scholarly journals VipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotype

2021 ◽  
Author(s):  
Arjun Khakhar ◽  
Cecily Wang ◽  
Ryan Swanson ◽  
Sydney Stokke ◽  
Furva Rizvi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Viral Vectors ◽  
Viral Vector ◽  
Tobacco Rattle Virus ◽  
Plant Size ◽  
Great Promise ◽  
Attractive Alternative ◽  
Gibberellin Biosynthesis ◽  
In Planta

Abstract Synthetic transcription factors have great promise as tools to help elucidate relationships between gene expression and phenotype by allowing tunable alterations of gene expression without genomic alterations of the loci being studied. However, the years-long timescales, high cost, and technical skill associated with plant transformation have limited their use. In this work we developed a technology called VipariNama (ViN) in which vectors based on the Tobacco Rattle Virus (TRV) are used to rapidly deploy Cas9-based synthetic transcription factors and reprogram gene expression in planta. We demonstrate that ViN vectors can implement activation or repression of multiple genes systemically and persistently over several weeks in Nicotiana benthamiana, Arabidopsis (Arabidopsis thaliana), and tomato (Solanum lycopersicum). By exploring strategies including RNA scaffolding, viral vector ensembles, and viral engineering, we describe how the flexibility and efficacy of regulation can be improved. We also show how this transcriptional reprogramming can create predictable changes to metabolic phenotypes, such as gibberellin biosynthesis in N. benthamiana and anthocyanin accumulation in Arabidopsis, as well as developmental phenotypes, such as plant size in N. benthamiana, Arabidopsis, and tomato. These results demonstrate how ViN vector-based reprogramming of different aspects of gibberellin signaling can be used to engineer plant size in a range of plant species in a matter of weeks. In summary, VipariNama accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.

scholarly journals VipariNama: RNA vectors to rapidly reprogram plant morphology and metabolism

2020 ◽  
Author(s):  
Arjun Khakhar ◽  
Cecily Wang ◽  
Ryan Swanson ◽  
Sydney Stokke ◽  
Furva Rizvi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Plant Morphology ◽  
Plant Size ◽  
Great Promise ◽  
Attractive Alternative ◽  
Biological Processes ◽  
In Planta ◽  
Transcriptional Reprogramming ◽  
Long Timescales

AbstractSynthetic transcription factors have great promise as tools to explore biological processes. By allowing precise alterations in gene expression, they can help elucidate relationships between gene expression and plant morphology or metabolism. However, the years-long timescales, high cost, and technical skill associated with plant transformation have dramatically slowed their use. In this work, we developed a new platform technology called VipariNama (ViN) in which RNA vectors are used to rapidly deploy synthetic transcription factors and reprogram gene expression in planta. We demonstrate how ViN vectors can direct activation or repression of multiple genes, systemically and persistently over several weeks, and in multiple plant species. We also show how this transcriptional reprogramming can create predictable changes to metabolic and morphological phenotypes in the model plants Nicotiana benthamiana and Arabidopsis thaliana in a matter of weeks. Finally, we show how a model of gibberellin signaling can guide ViN vector-based reprogramming to rapidly engineer plant size in both model species as well as the crop Solanum lycopersicum (tomato). In summary, using VipariNama accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.

Interaction of Arabidopsis TGA3 and WRKY53 transcription factors on Cestrum yellow leaf curling virus (CmYLCV) promoter mediates salicylic acid-dependent gene expression in planta

Planta ◽  
2017 ◽  
Vol 247 (1) ◽  
pp. 181-199 ◽  
Author(s):  
Shayan Sarkar ◽  
Abhimanyu Das ◽  
Prashant Khandagale ◽  
Indu B. Maiti ◽  
Sudip Chattopadhyay ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salicylic Acid ◽  
Transcription Factors ◽  
Yellow Leaf ◽  
In Planta ◽  
Leaf Curling

Gene therapy for neurodegenerative and ocular diseases using lentiviral vectors

2005 ◽  
Vol 110 (1) ◽  
pp. 37-46 ◽  
Author(s):  
G. Scott Ralph ◽  
Katie Binley ◽  
Liang-Fong Wong ◽  
Mimoun Azzouz ◽  
Nicholas D. Mazarakis
Keyword(s):  
Gene Therapy ◽  
Nervous System ◽  
Viral Vectors ◽  
Viral Vector ◽  
Lentiviral Vectors ◽  
Great Promise ◽  
Ocular Diseases ◽  
Vector Systems ◽  
Gene Therapy Application ◽  
Wide Range

