Transgene Copy Research Articles

Amplicon-Based RNA Interference Targeting V2 Gene of Cotton Leaf Curl Kokhran Virus-Burewala Strain Can Provide Resistance in Transgenic Cotton Plants.

The conserved coat or V2 gene of begomoviruses is responsible for viral movement in the plant cells. RNAi technology was used to silence V2 gene for resistance against these viruses in transgenic plants. The transformation of the RNAi-based gene construct targeting V2 gene of CLCuKoV-Bur, cloned under 35S promoter, was done in two elite cotton varieties MNH-786 and VH-289 using shoot apex cut method of gene transformation. The transformation efficiency was found to be 3.75 and 2.88 % in MNH-786 and VH-289, respectively. Confirmation of successful transformation was done through PCR in T 0, T 1, and T 2 generations using gene-specific primers. Transgenic cotton plants were categorized on the basis of the virus disease index in T 1 generation. Copy number and transgene location were observed using FISH and karyotyping in T 2 generation which confirmed random integration of V2 RNAi amplicon at chromosome 6 and 16. Real-time quantitative PCR analyses of promising transgenic lines showed low virus titer compared to wild-type control plants upon challenging them with viruliferous whiteflies in a contained environment. From the results, it was concluded that amplicon V2 RNAi construct was able to limit virus replication and can be used to control CLCuV in the field.

Production of insect-resistant transgenic rice plants for use in practical agriculture

Plant biotechnology provides a powerful solution to boost agricultural productivity and nutritional quality. The development process of a transgenic crop includes multiple steps that consist of gene isolation for a target trait, generation of T0 transgenic crops, characterization of the transgene, evaluation of agronomic performance of transgenic crops, selection of elite transgenic lines and assessment of target trait efficacy. Here, we developed elite insect-resistant transgenic rice plants that may satisfy the standards of biosafety assessments. We made a construct with the insecticide cry1Ac gene for a target trait. A total of 310 T0 transgenic lines were generated and underwent extensive analysis. We selected four T3 lines that contain a single-copy transgene inserted into intergenic regions of the rice genome. During this process, we critically analyzed the transgenic lines with five checkpoints that include single copy of transgene, its integration into intergenic region, clean T-DNA arrangement, stability of transgene through generations and substantial equivalence of transgenic plants in agronomic traits other than insect resistance. Consequently, we obtained insect-resistant transgenic rice plants that can be used in practical agriculture.

Application of Droplet Digital PCR for Estimating Vector Copy Number States in Stem Cell Gene Therapy.

Stable gene transfer into target cell populations via integrating viral vectors is widely used in stem cell gene therapy (SCGT). Accurate vector copy number (VCN) estimation has become increasingly important. However, existing methods of estimation such as real-time quantitative PCR are more restricted in practicality, especially during clinical trials, given the limited availability of sample materials from patients. This study demonstrates the application of an emerging technology called droplet digital PCR (ddPCR) in estimating VCN states in the context of SCGT. Induced pluripotent stem cells (iPSCs) derived from a patient with X-linked chronic granulomatous disease were used as clonable target cells for transduction with alpharetroviral vectors harboring codon-optimized CYBB cDNA. Precise primer–probe design followed by multiplex analysis conferred assay specificity. Accurate estimation of per-cell VCN values was possible without reliance on a reference standard curve. Sensitivity was high and the dynamic range of detection was wide. Assay reliability was validated by observation of consistent, reproducible, and distinct VCN clustering patterns for clones of transduced iPSCs with varying numbers of transgene copies. Taken together, use of ddPCR appears to offer a practical and robust approach to VCN estimation with a wide range of clinical and research applications.

Peptide-Grafted Polymers as Artificial Converter of Cellular Signals

Abstract Intracellular signal transduction systems consisting of sophisticated molecular networks are essential to provide almost all cellular functions. Any abnormal activation of enzymes included in this network can be directly linked to various disease states. Therefore, cellular function can be altered if we can modulate this signal transduction process. In this context, artificial signal converters, which respond to particular abnormal signaling to activate transgene transcription, are introduced. Such molecular systems use polymer materials grafted with cationic peptides, which are a specific substrate of target protein kinase or protease. This concept which is called D-RECS, DDS in response to cellular signals, could have potential for design of disease cell specific therapeutic or diagnostic (imaging) systems using pathological signaling as a target. Molecular design and structural factors affecting signal response in such systems are discussed.

