PF561 DUAL‐TARGETING OF PROMOTER AND ENHANCER DRIVEN PROCESSES SUPPRESSES MYELOMA CELL GROWTH AND VIABILITY VIA PERTURBATION OF THE MYELOMA PROLIFERATIVE PROGRAM
Authors: Fulciniti M. , Chakraborty C. , Samur M. , Munshi N. 
Published: June 2019

Background:

Cancer cells are characterized by perturbed transcriptional profiles. These dysregulated programs create dependencies on transcriptional regulators not predicted by genetic changes. Tumor cells, including multiple myeloma cells, tend to develop striking dependencies on super‐enhancer regulatory elements. In addition to super‐enhancers, promoter proximal transcription factors such as E2F1 and SP1 play a prominent role in myeloma cell biology via their control of proliferative and survival genes. Importantly, our genome‐wide profiling of the MM epigenome landscape revealed that promoter‐ and enhancer‐associated factors govern distinct biological functions providing a non‐overlapping control of the myeloma transcriptome.

Aims:

The goal of this study is to improve our understanding of global gene regulation in MM, with the aim of deploying novel therapeutics to target uncontrolled MM cell proliferation.

Methods:

We performed integrated genomic analysis using a combination of ChIP‐seq, ATAC‐seq, and RNA‐seq technologies as well as loss of function screening in MM cell lines and primary MM cells.

Results:

Global chromatin analysis of MM cells revealed two distinct regulatory axes, with SP1, DP1, E2F and MYC predominantly localized to promoters of growth/proliferation genes and CDK9, BETs and other factors disproportionately enriched at enhancer‐regulated tissue‐specific genes. This divergent enhancer and promoter axes is also observed in diffuse large B‐cell lymphoma, suggesting a broader transcriptome control process. Importantly, we have observed that dual inhibition of promoter and enhancer axes using RNA interference shows a superior inhibition of MM cell growth and viability both in vitro and in vivo compared to single perturbation alone, providing an important molecular mechanism for combination therapy. We have further gone on to target TFs SP1 with a small molecule inhibitor Terameprocol which inhibits its DNA binding activity and a cell‐permeable peptide to disrupt the heterodimerization of E2F1 with its partner DP1 responsible for the E2F transcriptional activity. These strategies have been successful in inhibiting MM cell growth and viability, and the effect was augmented in the presence of inhibitors of enhancers, such as the small molecule BRD4 inhibitor JQ1.

We have further investigated inhibitors of upstream regulators of the pRB‐E2F axis such as CDK4/6 to impact E2F1 activity. CDK4–6 complexes can phosphorylate RB, releasing the E2F and modulating the expression of E2F target genes. Therefore, we investigated the combination of CDK4/6 inhibitor Palbociclib with low doses of JQ1 and observed a profound effects on E2F promoter driven transcriptional activity, and a highly synergistic effect on growth and survival in a large panel of cell lines and primary MM cells from newly diagnosed and relapsed patients. Cell cycle analysis revealed complete G1 arrest after treatment. Importantly, the combination regimen had no significant effect on healthy donor PBMCs activated with PHA, suggesting a favorable therapeutic index.

Summary/Conclusion:

These data implicate the existence of a sequestered cellular function by promoter and enhancer driven processes providing non‐overlapping vulnerabilities. Simultaneous targeting of these processes using clinically applicable agents can synergistically impair the myeloma proliferative program, with potential for development of a promising therapeutic strategy.