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Efficient Development of Platform Cell Lines Using CRISPR-Cas9 and Transcriptomics Analysis

Andrew Tae-Jun Kwon, Kohta Mohri, Satoshi Takizawa, Takahiro Arakawa, Maiko Takahashi, Bogumil Kaczkowski, Masaaki Furuno, Harukazu Suzuki, Shunsuke Tagami, Hidefumi Mukai, Erik Arner
doi: https://doi.org/10.1101/2020.09.16.299248
Andrew Tae-Jun Kwon
1RIKEN Center for Integrative Medical Sciences, Japan
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Kohta Mohri
2RIKEN Center for Biosystems Dynamic Research, Japan
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Satoshi Takizawa
1RIKEN Center for Integrative Medical Sciences, Japan
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Takahiro Arakawa
1RIKEN Center for Integrative Medical Sciences, Japan
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Maiko Takahashi
2RIKEN Center for Biosystems Dynamic Research, Japan
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Bogumil Kaczkowski
1RIKEN Center for Integrative Medical Sciences, Japan
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Masaaki Furuno
1RIKEN Center for Integrative Medical Sciences, Japan
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Harukazu Suzuki
1RIKEN Center for Integrative Medical Sciences, Japan
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Shunsuke Tagami
2RIKEN Center for Biosystems Dynamic Research, Japan
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Hidefumi Mukai
2RIKEN Center for Biosystems Dynamic Research, Japan
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  • For correspondence: erik.arner@riken.jp hmukai@riken.jp
Erik Arner
1RIKEN Center for Integrative Medical Sciences, Japan
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  • For correspondence: erik.arner@riken.jp hmukai@riken.jp
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Abstract

Antibody-drug conjugates offers many advantages as a drug delivery platform that allows for highly specific targeting of cell types and genes. Ideally, testing the efficacy of these systems requires two cell types to be different only in the gene targeted by the drug, with the rest of the cellular machinery unchanged, in order to minimize other potential differences from obscuring the effects of the drug. In this study, we created multiple variants of U87MG cells with targeted mutation in the TP53 gene using the CRISPR-Cas9 system, and determined that their major transcriptional differences stem from the loss of p53 function. Using the transcriptome data, we predicted which mutant clones would have less divergent phenotypes from the wild type and thereby serve as the best candidates to be used as drug delivery testing platforms. Further in vitro and in vivo assays of cell morphology, proliferation rate and target antigen-mediated uptake supported our predictions. Based on the combined analysis results, we successfully selected the best qualifying mutant clone. This study serves as proof-of-principle of the approach and paves the way for extending to additional cell types and target genes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Corrected spelling error in the title

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 16, 2020.
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Efficient Development of Platform Cell Lines Using CRISPR-Cas9 and Transcriptomics Analysis
Andrew Tae-Jun Kwon, Kohta Mohri, Satoshi Takizawa, Takahiro Arakawa, Maiko Takahashi, Bogumil Kaczkowski, Masaaki Furuno, Harukazu Suzuki, Shunsuke Tagami, Hidefumi Mukai, Erik Arner
bioRxiv 2020.09.16.299248; doi: https://doi.org/10.1101/2020.09.16.299248
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Efficient Development of Platform Cell Lines Using CRISPR-Cas9 and Transcriptomics Analysis
Andrew Tae-Jun Kwon, Kohta Mohri, Satoshi Takizawa, Takahiro Arakawa, Maiko Takahashi, Bogumil Kaczkowski, Masaaki Furuno, Harukazu Suzuki, Shunsuke Tagami, Hidefumi Mukai, Erik Arner
bioRxiv 2020.09.16.299248; doi: https://doi.org/10.1101/2020.09.16.299248

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