A novel transgenic mouse model of lysosomal storage disorder.

Knockout technology has proven useful for delineating functional roles of specific genes. Here we describe and provide an explanation for striking pathology that occurs in a subset of genetically engineered mice expressing a rat CaVβ2a transgene under control of the cardiac α-myosin heavy chain promoter. Lesions were limited to mice homozygous for transgene and independent of native Cacnb2 genomic copy number. Gross findings included an atrophied pancreas; decreased adipose tissue; thickened, orange intestines; and enlarged liver, spleen, and abdominal lymph nodes. Immune cell infiltration and cell engulfment by macrophages were associated with loss of pancreatic acinar cells. Foamy macrophages diffusely infiltrated the small intestine's lamina propria, while similar macrophage aggregates packed liver and splenic red pulp sinusoids. Periodic acid-Schiff-positive, diastase-resistant, iron-negative, Oil Red O-positive, and autofluorescent cytoplasm was indicative of a lipid storage disorder. Electron microscopic analysis revealed liver sinusoids distended by clusters of macrophages containing intracellular myelin "swirls" and hepatocytes with enlarged lysosomes. Additionally, build up of cholesterol, cholesterol esters, and triglycerides, along with changes in liver metabolic enzyme levels, were consistent with a lipid processing defect. Because of this complex pathology, we examined the transgene insertion site. Multiple transgene copies inserted into chromosome 19; at this same site, an approximate 180,000 base pair deletion occurred, ablating cholesterol 25-hydroxylase and partially deleting lysosomal acid lipase and CD95 Loss of gene function can account for the altered lipid processing, along with hypertrophy of the immune system, which define this phenotype, and serendipitously provides a novel mouse model of lysosomal storage disorder.

English

Jatropha curcas L. oil has been shown to be suitable for the production of biodiesel. However, this species has not been domesticated yet. Genetic breeding through conventional methods is time consuming and costly, hence, genetic transformation could contribute positively to the improvement of interesting traits. Although in vitro regeneration and stable genetic transformation has been pursued for several years, variation in transformation efficiency remains strongly genotype-dependent and indicates that protocols optimization is still needed. Thus, this study was carried out to introduce a chitinase gene from the Trichoderma viride fungus into the genome of a J. curcas superior genotype by inoculating leaf explants with Agrobacterium tumefaciens EHA 105 strain in axenic conditions. Some key parameters such as pre-culture period and antibiotic doses were optimized with 500 mg.L-1 cefotaxime and 100 mg.L-1 kanamycin concentrations being suitable for A. tumefaciens inhibition and explant selection, respectively. The best transformation efficiency (50%) was obtained when leaf explants were incubated on a culture medium promoting shoot regeneration at 15 days before the induction of the transformation process. Plants where chitinase gene amplicons could be detected were assessed for transgene copy number and expression levels by quantitative real-time polymerase chain reaction (PCR). One, two and three copies of the introduced gene were confirmed in nine transgenic lines with two of them that were assessed for gene expression and showed quantitative variation for this variable. These results bring valuable information for further gene insertions in breeding programs of J. curcas for fungal disease resistance.

Comparison of droplet digital PCR with quantitative real-time PCR for determination of zygosity in transgenic maize

This study evaluated the applicability of droplet digital PCR (ddPCR) as a tool for maize zygosity determination using quantitative real-time PCR (qPCR) as a reference technology. Quantitative real-time PCR is commonly used to determine transgene copy number or GMO zygosity characterization. However, its effectiveness is based on identical reaction efficiencies for the transgene and the endogenous reference gene. Additionally, a calibrator sample should be utilized for accuracy. Droplet digital PCR is a DNA molecule counting technique that directly counts the absolute number of target and reference DNA molecules in a sample, independent of assay efficiency or external calibrators. The zygosity of the transgene can be easily determined using the ratio of the quantity of the target gene to the reference single copy endogenous gene. In this study, both the qPCR and ddPCR methods were used to determine insect-resistant transgenic maize IE034 zygosity. Both methods performed well, but the ddPCR method was more convenient because of its absolute quantification property.

Viral proteins expressed in the protozoan parasite Eimeria tenella are detected by the chicken immune system.

