107 GENETIC INACTIVATION OF THE Sry GENE IN ARGALI WILD AND ROMNEY DOMESTIC SHEEP WITH CRISPR/Cas SYSTEMS FOR PRODUCING SEX-REVERSED FEMALE ANIMALS

2014 ◽  
Vol 26 (1) ◽  
pp. 167 ◽  
Author(s):  
Z. Fan ◽  
S. Lee ◽  
H. Park ◽  
K. Lucibello ◽  
Q. Meng ◽  
...  

The Tibetan Argali (Ovis ammon hodgsoni), a wild sheep of the subfamily Caprinae (Bovidae), primarily found in the Tibetan Plateau, is categorized as near threatened on the International Union for Conservation of Nature (IUCN) Red List. For the conservation of this species, we have achieved the cloning of a full-term live Argali lamb (died shortly after birth) from a male Argali cell line that has been cryopreserved for more than 20 years. While working towards the goal of cloning a live Argali, we also recognised the need to establish a reproductive herd of animals by producing both fertile males and females. However, as in the case of Argali, it is difficult, and in some cases impossible, to obtain male and female cell lines from an endangered mammalian species. Therefore, for demonstrating a proof of concept of using an assisted reproduction technology (ART) for the conservation of endangered species or reviving extinct species, we used the Argali as an experimental model to produce both fertile males and females through ART. The Sry gene plays a central role in mammalian sex determination: mutations in the Sry gene result in the development of XY females; in mice, Sry knockout (KO) results in fertile XY females. Therefore, we created sex-reversed Argali cell lines through the KO of the Sry gene. In parallel, for potentially comparing the fertility of sex-reversed XY females between the Argali and domestic sheep [Romney (Ovis aries)], we also knocked out the Sry gene in the domestic sheep. Specifically, we used the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system to introduce mutations to the high-mobility group (HMG) box of the Sry gene. Skin fibroblasts from either adult Argali or Romney sheep were cultured in DMEM (HyClone) supplemented with 10% fetal bovine serum (FBS). Cells were harvested at 100% confluence with 0.25% trypsin-EDTA and transfected with the CRISPR/Cas DNA constructs by using the Amaxa Nucleofector system. For each experiment, 106 cells were transfected with 5 μg of CRISPR/Cas DNA constructs. After 72 hours post-transfection, cells were harvested, with half being used for genomic DNA isolation (for examining KO efficiency) and the other half for limited dilution for obtaining single-cell-derived colonies. With the Surveyor assay and a restriction enzyme digestion assay (successfully knocked-out cells lose the Dde I site in the HMG box of the Sry gene, rendering resistance to Dde I digestion), we demonstrated that the Sry KO efficiency was about 10% both in Argali and Romney sheep. By screening single-cell-derived colonies from the transfected Romney sheep cells, an Sry-KO cell line harboring a 2-nucleotide deletion in the HMG box was successfully established. Multiple vials of cells from this Sry-KO cell line have been cryopreserved and will be used for animal cloning via somatic cell nuclear transfer (SCNT) in the sheep-breeding season this fall.

2019 ◽  
Author(s):  
Ruixin Wang ◽  
Dongni Wang ◽  
Dekai Kang ◽  
Xusen Guo ◽  
Chong Guo ◽  
...  

