Abstract 3755: Genome-wide transcriptome analysis reveals the distinct gene expression profiles and specific biological effects of fluorescent polyamides, HxIP and azaHxPI

• Published in: Cancer research (Chicago, Ill.) Ill.), 2016-07, Vol.76 (14_Supplement), p.3755-3755
• Main Authors: Pett, Luke, Satam, Vijay, Patil, Pravin, Lee, Moses, Hartley, John A., Kiakos, Konstantinos
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2016-3755

DNA-binding polyamides target predetermined sequences to inhibit specific transcription factor-DNA interactions and modulate gene expression. Inherently non-genotoxic, these non-covalent binding small molecules exert their biological activity without inflicting DNA damage and provide the basis for potentially less toxic DNA-targeting anticancer therapeutics. However, the genome-wide specificity of polyamide binding remains an outstanding issue in delivering the desired biological response without inducing widespread off-target effects. In this study, we used RNA-seq transcriptome analysis to assess the global effects of fluorescent polyamides HxIP and azaHxPI, having previously shown that they bind with high affinity and selectivity to their respective target DNA sequences 5’-WWCGWW-3’ and 5’-WCGCGW-3’ (W = A/T)1,2. Changes to the MDA-MB-231 breast adenocarcinoma transcriptome were measured following 24 h treatment with 2 and 5 μM HxIP or azaHxPI. At 5 μM, HxIP affected 349 genes by two-fold (p 100 μM), whereas azaHxPI causes growth inhibition (GI50 = 20.3 μM) and induces apoptosis. Immunoblotting analysis of γ;H2AX showed no evidence of DNA damage, further corroborated by the absence of chk2 phosphorylation. In addition, no ATR-chk1 activation was detected suggesting that azaHxPI does not induce replication stress, despite inhibiting DNA synthesis as shown using the BrdU incorporation assay. Levels of phospho-AKT (Ser472) decreased in response to polyamide treatment, whilst p21 is significantly upregulated and both may be implicated in the mechanism of azaHxPI induced-apoptosis. Taken together these results emphasise the potential application of polyamides as apoptosis-inducing DNA-targeting agents benefiting from enhanced sequence selectivi