An Unbiased Method for Detection of Genome-Wide Off-Target Effects in Cell Lines Treated with Zinc Finger Nucleases

2014 ◽  
pp. 353-369 ◽  
Author(s):  
Cory R. Lindsay ◽  
David B. Roth
Keyword(s):  
Cell Lines ◽  
Zinc Finger ◽  
Zinc Finger Nucleases ◽  
Genome Wide ◽  
Target Effects

scholarly journals Genetic Dependency of Alzheimer’s Disease-associated Genes Across Cells and Tissue Types

2021 ◽  
Author(s):  
Suraj K Jaladanki ◽  
Abdulkadir Elmas ◽  
Gabriel Santos Malave ◽  
Kuan-lin Huang
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Cell Lines ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Activity Levels ◽  
Genome Wide ◽  
Disease Associated Genes ◽  
Network Studies ◽  
Target Effects

Abstract Background Multiple genes with genetic variants or expression changes associated with Alzheimer’s disease (AD) have been identified. Altering their expression and activity levels serve as potential therapeutic strategies, yet the cellular implications of such alterations remain largely unknown. Methods Cellular dependencies of 105 AD-associated genes, previously identified by genome-wide association studies (GWAS) and gene expression network studies, were evaluated in over 700 cell lines with CRISPR knockout/RNAi knockdown screen data. Expression-driven dependencies were examined within multiple tissue lineages. ResultsMultiple genes showed widespread cell dependencies across tissue lineages, suggesting their inhibition may yield off-target effects. SPI1, MEF2C, GAB2, and ABCC11 were identified as genes of interest since their genetic knockouts specifically affected high-expressing cells of the hematopoietic and lymphoid lineage related to microglia. Other genes exhibiting expression-driven dependencies include ACTG1 in autonomic ganglia and GLS in central nervous system lineages. Conclusions Analyses of genetic screen data identified AD-associated genes whose knockout or knockdown selectively affected cell lines of relevant tissue lineages, prioritizing targets for potential AD treatments.

Highly efficient deletion of FUT8 in CHO cell lines using zinc-finger nucleases yields cells that produce completely nonfucosylated antibodies

2010 ◽  
Vol 106 (5) ◽  
pp. 774-783 ◽  
Author(s):  
Laetitia Malphettes ◽  
Yevgeniy Freyvert ◽  
Jennifer Chang ◽  
Pei-Qi Liu ◽  
Edmond Chan ◽  
...  
Keyword(s):  
Cell Lines ◽  
Zinc Finger ◽  
Zinc Finger Nucleases ◽  
Cho Cell ◽  
Highly Efficient

Genomic Knockout of Endogenous Canine P-Glycoprotein in Wild-Type, Human P-Glycoprotein and Human BCRP Transfected MDCKII Cell Lines by Zinc Finger Nucleases

2014 ◽  
Vol 32 (6) ◽  
pp. 2060-2071 ◽  
Author(s):  
Dominik Gartzke ◽  
Jürgen Delzer ◽  
Loic Laplanche ◽  
Yasuo Uchida ◽  
Yutaro Hoshi ◽  
...  
Keyword(s):  
Cell Lines ◽  
Zinc Finger ◽  
Zinc Finger Nucleases ◽  
Wild Type ◽  
P Glycoprotein

scholarly journals Zinc-finger nucleases: new strategies to target the rat genome

2010 ◽  
Vol 119 (8) ◽  
pp. 303-311 ◽  
Author(s):  
Aron M. Geurts ◽  
Carol Moreno
Keyword(s):  
Zinc Finger ◽  
Human Disease ◽  
Association Studies ◽  
Genetic Research ◽  
Zinc Finger Nucleases ◽  
Genome Wide Association Studies ◽  
Genetic Determinants ◽  
Rat Models ◽  
Genome Wide ◽  
Rat Genome

The importance of genetic laboratory models, such as mice and rats, becomes evident when there is a poor understanding of the nature of human disease. Many rat models for human disease, created over the years by phenotype-driven strategies, now provide a foundation for the identification of their genetic determinants. These models are especially valuable with the emerging need for validation of genes found in genome-wide association studies for complex diseases. The manipulation of the rat genome using engineered zinc-finger nucleases now introduces a key technology for manipulating the rat genome, which is broadly applicable. The ability to generate knockout rat models using zinc-finger nuclease technology will now enable its full emergence as an exceptional physiological and genetic research model.

scholarly journals P11.26 Genome-wide shRNA screen identifies candidate genes driving glioblastoma invasion

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii48-iii48
Author(s):  
A Schuster ◽  
V Neirinckx ◽  
E Klein ◽  
P V Nazarov ◽  
A Oudin ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Cell Lines ◽  
Zinc Finger ◽  
Gene Knockdown ◽  
Non Invasive ◽  
Genome Wide ◽  
Zinc Finger Motifs ◽  
A Genome ◽  
Shrna Screen

Abstract BACKGROUND A major hallmark of glioblastoma (GBM) is its highly invasive capacity, contributing to its aggressive behaviour. Since invasive cells cannot be easily removed by surgery or irradiation, they are left behind and eventually result in lethal recurrence. Therefore, a better understanding of the invasion process and of the key molecular players underlying the invasive capacities of GBM may lead to the identification of new therapeutic targets for GBM patients. MATERIAL AND METHODS To identify candidate genes responsible for invasion, a genome-wide shRNA screen was performed in patient-derived GBM sphere cultures. The phenotype of the most promising candidate was validated in in vitro invasion assays, ex vivo brain slice cultures and in vivo orthotopic xenografts in mice. Gene knockdown in invasive GBM cell lines was compared with overexpression in non-invasive cells. RNA sequencing of knockdown cells, along with the generation of deletion constructs were applied to uncover the mechanisms regulating invasion. RESULTS Through a whole genome shRNA screen, a zinc-finger containing protein was identified as an invasion essential candidate gene. Knockdown of this gene confirmed a strong decrease in invasion capacity in two highly invasive GBM cell lines. In contrast, gene overexpression switched non-invasive GBM cells to an invasive phenotype. Deletion of either one or both zinc-finger motifs led to decreased invasion indicating that the two zinc-finger motifs are essential for regulating invasion. Mutation of the nuclear localisation signal resulted in retention of the protein in the cytoplasm and loss of the invasion phenotype demonstrating that the protein activity is required in the nucleus. Gene expression analyses revealed that invasion-related genes are significantly regulated by the candidate gene once it is localized in the nucleus. CONCLUSION We identified a zinc-finger containing protein as a novel driver of GBM invasion, presumably through a transcription factor activity resulting in the induction of an invasive transcriptional program. This protein and its downstream pathway may represent a novel promising target to overcome invasive capacities in GBM.

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