BACKGROUND In vitro human cell line models have been widely used for biomedical research to predict clinical response, identify novel mechanisms and drug response. However, one-fifth to one-third of cell lines have been cross-contaminated, which can seriously result in invalidated experimental results, unusable therapeutic products and waste of research funding. Cell line misidentification and cross-contamination may occur at any time, but authenticating cell lines is infrequent performed because the recommended genetic approaches are usually require extensive expertise and may take a few days. Conversely, the observation of live-cell morphology is a direct and real-time technique. OBJECTIVE The purpose of this study was to construct a novel computer vision technology based on deep convolutional neural networks (CNN) for “cell face” recognition. This was aimed to improve cell identification efficiency and reduce the occurrence of cell-line cross contamination. METHODS Unstained optical microscopy images of cell lines were obtained for model training (about 334 thousand patch images), and testing (about 153 thousand patch images). The AI system first trained to recognize the pure cell morphology. In order to find the most appropriate CNN model,we explored the key image features in cell morphology classification tasks using the classical CNN model-Alexnet. After that, a preferred fine-grained recognition model BCNN was used for the cell type identification (seven classifications). Next, we simulated the situation of cell cross-contamination and mixed the cells in pairs at different ratios. The detection of the cross-contamination was divided into two levels, whether the cells are mixed and what the contaminating cell is. The specificity, sensitivity, and accuracy of the model were tested separately by external validation. Finally, the segmentation model DialedNet was used to present the classification results at the single cell level. RESULTS The cell texture and density were the influencing factors that can be better recognized by the bilinear convolutional neural network (BCNN) comparing to AlexNet. The BCNN achieved 99.5% accuracy in identifying seven pure cell lines and 86.3% accuracy for detecting cross-contamination (mixing two of the seven cell lines). DilatedNet was applied to the semantic segment for analyzing in single-cell level and achieved an accuracy of 98.2%. CONCLUSIONS This study successfully demonstrated that cell lines can be morphologically identified using deep learning models. Only light-microscopy images and no reagents are required, enabling most labs to routinely perform cell identification tests.


2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Noemi Andor ◽  
Billy T Lau ◽  
Claudia Catalanotti ◽  
Anuja Sathe ◽  
Matthew Kubit ◽  
...  

Abstract Cancer cell lines are not homogeneous nor are they static in their genetic state and biological properties. Genetic, transcriptional and phenotypic diversity within cell lines contributes to the lack of experimental reproducibility frequently observed in tissue-culture-based studies. While cancer cell line heterogeneity has been generally recognized, there are no studies which quantify the number of clones that coexist within cell lines and their distinguishing characteristics. We used a single-cell DNA sequencing approach to characterize the cellular diversity within nine gastric cancer cell lines and integrated this information with single-cell RNA sequencing. Overall, we sequenced the genomes of 8824 cells, identifying between 2 and 12 clones per cell line. Using the transcriptomes of more than 28 000 single cells from the same cell lines, we independently corroborated 88% of the clonal structure determined from single cell DNA analysis. For one of these cell lines, we identified cell surface markers that distinguished two subpopulations and used flow cytometry to sort these two clones. We identified substantial proportions of replicating cells in each cell line, assigned these cells to subclones detected among the G0/G1 population and used the proportion of replicating cells per subclone as a surrogate of each subclone's growth rate.


2019 ◽  
Vol 36 (5) ◽  
pp. 1607-1613 ◽  
Author(s):  
Joseph C Boyd ◽  
Alice Pinheiro ◽  
Elaine Del Nery ◽  
Fabien Reyal ◽  
Thomas Walter

Abstract Motivation High-content screening is an important tool in drug discovery and characterization. Often, high-content drug screens are performed on one single-cell line. Yet, a single-cell line cannot be thought of as a perfect disease model. Many diseases feature an important molecular heterogeneity. Consequently, a drug may be effective against one molecular subtype of a disease, but less so against another. To characterize drugs with respect to their effect not only on one cell line but on a panel of cell lines is therefore a promising strategy to streamline the drug discovery process. Results The contribution of this article is 2-fold. First, we investigate whether we can predict drug mechanism of action (MOA) at the molecular level without optimization of the MOA classes to the screen specificities. To this end, we benchmark a set of algorithms within a conventional pipeline, and evaluate their MOA prediction performance according to a statistically rigorous framework. Second, we extend this conventional pipeline to the simultaneous analysis of multiple cell lines, each manifesting potentially different morphological baselines. For this, we propose multi-task autoencoders, including a domain-adaptive model used to construct domain-invariant feature representations across cell lines. We apply these methods to a pilot screen of two triple negative breast cancer cell lines as models for two different molecular subtypes of the disease. Availability and implementation https://github.com/jcboyd/multi-cell-line or https://zenodo.org/record/2677923. Supplementary information Supplementary data are available at Bioinformatics online.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3363-3363
Author(s):  
Dominik Schnerch ◽  
Julia Felthaus ◽  
Lara Mentlein ◽  
Monika Engelhardt ◽  
Ralph M. Waesch

