94 PRODUCTION OF AN α1,3-GALACTOSYLTRANSFERASE GENE KNOCKOUT CALF USING A SINGLE TARGETING VECTOR AND REJUVENATED CELL LINES

2007 ◽  
Vol 19 (1) ◽  
pp. 164
Author(s):  
M. Urakawa ◽  
Y. Sendai ◽  
T. Sawada ◽  
Y. Shinkai ◽  
A. Ideta ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Cell Line ◽  
Southern Blot ◽  
Gene Targeting ◽  
Cell Lines ◽  
Gene Knockout ◽  
Antibiotic Resistance Gene ◽  
Blastocyst Stage ◽  
Fetal Fibroblasts ◽  
Targeting Vector

Gene targeting in large animals has the potential to be useful in agriculture. In this study, we examined whether an �1,3-galactosyltransferase-gene knockout (null) calf could be produced using a single targeting vector for disruption of both alleles and a rejuvenation of cell line by production of cloned fetuses. A promoter-less positive selection vector (pGT-22) containing an IRES (internal ribosome entry site)-antibiotic resistance gene(neo) cassette and loxP sequences was used to disrupt the bovine �1,3-galactosyltransferase (�1,3-GT) gene. In gene-targeting (GT), Japanese Black fetal fibroblasts were transfected with pGT-22, and were selected with 0.4 mg mL-1 G418. G418-resistant cells were monitored by PCR and Southern blot analysis. After PCR selection, a portion of the PCR-positive colonies were infected with the adenovirus AxCANCre, which transiently expresses Cre recombinase in the infected cells, to excise the antibiotic-resistance gene cassette (IRES/lacZ-neo) from the targeted allele. The targeted cells in which homologous recombination occurred were used for somatic cell nuclear transfer (SCNT). The cell cycle synchronization of donor cells in the early G1 phase and SCNT were performed according to the established procedure in our laboratory (Urakawa et al. 2004 Theriogenology 62, 714–728). As a result, in the first GT, one PCR-Southern blot-positive clone (0.26%, in 380 G418-resistant colony) was used for SCNT. Of 35 pulsed SCNT embryos, 4 (11.4%) developed to the blastocyst stage and 3 blastocysts were nonsurgically transferred to a recipient heifer; one fetus was recovered on Day 41. The cell line (�1,3-GT+/-) was established and was transfected with pGT-22 in the second GT. As a result, 8 PCR-Southern blot-positive clones (1.6%, in 508 G418-resistant colony) were recovered. The 2nd GT and the following SCNT were accomplished by the same methods used in the 1st GT and SCNT procedure. Of 36 pulsed SCNT embryos, 7 (19.4%) developed to the blastocyst stage and 3 blastocysts were nonsurgically transferred to a recipient heifer; one fetus was recovered on Day 41. The cell line (�1,3-GT-/-) was established, and was used for SCNT to obtain the �1,3-GT homozygous knockout offspring. Finally, 52 of 148 pulsed SCNT embryos (35.1%) developed to the blastocyst stage and 6 cloned embryos were transferred into 3 recipient heifers. A single knockout female offspring with normal morphology in all organs was born (Day 287) but died about one hour after birth. In this study, we established both heterozygous and homozygous �1,3-GT knockout cell lines from primary fetal fibroblasts and produced an �1,3-GT knockout offspring using a single targeting vector and rejuvenated cell lines.

scholarly journals A CRISPR/Cas9 genome editing pipeline in the EndoC-βH1 cell line to study genes implicated in beta cell function

2019 ◽  
Vol 4 ◽  
pp. 150 ◽  
Author(s):  
Antje K. Grotz ◽  
Fernando Abaitua ◽  
Elena Navarro-Guerrero ◽  
Benoit Hastoy ◽  
Daniel Ebner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Beta Cell ◽  
Er Stress ◽  
Cell Line ◽  
Cell Lines ◽  
Target Genes ◽  
Gene Knockout ◽  
Mrna Levels ◽  
Beta Cell Line ◽  
Human Beta Cell

