Transcriptional inhibition of progressive renal disease by gene silencing pyrrole–imidazole polyamide targeting of the transforming growth factor-β1 promoter

Abstract

Pyrrole-imidazole (PI) polyamides are small synthetic molecules that recognize and attach to the minor groove of DNA, thereby inhibiting gene transcription by blocking transcription factor binding. These derivatives can act as gene silencers inhibiting target gene expression under stimulatory conditions such as disease. To evaluate PI polyamides as treatments for the progression of renal diseases, we examined morphological effects, pharmacological properties, and the specificity of PI polyamides targeted to the transforming growth factor (TGF)-β1 promoter during salt-induced hypertensive nephrosclerosis in Dahl salt-sensitive rats. The targeted PI polyamide markedly reduced glomerulosclerosis and interstitial fibrosis without side effects. PI polyamide significantly decreased expression of TGF-β1 and extracellular matrix in the renal cortex. Microarray analysis found that only 3% of the transcripts were affected by PI polyamide, but this included decreased expression of extracellular matrix, TGF-β1-related cytokines, angiogenic, and cell stabilizing factors, proteinases, and renal injury-related factors. Thus, targeted PI polyamides are potential gene silencers for diseases not treatable by current remedies.

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

“…Genome-wide analysis showed a total of 168 genes to be affected by the Py-Im polyamide 1 in xenografts, which corresponds to 0.76% of the NCBI reference sequence (refSeq) annotation (p < 0.05, at least twofold change). For comparison, Matsuda et al reported gene expression changes in rat kidney cortex for 3% of genes interrogated by microarray (14).…”

“…administration (12). Matsuda et al further showed that a Py-Im polyamide targeted to the TGF-β1 promoter affected target gene expression in vivo (rat renal cortex) without evidence of systemic toxicity (13,14). The present study focuses on the question of whether Py-Im polyamides affect gene expression in vivo, specifically in a xenograft model environment, employing a luciferaseexpressing derivative of the commonly used lung nonsmall cell carcinoma line A549.…”

Targeting TGF-β Signaling for Therapeutic Gain

“…2; Table 1), including a pyrrole-imidazole polyamide drug that blocks transcription of the TGFB1 target gene (Yao et al 2009;Chen et al 2010;Matsuda et al 2011;Washio et al 2011;Igarashi et al 2015), antisense RNAs that target TGFB1 or TGFB2 mRNAs for degradation (Hau et al 2009;Vallieres 2009;Schlingensiepen et al 2011), antibodies against TGF-b ligands or receptors that block ligand -receptor engagement, and many small molecule ATP-mimetic TbRI kinase inhibitors (Fig. 2).…”

Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders

“…Displacement of NF-kB by polyamides was also shown by electrophoretic mobility shift assays (16,17). Matsuda and co-workers independently demonstrated that a Py-Im polyamide could be used to target the TGF-β promoter (18). Small molecule inhibitors mostly act upstream of the NF-κB DNA-binding event.…”