Viral vector

Summary

Viral vectors are tools commonly used by molecular biologists to deliver genetic material into cells. This process can be performed inside a living organism (in vivo) or in cell culture (in vitro). Viruses have evolved specialized molecular mechanisms to efficiently transport their genomes inside the cells they infect. Delivery of genes or other genetic material by a vector is termed transduction and the infected cells are described as transduced. Molecular biologists first harnessed this machinery in the 1970s. Paul Berg used a modified SV40 virus containing DNA from the bacteriophage λ to infect monkey kidney cells maintained in culture. In addition to their use in molecular biology research, viral vectors are used for gene therapy and the development of vaccines. Vectors can either integrate into a cell's genome or transiently express a gene with non-integrative vectors. Key properties of a viral vector Viral Vectors are tailored to their specific applications but genera

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Transgenic SOD1 mice as a model for developing amyotrophic lateral sclerosis therapies

Sandrine Guillot

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by a loss of motor neurons in the brain (brainstem and cortex) and the spinal cord that leads to a motor neurological symptomatology. Approximately 10% of ALS cases have a familial form of ALS. Among the familial cases, 20% are caused by dominantly inherited mutations (around 100 different mutations) in the protein Cu/Zn superoxide dismutase (SOD1). To date, genetic ALS models on mutated SOD1 (SOD1G93A, SOD1G85R and SOD1G37R) transgenesis in rodents have been successful in recapitulating the main features of the human pathology, especially the loss of spinal or facial motoneurons, the increased astrogliosis, the activation of microglia and the cellular and molecular disruptions in motoneurons. The therapies toward a treatment or cure for ALS have been met with limited success. In the present study, SOD1G93A transgenic mice have been used to test new gene therapies to slow disease progression and pharmacological approach to obtain a better comprehension of the pathological process, more precisely, to define the involvement of microglial activation in the spread of the disease. For the approach by gene therapy, injection of viral vectors in a localized region of central nervous system (CNS) constitutes an excellent tool for the development of new therapies. In the present study, the viral-mediated expression of potential neuroprotective factors was explored in the lumbar spinal cord or facial nucleus of SOD1G93A transgenic mice. As HIV-1-derived lentiviral vectors can efficiently transduce neurons in CNS, these retroviral vectors were used to over-express the neurotrophic factor GDNF (glial cell line-derived neurotrophic factor) to supply a trophic support to lumbar and facial motoneurons, or RNAi molecules specifically targeting the SOD1G93A gene to inhibit the mutant SOD1 expression, the cause of the disease, in the lumbar spinal cord of SOD1G93A transgenic mice. For the study of the level of microglial involvement in the pathology, SOD1G93A transgenic mice had a daily pharmacological treatment with an inhibitor of microglial activation, the minocycline. The present thesis demonstrates that, on the one hand, at the difference of laboratories that delayed the disease progression by intramuscular injection of adenoviral vectors or adenoassociated vectors encoding for GDNF, the intraspinal injection of lentivirus encoding for GDNF did not lead to a protection of lumbar motoneurons and a delay of the disease. But this study showed a significantly rescue of facial motoneurons by the injection of lentivirus encoding for GDNF directly in facial nucleus. A selective vulnerability between motoneurons in facial nucleus and these in lumbar spinal cord has been therefore underlined. On the other hand, we showed that the therapeutic approach to inhibit the mutant SOD1 expression look as the most effective to delay the progression of the ALS pathology. Both studies of gene therapy, compared to others studies using the same therapeutic factors, demonstrated clearly that to optimize a therapeutic treatment, it seems better to act at muscular junction level with a retrograde transport form muscle to motoneuronal bodies of the therapeutic molecule or viral vector. Nevertheless, motoneuron-restricted silencing of mutant SOD1 would be useful for better understanding of neuronal and glial cellular mechanism mediating ALS-linked mutated SOD1 toxicity. Regarding the involvement of microglia in the pathological process, the inhibition of microglial activation by the minocycline treatment, suggests, on the one hand, that microglial activation do not initiate the pathological process and that this microgliosis might be a consequence and triggered by multiple disruptions. On the other hand, that minocycline could protect completely facial motoneurons and partially spinal motoneurons by its anti-apoptotic property. Therapeutic approaches aiming to act directly on the cause of the disease as well as a better comprehension of the role of non-neuronal cells in the pathological process may therefore open new perspectives for the treatment of ALS pathology.

