Gene Transfer Methodologies Research Articles

Genetic manipulations of nonmodel gut microbes.

Hundreds of microbiota gene expressions are significantly different between healthy and diseased humans. The "bottleneck" preventing a mechanistic dissection of how they affect host biology/disease is that many genes are encoded by nonmodel gut commensals and not genetically manipulatable. Approaches to efficiently identify their gene transfer methodologies and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. This paper will introduce a step-by-step protocol to identify gene transfer conditions and build the gene manipulation tools for nonmodel gut microbes, focusing on Gram-negative Bacteroidia and Gram-positive Clostridia organisms. This protocol enables us to identify gene transfer methods and develop gene manipulation tools without prior knowledge of their genome sequences, by targeting bacterial 16s ribosomal RNAs or expanding their compatible replication origins combined with clustered regularly interspaced short palindromic repeats machinery. Such an efficient and generalizable approach will facilitate functional studies that causally connect gut microbiota genes to host diseases.

A Regional and Projection-Specific Role of RGSz1 in the Ventrolateral Periaqueductal Grey in the Modulation of Morphine Reward.

Opioid analgesics exert their therapeutic and adverse effects by activating μ opioid receptors (MOPR); however, functional responses to MOPR activation are modulated by distinct signal transduction complexes within the brain. The ventrolateral periaqueductal gray (vlPAG) plays a critical role in modulation of nociception and analgesia, but the exact intracellular pathways associated with opioid responses in this region are not fully understood. We previously showed that knockout of the signal transduction modulator Regulator of G protein Signaling z1 (RGSz1) enhanced analgesic responses to opioids, whereas it decreased the rewarding efficacy of morphine. Here, we applied viral mediated gene transfer methodology and delivered adeno-associated virus (AAV) expressing Cre recombinase to the vlPAG of RGSz1fl\fl mice to demonstrate that downregulation of RGSz1 in this region decreases sensitivity to morphine in the place preference paradigm, under pain-free as well as neuropathic pain states. We also used retrograde viral vectors along with flippase-dependent Cre vectors to conditionally downregulate RGSz1 in vlPAG projections to the ventral tegmental area (VTA) and show that downregulation of RGSz1 prevents the development of place conditioning to low morphine doses. Consistent with the role for RGSz1 as a negative modulator of MOPR activity, RGSz1KO enhances opioid-induced cAMP inhibition in periaqueductal gray (PAG) membranes. Furthermore, using a new generation of bioluminescence resonance energy transfer (BRET) sensors, we demonstrate that RGSz1 modulates Gαz but not other Gαi family subunits and selectively impedes MOPR-mediated Gαz signaling events invoked by morphine and other opioids. Our work highlights a regional and circuit-specific role of the G protein-signaling modulator RGSz1 in morphine reward, providing insights on midbrain intracellular pathways that control addiction-related behaviors. SIGNIFICANCE STATEMENT: This study used advanced genetic mouse models to highlight the role of the signal transduction modulator named RGSz1 in responses to clinically used opioid analgesics. We show that RGSz1 controls the rewarding efficacy of opioids by actions in ventrolateral periaqueductal gray projections to the ventral tegmental area, a key component of the midbrain dopamine pathway. These studies highlight novel mechanisms by which pain-modulating structures control the rewarding efficacy of opioids.

Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome

Hundreds of microbiota genes are associated with host biology/disease. Unraveling the causal contribution of a microbiota gene to host biology remains difficult because many are encoded by nonmodel gut commensals and not genetically targetable. A general approach to identify their gene transfer methodology and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. We developed a pipeline that identifies the gene transfer methods for multiple nonmodel microbes spanning five phyla, and we demonstrated the utility of their genetic tools by modulating microbiome-derived short-chain fatty acids and bile acids invitro and in the host. In a proof-of-principle study, by deleting a commensal gene for bile acid synthesis in a complex microbiome, we discovered an intriguing role of this gene in regulating colon inflammation. This technology will enable genetically engineering the nonmodel gut microbiome and facilitate mechanistic dissection of microbiota-host interactions.

Engineering NK Cells for CAR Therapy-Recent Advances in Gene Transfer Methodology.

