Harnessing iron/2-oxoglutarate dependent demethylases to overcome cancer therapy resistance

The development of resistance has been and unfortunately still is a major drawback in standard-of-care cancer therapy. In the era of precision medicine, targeted therapy is becoming a front-line approach for treating different types of cancer. Despite high initial efficacy, intrinsic or acquired resistance eventually limits the success of targeted therapy, analogously to broad-spectrum chemotherapy. Examples of tumour types that become refractory to targeted therapies or conventional platinum-based chemotherapy are melanoma bearing BRAF mutations and malignant pleural mesothelioma (MPM), respectively. It is imperative to elucidate the mechanisms of anti-tumour drug resistance to develop therapeutic approaches that overcome or prevent treatment failure. New roadmaps to combat drug resistance in cancer can be drawn by outlining the consequences of therapy-imposed selective pressures on DNA and histone epigenetic patterns. Epigenetic modifications are responsible for establishing specific transcriptional programs in response to environmental cues, including chemotherapeutic agents. Epigenetic enzymes are sensors of metabolic perturbations as their catalytic mechanism are critically dependent on the use of metabolites as cofactor/cosubstrates. In this way, the availability of metabolites connects metabolism to chromatin structure and gene expression via epigenetics. Our interest is for DNA hydroxylases and histone lysine demethylases (KDMs) involved in the removal of repressive epigenetic marks and belonging to the superfamily of Fe(II)/2-oxoglutarate (2OG)- dependent dioxygenases. Specifically, TET1,2,3 erase DNA methylation patterns by producing 5-hydroxymethylcytosine (5hmC) whereas KDM4D and 6B demethylate trimethylated histone H3 in lysine 9 and 27 (H3K9/27me3), respectively. To date, these enzymes have often been considered independent of each other, but we hypothesise that metabolic changes occurring during the acquirement of drug resistance may promote an intricate epigenetic remodelling through 2OG signalling. We, therefore, aim to unveil the role of TETs and KDM4D/6B in drug resistance, shedding light on the integrated cross-talk between epigenetic modifiers that remove repressive chromatin marks sharing Fe(II)/2OG-dependent catalytic mechanism. The proponent researchers of this project will work in synergy to delineate a comprehensive epigenetic scenario in acquired drug resistance of melanoma and MPM. We will use these cellular models because they represent two different tumours currently treated by a targeted vs broad-spectrum therapeutic approach. Using three-dimensional multicellular spheroid cultures, transcriptomic/epigenomic analyses and treatments with compounds that can simultaneously affect TETs/KDMs enzymatic activity, we aim to highlight new intervention targets to overcome therapy resistance by harnessing DNA/histone demethylation pathways.