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The three-dimensional organization of the genome contributes to its maintenance and regulation. While chromosomal regions associate with nucleolar ribosomal RNA genes (rDNA), the biological significance of rDNA-genome interactions and whether they are dynamically regulated during disease remain unclear. rDNA chromatin exists in multiple inactive and active states and their transition is regulated by the RNA polymerase I transcription factor UBTF. Here, using a MYC-driven lymphoma model, we demonstrate that during malignant progression the rDNA chromatin converts to the open state, which is required for tumor cell survival. Moreover, this rDNA transition co-occurs with a reorganization of rDNA-genome contacts which correlate with gene expression changes at associated loci, impacting gene ontologies including B-cell differentiation, cell growth and metabolism. We propose that UBTF-mediated conversion to open rDNA chromatin during malignant transformation contributes to the regulation of specific gene pathways that regulate growth and differentiation through reformed long-range physical interactions with the rDNA

Our laboratory has demonstrated that a small molecule (CX-5461, Senhwa Biosciences; currently in phase I clinical trial for haematological malignancies) that inhibits ribosomal RNA gene (rDNA) transcription by RNA Polymerase I (Pol I), is highly efficacious in various cancer types in preclinical studies. Although CX-5461 has entered the clinic and its therapeutic effects in preclinical study are promising, it is still unclear: 1) what mechanisms confer sensitivity or resistance to Pol I therapy, 2) which patients will benefit the most from CX-5461 and 3) what combination therapies will improve the response rates and survival. The goal of my thesis is to begin to address these questions, by focusing on an aggressive acute myeloid leukaemia (AML), a refractory disease associated with low survival rates and high risk of relapse. We have demonstrated that in AML, CX-5461 acts in part to elicit a nucleolar specific DNA damage response (DDR) via ATM and ATR signaling, resulting in the arrest of leukemia cells in S and G2/M phases (Hein et al, 2017). Importantly, pharmacologic inhibitors targeting DDR were shown to sensitise cancer cells to CX-5461 treatment (Quin et al, 2017). It has been demonstrated that mechanistic interactions underlying the DDR rely on context-specific chromatin structure, including chromatin’s structural rearrangement by histone chaperones and the bromodomain and extra-terminal (BET) proteins. Due to the specialised transcriptional context of rDNA, we hypothesise that targeting epigenetic and transcriptional regulators (eg., bromodomain inhibitors) in combination with CX-5461 may render cancer cells highly sensitive to ATM/ATR activation and result in enhanced anti-tumour activity. Here we used IBET-151 (GSK) to block BET protein binding to acetylated chromatin marks in combination with CX-5461 in a disease model of AML. We observed strong synergy between CX-5461 and IBET-151 across a human AML cell line panel. Importantly, co-treatment with CX-5461