5 (IL-5) gene was isolated from a genomic lambda phage library and a fragment containing all four exons was inserted into the retroviral vector pXT1, resulting in pXTRIL5. Upon retroviral gene transfer into two IL-5-dependent mouse cell lines, B13 and T88M, autonomously growing cells were established and B-cell growth factor activity was detected in the supernatants of the infected cells. "cDNA" versions of the rat IL-5 gene were rescued by the polymerase chain reaction (PCR) with primers specific for the flanking regions of the cloning site in pXT1. Restriction or DNA sequence analysis of five different clones revealed precise splicing in two cases, while three of the clones had retained the first intron. In addition, in two of these about 400 bp of rat IL-5 5' flanking regions were deleted. The sequence comparison of rat, mouse, and human IL-5 genes revealed a high degree of conservation (e.g., mouse and rat were 92% homologous at the amino acid level). The combination of retroviral gene transfer and PCR may offer an alternative, efficient method for the cloning of cDNAs.     

Genetic rearrangements occurring during a single cycle of murine leukemia virus vector replication: characterization and implications.

Retroviruses evolve at rapid rates, which is presumably advantageous for responding to selective pressures. Understanding the basic mutational processes involved during retroviral replication is important for comprehending the ability of retroviruses to escape immunosurveillance and antiviral drug treatment. Moreover, since retroviral vectors are important vehicles for somatic cell gene therapy, knowledge of the mechanism of retroviral variation is critical for anticipating untoward mutational events occurring during retrovirus-medicated gene transfer. The focus of this report is to examine the spectrum of genomic rearrangements arising during a single cycle of Moloney murine leukemia virus (MoMLV) vector virus replication. An MoMLV vector containing the herpes simplex virus thymidine kinase (tk) gene was constructed. MoMLV vector virus was produced in packaging lines, and target cells were infected. From a total of 224 mutant proviruses analyzed, 114 had gross rearrangements readily detectable by Southern blotting. The remaining proviruses were of parental size. PCR and DNA sequence analysis of 73 of the grossly rearranged mutant proviruses indicated they resulted from deletions, combined with insertions, duplications, and complex mutations that were a result of multiple genomic alterations in the same provirus. Complex hypermutations distinct from those previously described for spleen necrosis virus and human immunodeficiency virus were detected. There was a correlation between the mutation breakpoints and single-stranded regions in the predicted viral RNA secondary structure. The results also confirmed that the tk gene is inactivated at an average rate of about 8.8% per cycle of retroviral replication, which corresponds to a rate of mutation of 3%/kbp.     

携带FMDV前导蛋白基因逆转录病毒载体的构建及其在牛肾细胞中的表达

以口蹄疫病毒株OA/58 RNA为模板, 反转录并扩增目的cDNA。通过分子克隆技术将前导蛋白编码序列Lab与逆转录病毒载体pBPSTR1连接, 将构建正确的重组载体命名为pBPSTR1-Lab。通过分别利用不同浓度的嘌呤霉素和四环素来确定最佳筛选浓度和最佳调控浓度, 结果显示嘌呤霉素的最佳筛选浓度为3 mg/mL, 四环素的最佳调控浓度为1 mg/mL。利用pBPSTR1-Lab和包装质粒pVSV-G双质粒瞬时转染Gp2-293包装细胞来获得重组逆转录病毒。利用重组逆转录病毒来感染牛肾细胞, 并连续筛选12天来获得阳性克隆。通过除去四环素来诱导目的基因在牛肾细胞中表达, 发现牛肾细胞病变死亡。经过PCR和蛋白质免疫印迹证实稳定表达前导蛋白的牛肾细胞系已经建立, 为今后研究前导蛋白致病机理提供了平台。     

携带FMDV前导蛋白基因逆转录病毒载体的构建及其在牛肾细胞中的表达

以口蹄疫病毒株OA/58 RNA为模板, 反转录并扩增目的cDNA。通过分子克隆技术将前导蛋白编码序列Lab与逆转录病毒载体pBPSTR1连接, 将构建正确的重组载体命名为pBPSTR1-Lab。通过分别利用不同浓度的嘌呤霉素和四环素来确定最佳筛选浓度和最佳调控浓度, 结果显示嘌呤霉素的最佳筛选浓度为3 mg/mL, 四环素的最佳调控浓度为1 mg/mL。利用pBPSTR1-Lab和包装质粒pVSV-G双质粒瞬时转染Gp2-293包装细胞来获得重组逆转录病毒。利用重组逆转录病毒来感染牛肾细胞, 并连续筛选12天来获得阳性克隆。通过除去四环素来诱导目的基因在牛肾细胞中表达, 发现牛肾细胞病变死亡。经过PCR和蛋白质免疫印迹证实稳定表达前导蛋白的牛肾细胞系已经建立, 为今后研究前导蛋白致病机理提供了平台。     

Cre recombinase‐mediated site‐specific modification of a cellular genome using an integrase‐defective retroviral vector

Retroviral integrase is an enzyme responsible for the integration of retroviruses. A single mutation in the integrase core domain can severely compromise its integration ability, leading to the accumulation of circular retroviral cDNA in the nuclei of infected cells. We therefore attempted to use those cDNA as substrates for Cre recombinase to perform a recombinase‐mediated cassette exchange (RMCE), thereby targeting retroviral vectors to a predetermined site. An expression unit containing a promoter, an ATG codon and marker genes (hygromycin resistance gene and red fluorescent protein gene) flanked by wild‐type and mutant loxP sites was first introduced into cellular chromosome to build founder cell lines. We then constructed another plasmid for the production of integrase‐defective retroviral vectors (IDRV), which contains an ATG‐deficient neomycin resistance gene and green fluorescent protein gene, flanked by a compatible pair of loxPs. After providing founder cells with Cre and infecting with IDRV later, effective RMCE occurred, resulting in the appearance of G418‐resistant colonies and a change in the color of fluorescence from red to green. Southern blot and PCR analyses on selected clones further confirmed site‐specific recombination. The successful substitution of the original viral integration machinery with a non‐viral mechanism could expand the application of retroviral vectors. Biotechnol. Bioeng. 2010;107:717–729. © 2010 Wiley Periodicals, Inc.