Abstract A31: Elucidating mechanisms that cooperate with the therapeutic inhibition of RNA polymerase I to treat MYC-driven hematological malignancies
Authors: Poortinga Gretchen , Diesch Jeannine , Sanij Elaine , Hein Nadine , Sornkum Jirawas , Cameron Donald , Bywater Megan J. , Johnstone Ricky , Drygin Denis , O'Brien Sean , Pearson Richard B. , McArthur Grant A. , Hannan Ross D. 
Published: October 2015

Abstract
The MYC oncoprotein and transcription factor has a well-described role in harnessing and driving ribosome biogenesis (RiBi) via its regulation of all three RNA polymerases, and it is proposed that this is a crucial output of MYC's malignant function. Thus, the potential for therapeutic intervention in a broad range of MYC-driven cancers may converge on targeting the RiBi program, potentially as monotherapy or, more likely, as a basis for rational combination therapies. Indeed, small molecule (CX-5461) inhibition of RNA Polymerase I (Pol I), a major MYC target, selectively kills MYC-driven lymphoma in vivo via activation of a p53-dependent nucleolar stress response.
While CX-5461 potently inhibits ribosome biogenesis in a MYC-driven B-cell lymphoma via p53-dependent apoptosis, it is unclear whether all malignancies will respond similarly. Furthermore, as we predict resistance to CX-5461 and tumor relapse from our in vivo mouse studies, the need to identify pathways responsible for mediating resistance to Pol I inhibition in the background of oncogenic MYC is necessary for future development of rational combination therapies. To address these key questions, we have undertaken multiple approaches. Firstly, we are utilizing model systems of acute myeloid leukemia (AML) to take both an unbiased and a direct approach to understanding the role of MYC in mediating CX-5461 sensitivity. Secondly, to identify factors conferring acquired resistance to CX-5461 we have used the well-characterized Eµ-Myc mouse model of MYC-mediated lymphoma where, following a period of disease remission, prolonged dosing of CX-5461 in mice bearing lymphomas results in eventual relapse due to acquired drug resistance. Thus, we compared whole-exome sequencing data between isogenic sensitive and CX-5461 resistant B-cell lymphomas to identify additional mutations conferring drug resistance.
Finally, we are using the Eµ-Myc model to investigate the regulation of rDNA transcription itself during cancer progression. Compared to wild type B-cells, malignant MYC over-expressing B-cells have hyper-activated Pol I and increased rDNA transcription. This increase in transcription is associated with a dramatic increase in the number of transcriptionally active rDNA repeats, indicating changes in chromatin structure during transformation. In order to assess epigenetic changes at the rDNA loci and to identify long distance rDNA interactions occurring during malignant progression, we have used ChIP-seq and circularized chromosome conformation capture sequencing (4C-seq) at all cell stages of malignancy in vivo (wild type, pre-malignant and malignant Eµ-Myc B-cells). We demonstrate that transition from premalignancy to malignancy is associated with robust changes in rDNA chromatin as well as reorganization of rDNA-genome interactions with a significant increase in these interactions being detected in malignant cells. Our data provide evidence for MYC-driven activation of rDNA in cancer progression beyond ribosome biogenesis and offer novel insights into the spatial and transcriptional dynamics of the rDNA-associated genome during malignant transformation.
We will present our latest data on all fronts aimed at understanding the critical role that MYC plays in therapeutic inhibition of Pol I transcription.
Citation Format: Gretchen Poortinga, Jeannine Diesch, Elaine Sanij, Nadine Hein, Jirawas Sornkum, Donald Cameron, Megan J. Bywater, Ricky Johnstone, Denis Drygin, Sean O'Brien, Richard B. Pearson, Grant A. McArthur, Ross D. Hannan. Elucidating mechanisms that cooperate with the therapeutic inhibition of RNA polymerase I to treat MYC-driven hematological malignancies. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr A31.