The development of chimeric antigen receptor (CAR) T cell therapy has introduced a new and effective strategy to guide and promote the immune response against tumors in the clinic. More recently, in an attempt to enhance its utility, this method has been expanded to novel cell types. One of the more successful variants has proven to be the expression of CARs in Natural Killer (NK) cells (CAR-NK). Gene engineering NK cells to express an exogenous CAR receptor allows the innate anti-tumor ability of NK cells to be harnessed and directed against a target tumor antigen. In addition, the biology of NK cells allows the development of an allogeneic cell therapeutic product useable with most or all patient haplotypes. NK cells cause little or no graft versus host disease (GvHD) and are therefore suitable for development of an “off the shelf” therapeutic product. Initial trials have also shown that CAR-NK cells rarely cause cytokine release syndrome. However, despite their potential NK cells have proven to be difficult to engineer, with high sensitivity to apoptosis and low levels of gene expression. The creation of optimized methods to introduce genes into NK cells will promote the widespread application of CAR-NK in research laboratories and the clinics.

Viral and Nonviral Transfer of Genetic Materials to Adipose Tissues: Toward a Gold Standard Approach.

Gene transfer using viral or nonviral vectors enables the ability to manipulate specific cells and tissues for gene silencing, protein overexpression, or genome modification. Despite the widespread application of viral- and non-viral-mediated gene transfer to liver, heart, skeletal muscle, and the central nervous system, its use in adipose tissue has been limited. This is largely because adipose tissue is distributed throughout the body in distinct depots and adipocytes make up a minority of the cells within the tissue, making transduction difficult. Currently, there is no consensus methodology for efficient gene transfer to adipose tissue and many studies report conflicting information with regard to transduction efficiency and vector biodistribution. In this review, we summarize the challenges associated with gene transfer to adipose tissue and report on innovations that improve efficacy. We describe how vector and route of administration are the two key factors that influence transduction efficiency and outline a "gold standard" approach and experimental workflow for validating gene transfer to adipose tissue. Lastly, we speculate on how CRISPR/Cas9 can be integrated to improve adipose tissue research.

Isolation and Nanoscale Electroporation of Primary Neuronal Cultures In Situ.

Developing effective gene therapies for disorders of the central nervous system (CNS) is extremely challenging due to the lack of safe and efficient gene delivery methods to neurons and glial cells, hampering the study of CNS physiology and the identification of novel therapeutic targets. Current gene transfer methodologies for neuronal cultures rely on synthetic nanoparticles or viral transduction. These approaches present low gene transfer efficiency, are highly toxic, and may induce adverse immune responses. Electroporation has been implemented as an alternative approach; however, this method is restricted for the most part to cells in suspension, and electrical overstimulation of the neuronal membrane may have detrimental consequences. To overcome these barriers, here we describe the implementation of nanochannel-based electroporation for gene delivery into primary neural cultures safely and efficiently. We outline the preparation of viable primary neuronal cultures from the hippocampus of E18.5 mouse embryos and describe the optimal parameter for transfection using a nanochannel-based electroporation platform.

Millets genetic engineering: the progress made and prospects for the future

Millets comprise a highly variable small-seeded group of Poaceae members that can grow in extreme environmental conditions of drought, high temperature and low soil fertility hence, recognized as climate-resilient. Among millets, the phylogenetic closeness of Setaria with other agronomically important grasses like maize, sugarcane, and sorghum helped in its adoption as a translational model plant. Established efficient gene transfer methodology is a prerequisite for embracing plant species as models. However, genetic engineering of some of the economically important millets has been started in the 1990s, but inadequate progress made this group lag behind other members of Poaceae as rice, maize and wheat. Genetic transformation in millets has generally been achieved by a physical method of microprojectile bombardment, recently Agrobacterium-mediated gene transfer technique has also established in some of the millets but with very few reports. The central hindrance in millet transformation is its recalcitrant nature to regeneration through tissue culture techniques. Optimization of highly efficient regeneration procedure for each millet species is thus, necessary to establish advanced transformation system for them. The possibility of alternative transformation approaches is also discussed. The establishment of robust gene transfer methods whether it’s conventional in-vitro tissue culture dependent or in-planta are important for functional validation studies and would enable development of crop improvement strategies. This review presents the progress made on millet genetic transformation, discussing the major challenges that need to be overcome and future opportunities of transgenic techniques in various millets.

Intranasal Delivery of Adenoviral and AAV Vectors for Transduction of the Mammalian Peripheral Olfactory System.

Intranasal delivery of solutions is a straightforward methodology for viral vector transduction and gene transfer to the epithelia within the nasal cavity. Beyond the simplicity of the technique, intranasal delivery has demonstrated restricted transduction of the olfactory and respiratory epithelial tissues. Here we outline the procedure of viral vector intranasal delivery in early postnatal and adult mice, as well as adult rats. The procedure allows for robust transduction and ectopic gene delivery that can be used for the visualization of cellular structures, protein distribution, and assessment of viral vector-mediated therapies.