EPFL2005

Excess fat mass in obese individuals, which is characterized by an increase of white adipocyte cell size and number, significantly raises the risk of developing metabolic syndrome symptoms as well as cancer. A detailed understanding of the transcriptional mechanisms mediating white adipocyte differentiation (i.e., adipogenesis) is required to counteract the growing obesity epidemics. In this thesis, we have implemented two combinatory approaches to detect new protein-DNA interactions in the mouse, one of which targets the adipogenic gene regulatory network (GRN) that underlies the white adipocyte differentiation process. As a first approach to shed light on GRNs, we have developed and validated a powerful approach that combines a high-throughput yeast one-hybrid-based (Y1H) system to detect transcription factors (TFs)-DNA element interactions, together with a novel microfluidics-based technique, enabling the identification and characterization of individual binding sites for detected TFs within the respective regulatory sequences at unprecedented throughput and resolution. Using well-described regulatory elements as well as an uncharacterized enhancer which can play also a role in adipogenesis, we show that our approach in a first phase uncovers many known as well as novel TF-DNA interactions, of which a large proportion were independently validated. In addition, we further demonstrate how our approach can be used in a second phase to characterize detected interactions by enabling the generation of a relative DNA occupancy landscape over the length of the respective DNA element. Furthermore, we provide evidence that this system enables the detection of novel interactions that may have in vivo relevance. Given the strict requirements for direct and well-characterized protein-DNA interaction data to generate and model gene regulatory networks, the presented two-tiered approach should be of great value to enhance our understanding of the regulatory principles underlying mouse gene expression. To identify transcription factors involved in white adipocyte differentiation, we overexpressed TFs in preadipocytes and quantified their effect on differentiation. To this end, we have created a mouse open-reading frame resource consisting of more than 750 fully sequence-verified TF clones. We transferred these TF clones to a Tet-On lentiviral vector and used them to infect white preadipocytes. Based on microscopy-assisted quantification of lipids after induction of differentiation, we identified putatively novel TF candidates that strongly enhanced differentiation based on the increased lipid accumulation, indicating a potential role in adipogenesis. Gene expression and ChIP-seq experiments have been performed for the three top candidates (ZEB1, ZFP30 and ZFP277) to further study their function within the adipogenic regulatory network. To assess whether the effect of these TFs on adipogenesis could be reproduced in vivo, murine adipose stromal-vascular fraction containing adipocyte precursor cells were implanted into mice fed a high-fat diet, after each of the three TF candidates were knockdown or overexpressed in these cells. This experiment and the RNA-seq analyses are currently being processed while this thesis is being written. Furthermore, due to the absence of quantitative real-time PCR (qPCR) primer designing tools that would allow for gene-specific expression profiling in a high-throughput fashion, we design a user-friendly platform: GETPrime. This platform uniquely combines and automates several features critical to optimal qPCR primer design for all annotated Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster and Danio rerio genes in the Ensembl database. GETPrime primers have been extensively validated experimentally, demonstrating their high quality as well as high transcript specificity in complex samples.