Abstract Abstract 3363 Proper mitotic control is a prerequisite to guarantee the equal distribution of the genetic material onto the two developing daughter cells. A mitotic key regulator is cyclin B. High levels of cyclin B facilitate entry into mitosis whereas its controlled degradation coordinates chromosome separation and cytokinesis. The latter events are coordinated by the anaphase- promoting complex / cyclosome (APC/C), a ubiquitin ligase that couples ubiquitin chains to cyclin B, mediating its proteasomal degradation. The regulation of the APC/C-activity by complex protein networks, such as the spindle assembly checkpoint, therefore presents the basis for an accurate mitosis. Mitotic errors give rise to daughter cells with an aberrant set of chromosomes and contribute to genetic instability. Genetic instability is a hallmark of cancer cells and plays an important role in the onset and progression of acute myeloid leukemia (AML). In rare cases, de novo AMLs present with multiple cytogenetic aberrations (complex karyotype). However, a larger number of patients develop karyotype deviations in the course of the disease, sometimes even under therapy, which comes along with an adverse prognosis. Understanding the biology that drives the gain and loss of genetic material therefore bears the potential of identifying new therapeutic targets. We compared a number of lymphoblastic and myeloid cell lines and found AML cell lines to be deficient in arresting at metaphase in the presence of the microtubule-disrupting agent nocodazole. Cyclin B was expressed at much lower levels in the AML cell line Kasumi-1 and did not accumulate following spindle disruption as observed in the lymphoblastic cell line DG-75. We could show that Kasumi-1 cells, when challenged with nocodazole, were not capable of properly maintaining chromatid-cohesion and underwent premature sister chromatid separation. These findings suggest that mitotic control mechanisms do not work tightly enough in AML cells to prevent chromosome separation in the presence of spindle disruption. We applied live-cell imaging to exactly characterize mitotic timing in Kasumi-1 cells at a single cell level. The expression of a GFP-tagged derivative of histone H2 served to visualize the nuclear envelope breakdown and anaphase onset. Detection of the latter events allowed the faithful measurement of mitotic timing. We could find a significant shortening of mitosis in Kasumi-1 cells as compared to the lymphoblastic cell line DG-75. In both AML cell lines and primary AML blasts we identified the spindle assembly checkpoint components BubR1 and Bub1 to be downregulated. Interestingly, re-expression of BubR1 in Kasumi-1 cells led to a significant stabilization of cyclin B on western blots. To address the question whether an increased expression of cyclin B leads to a more pronounced mitotic delay in the presence of spindle-disruption in AML cells is subject of current experiments. It was reported that different cell types can escape from a mitotic block as a consequence of cyclin B degradation. In the literature, this phenomenon was referred to as mitotic slippage and is known to drive genetic instability. To monitor cyclin B turnover and localization at a single cell level, we generated a chimeric cyclin B-molecule, SNAP-cyclin B, which can couple to a suitable fluorochrome in a self-labeling reaction after addition to the growth medium. In this system, the fluorescence intensity reflects the amount of chimeric cyclin B and allows the monitoring of APC/C-dependent proteolysis. In our current approaches we aim at studying cyclin B-turnover at a single cell level in AML cell lines as well as primary leukemia cells by using live-cell imaging before and after BubR1- and Bub1-rescue. An aberrant cell cycle control is found in most human malignancies and might be an important driving force in leukemogenesis. We hypothesize that BubR1, in concert with different other regulators, might lead to inaccuracies in mitotic control. This hypothesis is underlined by the shortened time to anaphase in Kasumi-1 cells and a decreased expression of cyclin B, both of which are characteristics of BubR1-depletion. Mitotic regulators are already targets in AML therapy and a deeper understanding of mitotic processes in AML might lead to improved approaches. Disclosures: No relevant conflicts of interest to declare.


2007 ◽  
Vol 88 (1) ◽  
pp. 40-45 ◽  
Author(s):  
Naomi S. Taus ◽  
David R. Herndon ◽  
Donald L. Traul ◽  
James P. Stewart ◽  
Mathias Ackermann ◽  
...  