Setaria viridis.

Interest in plant model systems for genetic, biological, and functional genomics studies stems from advantages they provide in terms of fast generation time, small stature, and simple growth requirements. A model species would be especially advantageous for the studies of C4 photosynthetic grasses, which currently present practical challenges. These include long seed-to-seed generation times, and because of their large size at maturity they require large growing areas. One potential model of interest for C4 photosynthetic grasses is Setaria viridis. It has all the desirable aforementioned attributes for a model; however, for it to be adopted as a model for functional genomics studies, gene transfer methodology is also needed. In this chapter, we describe methods for Agrobacterium tumefaciens-mediated transformation of seed-derived callus. Vectors used for gene constructs contained the hygromycin phosphotransferase gene as a selectable marker. The transition of transgenic lines to soil was straightforward; plants started to flower in 1-3 weeks, with seeds ready to harvest approximately 5 weeks later.

Genetic Modification of T Cells

Gene transfer technology has advanced rapidly from simple physical-chemical laboratory methods in the 1970s and 1980s to the sophisticated viral and nonviral methods currently in clinical practice. Herein, we review 4 gene transfer methodologies applied in human gene therapy clinical trials transferring chimeric antigen receptors into T cells for the treatment of B-cell malignancies. The 4 methods include 2 viral vector gene transfer technologies, gamma retroviral vectors and lentiviral vectors, and 2 nonviral methods, transposons and mRNA electroporation.

Hematopoietic Stem Cell Gene Therapy: Assessing the Relevance of Preclinical Models

The modern laboratory mouse has become a central tool of for biomedical research with a notable influence in the field of hematopoiesis. Application of retroviral-based gene transfer approaches to mouse hematopoietic stem cells (HSCs) has led to a sophisticated understanding of the hematopoietic hierarchy in this model. However, the assumption that gene transfer methodologies developed in the mouse could be similarly applied to human HSCs for the treatment of human diseases left the field of gene therapy in a decade-long quandary. It is not until more relevant humanized xenograft mouse models and phylogenetically related large animal species were used to optimize gene transfer methodologies that unequivocal clinical successes were achieved. However, the subsequent reporting of severe adverse events in these clinical trials cast doubts on the predictive value of conventional preclinical testing, and encouraged the development of new assays for assessing the relative genotoxicity of various vector designs.

Genetic modification of human T lymphocytes for the treatment of hematologic malignancies

Modern chemotherapy regimens and supportive care have produced remarkable improvements in the overall survival of patients with hematologic malignancies. However, the development of targeted small molecules, monoclonal antibodies, and biological therapies that demonstrate greater efficacy and lower toxicity remains highly desirable in hematology, and oncology in general. In the context of biological therapies, T-lymphocyte based treatments have enormous potential. Donor lymphocyte infusion in patients relapsed after allogeneic hematopoietic stem cell transplant pioneered the concept that T lymphocytes can effectively control tumor growth, and this was then followed by the development of cell culture strategies to generate T lymphocytes with selective activity against tumor cells. Over the past decade, it has become clear that the adoptive transfer of ex vivo expanded antigen-specific cytotoxic T lymphocytes promotes sustained antitumor effects in patients with virus-associated lymphomas, such as Epstein-Barr virus related post-transplant lymphomas and Hodgkin's lymphomas. Because of this compelling clinical evidence and the concomitant development of methodologies for robust gene transfer to human T lymphocytes, the field has rapidly evolved, offering new opportunities to extend T-cell based therapies. This review summarizes the most recent biological and clinical developments using genetically manipulated T cells for the treatment of hematologic malignancies.

Overview on the efforts to generate transgenic chicken

After 25 years, the search for the avian cell that can be cultured indefinitely, genetically modified, and clonally derived while retaining its ability to enter the germ line has ended. Van de Lavoir et al. have defined the conditions for culture and genetic modification of primordial germ cells (PGCs) and showed that these cells are transmitted at high rates through the germline. The advent of this technology provides the ability to introduce transgenes of any size and to make site-specific changes to the genome. In this review, general avian reproduction and establishment of germ cells are described for possible routes to gene transfer. Also, the current gene transfer methodologies were summarized with a focus on PGC gene transfer. Finally, the application of transgenics to poultry was considered. Key words: Transgenic chickens, bioreactors, PGC.