EPFL2013

Studies on lentiviral-mediated transgenesis

Marc-Olivier Sauvain

Transgenic animals are essential research tools, whether to address basic biological questions or to develop preclinical models of human diseases. Their generation through the injection of naked plasmid DNA into the male pronucleus of a fertilized oocyte has been the standard practice for almost 3 decades. However, this approach is invasive, largely limited to the mouse and results in low rates of transgene integration. Although the inefficiency of pronuclear injection can be overcome in small animals by high-throughput screening for transgene integration, this becomes economically more challenging in larger animals, such as sheep, pigs or cows, because of the extreme costs associated with this procedure (

60'000-

300'000). Thus, new strategies to enhance the production and the variety of transgenic animals would be an important asset. One such approach has emerged through the use of lentiviral vectors, a gene delivery system that can efficiently transfer and stably integrate its cargo into a wide variety of cell types from numerous species, and has been successfully applied to generate transgenic mice, rats, pigs and cows. The increasing use of lentivector-mediated transgenesis warrants a full analysis of its modalities. As a step towards this goal, the present study aimed at characterizing the genotypic features of transgenic mice generated by lentiviral infection of zygotes. First, as an indirect method to measure the kinetics of lentiviral integration in early embryos, we examined the rates of transmission of individual proviruses from G0 transgenic mice to their G1 progeny using a PCR-based technique specific for each integrant. The mean rate of transmission of 44% for individual proviruses suggests that vector integration was most often established between the post-S phase of the one-cell stage and pre-S phase of the two-cell stage. We then moved on to define proviral integration site selection in lentivector-generated transgenic mice. Using LAM-PCR-mediated amplification and sequencing of the host genome-provirus junctions, we found that the frequency of proviral integration inside a gene was 1.75- and 1.88-fold higher in transgenic mice and 3T3 fibroblasts, respectively, than expected from the distribution of annotated genes in the mouse genome (Pmice .03e 09; P3T3 5.55e 16). Moreover, integration was not influenced by the transcriptional orientation of the target gene and tended to favour the middle of transcribed regions. We also observed a subtle difference in the integration patterns of lentiviral vectors in 3T3 fibroblasts and transgenic mice, with the latter exhibiting a slightly higher frequency of integration into repeats. Although this difference was statistically not significant, it might reflect the elevated transcriptional activity of repetitive elements in preimplantation embryos. Since proviruses favour intragenic localization, we analyzed G2 mice homozygous for specific lentiviral integrants using PCR-based techniques and observed that the frequency of homozygosity was below the expected mendelian transmission rate of 25%. This suggested that some of the homozygous G2 mice must be nonviable due to the potential of retrovirus integrants to inactivate target genes. However, the normal rates of G1 representation of proviruses that did not achieve homozygosity in G2 suggested an absence of toxicity in the heterozygous state. Processes governing the earliest steps of mammalian development are still incompletely understood. In particular, the stage at and modalities by which early blastomeres become committed to either the inner cell mass (ICM), which subsequently yields the embryo proper, or the trophectoderm, which serves as precursor of extra-embryonic tissues, is unclear. The long held "random" hypothesis for development of the embryonic-abembryonic axis states that, within these two structures, early blastomeres are equally represented. However, recent lineage-tracing experiments support a model of "developmental bias", in which the progeny of the early blastomeres is allocated in a biased fashion. In our study, we took advantage of the specific integration pattern of lentiviral vector – i.e. each lentiviral vector integrates the host genome at specific sites – to "fingerprint" individual blastomeres and to follow them during embryogenesis. For this, we injected lentiviral vectors into embryos at either the one-cell or the two-cell stage. The Southern Blot (SB) analysis performed at E12.5 revealed that the infection at the one-cell stage yielded integrants shared for their majority by both embryonic and extra-embryonic tissues (74% of similar bands), while the infection at the two-cell stage induced a drastically different picture, with only a minority of common integrants between both types of tissues (22% of similar bands). This suggests that early blastomeres – from the two-cell stage on – contribute differentially to these lineages, which argues against a purely stochastic model. However, we still obtained 22% of shared integrations after infection at the two-cell stage, with only 8 out of 27 embryos showing a complete segregation of the proviral integration patterns. This rules out a "fully determined" model. Thus, our observations rather support the "developmental bias" hypothesis.

EPFL2009