BackgroundEimeria species are parasitic protozoa that cause coccidiosis, an intestinal disease commonly characterised by malabsorption, diarrhoea and haemorrhage that is particularly important in chickens. Vaccination against chicken coccidiosis is effective using wild-type or attenuated live parasite lines. The development of protocols to express foreign proteins in Eimeria species has opened up the possibility of using Eimeria live vaccines to deliver heterologous antigens and function as multivalent vaccine vectors that could protect chickens against a range of pathogens.ResultsIn this study, genetic complementation was used to express immunoprotective virus antigens in Eimeria tenella. Infectious bursal disease virus (IBDV) causes Gumboro, an immunosuppressive disease that affects productivity and can interfere with the efficacy of poultry vaccination programmes. Infectious laryngotracheitis virus (ILTV) causes a highly transmissible respiratory disease for which strong cellular immunity and antibody responses are required for effective vaccination. Genes encoding the VP2 protein from a very virulent strain of IBDV (vvVP2) and glycoprotein I from ILTV (gI) were cloned downstream of 5’Et-Actin or 5’Et-TIF promoter regions in plasmids that also contained a mCitrine fluorescent reporter cassette under control of the 5’Et-MIC1 promoter. The plasmids were introduced by nucleofection into E. tenella sporozoites, which were then used to infect chickens. Progeny oocysts were sorted by FACS and passaged several times in vivo until the proportion of fluorescent parasites in each transgenic population reached ~20 % and the number of transgene copies per parasite genome decreased to < 10. All populations were found to transcribe and express the transgene and induced the generation of low titre, transgene-specific antibodies when used to immunise chickens.ConclusionsE. tenella can express antigens of other poultry pathogens that are successfully recognised by the chicken immune system. Nonetheless, further work has to be done in order to improve the levels of expression for its future use as a multivalent vaccine vector.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-016-1756-2) contains supplementary material, which is available to authorized users.

Determination of Cry1Ac copy number in transgenic pigeonpeaplants using quantitative real time PCR.

Copy number of Cry1Ac in transgenic pigeonpea plants was determined by quantitative real time PCR using Syber Green as fluorescence indicator. Gene specific primers designed to amplify relatively long amplicons (400 – 600 bp), for Cry1Ac was used to increase specificity and sensitivity of Real time PCR. Estimated copy number in transgenic lines using real-time quantitative PCR and southern hybridization was correlated and found to be same i.e. single copy number. This study shows effectivness of real-time PCR method for estimating the transgene copy number in transgenic pigeonpea plants by a simple, accurate and cost effective manner.Keywords: Copy number, Cry1Ac, Pigeonpea transformation, Real-time PCR, Syber green.

Characterization of Growth and Reproduction Performance, Transgene Integration, Expression, and Transmission Patterns in Transgenic Pigs Produced by piggyBac Transposition-Mediated Gene Transfer

ABSTRACTPreviously we successfully produced a group of EGFP-expressing founder transgenic pigs by a newly developed efficient and simple pig transgenesis method based on cytoplasmic injection of piggyBac plasmids. In this study, we investigated the growth and reproduction performance and characterized the transgene insertion, transmission, and expression patterns in transgenic pigs generated by piggyBac transposition. Results showed that transgene has no injurious effect on the growth and reproduction of transgenic pigs. Multiple copies of monogenic EGFP transgene were inserted at noncoding sequences of host genome, and passed from founder transgenic pigs to their transgenic offspring in segregation or linkage manner. The EGFP transgene was ubiquitously expressed in transgenic pigs, and its expression intensity was associated with transgene copy number but not related to its promoter DNA methylation level. To the best of our knowledge, this is first study that fully described the growth and reproduction performance, transgene insertion, expression, and transmission profiles in transgenic pigs produced by piggyBac system. It not only demonstrates that piggyBac transposition-mediated gene transfer is an effective and favorable approach for pig transgenesis, but also provides scientific information for understanding the transgene insertion, expression and transmission patterns in transgenic animals produced by piggyBac transposition.