Type 2 diabetes (T2D) is a global pandemic with a strong genetic component, but most causal genes influencing the disease risk remain unknown. It is clear, however, that the pancreatic beta cell is central to T2D pathogenesis. In vitro gene-knockout (KO) models to study T2D risk genes have so far focused on rodent beta cells. However, there are important structural and functional differences between rodent and human beta cell lines. With that in mind, we have developed a robust pipeline to create a stable CRISPR/Cas9 KO in an authentic human beta cell line (EndoC-βH1). The KO pipeline consists of a dual lentiviral sgRNA strategy and we targeted three genes (INS, IDE, PAM) as a proof of concept. We achieved a significant reduction in mRNA levels and complete protein depletion of all target genes. Using this dual sgRNA strategy, up to 94 kb DNA were cut out of the target genes and the editing efficiency of each sgRNA exceeded >87.5%. Sequencing of off-targets showed no unspecific editing. Most importantly, the pipeline did not affect the glucose-responsive insulin secretion of the cells. Interestingly, comparison of KO cell lines for NEUROD1 and SLC30A8 with siRNA-mediated knockdown (KD) approaches demonstrate phenotypic differences. NEUROD1-KO cells were not viable and displayed elevated markers for ER stress and apoptosis. NEUROD1-KD, however, only had a modest elevation, by 34%, in the pro-apoptotic transcription factor CHOP and a gene expression profile indicative of chronic ER stress without evidence of elevated cell death. On the other hand, SLC30A8-KO cells demonstrated no reduction in KATP channel gene expression in contrast to siRNA silencing. Overall, this strategy to efficiently create stable KO in the human beta cell line EndoC-βH1 will allow for a better understanding of genes involved in beta cell dysfunction, their underlying functional mechanisms and T2D pathogenesis.

scholarly journals 231EXPRESSION PATTERN OF CERTAIN DEVELOPMENTALLY IMPORTANT GENES IN BOVINE NUCLEAR TRANSFER EMBRYOS PRODUCED USING CELL LINES OF DIFFERENT EFFICIENCY

2004 ◽  
Vol 16 (2) ◽  
pp. 236 ◽  
Author(s):  
Z. Beyhan ◽  
N.L. First
Keyword(s):  
Gene Expression ◽  
Statistical Analysis ◽  
Cell Line ◽  
Cell Lines ◽  
Live Birth ◽  
Nuclear Transfer ◽  
Expression Patterns ◽  
Blastocyst Stage ◽  
Gene Expression Patterns ◽  
Donor Cells

Developmental abnormalities associated with the cloning process suggest that reprogramming of donor nuclei into an embryonic state may not be fully completed in most of the cloned animals. One of the areas of interest in this respect is the analysis of gene expression patterns in nuclear transfer embryos to dissect the processes that failed and to develop means to overcome the limitations imposed by these factors. In this study, we investigated the expression patterns of histone deacetylase-1,-2,-3 (HDAC-1,-2,-3), DNA methyltransferase-3A (DNMT3A) and octamer binding protein-4 gene (POU5F1) in donor cells with different cloning efficiencies (low: no-pregnancy, medium: pregnancy but no live birth and high: live birth) and nuclear transfer embryos derived from these cell lines using a real time reverse transcription-polymerase chain reaction (RT-PCR) assay with SYBR green chemistry. Employing standard protocols, we produced nuclear transfer embryos from three different cell lines categorized as having varying efficiencies in supporting development to term. Embryos were collected at morula, blastocyst and hatched blastocyst stages and total RNA was extracted from pools of 4–5 embryos using Absolutely RNA nanoprep kit (Stratagene, La Jolla, CA, USA). Relative level of expression at these stages was analyzed using ΔΔCT method with HH2A as the reference gene and in vitro-fertilized embryos as the control samples. Statistical analysis was performed on ranked expression data employing SAS statistical analysis software procedure ANOVA. Same set of genes were also analyzed on donor cells using standard curve method. All genes investigated were affected by nuclear transfer and followed somewhat altered expression patterns. In general, expression of HDAC genes was elevated especially at the compact morula stage but became comparable to control embryos at the hatched blastocyst stage. DNMT3A expression in NT embryos was lower than in IVF embryos at all stages. POU5F1 transcript levels were also reduced in nuclear transfer embryos at the compact morula and blastocyst stages. The difference, however, disappeared at the hatched blastocyst stage. There was a cell line effect on the expression patterns of all genes investigated. Cell lines efficient in producing offspring tended to resemble control embryos in gene expression patterns compared to inefficient cell lines. These results agree with several studies reporting altered gene expression patterns for certain genes in cloned embryos. Our data also suggest that cell line differences in developmental competency observed in cloning experiments might be related to physiological differences in transcriptional regulation and nuclear remodeling, DNA methylation, and lineage differentiation in embryos cloned from these cell lines.