A Tightly Controlled Conditional Knockdown System Using the Tol2 Transposon-Mediated Technique

BackgroundGene knockdown analyses using the in utero electroporation method have helped reveal functional aspects of genes of interest in cortical development. However, the application of this method to analyses in later stages of brain development or in the adult brain is still difficult because the amount of injected plasmids in a cell decreases along with development due to dilution by cell proliferation and the degradation of the plasmids. Furthermore, it is difficult to exclude the influence of earlier knockdown effects.Methodology/Principal FindingsWe developed a tightly controlled conditional knockdown system using a newly constructed vector, pT2K-TBI-shRNAmir, based on a Tol2 transposon-mediated gene transfer methodology with the tetracycline-inducible gene expression technique, which allows us to maintain a transgene for a long period of time and induce the knockdown of the gene of interest. We showed that expression of the endogenous amyloid precursor protein (APP) was sharply decreased by our inducible, stably integrated knockdown system in PC12 cells. Moreover, we induced an acute insufficiency of Dab1 with our system and observed that radial migration was impaired in the developing cerebral cortex. Such inhibitory effects on radial migration were not observed without induction, indicating that our system tightly controlled the knockdown, without any expression leakage in vivo.Conclusions/SignificanceOur system enables us to investigate the brain at any of the later stages of development or in the adult by utilizing a knockdown technique with the aid of the in utero electroporation gene transfer methodology. Furthermore, we can perform knockdown analyses free from the influence of undesired earlier knockdown effects.

Efficiency of High- and Low-Voltage Pulse Combinations for Gene Electrotransfer in Muscle, Liver, Tumor, and Skin

Gene electrotransfer is gaining momentum as an efficient methodology for nonviral gene transfer. In skeletal muscle, data suggest that electric pulses play two roles: structurally permeabilizing the muscle fibers and electrophoretically supporting the migration of DNA toward or across the permeabilized membrane. To investigate this further, combinations of permeabilizing short high-voltage pulses (HV; hundreds of V/cm) and mainly electrophoretic long low-voltage pulses (LV; tens of V/cm) were investigated in muscle, liver, tumor, and skin in rodent models. The following observations were made: (1) Striking differences between the various tissues were found, likely related to cell size and tissue organization; (2) gene expression is increased, if there was a time interval between the HV pulse and the LV pulse; (3) the HV pulse was required for high electrotransfer to muscle, tumor, and skin, but not to liver; and (4) efficient gene electrotransfer was achieved with HV field strengths below the detectability thresholds for permeabilization; and (5) the lag time interval between the HV and LV pulses decreased sensitivity to the HV pulses, enabling a wider HV amplitude range. In conclusion, HV plus LV pulses represent an efficient and safe option for future clinical trials and we suggest recommendations for gene transfer to various types of tissues.

EFFICIENCY OF HIGH AND LOW VOLTAGE PULSE COMBINATIONS FOR GENE ELECTROTRANSFER IN MUSCLE, LIVER, TUMOR AND SKIN

Gene electrotransfer is gaining momentum as an efficient methodology for nonviral gene transfer. In skeletal muscle, data suggest that electric pulses play two roles: structurally permeabilizing the muscle fibers and electrophoretically supporting the migration of DNA toward or across the permeabilized membrane. To investigate this further, combinations of permeabilizing short high-voltage pulses (HV; hundreds of V/cm) and mainly electrophoretic long low-voltage pulses (LV; tens of V/cm) were investigated in muscle, liver, tumor, and skin in rodent models. The following observations were made: (1) Striking differences between the various tissues were found, likely related to cell size and tissue organization; (2) gene expression is increased, if there was a time interval between the HV pulse and the LV pulse; (3) the HV pulse was required for high electrotransfer to muscle, tumor, and skin, but not to liver; and (4) efficient gene electrotransfer was achieved with HV field strengths below the detectability thresholds for permeabilization; and (5) the lag time interval between the HV and LV pulses decreased sensitivity to the HV pulses, enabling a wider HV amplitude range. In conclusion, HV plus LV pulses represent an efficient and safe option for future clinical trials and we suggest recommendations for gene transfer to various types of tissues.

Current Status of the Development of an Artificial Salivary Gland

Salivary glands (SGs) secrete more than half a liter of saliva daily. Saliva has many functions in maintaining the normal homeostasis of the oral cavity. Several causes underlie salivary impairment, where irradiation therapy to head and neck cancer patients is one of the most debilitating causes leading to considerable decrease in the patients' quality of life. In the last decade, others and we have focused on implementing tissue engineering principles combined with gene transfer and stem cell methodologies to develop an artificial SG device. This manuscript provides an overview of the current status of engineering an artificial SG.