Abstract 1200: HER-2 isoform interaction in mammary carcinoma onset and progression

Abstract Human breast cancer cells express full-length HER-2 along with proteins resulting from mutation, alternative splicing, alternative initiation of translation and post-translational modification. The Delta16 splice variant, lacking exon 16, has the properties of an activated oncogene, but it could also play beneficial roles in the response to targeted therapeutic agents. To study mammary carcinogenesis in a mouse model that mimics human coexpression of full-length HER-2 and Delta16 isoforms, we produced hybrid mice bearing heterozygous copies of both human transgenes (F1 mice), and we compared them to parental mice (Delta16 and HER-2 transgenic mice, respectively). Tumor onset in F1 and Delta16 mice was much faster than in HER-2 mice (30 vs &amp;gt;80 weeks), but the growth of established tumors and metastatic spread were not enhanced. Each mammary carcinoma of F1 mice expressed both isoforms at variable ratios. Most (∼80%) expressed high levels of Delta16 and low levels of full length HER-2, a few (∼5%) expressed full-length HER-2 and little, if any, Delta 16, and the remainder (∼15%) coexpressed at high level both isoforms. The study of tumor vascularization showed that full-length HER-2 tumors mainly contained few large vessels or vascular lacunae, whereas Delta16 tumors were perfused by numerous endothelium-lined small vessels. F1 tumors with high full-length HER-2 expression made few large vessels, whereas tumors with low full-length HER-2 and high Delta16 contained numerous small vessels and expressed high levels of both VEGF and VEGFR2. Administration of trastuzumab to young F1 mice effectively prevented mammary carcinoma onset in ∼85% of mice at 1 year of age. The preventive effect of trastuzumab was stronger in F1 mice than in both parental strain. To analyze the intrinsic sensitivity of F1 mammary carcinoma cells to targeted drugs in 3D, we established cell lines expressing different HER-2 isoform ratios. High Delta16 expression caused high sensitivity to HER-2 inhibitors (trastuzumab, neratinib, lapatinib), whereas high full-length HER-2 was associated with a lower sensitivity. Interestingly, high levels of both isoforms was associated with resistance to trastuzumab, but sensitivity to small molecule inhibitors. In conclusion, the coexpression of full-length HER-2 and Delta16 controls several determinants of mammary carcinoma development, progression and sensitivity to targeted agents, as revealed by the study of F1 mice. Citation Format: Arianna Palladini, Massimiliano Dall’Ora, Tania Balboni, Giordano Nicoletti, Marianna Ianzano, Roberta Laranga, Lorena Landuzzi, Veronica Giusti, Alessia Lamolinara, Carla De Giovanni, Augusto Amici, Serenella M. Pupa, Manuela Iezzi, Patrizia Nanni, Pier-Luigi Lollini. HER-2 isoform interaction in mammary carcinoma onset and progression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1200.

Presenilin 1 transgene addition to amyloid precursor protein overexpressing transgenic rats increases amyloid beta 42 levels and results in loss of memory retention.

BackgroundWe previously reported the production of transgenic rats (APP21 line) that over-express human amyloid precursor protein (APP) containing Swedish and Indiana mutations. In order to generate a better model for Alzheimer’s disease (AD), the APP21 rat line was used to generate double transgenic line that over-expressed Presenilin 1 (PS1) with L166P mutation in addition to APP transgene (APP + PS1 line).ResultsThirty-two double transgenic founders were generated and the ultimate transgenic founder was selected based on PS1 transgene copy number and level of amyloid-beta (Aβ)42 peptide. The APP + PS1 double transgenic rats had 38 times more PS1 in brains compared to APP rats. Behavioral assessment using Barnes maze showed that APP + PS1 rats exhibited a larger learning and memory deficit than APP21 rats. Double transgenic rats also produced more Aβ42. Histological examination of the brains showed that the APP21 rat line displayed neurofibrillary tangles and in contrast, the APP + PS1 line showed chromatolysis in hippocampal neurons and neuronal loss in CA3 region of hippocampus.ConclusionsDue to the separate segregation of APP and PS1 transgenes in APP + PS1 double transgenic rats, this transgenic line may be a valuable model for studying the effects of various levels of APP and PS1 transgenes on various aspects of brain pathologies associated with the AD phenotype.Electronic supplementary materialThe online version of this article (doi:10.1186/s12868-016-0281-8) contains supplementary material, which is available to authorized users.

Genetically modified (GM) crops: milestones and new advances in crop improvement.

