Abstract 2191: Transcriptome analysis demonstrates the ability of the bromodomain inhibitor JQ1 to attenuate expression of common oncogenes heterogeneously expressed among chronic lymphocytic leukemia subsets
Authors: Shull Austin Y. , Choi Jeong-Hyeon , Buckley Brian , Pei Lirong , Awan Farrukh T. , Shi Huidong 
Published: August 2015

Abstract
Chronic lymphocytic leukemia (CLL), the most common adult leukemia in the western world, is characterized by the ability of B-cells to escape their regulated apoptotic fate and oncogenically expand via microenvironment interactions in the lymph node. With recent studies demonstrating BET bromodomains as effective therapeutic targets in cancers, our goal was to investigate the potential therapeutic benefits of JQ1 and determine how this bromodomain inhibitor alters the transcriptional landscape in CLL. We performed in vitro proliferation assays in the MEC1, MEC2, and WAC3 CLL cell lines. Based on dose and time dependent variables, we determined that 1uM of JQ1 could fully inhibit proliferation in all 3 cell lines. Cell cycle and Annexin V/DAPI analysis with 500nM and 1uM of JQ1 caused G1 cell cycle arrest in MEC1 and MEC2 after 72 hours while inducing little apoptosis. This result was supported mechanistically by the fact that cyclin D3 protein expression was lost in MEC1 after 24hr treatment while BCL2 expression remained stable. Based on the phenotypic results, we then treated MEC1, an immortalized clone of primary CLL, and MEC2, an immortalized clone of progressed CLL, with 1uM of JQ1 and performed a time course-based RNAseq analysis to determine how JQ1 affects the CLL transcriptional landscape. We compared the treatment analysis against 47 clinical CLL and 5 healthy donor samples in order to conduct a meta-analysis comparison between transcripts significantly upregulated in the clinical CLL RNAseq and transcripts significantly downregulated in the JQ1-treated MEC1 and MEC2 RNAseq. Pathway analysis comparison between transcripts upregulated in clinical CLL samples and transcripts downregulated in the treated cell lines demonstrated that JQ1 disrupted expression of signaling cascades involved with the NFKB, NFAT, and PI3K pathways, as well as disrupting pathways activated by IL2, IL4, and CD40L. Interestingly, we determined that, though the clinically relevant pathways affected by JQ1 treatment were similar in the two cell lines, the specific transcriptional targets affected by JQ1 differ greatly between MEC1 and MEC2. Specifically, JQ1 downregulated ZAP70, LCK, BTK, and CXCR4 expression in MEC1, whereas JQ1 downregulated CD274 (PDL1), MIR155HG, TRAF1, MALAT1, and CCR7 expression in MEC2. Interestingly, the only transcripts that overlapped in the three-way comparison were DACT1 and the CD23 activation marker gene FCER2. Based on our analysis, JQ1 may have the potential to indiscriminately inhibit certain CLL oncogenes that drive heterogeneous CLL subsets. These results and our ongoing genome-wide ChIPseq analysis of H3K27Ac marks in MEC1 and MEC2 will help determine whether bromodomain inhibition could potentially serve as a promising therapeutic against CLL clonal and subclonal expansion.
Citation Format: Austin Y. Shull, Jeong-Hyeon Choi, Brian Buckley, Lirong Pei, Farrukh T. Awan, Huidong Shi. Transcriptome analysis demonstrates the ability of the bromodomain inhibitor JQ1 to attenuate expression of common oncogenes heterogeneously expressed among chronic lymphocytic leukemia subsets. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2191. doi:10.1158/1538-7445.AM2015-2191