300 HEMIZYGOUS PRION PROTEIN GENE (PRNP) KNOCKOUT IN CATTLE FIBROBLASTS

2008 ◽  
Vol 20 (1) ◽  
pp. 230
Author(s):  
D. Brunetti ◽  
G. Rossi ◽  
I. Lagutina ◽  
R. Duchi ◽  
S. Colleoni ◽  
...  
Keyword(s):  
Southern Blot ◽  
Prion Protein ◽  
Cell Lines ◽  
Protein Gene ◽  
Spongiform Encephalopathy ◽  
Prion Protein Gene ◽  
Drug Resistant ◽  
Bovine Strain ◽  
Fetal Fibroblasts ◽  
Adult Fibroblasts

Bovine spongiform encephalopathy (BSE) represents a real threat for human health, as has been demonstrated by the causal link with the variant form of Creutzfeldt-Jakob disease. The aim of our project is to create a bovine strain knockout for the prion protein gene (PRNP) that should be resistant to BSE infection. We combined the use of homologous recombination by PRNP targeting vectors in bovine fibroblasts with the subsequent use of nuclear transfer (NT). We transfected fetal (male) and adult (female) bovine fibroblasts by nucleofection, using targeting vectors disrupting the PRNP by means of loxP flanked cassettes. They expressed resistance to different drugs driven by a PGK or TK promoter and the thymidine kinase gene as a negative selection marker. We screened, by PCR, 907 drug-resistant colonies, from which we identified 8 Neo-resistant colonies with a recombined PRNP allele (overall efficiency 3.2%; 7/108 from fetal, 1/145 from adult; P < 0.5). Fibroblasts PRNP+/– Neo were used to produce NT blastocysts from which neural precursors cell lines were established (Lazzari et al. 2006 Stem Cells 24, 2514–2521). These lines were capable of extensive proliferation (over 120 doublings during 4 months of culture) and provided unlimited material for Southern blot analysis to confirm PCR findings. Three clones (2 from fetal and 1 from adult) were further analyzed and confirmed PRNP+/– by Southern blot and were subsequently used for NT to generate blastocysts for transfer to recipient heifers. On Day +40 of gestation, the pregnancy rate was 33.3% (9/30) for the fetal line and 50% (2/4) for the adult line. One of the fetuses originating from fetal fibroblasts was removed on Day +45 to establish a rejuvenated fibroblast cell line used for a second round of gene targeting to obtain a PRNP –/– clone. We nucleofected these fibroblasts with Puro, Hygro, and promoterless Hygro cassette-carrying targeting vectors. We screened 625 drug-resistant colonies by PCR but none tested positive for the second targeting. In conclusion, we have obtained heterozygous PRNP+/– fibroblasts with the Neo vector both in fetal and adult fibroblasts, but failed with other vectors. In the first targeting, the efficiency was 10 times greater in fetal v. adult fibroblasts. The derivation of neural precursor cell lines from cloned blastocysts is a useful procedure to have sufficient material for molecular analysis without the need of rejuvenating the cell through the production of a fetus. None of the vectors used for the targeting of the second allele was successful.

