Transcriptomic Signature and PROTAC Strategy Revealed Histone Lysine Demethylase as a Target of Anticancer Activity of Deferiprone

Deferiprone (DFP) is an iron chelator approved for treating iron overload in thalassemia patients. Recent observations have suggested that DFP has promising anticancer activities ascribed to several mechanisms including reduction of the intracellular free labile iron and zinc ion pools and inhibition of the activities of other intracellular targets, including ribonucleotide reductase (RNR). We previously reported that DFP inhibits the demethylase activities of several Fe(II)/α- ketoglutarate dependent histone lysine demethylases (KDMs) at much lower concentrations at which it inhibits RNR activities and/or reduces the labile intracellular iron and zinc ion pools. In this study, we used RNA sequencing (RNA seq) and PROTACs strategies to validate and quantify the contribution of intracellular KDM inhibition to the antiproliferative activities of DFP. We report herein that DFP elicited gene expression signature that is largely similar to that of JIB-04, an established KDM inhibitor (KDMi), in two breast cancer (BCa) cells (MCF-7 and MDA-MD-231). Importantly, RNA seq revealed that DFP and JIB-04 downregulated the expression of hypoxia-inducible factor 1α (HIF-1α), an oncogene whose expression is commonly modulated through histone demethylation mediated by KDMs and degraded by several KDMi.

Moreover, DFP-derived PROTACs elicited enhanced cancer cell selective antiproliferative activities and intracellular on-target effects, downregulating several KDMs implicated in the etiology of BCa cells, including a strong degradation of KDMs 2A, 3A and 5B, and a moderate degradation of KDMs 4A-C, 5C, 6B. Collectively, our data supports KDM inhibition as a key mechanism of anticancer activity of DFP and identifies PROTAC is a viable strategy to obtain novel DFP analogs with improved potency and therapeutic index.