The rhadinovirus Ovine herpesvirus 2 (OvHV-2) is the causative agent of sheep-associated malignant catarrhal fever. OvHV-2 primarily affects ruminants and has a worldwide distribution. In this study, a composite sequence of OvHV-2 genomic DNA isolated from nasal secretions of sheep experiencing virus-shedding episodes was determined and compared with the sequence of OvHV-2 DNA isolated from a lymphoblastoid cell line derived from a clinically affected cow. The study confirmed the OvHV-2 sequence information determined for the cell line-isolated DNA and showed no apparently significant changes in the OvHV-2 genome during passage through a clinically susceptible species with subsequent maintenance in vitro. Amino acid identity between the predicted open reading frames (ORFs) of the two genomes was 94–100 %, except for ORF73, which had an identity of 83 %. Polymorphism in ORF73 was due primarily to variability in the G/E-rich repetitive central region of the ORF.


2014 ◽  
Author(s):  
Jee-Hyub Kim

A cell line is a cell culture developed from a single cell and therefore consisting of cells with a uniform genetic make-up. A cell line has an important role as a research resource such as organisms, antibodies, constructs, knockdown reagents, etc. Unique identification of cell lines in the biomedical literature is important for the reproducibility of science. As data citation, resource citation is also important for resource re-use. In this paper, we mention the challenges of identifying cell lines and describe a system for cell line annotation with preliminary results.


Cancers ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 144
Author(s):  
Patrícia Neuperger ◽  
József Á. Balog ◽  
László Tiszlavicz ◽  
József Furák ◽  
Nikolett Gémes ◽  
...  

Intratumoral heterogeneity (ITH) is responsible for the majority of difficulties encountered in the treatment of lung-cancer patients. Therefore, the heterogeneity of NSCLC cell lines and primary lung adenocarcinoma was investigated by single-cell mass cytometry (CyTOF). First, we studied the single-cell heterogeneity of frequent NSCLC adenocarcinoma models, such as A549, H1975, and H1650. The intra- and inter-cell-line single-cell heterogeneity is represented in the expression patterns of 13 markers—namely GLUT1, MCT4, CA9, TMEM45A, CD66, CD274 (PD-L1), CD24, CD326 (EpCAM), pan-keratin, TRA-1-60, galectin-3, galectin-1, and EGFR. The qRT-PCR and CyTOF analyses revealed that a hypoxic microenvironment and altered metabolism may influence cell-line heterogeneity. Additionally, human primary lung adenocarcinoma and non-involved healthy lung tissue biopsies were homogenized to prepare a single-cell suspension for CyTOF analysis. The CyTOF showed the ITH of human primary lung adenocarcinoma for 14 markers; particularly, the higher expressions of GLUT1, MCT4, CA9, TMEM45A, and CD66 were associated with the lung-tumor tissue. Our single-cell results are the first to demonstrate TMEM45A expression in human lung adenocarcinoma, which was verified by immunohistochemistry.


2019 ◽  
Vol 2 (2) ◽  
pp. 7-11 ◽  
Author(s):  
V. Melnychuk

The article presents the results of studies on the indicators of invasiveness of domestic sheep Ovis aries (Linnaeus, 1758), the causative agent of Haemonchus contortus (Rudolphi 1803; Cobb 1898) and its characteristics depending on the season in the climatic and geographical conditions of the Zaporizhzhya region. The research was conducted during 2015–2019 on the basis of laboratories of the departments of parasitology and ichthyopathology of the Stepan Gzhytskyi National University of Veterinary Medicine and Biotechnologies Lviv and Parasitology and Veterinary-Sanitary Examination of the Poltava State Agrarian Academy. Helminths were isolated by the results of complete helminthological sections of the digestive organs of the dead or slaughtered sheep, and the indicators of the extent and intensity of the invasion were established. Specific identification of the identified nematodes was performed taking into account the morphological features of mature males and females. It is proved that H. contortus is a fairly widespread species of nematodes in the population of domestic sheep in the territory of the studied region. The magnitude of the invasion of animals reached 66.36 %, the intensity of the invasion – 25.56 ± 1.51 samples/animal (for fluctuations from 1 to 79 sp./an.). It is noted that the causative agent of Haemonchosis is registered during the year. At the same time, the degree of sheep infection depends on the season of the year and is characterized by certain patterns in the extent and intensity of H. contortus invasion of sheep. The peak of the animals with the nematodes was detected in the autumn-winter period of the year, EI ranged from 73.23 to 78.57 %. The decline in invasion magnitude was observed in spring (52.63 %) and summer (59.68 %). Seasonal fluctuations in the infestation rates had some differences and were characterized by maximum values in the summer and autumn seasons ranging from 27.49 ± 2.52 to 37.35 ± 2.36 samples/animal. During the winter, the intensity of H. contortus infestation in sheep gradually decreased (13.73 ± 2.12 sp/an) and gained minimum values in the spring of the year (10.85 ± 1.78 sp./an). The conducted researches illuminate the current epizootic condition of sheep haemorrhage in the territory of Zaporizhzhya region, expand and supplement the already existing data that will allow to increase the effectiveness of the use of therapeutic and preventive measures in this invasion.


Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1948
Author(s):  
Mariam Jaafar ◽  
Hermes Paraqindes ◽  
Mathieu Gabut ◽  
Jean-Jacques Diaz ◽  
Virginie Marcel ◽  
...  

Recent findings suggest that ribosomes, the translational machineries, can display a distinct composition depending on physio-pathological contexts. Thanks to outstanding technological breakthroughs, many studies have reported that variations of rRNA modifications, and more particularly the most abundant rRNA chemical modification, the rRNA 2′O-ribose methylation (2′Ome), intrinsically occur in many organisms. In the last 5 years, accumulating reports have illustrated that rRNA 2′Ome varies in human cell lines but also in living organisms (yeast, plant, zebrafish, mouse, human) during development and diseases. These rRNA 2′Ome variations occur either within a single cell line, organ, or patient’s sample (i.e., intra-variability) or between at least two biological conditions (i.e., inter-variability). Thus, the ribosomes can tolerate the absence of 2′Ome at some specific positions. These observations question whether variations in rRNA 2′Ome could provide ribosomes with particular translational regulatory activities and functional specializations. Here, we compile recent studies supporting the heterogeneity of ribosome composition at rRNA 2′Ome level and provide an overview of the natural diversity in rRNA 2′Ome that has been reported up to now throughout the kingdom of life. Moreover, we discuss the little evidence that suggests that variations of rRNA 2′Ome can effectively impact the ribosome activity and contribute to the etiology of some human diseases.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marina Zoppo ◽  
Nicole Okoniewski ◽  
Stanislav Pantelyushin ◽  
Johannes vom Berg ◽  
Kristin Schirmer

Abstract Background The advent of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology marked the beginning of a new era in the field of molecular biology, allowing the efficient and precise creation of targeted mutations in the genome of every living cell. Since its discovery, different gene editing approaches based on the CRISPR/Cas9 technology have been widely established in mammalian cell lines, while limited knowledge is available on genetic manipulation in fish cell lines. In this work, we developed a strategy to CRISPR/Cas9 gene edit rainbow trout (Oncorhynchus mykiss) cell lines and to generate single cell clone-derived knock-out cell lines, focusing on the phase I biotransformation enzyme encoding gene, cyp1a1, and on the intestinal cell line, RTgutGC, as example. Results Ribonucleoprotein (RNP) complexes, consisting of the Cas9 protein and a fluorescently labeled crRNA/tracrRNA duplex targeting the cyp1a1 gene, were delivered via electroporation. A T7 endonuclease I (T7EI) assay was performed on flow cytometry enriched transfected cells in order to detect CRISPR-mediated targeted mutations in the cyp1a1 locus, revealing an overall gene editing efficiency of 39%. Sanger sequencing coupled with bioinformatic analysis led to the detection of multiple insertions and deletions of variable lengths in the cyp1a1 region directed by CRISPR/Cas9 machinery. Clonal isolation based on the use of cloning cylinders was applied, allowing to overcome the genetic heterogeneity created by the CRISPR/Cas9 gene editing. Using this method, two monoclonal CRISPR edited rainbow trout cell lines were established for the first time. Sequencing analysis of the mutant clones confirmed the disruption of the cyp1a1 gene open reading frame through the insertion of 101 or 1 base pair, respectively. Conclusions The designed RNP-based CRISPR/Cas9 approach, starting from overcoming limitations of transfection to achieving a clonal cell line, sets the stage for exploiting permanent gene editing in rainbow trout, and potentially other fish cells, for unprecedented exploration of gene function.


Sign in / Sign up

Export Citation Format

Share Document