New advances in crop genetic engineering can significantly pace up the development of genetically improved varieties with enhanced yield, nutrition and tolerance to biotic and abiotic stresses. Genetically modified (GM) crops can act as powerful complement to the crops produced by laborious and time consuming conventional breeding methods to meet the worldwide demand for quality foods. GM crops can help fight malnutrition due to enhanced yield, nutritional quality and increased resistance to various biotic and abiotic stresses. However, several biosafety issues and public concerns are associated with cultivation of GM crops developed by transgenesis, i.e., introduction of genes from distantly related organism. To meet these concerns, researchers have developed alternative concepts of cisgenesis and intragenesis which involve transformation of plants with genetic material derived from the species itself or from closely related species capable of sexual hybridization, respectively. Recombinase technology aimed at site-specific integration of transgene can help to overcome limitations of traditional genetic engineering methods based on random integration of multiple copy of transgene into plant genome leading to gene silencing and unpredictable expression pattern. Besides, recently developed technology of genome editing using engineered nucleases, permit the modification or mutation of genes of interest without involving foreign DNA, and as a result, plants developed with this technology might be considered as non-transgenic genetically altered plants. This would open the doors for the development and commercialization of transgenic plants with superior phenotypes even in countries where GM crops are poorly accepted. This review is an attempt to summarize various past achievements of GM technology in crop improvement, recent progress and new advances in the field to develop improved varieties aimed for better consumer acceptance.

Synergistic Action of D-Glucose and Acetosyringone on Agrobacterium Strains for Efficient Dunaliella Transformation.

An effective transformation protocol for Dunaliella, a β-carotene producer, was developed using the synergistic mechanism of D-glucose and Acetosyringone on three different Agrobacterium strains (EHA105, GV3101 and LBA4404). In the present study, we investigated the pre-induction of Agrobacterium strains harboring pMDC45 binary vector in TAP media at varying concentrations of D-glucose (5 mM, 10 mM, and 15mM) and 100 μM of Acetosyringone for co-cultivation. Induction of Agrobacterium strains with 10 mM D-glucose and 100 μM Acetosyringone showed higher rates of efficiency compared to other treatments. The presence of GFP and HPT transgenes as a measure of transformation efficiency from the transgenic lines were determined using fluorescent microscopy, PCR, and southern blot analyzes. Highest transformation rate was obtained with the Agrobacterium strain LBA4404 (181 ± 3.78 cfu per 106 cells) followed by GV3101 (128 ± 5.29 cfu per 106 cells) and EHA105 (61 ± 5.03 cfu per 106 cells). However, the Agrobacterium strain GV3101 exhibited more efficient single copy transgene (HPT) transfer into the genome of D. salina than LBA4404. Therefore, future studies dealing with genetic modifications in D. salina can utilize GV3101 as an optimal Agrobacterium strain for gene transfer.

Abstract 397: Transgenic Expression of Cholesteryl Ester Transfer Protein in Female Mice Disrupts Liver and Plasma Triglyceride Metabolism With Estrogen Treatment in a Liver Network Involving Estrogen Receptor Alpha and Small Heterodimer Partner

Background: Triglycerides are an important risk factor for cardiovascular disease, especially in women. Hormone replacement therapy raises triglycerides (TG) in postmenopausal women, but mechanisms responsible remain poorly understood. Cholesteryl Ester Transfer Protein (CETP) is a serum protein that shuttles TG and cholesteryl ester between lipoproteins in humans and plays an important role in lipoprotein metabolism. The role of CETP in regulating whole body triglyceride homeostasis remains unclear. Mice (which naturally lack CETP) expressing a transgenic copy of CETP or their wild-type (WT) littermates were used to determine the role of CETP in regulating plasma and liver TG metabolism in response to estrogen. Methods and Results: Female CETP and WT mice were ovariectomized and given vehicle or estrogen treatment. Estrogen raised plasma TG in CETP females, but not in WT females. CETP expression impaired TG clearance independent of estrogen. Estrogen treatment raised very-low density lipoprotein (VLDL) TG production in CETP females, but not in WT females. Estrogen treatment augmented mRNA expression and protein activity of VLDL assembly and secretion targets (Apob, Mttp, PDI) in CETP females, but not in WT females. Additionally, CETP expression lowered liver TG content and increased mRNA expression of TG oxidation targets (Ppara, Acox1, Acadm, Cpt2). Deletion of liver estrogen receptor alpha prevented CETP-mediated decreases in liver TG content and increases in mRNA expression of TG oxidation targets. Liver-specific deletion of estrogen receptor alpha did not attenuate estrogen-mediated increases in plasma TG and VLDL-TG production in female mice expressing CETP. Deletion of liver small heterodimer partner attenuated CETP-mediated increases in plasma TG and VLDL-TG production with estrogen treatment. Deletion of small heterodimer partner also attenuated CETP-mediated increases in mRNA expression and protein activity of VLDL synthesis and assembly targets with estrogen treatment. Conclusion: These studies indicate several novel functions of CETP in regulating plasma and liver TG homeostasis. We also discovered that CETP expression in female mice also augments several aspects of estrogen action in liver that impact liver TG biology.