Gene therapy holds great promise for the treatment of a wide range of inherited and acquired disorders. The development of viral vector systems to mediate safe and long-lasting expression of therapeutic transgenes in specific target cell populations is continually advancing. Gene therapy for the nervous system is particularly challenging due to the post-mitotic nature of neuronal cells and the restricted accessibility of the brain itself. Viral vectors based on lentiviruses provide particularly attractive vehicles for delivery of therapeutic genes to treat neurological and ocular diseases, since they efficiently transduce non-dividing cells and mediate sustained transgene expression. Furthermore, novel routes of vector delivery to the nervous system have recently been elucidated and these have increased further the scope of lentiviruses for gene therapy application. Several studies have demonstrated convincing therapeutic efficacy of lentiviral-based gene therapies in animal models of severe neurological disorders and the push for progressing such vectors to the clinic is ongoing. This review describes the key features of lentiviral vectors that make them such useful tools for gene therapy to the nervous system and outlines the major breakthroughs in the potential use of such vectors for treating neurodegenerative and ocular diseases.

Prediction of key transcription factors during skin regeneration by combining gene expression data and regulatory network information analysis

2019 ◽  
Vol 12 (03) ◽  
pp. 1950024
Author(s):  
Ping Huang ◽  
Peng Ge ◽  
Qing-Fen Tian ◽  
Guo-Bao Huang
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Expression Data ◽  
Regulatory Network ◽  
Skin Regeneration ◽  
Local Network ◽  
Great Promise ◽  
Expression Data ◽  
Network Information ◽  
Ppi Networks

Purpose: Burn is one of the most common injuries in clinical practice. The use of transcription factors (TFs) has been reported to reverse the epigenetic rewiring process and has great promise for skin regeneration. To better identify key TFs for skin reprogramming, we proposed a predictive system that conjoint analyzed gene expression data and regulatory network information. Methods: Firstly, the gene expression data in skin tissues were downloaded and the LIMMA package was used to identify differential-expressed genes (DEGs). Then three ways, including identification of TFs from the DEGs, enrichment analysis of TFs by a Fisher’s test, the direct and network-based influence degree analysis of TFs, were used to identify the key TFs related to skin regeneration. Finally, to obtain most comprehensive combination of TFs, the coverage extent of all the TFs were analyzed by Venn diagrams. Results: The top 30 TFs combinations with higher coverage were acquired. Especially, TFAP2A, ZEB1, and NFKB1 exerted greater regulatory influence on other DEGs in the local network and presented relatively higher degrees in the protein–protein interaction (PPI) networks. Conclusion: These TFs identification could give a deeper understanding of the molecular mechanism of cell trans-differentiation, and provide a reference for the skin regeneration and burn treatment.

scholarly journals Viral-Vector Delivered anti-Angiogenic Therapies to the Eye

2020 ◽  
Author(s):  
Sanna Koponen ◽  
Emmi Kokki ◽  
Kati Kinnunen ◽  
Seppo Ylä-Herttuala
Keyword(s):  
Gene Therapy ◽  
Clinical Studies ◽  
Viral Vectors ◽  
Vision Loss ◽  
Viral Vector ◽  
Great Promise ◽  
Ocular Neovascularization ◽  
Vessel Growth ◽  
Lentivirus Vectors ◽  
Endothelial Growth Factors

Pathological vessel growth harms vision and may finally lead to vision loss. Anti-angiogenic gene therapy with viral vectors for ocular neovascularization has shown great promise in pre-clinical studies. Most of the studies has conducted with different adeno-associate serotype vectors. In addition, Adeno and lentivirus vectors have been used. Therapy has targeted to block vascular endothelial growth factors or other pro-angiogenic factors. Clinical trials of intraocular gene therapy for neovascularization have shown the treatment to be safe without severe adverse events or systemic effects. Nevertheless, clinical studies have not proceeded phase 2 trials further.

scholarly journals Reprogramming of Human Huntington Fibroblasts Using mRNA

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Antje Arnold ◽  
Yahaira M. Naaldijk ◽  
Claire Fabian ◽  
Henry Wirth ◽  
Hans Binder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Viral Vectors ◽  
Viral Vector ◽  
Ips Cells ◽  
Expression Array ◽  
Healthy Donors ◽  
Pluripotency Gene ◽  
Cell Sources ◽  
Induced Pluripotent

The derivation of induced pluripotent stem cells (iPS) from human cell sources using transduction based on viral vectors has been reported by several laboratories. Viral vector-induced integration is a potential cause of genetic modification. We have derived iPS cells from human foreskin, adult Huntington fibroblasts, and adult skin fibroblasts of healthy donors using a nonviral and nonintegrating procedure based on mRNA transfer. In vitro transcribed mRNA for 5 factors, oct-4, nanog, klf-4, c-myc, sox-2 as well as for one new factor, hTERT, was used to induce pluripotency. Reprogramming was analyzed by qPCR analysis of pluripotency gene expression, differentiation, gene expression array, and teratoma assays. iPS cells were shown to express pluripotency markers and were able to differentiate towards ecto-, endo-, and mesodermal lineages. This method may represent a safer technology for reprogramming and derivation of iPS cells. Cells produced by this method can more easily be transferred into the clinical setting.

