Epigenetic Therapy Increases Therapeutic Efficacy in Myeloproliferative Neoplasms Through Inhibition of Aberrant Inflammatory Signaling

The mechanisms that mediate transformation in MPN are not fully delineated and clinically utilized JAK inhibitors have limited ability to reduce disease burden or reverse myelofibrosis. Here we show that MPN progenitor cells are characterized by marked alterations in gene regulation through differential enhancer utilization, and identify Nfb signaling as a key pathway activated in malignant and non-malignant cells in MPN. Genetic and functional studies underscore the central role of JAK/STAT signaling in myeloproliferative neoplasms (MPNs). However, the mechanisms that mediate transformation in MPNs are not fully delineated, and clinically utilized JAK inhibitors have limited ability to reduce disease burden or reverse myelofibrosis. Here we show that MPN progenitor cells are characterized by marked alterations in gene regulation through differential enhancer utilization, and identify nuclear factor kB (NF-kB) signaling as a key pathway activated in malignant and non-malignant cells in MPN. Inhibition of BET bromodomain proteins attenuated NF-kB signaling and reduced cytokine production in vivo. Most importantly, combined JAK/BET inhibition resulted in a marked reduction in the serum levels of inflammatory cytokines, reduced disease burden, and reversed bone marrow fibrosis in vivo. Mutant (GFP-positive) megakaryocytic-erythroid progenitors (MEP) were separated by fluorescent-activated cell sorting (FACS) using green fluorescent protein (GFP) to identify MPLW515L-expressing cells and specific cell surface marker; Epigenetic profiling using H3K27Ac and H3K4Me1 are performed. FASTQ reads are aligned to mouse reference genome (build mm9) RNA-seq of human SET-2 cell line treated with vehicle, ruxolitinib, JQ1, or combination therapy (n=12) RNA-seq of JAK2fl/WT Cre-negative and Cre-positive MEPs (n=6) RNA-seq of MEP MPLW515L GFP+ cells treated with vehicle, ruxolitinib, JQ1, or combination therapy (n=9) RNA-seq of control MIGR1 and MPLW515L-positive MEPs (n=6)