Recombinant production of Streptococcus equisimilis streptokinase by Streptomyces lividans

BackgroundStreptokinase (SK) is a potent plasminogen activator with widespread clinical use as a thrombolytic agent. It is naturally secreted by several strains of beta-haemolytic streptococci. The low yields obtained in SK production, lack of developed gene transfer methodology and the pathogenesis of its natural host have been the principal reasons to search for a recombinant source for this important therapeutic protein. We report here the expression and secretion of SK by the Gram-positive bacterium Streptomyces lividans. The structural gene encoding SK was fused to the Streptomyces venezuelae CBS762.70 subtilisin inhibitor (vsi) signal sequence or to the Streptomyces lividans xylanase C (xlnC) signal sequence. The native Vsi protein is translocated via the Sec pathway while the native XlnC protein uses the twin-arginine translocation (Tat) pathway.ResultsSK yield in the spent culture medium of S. lividans was higher when the Sec-dependent signal peptide mediates the SK translocation. Using a 1.5 L fermentor, the secretory production of the Vsi-SK fusion protein reached up to 15 mg SK/l. SK was partially purified from the culture supernatant by DEAE-Sephacel chromatography. A 44-kDa degradation product co-eluted with the 47-kDa mature SK. The first amino acid residues of the S. lividans-produced SK were identical with those of the expected N-terminal sequence. The Vsi signal peptide was thus correctly cleaved off and the N-terminus of mature Vsi-SK fusion protein released by S. lividans remained intact. This result also implicates that the processing of the recombinant SK secreted by Streptomyces probably occurred at its C-terminal end, as in its native host Streptococcus equisimilis. The specific activity of the partially purified Streptomyces-derived SK was determined at 2661 IU/mg protein.ConclusionHeterologous expression of Streptococcus equisimilis ATCC9542 skc-2 in Streptomyces lividans was successfully achieved. SK can be translocated via both the Sec and the Tat pathway in S. lividans, but yield was about 30 times higher when the SK was fused to the Sec-dependent Vsi signal peptide compared to the fusion with the Tat-dependent signal peptide of S. lividans xylanase C. Small-scale fermentation led to a fourfold improvement of secretory SK yield in S. lividans compared to lab-scale conditions. The partially purified SK showed biological activity. Streptomyces lividans was shown to be a valuable host for the production of a world-wide important, biopharmaceutical product in a bio-active form.

Cre Recombinase Gene Transfer In Vitro and Detection of loxP-Dependent Recombination: Figure 1.

INTRODUCTIONAltering the genome of intact cells and organisms by site-specific DNA recombination has become an important gene-transfer methodology. The inclusion of exogenous recombinase target sequences within transferred DNA segments allows subsequent modifications to previously altered genomic structure that increase the utility of gene transfer and enhance experimental design. In this protocol, correctly targeted mouse embryonic stem (ES) cell clones bearing the F[tkneo] allele (containing several loxP sites) are subjected to in vitro Cre gene transfer to generate ES cell subclones bearing either Type 1 (Δ) or Type 2 (F) alleles. Type 2 ES cells are used to generate chimeric mice that are then crossed to germ-line Cre-expressing mice, such as ZP3-Cre transgenic mates. The additional time needed to breed the mice (~2-3 mo) is typically less troublesome than the cost and effort of maintaining multiple clone-derived lines of mice.

Conditional Mutagenesis of the Genome Using Site-Specific DNA Recombination: Figure 1.

INTRODUCTIONAltering the genome of intact cells and organisms by site-specific DNA recombination has become an important gene-transfer methodology. DNA modifications produced by gene transfer and homologous recombination are typically static once integrated among target cell chromosomes. In contrast, the inclusion of exogenous recombinase target sequences within transferred DNA segments allows subsequent modifications to previously altered genomic structure that increase the utility of gene transfer and enhance experimental design. Creating tissue- and cell-type-specific genetic lesions in animal models, indelibly marking progenitors for cell fate mapping, inducing large-scale chromosomal rearrangements, and complementing gene defects in studies of phenotypic maintenance and reversion are all possible by directing recombinase expression using gene transfer among experimentally modified genomes. Moreover, this approach is effective in providing controlled data establishing genotype-phenotype relationships and allows for the excision of introduced marker genes that can affect neighboring chromatin structure and function. Although early work involved the yeast Flp recombinase, most studies in mammalian systems have used the Cre recombinase derived from bacteriophage P1. Both enzymes are members of the integrase family of recombinases but bind to distinct DNA target signals. Cre recombinase operates on the 34-bp loxP sequence and, like Flp, performs conservative recombination involving DNA segments positioned among these target sites.