DNA topoisomerase inhibition with the HIF inhibitor acriflavine promotes transcription of lncRNAs in endothelial cells

• Published in: Molecular therapy. Nucleic acids 2022-03, Vol.27, p.1023-1035
• Main Authors: Seredinski, Sandra, Boos, Frederike, Günther, Stefan, Oo, James A., Warwick, Timothy, Izquierdo Ponce, Judit, Lillich, Felix F., Proschak, Ewgenij, Knapp, Stefan, Gilsbach, Ralf, Pflüger-Müller, Beatrice, Brandes, Ralf P., Leisegang, Matthias S.
• Format: Article
• Language: English
• Subjects: acriflavine; angiogenesis; chromatin; endothelial cells; hypoxia; long non-coding RNA; Original; topoisomerase inhibitor
• ISSN: 2162-2531; 2162-2531
• DOI: 10.1016/j.omtn.2022.01.016

The transcription factor hypoxia-inducible factor 1 (HIF1) is an important driver of cancer and is therefore an attractive drug target. Acriflavine (ACF) has been suggested to inhibit HIF1, but its mechanism of action is unknown. Here we investigated the interaction of ACF with DNA and long non-coding RNAs (lncRNAs) and its function in human endothelial cells. ACF promoted apoptosis and reduced proliferation, network formation, and angiogenic capacity. It also induced changes in gene expression, as determined by RNA sequencing (RNA-seq), which could not be attributed to specific inhibition of HIF1. A similar response was observed in murine lung endothelial cells. Although ACF increased and decreased a similar number of protein-coding genes, lncRNAs were preferentially upregulated under normoxic and hypoxic conditions. An assay for transposase accessibility with subsequent DNA sequencing (ATAC-seq) demonstrated that ACF induced strong changes in chromatin accessibility at lncRNA promoters. Immunofluorescence showed displacement of DNA:RNA hybrids. Such effects might be due to ACF-mediated topoisomerase inhibition, which was indeed the case, as reflected by DNA unwinding assays. Comparison with other acridine derivatives and topoisomerase inhibitors suggested that the specific function of ACF is an effect of acridinium-class compounds. This study demonstrates that ACF inhibits topoisomerases rather than HIF specifically and that it elicits a unique expression response of lncRNAs. [Display omitted] Seredinski et al. demonstrate that acriflavine inhibits topoisomerases rather than blocking hypoxia signaling by specifically inhibiting hypoxia-inducible factor. Acriflavine-induced changes in chromatin accessibility induced pronounced upregulation of long non-coding RNAs. Functionally, this resulted in inhibition of proliferation, migration, spheroid outgrowth, and network formation of human endothelial cells.