Epigenetic regulation of cancer metabolism

The revolution of epigenetics has revitalized cancer research, shifting focus away from somatic mutation toward a novel perspective involving the dynamic states of chromatin. Regardless of aetiology, the progression of hepatocellular carcinoma (HCC) is highly variable and is influenced by numerous non-genetic factors such as age, diet, and inflammation. This phenotype points to the epigenetic nature of HCC and highlights the need to further our insight into how epigenetic mechanisms may influence HCC development. The overall goal of this project is to identify epi-modulator compounds with a therapeutic potential, either as a stand-alone regimen or in combination with conventional chemotherapy.

We have established liver cancer cell lines resistant to common chemotherapeutic drugs. Transcriptomic profiling revealed the deregulation of histone-modifying enzymes in chemoresistant cells. We have screened 182 small molecule epigenetic modulators on liver cancer cells and found that inhibitors of a specific histone demethylase (KDM) induce cell death. microRNA profiling revealed potential regulators of the KDM, and preliminary in vitro functional studies propose an oncogenic role of KDM in liver cancer. Furthermore, RNA-Sequencing and bioinformatic analysis revealed that metabolic pathways are regulated by the KDM.

Aim 1: To investigate KDM regulation at the transcriptional and post-transcriptional level. Computational analysis, deletion promoter luciferase-based assays and Chromatin Immunoprecipitation (ChIP) will be employed to identify functional elements responsible for the regulation of KDM transcription. Additionally, we will explore the post-transcriptional regulation of KDM based on our microRNA preliminary data using western blot, RT-qPCR and 3’UTR reporter assays.

Aim 2: To characterize the molecular mechanisms regulated by KDM. We will perform ChIP-Sequencing analyses to assess the genome-wide distribution of histone modifications catalysed by the KDM. To validate our RNA-Sequencing data, we will perform metabolic profiling upon KDM depletion. Integration of ChIP-Sequencing with the RNA-Sequencing and metabolic profiling data will reveal the molecular pathways regulated by KDM.

Aim 3: To explore the therapeutic potential of KDM inhibition in liver cancer. To this end, we will perform a screen of combinatorial treatments, KDM inhibitors with conventional chemotherapeutic compounds, and assess their effects on chemoresistant cell growth. Importantly, to provide insight into human disease we will investigate the therapeutic potential of targeting KDM by employing a novel organ-on-a-chip technology. We will develop nanoparticles to improve efficacy and target specificity of the therapeutic combinations. Nanoparticles will be used to deliver KDM inhibitors, microRNA mimics or their combination on a liver cancer-on-a-chip.