Transcriptomic Analysis of CRISPR/Cas9-Mediated TDP1-Knockout HEK293A Cells

Nadezhda S. Dyrkheeva; Alexandra L. Zakharenko; Anastasia A. Malakhova; Larisa S. Okorokova; Dmitry N. Shtokalo; Sergey P. Medvedev; Alexey A. Tupikin; Marsel R. Kabilov; Olga I. Lavrik

doi:10.20944/preprints202312.0002.v1

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preprints.org > biology and life sciences > biochemistry and molecular biology > doi: 10.20944/preprints202312.0002.v1

Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Transcriptomic Analysis of CRISPR/Cas9-Mediated TDP1-Knockout HEK293A Cells

Nadezhda S. Dyrkheeva

Alexandra L. Zakharenko

Anastasia A. Malakhova

Version 1 : Received: 28 November 2023 / Approved: 1 December 2023 / Online: 1 December 2023 (04:53:45 CET)

How to cite: Dyrkheeva, N. S.; Zakharenko, A. L.; Malakhova, A. A.; Okorokova, L. S.; Shtokalo, D. N.; Medvedev, S. P.; Tupikin, A. A.; Kabilov, M. R.; Lavrik, O. I. Transcriptomic Analysis of CRISPR/Cas9-Mediated TDP1-Knockout HEK293A Cells. Preprints 2023, 2023120002. https://doi.org/10.20944/preprints202312.0002.v1 Dyrkheeva, N. S.; Zakharenko, A. L.; Malakhova, A. A.; Okorokova, L. S.; Shtokalo, D. N.; Medvedev, S. P.; Tupikin, A. A.; Kabilov, M. R.; Lavrik, O. I. Transcriptomic Analysis of CRISPR/Cas9-Mediated TDP1-Knockout HEK293A Cells. Preprints 2023, 2023120002. https://doi.org/10.20944/preprints202312.0002.v1

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MDPI and ACS Style

Dyrkheeva, N. S.; Zakharenko, A. L.; Malakhova, A. A.; Okorokova, L. S.; Shtokalo, D. N.; Medvedev, S. P.; Tupikin, A. A.; Kabilov, M. R.; Lavrik, O. I. Transcriptomic Analysis of CRISPR/Cas9-Mediated TDP1-Knockout HEK293A Cells. Preprints 2023, 2023120002. https://doi.org/10.20944/preprints202312.0002.v1

APA Style

Dyrkheeva, N. S., Zakharenko, A. L., Malakhova, A. A., Okorokova, L. S., Shtokalo, D. N., Medvedev, S. P., Tupikin, A. A., Kabilov, M. R., & Lavrik, O. I. (2023). Transcriptomic Analysis of CRISPR/Cas9-Mediated TDP1-Knockout HEK293A Cells. Preprints. https://doi.org/10.20944/preprints202312.0002.v1

Chicago/Turabian Style

Dyrkheeva, N. S., Marsel R. Kabilov and Olga I. Lavrik. 2023 "Transcriptomic Analysis of CRISPR/Cas9-Mediated TDP1-Knockout HEK293A Cells" Preprints. https://doi.org/10.20944/preprints202312.0002.v1

Abstract

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a human DNA repair protein. It is a member of the phospholipase D family based on the structure similarity. TDP1 is a key enzyme involved in repairing stalled topoisomerase 1 (TOP1)-DNA complexes. Previously we obtained with the CRISPR/Cas9 method HEK293A cells with the homozygous knockout of the Tdp1 gene and used knockout cells as a cellular model for studying the mechanisms of anticancer therapy. In this work we studied for the first time by transcriptomic analysis the effect of Tdp1 gene knockout on genes expression changes in human HEK293A cell line. We received original data that may indicate a role of TDP1 in other process besides repair of DNA-TOP1 complex. The differentially expressed genes (DEGs) analysis revealed that TDP1 could be involved in different processes such as cell adhesion and communication, spermatogenesis, mitochondrial function, neurodegeneration, cytokine response, and MAPK pathway signaling.

Keywords

tyrosyl-DNA phosphodiesterase 1; topoisomerase 1; HEK293A; transcriptome; TDP1 knockout

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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