Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide

Abstract

Gene regulation by DNA binding small molecules could have important therapeutic applications. This study reports the investigation of a DNA-binding pyrrole-imidazole polyamide targeted to bind the DNA sequence 5′-WGGWWW-3′ with reference to its potency in a subcutaneous xenograft tumor model. The molecule is capable of trafficking to the tumor site following subcutaneous injection and modulates transcription of select genes in vivo. An FITC-labeled analogue of this polyamide can be detected in tumor-derived cells by confocal microscopy. RNA deep sequencing (RNA-seq) of tumor tissue allowed the identification of further affected genes, a representative panel of which was interrogated by quantitative reverse transcription-PCR and correlated with cell culture expression levels.tumor RNA-sequencing | eXpress | in vivo circulation | efficacy

Nuclear Localization and Gene Expression Modulation by a Fluorescent Sequence-Selective p-Anisyl-benzimidazolecarboxamido Imidazole-Pyrrole Polyamide

“…HxIP rapidly localizes in the nucleus of different cell types in a dose-and time-dependent manner. Fast uptake (15 min) of a fluorescent polyamide by cells in culture has also been reported elsewhere (Matsuda et al, 2011), while another fluorescent hairpin polyamide was retained and detected in xenograft tumor-derived cells days after injection in mice (Raskatov et al, 2012a(Raskatov et al, , 2012b. HxIP was able to upregulate topo IIa gene expression in both NIH3T3 and A549 cells and appears to do so by selectively targeting the confluence-specific resistant phenotype, as it is only effective in the context of cellular confluency while having no effect on exponentially growing cells (Figures 6 and S4).…”

“…These agents can act as synthetic gene expression regulators by interfering with the binding of a number of endogenous transcription factors to their target DNA elements in designated promoters. Polyamides can display affinities and DNA sequence specificities rivaling those of native proteins (Trauger et al, 1996;Dervan and Bü rli, 1999;Dervan and Edelson, 2003), and have been successfully used for the modulation of gene expression in both cell culture Raskatov et al, 2012aRaskatov et al, , 2012b and tumor xenografts (Raskatov et al, 2012a(Raskatov et al, , 2012b.…”

The progress of angiogenic factors in the development of leukemias

“…It is an interesting target for novel drug therapies because of its oncogenic activities and overexpression in a majority of human cancers (47). Binding inhibition of c-myc on gene promoters by some small molecule inhibitors has been tried (48,49), and found that some of them were effective in disrupting essential protein-DNA interactions, for example, Pyrroleimidazole (PI) polyamides, specific sequence DNAbinding small molecules (50)(51)(52), and can inhibit a part of E-box-mediated c-myc downstream gene expression (47). EGFR variant III (EGFRvIII), which strongly induces neovascularization in tumors, could induce Angptl4 expression through the ERK/c-myc pathway.…”

Antitumor activity of a pyrrole-imidazole polyamide

“…Py-Im polyamides have been used as molecular probes in cell culture to modulate inducible gene-expression pathways (12)(13)(14)(15). In rodents, eight-ring hairpin Py-Im polyamides circulate in blood for several hours after administration and affect changes in gene expression in tissues (16)(17)(18).…”