309 PRODUCTION OF CATTLE BY NUCLEAR TRANSFER FROM CELLS IN WHICH A GENE IS DISRUPTED

2009 ◽  
Vol 21 (1) ◽  
pp. 251
Author(s):  
M. Urakawa ◽  
Y. Sendai ◽  
A. Ideta ◽  
K. Hayama ◽  
Y. Shinkai ◽  
...  
Keyword(s):  
Pregnancy Rate ◽  
Gene Targeting ◽  
Prion Protein ◽  
Nuclear Transfer ◽  
Antibiotic Resistance Gene ◽  
Control Group ◽  
Gestation Length ◽  
Entry Site ◽  
Donor Cells ◽  
Fetal Fibroblasts

Gene-targeted animals provide a powerful model to examine gene functionality. In this study, we examined the effect of gene targeting of donor cells for nuclear transfer (NT) on the pregnancy rate and on viability of the offspring after embryo transfer. Gene-targeted (tg; targeting of both alleles of the gene encoding bovine prion protein) or non-manipulated (control) bovine fetal fibroblasts were used for NT. A promoterless positive selection vector (pPrP5.2) containing an internal ribosome entry site-antibiotic resistance gene (neo) cassette and loxP sequences was used to disrupt the bovine prion protein gene. The cells (tg) in which homologous recombination was occurred were used for NT. The tg and control cells were cultured in DMEM with 10% FCS and were prepared in the early G1 phase to our previous report (Urakawa M et al. 2004 Theriogenology 62, 714–728). Each donor cell was inserted into an enucleated in vitro-matured (19 h) oocyte. Cell fusion (DC, 200 V mm–1, 10 μs) and activation (DC, 100 V mm–1 , 60 μs) were done in 0.3 m mannitol solution. The NT embryos were then activated with 5 μm Ca-ionophore and 10 μg of mL–1 cycloheximide and were cultured with bovine oviduct epithelial cells in CR1aa with 5% CS. The blastocyst rates were judged at 6 days after NT. The blastocysts were non-surgically transferred to recipient heifers. The recipients were monitored daily for heat behavior, examined by ultrasound at Day 30 and 60, and then observed monthly to confirm pregnancy. The offspring born in the tg group were confirmed by PCR to be transgenic. Statically significance was tested using a chi-square test or t-test. Developmental rate to the blastocyst stage, pregnancy rate at Day 30 and 60, and calving rate did not differ significantly between tg and the control group (Table 1). Gestation length (tg; 290.0 ± 2.2 days v. control; 290.5 ± 3.9 days) and birth weight (tg; 39.6 ± 8.0 kg v. control; 40.2 ± 4.1 kg) were not significantly different. These results indicate that gene targeting of donor cells used for NT does not significantly affect the development of embryos, pregnancy rate, or the viability of the offspring. Table 1.Development of NT embryos with tg or control cells

scholarly journals A Universal Positive-Negative Selection System for Gene Targeting in Plants Combining an Antibiotic Resistance Gene and Its Antisense RNA

2015 ◽  
Vol 169 (1) ◽  
pp. 362-370 ◽  
Author(s):  
Ayako Nishizawa-Yokoi ◽  
Satoko Nonaka ◽  
Keishi Osakabe ◽  
Hiroaki Saika ◽  
Seiichi Toki
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Gene Targeting ◽  
Antisense Rna ◽  
Negative Selection ◽  
Antibiotic Resistance Gene ◽  
Selection System

scholarly journals ELIMINATOR: Essentiality anaLysIs using MultIsystem Networks And inTeger prOgRamming

2021 ◽  
Author(s):  
Asier Antoranz ◽  
Maria Ortiz ◽  
Jon Pey
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
In Silico ◽  
Large Scale ◽  
Gene Knockout ◽  
Patient Specific ◽  
Gene Essentiality ◽  
Molecular Features ◽  
The Impact