scholarly journals Viral vectors as a novel tool for clinical and neuropsychiatric research applications

2018 ◽  
Vol 31 (2) ◽  
pp. e000015 ◽  
Author(s):  
Yao Wang ◽  
Zhiwei Hu ◽  
Peijun Ju ◽  
Shan Yin ◽  
Fujie Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Viral Vectors ◽  
Molecular Mechanisms ◽  
Gene Expression Regulation ◽  
Viral Vector ◽  
Neurological Diseases ◽  
Basic Research ◽  
Research Field ◽  
Research Fields ◽  
Pathogenic Genes

BackgroundA viral vector is a genetically modified vector produced by genetic engineering. As pathogenic genes in the virus are completely or largely eliminated, it is safe to be widely used in multidisciplinary research fields for expressing genes, such as neuroscience, metabolism, oncology and so on. Neuroscience and psychiatry are the most closely related disciplines in either basic research or clinical research, but the application of viral vectors in neuropsychiatry has not received much attention or not been widely accepted.ObjectiveThis article will focus on the application of viral vectors in basic and clinical neuropsychiatric research.MethodsBy using viral vectors, scientists can perform neurological labelling, gene expression regulation and physiological manipulation for investigating phenomenon from molecular mechanisms to behaviours. At the same time, to treat mental or neurological disorders, viral vectors can be designed for gene therapy, which alter gene expression levels or repair mutated genes in the brains of patients.PerspectiveViral vectors play an important role in basic research and clinical applications. To further understand brain function and prevent mental and neurological diseases, we hypothesize that viral vectors could be used along with various advanced technologies, such as sequencing and high-throughput expression analysis in the neuroscience research field.

scholarly journals Viral-Vector-Delivered Anti-Angiogenic Therapies to the Eye

Pharmaceutics ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 219
Author(s):  
Sanna Koponen ◽  
Emmi Kokki ◽  
Kati Kinnunen ◽  
Seppo Ylä-Herttuala
Keyword(s):  
Gene Therapy ◽  
Viral Vectors ◽  
Vision Loss ◽  
Viral Vector ◽  
Great Promise ◽  
Vascular Endothelial ◽  
Ocular Neovascularization ◽  
Vessel Growth ◽  
Lentivirus Vectors ◽  
Endothelial Growth Factors

Pathological vessel growth harms vision and may finally lead to vision loss. Anti-angiogenic gene therapy with viral vectors for ocular neovascularization has shown great promise in preclinical studies. Most of the studies have been conducted with different adeno-associated serotype vectors. In addition, adeno- and lentivirus vectors have been used. Therapy has been targeted towards blocking vascular endothelial growth factors or other pro-angiogenic factors. Clinical trials of intraocular gene therapy for neovascularization have shown the treatment to be safe without severe adverse events or systemic effects. Nevertheless, clinical studies have not proceeded further than Phase 2 trials.

scholarly journals Efficiency of cell-type specific and generic promoters in transducing oxytocin neurons and monitoring their neural activity during lactation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Keerthi Thirtamara Rajamani ◽  
Amanda B. Leithead ◽  
Michelle Kim ◽  
Marie Barbier ◽  
Michael Peruggia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Neural Activity ◽  
Viral Vectors ◽  
Fluorescent Protein ◽  
Viral Vector ◽  
Female Rats ◽  
Cell Populations ◽  
Specific Cell ◽  
Functional Studies ◽  
Drive Gene

AbstractHypothalamic oxytocin (OXT) and arginine-vasopressin (AVP) neurons have been at the center of several physiological and behavioral studies. Advances in viral vector biology and the development of transgenic rodent models have allowed for targeted gene expression to study the functions of specific cell populations and brain circuits. In this study, we compared the efficiency of various adeno-associated viral vectors in these cell populations and demonstrated that none of the widely used promoters were, on their own, effective at driving expression of a down-stream fluorescent protein in OXT or AVP neurons. As anticipated, the OXT promoter could efficiently drive gene expression in OXT neurons and this efficiency is solely attributed to the promoter and not the viral serotype. We also report that a dual virus approach using an OXT promoter driven Cre recombinase significantly improved the efficiency of viral transduction in OXT neurons. Finally, we demonstrate the utility of the OXT promoter for conducting functional studies on OXT neurons by using an OXT specific viral system to record neural activity of OXT neurons in lactating female rats across time. We conclude that extreme caution is needed when employing non-neuron-specific viral approaches/promoters to study neural populations within the paraventricular nucleus of the hypothalamus.

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