Downregulation of human IL4 and IL13 expression by CRISPR/Cas9-mediated deletion of DNase I hypersensitive site HS11/12 from a transgenic human Th2 cytokine locus

Abstract Production of the Th2 cytokines IL4 and IL13 is frequently dysregulated in allergy and asthma. Multiple genetic elements regulating expression of murine Th2 cytokines have been characterized by gene targeting. To study the regulation of human Th2 cytokines, we created BAC transgenic mice (BAC5TG) carrying a 160 kb fragment of the human Th2 locus encompassing RAD50, IL13 and IL4. This transgene includes all the regulatory elements required for physiological expression of mouse Th2 cytokines. BAC5TG mice appear normal, are born at the expected Mendelian ratio, and demonstrate tissue-specific and transgene copy number-dependent expression of human Th2 cytokines. DNA methylation profiles across the transgenic human Th2 locus are highly comparable if not identical to those observed in human cells. A DNase I hypersensitive site (HS) in the human IL13-IL4 intergenic region, previously identified in our lab and designated HS11/12, colocalizes with an area of extensive and profound CpG hypomethylation both in human and mouse transgenic T cells. However, unlike most Th2 regulatory elements identified to date, HS11/12 is not conserved between humans and mice. Using the CRISPR/Cas9 approach, we deleted HS11/12 from the human Th2 transgene in BAC5TG mice. Notably, production of both human IL13 and IL4 by in vitro differentiated Th2 cells from BAC5DHS11/12 TG mice was reduced by ~50%. Our results suggest that HS11/12 represents a novel cis-regulatory element required for optimal production of the human Th2 cytokines IL4 and IL13. The application of CRISPR/Cas9 technology to BAC transgenic mice may provide a powerful tool to study human gene regulation.

8. Further Characterization of U2 snRNP Mediated Restriction of AAV Vector Transduction

Improving adeno-associated virus (AAV) vector transduction efficiency is central to the development of its continued, widespread use in gene therapy. More effective AAV transduction would reduce vector doses required for efficient gene delivery, minimizing the risks associated with high dose AAV vectors. Several treatments have been reported to increase AAV vector transduction, including adenoviral co-infection. Through screening of a siRNA library, we recently identified U2 snRNP as a host restriction factor for AAV vector transduction. Disruption of U2 snRNP spliceosome and associated proteins, including PHF5A, SF3B1, SF3B2 and U2AF1, potently enhanced AAV vector transduction. Relevant to gene therapy applications of AAV vectors, meayamycin B, a powerful SF3B1 inhibitor, allowed for substantial increases in AAV vector transduction (up to 400-fold). This post-entry restriction appeared to occur after the second-strand synthesis but before transgene expression or accumulation of transgene transcripts and independently of the cellular splicing machinery. No notable changes were found in the cytoplasmic trafficking, nuclear entry, or genome release of AAV vector infection by U2 snRNP inhibition. Here, we further studied the mechanism(s) underlying the U2 snRNP-mediated block of AAV vectors. We first tested another commercially available U2 snRNP inhibitor, pladienolide B (PladB) and verified that PladB treatment also showed substantial dose dependent increases (up to 700-fold) in AAV vector transduction. We next studied the relationship between adenoviral co-infection and U2 snRNP inhibition. Adenoviral co-infection alone enhanced AAV vector transduction up to 30-fold, while adenoviral co-infection, in addition to genetic or pharmacological U2 snRNP inhibition, showed marginal additive effects, suggesting a common pathway targeted by adenoviral co-infection and U2 snRNP inhibition in enhanced AAV vector infection. Using a series of plasmids providing adenoviral helper functions, we have identified Ad5 E4, but not the E2A and VA RNA genes, as partially responsible for the enhanced AAV transduction by adenoviral co-infection through U2 snRNP inhibition. Since the effects of U2 snRNP inhibition are most likely on the regulation of transgene expression, we also assessed the epigenetic modifications of the AAV2 genome in the presence or absence of PladB. Through chromosome immunoprecipitation (ChIP) assays we mapped histone recruitment patterns at different regions of the AAV vector epigenome. PladB treatment reproducibly enhanced recruitment of histone H2b and H3 proteins to the AAV CMV promoter, luciferase transgene, and polyA regions up to 3-fold. Our preliminary study also suggested that U2 snRNP inhibition altered specific histone modification patterns on the AAV vector genome. We are in the process of verifying the influence of U2 snRNP inhibition, as well as AAV capsid variations, on epigenetic modifications of the AAV vector epigenome. Better understanding the underlying mechanism would provide novel insights into host-virus interactions and could lead to the rational design of next generation AAV vectors with improved transduction efficiencies and safety profiles.

