Super enhancer-associated molecular signatures reveal a dependency on immune and metabolic mechanisms in chronic lymphatic leukemia

Abstract

Chronic lymphocytic leukemia (CLL), characterized by the progressive and uncontrolled accumulation of CD19+ B cells, currently remains as an incurable malignancy despite recent advancements in treatment options. The difficulties of eliciting curative measures in CLL are partly driven by the adaptability of the transcriptional response in CLL cells. In this study, we sought to better understand the complexities of the CLL transcriptional profile by defining the large histone H3 lysine-27 acetylation regions known as “super enhancers” within B cells and determining which genes overexpressed in CLL overlapped with super enhancers. From this analysis, we identified 190 super enhancer-associated genes overexpressed in CLL and determined that many of the genes identified were either involved in immune signaling cascades (e.g. LCK, FCER2) or metabolic regulation (e.g. LSR, ENO2). These processes corresponded with our reverse phase protein array (RPPA) profile of CLL patients, which shows overexpression of immune signaling kinases (e.g. LCK) as well as alteration of metabolically sensitive translation regulators (e.g. 4E-BP1 phosphorylation). Additionally, we determined that CLL cells are apoptotically sensitive to dual PI3K/mTOR inhibition when compared to upstream B cell receptor pathway inhibition due to their differential effects on 4E-BP1 phosphorylation. Based on the derived information from our super enhancer expression signature, we then compared the effects of preferentially targeting super enhancers with either the BET bromodomain inhibitor JQ1 or the cyclin dependent kinase-7 (CDK7) inhibitor THZ1. From this comparison, we saw that JQ1 could inhibit cell cycle progression in CLL cell lines as well as differentially disrupt transcription of genes involved in immune signaling. Contrastingly, we saw that THZ1 elicited a different response in CLL cells by inducing apoptosis and differentially downregulating genes involved in metabolism. The specific super enhancer-associated genes disrupted by the respective treatments further highlighted the dichotomy of JQ1 and THZ1-mediated effects, as JQ1 suppressed the B cell activation marker gene FCER2 whereas THZ1 suppressed the glycolytic enolase gene ENO2. Collectively, these results reveal that super enhancers play a role in mediating both immune signaling and metabolic expression signatures in CLL and that super enhancers can be differentially disrupted by BET bromodomain or CDK7 inhibition.