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Transcriptomic analysis of HEK293A cells with a CRISPR/Cas9-mediated TDP1 knockout
Nadezhda S Dyrkheeva1, Alexandra L Zakharenko1, Anastasia A Malakhova2
1Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
Biochimica Et Biophysica Acta. General Subjects
|April 15, 2024
Summary
Tyrosyl-DNA phosphodiesterase 1 (TDP1) gene knockout alters DNA repair gene expression. TDP1 impacts cell adhesion, mitochondrial function, and the MAPK pathway, suggesting broader roles beyond DNA repair.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a human DNA repair enzyme.
- TDP1 is crucial for repairing stalled topoisomerase 1 (TOP1)-DNA complexes.
- Previous studies utilized TDP1 knockout HEK293A cells for anticancer therapy research.
Purpose of the Study:
- To investigate the impact of TDP1 gene knockout on the expression of DNA repair-related genes.
- To explore potential novel functions of TDP1 beyond its established role in DNA repair.
Main Methods:
- CRISPR/Cas9 gene editing to create TDP1 knockout HEK293A cells.
- Transcriptomic analysis (RNA sequencing) to assess global gene expression changes.
- Differential gene expression analysis to identify affected pathways.
Main Results:
- TDP1 knockout significantly altered the expression of numerous genes.
- Evidence suggests TDP1 involvement in cell adhesion and communication.
- TDP1 knockout impacts pathways including spermatogenesis, mitochondrial function, neurodegeneration, cytokine response, and MAPK signaling.
Conclusions:
- The TDP1 gene knockout has a profound effect on the transcriptome of HEK293A cells.
- TDP1 plays a role in cellular processes beyond the repair of TOP1-DNA complexes.
- These findings open new avenues for understanding TDP1's multifaceted biological functions.