High levels of histone H3 acetylation at the CMV promoter are predictive of stable expression in Chinese hamster ovary cells

Chinese hamster ovary cells (CHO) are widely used in the production of glycosylated therapeutic proteins such as antibodies. During expansion and maintenance, CHO cell lines are prone to production instability, which may be caused by promoter silencing, loss of transgene copies, or post-transcriptional effects. Silencing of recombinant genes may be accompanied by DNA methylation and histone modification. Previously, we demonstrated that cytosine methylation of the human cytomegalovirus major immediate early promoter/enhancer (hCMV-MIE) can be used to predict instability of antibody-producing CHO cell lines. However, the high rate of false prediction motivates the search for further markers of stable promoter activity. To this end, we correlated a variety of histone modifications in the vicinity of hCMV-MIE with production stability over time. Our results suggest that acetylation of histone H3 (H3ac) is a more effective indicator of production stability than DNA methylation. Selecting cell lines with highest CMV promoter H3ac levels enriches stable expressors and improves the average stability of production cell lines. For histone H3 acetylation measurement we employed a method based on chromatin immunoprecipitation (ChIP). In its current form, the method is suitable to evaluate 10-20 cell lines within a few days. We propose to determine H3 acetylation once the number of candidate cell lines has been narrowed based on productivity and product quality. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:776-786, 2016.

The utility of flow sorting to identify chromosomes carrying a single copy transgene in wheat.

BackgroundIdentification of transgene insertion sites in plant genomes has practical implications for crop breeding and is a stepping stone to analyze transgene function. However, single copy sequences are not always easy to localize in large plant genomes by standard approaches.ResultsWe employed flow cytometric chromosome sorting to determine chromosomal location of barley sucrose transporter construct in three transgenic lines of common wheat. Flow-sorted chromosomes were used as template for PCR and fluorescence in situ hybridization to identify chromosomes with transgenes. The chromosomes carrying the transgenes were then confirmed by PCR using DNA amplified from single flow-sorted chromosomes as template.ConclusionsInsertion sites of the transgene were unambiguously localized to chromosomes 4A, 7A and 5D in three wheat transgenic lines. The procedure presented in this study is applicable for localization of any single-copy sequence not only in wheat, but in any plant species where suspension of intact mitotic chromosomes suitable for flow cytometric sorting can be prepared.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-016-0124-8) contains supplementary material, which is available to authorized users.

Pharmacodynamics of anti-HIV gene therapy using viral vectors and targeted endonucleases.

A promising curative approach for HIV is to use designer endonucleases that bind and cleave specific target sequences within latent genomes, resulting in mutations that render the virus replication incompetent. We developed a mathematical model to describe the expression and activity of endonucleases delivered to HIV-infected cells using engineered viral vectors in order to guide dose selection and predict therapeutic outcomes. We developed a mechanistic model that predicts the number of transgene copies expressed at a given dose in individual target cells from fluorescence of a reporter gene. We fitted the model to flow cytometry datasets to determine the optimal vector serotype, promoter and dose required to achieve maximum expression. We showed that our model provides a more accurate measure of transduction efficiency compared with gating-based methods, which underestimate the percentage of cells expressing reporter genes. We identified that gene expression follows a sigmoid dose-response relationship and that the level of gene expression saturation depends on vector serotype and promoter. We also demonstrated that significant bottlenecks exist at the level of viral uptake and gene expression: only ∼1 in 220 added vectors enter a cell and, of these, depending on the dose and promoter used, between 1 in 15 and 1 in 1500 express transgene. Our model provides a quantitative method of dose selection and optimization that can be readily applied to a wide range of other gene therapy applications. Reducing bottlenecks in delivery will be key to reducing the number of doses required for a functional cure.