A gene is considered as essential when it is indispensable for cells to grow and replicate under a certain environment. However, gene essentiality is not a structural property but rather a contextual one, which depends on the specific biological conditions affecting the cell. This circumstantial essentiality of genes is what brings the attention of scientist since we can identify genes essential for cancer cells but not essential for healthy cells. This same contextuality makes their identification extremely challenging. Huge experimental efforts such as Project Achilles where the essentiality of thousands of genes is measured in over one thousand cell lines together with a plethora of molecular data (transcriptomics, copy number, mutations, etc.) can shed light on the causality behind the essentiality of a gene in a given environment by associating the measured essentiality to molecular features of the cell line. Here, we present an in-silico method for the identification of patient-specific essential genes using constraint-based modelling (CBM). Our method expands the ideas behind traditional CBM to accommodate multisystem networks, that is a biological network that focuses on complex interactions within several biological systems. In essence, it first calculates the minimum number of non-expressed genes required to be active by the cell to sustain life as defined by a set of requirements; and second, it performs an exhaustive in-silico gene knockout to find those that lead to the need of activating extra non-expressed genes. We validated the proposed methodology using a set of 452 cancer cell lines derived from the Cancer Cell Line Encyclopedia where an exhaustive experimental large-scale gene knockout study using CRISPR (Achilles Project) evaluates the impact of each removal. We also show that the integration of different essentiality predictions per gene, what we called Essentiality Congruity Score, (derived from multiple pathways) reduces the number of false positives. Finally, we explored the gene essentiality predictions for a breast cancer patient dataset, and our results showed high concordance with previous publications. These findings suggest that identifying genes whose activity are fundamental to sustain cellular life in a patient-specific manner is feasible using in-silico methods. The patient-level gene essentiality predictions can pave the way for precision medicine by identifying potential drug targets whose deletion can induce death in tumour cells.

scholarly journals Non-Clinical In Vitro Evaluation of Antibiotic Resistance Gene-Free Plasmids Encoding Human or Murine IL-12 Intended for First-in-Human Clinical Study

Pharmaceutics ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1739
Author(s):  
Spela Kos ◽  
Masa Bosnjak ◽  
Tanja Jesenko ◽  
Bostjan Markelc ◽  
Urska Kamensek ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Antibiotic Resistance ◽  
Antitumor Activity ◽  
Cell Line ◽  
Resistance Gene ◽  
Carcinoma Cell ◽  
Antibiotic Resistance Gene ◽  
Gene Electrotransfer ◽  
Localized Delivery

Interleukin 12 (IL-12) is a key cytokine that mediates antitumor activity of immune cells. To fulfill its clinical potential, the development is focused on localized delivery systems, such as gene electrotransfer, which can provide localized delivery of IL-12 to the tumor microenvironment. Gene electrotransfer of the plasmid encoding human IL-12 is already in clinical trials in USA, demonstrating positive results in the treatment of melanoma patients. To comply with EU regulatory requirements for clinical application, which recommend the use of antibiotic resistance gene-free plasmids, we constructed and developed the production process for the clinical grade quality antibiotic resistance gene-free plasmid encoding human IL-12 (p21-hIL-12-ORT) and its ortholog encoding murine IL-12 (p21-mIL-12-ORT). To demonstrate the suitability of the p21-hIL-12-ORT or p21-mIL-12-ORT plasmid for the first-in-human clinical trial, the biological activity of the expressed transgene, its level of expression and plasmid copy number were determined in vitro in the human squamous cell carcinoma cell line FaDu and the murine colon carcinoma cell line CT26. The results of the non-clinical evaluation in vitro set the basis for further in vivo testing and evaluation of antitumor activity of therapeutic molecules in murine models as well as provide crucial data for further clinical trials of the constructed antibiotic resistance gene-free plasmid in humans.

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