# Transcriptomic Analysis of TDP1-Knockout HEK293A Cells Treated with the TDP1 Inhibitor (Usnic Acid Derivative)

## TL;DR

This study examines how knocking out the TDP1 gene and using a TDP1 inhibitor affect gene expression in HEK293A cells, revealing potential mechanisms for anticancer effects.

## Contribution

The study introduces a novel TDP1 inhibitor and explores its impact on transcriptome changes in TDP1-knockout and wild-type HEK293A cells.

## Key findings

- OL9-119 reduces cell motility by downregulating specific genes, suggesting an antimetastatic effect.
- DEGs related to electron transport, mitochondrial function, and protein folding were identified under TDP1 inhibitor treatment.
- Transcriptome analysis revealed gene expression changes in TDP1 knockout cells treated with OL9-119.

## Abstract

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a key enzyme for the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, we obtained HEK293A cells with homozygous knockout of the TDP1 gene by the CRISPR/Cas9 method and used them as a cell model to study the mechanisms of anticancer therapy and to investigate the effect of TDP1 gene knockout on gene expression changes in the human HEK293A cell line by transcriptome analysis. In this study, we investigated the effect of a TDP1 inhibitor ((R,E)-2-acetyl-6-(2-(2-(4-bromobenzyliden) hydrazinyl) thiazol-4-yl)-3,7,9-trihydroxy-8,9b-dimethyldibenzo[b,d] furan-1(9bH)-one, OL9-119, an usnic acid derivative), capable of potentiating the antitumor effect of topotecan, as well as its combination with topotecan, on the transcriptome of wild-type and TDP1 knockout HEK293A cells. OL9-119 was found to be able to reduce cell motility by decreasing the expression of a number of genes, which may explain the antimetastatic effect of this compound. Differentially expressed genes (DEGs) related to electron transport, mitochondrial function, and protein folding were also identified under TDP1 inhibitor treatment.