CCTC-binding factor (CTCF) is a key regulator of gene expression through organization of the chromatin structure. Still, it is unclear how CTCF binding is perturbed in leukemia or in cancer in general. We studied CTCF binding by chromatin immunoprecipitation sequencing in cells from patients with acute myeloid leukemia (AML) and in normal bone marrow (NBM) in the context of gene expression, DNA methylation, and azacitidine exposure. CTCF binding was increased in AML compared with NBM. Aberrant CTCF binding was enriched for motifs for key myeloid transcription factors such as CEBPA, PU.1, and RUNX1. AML with TET2 mutations was characterized by a particularly strong gain of CTCF binding, highly enriched for gain in promoter regions, while AML in general was enriched for changes at enhancers. There was a strong anticorrelation between CTCF binding and DNA methylation. Gain of CTCF occupancy was associated with increased gene expression; however, the genomic location (promoter vs distal regions) and enrichment of motifs (for repressing vs activating cofactors) were decisive for the gene expression pattern. Knockdown of CTCF in K562 cells caused loss of CTCF binding and transcriptional repression of genes with changed CTCF binding in AML, as well as loss of RUNX1 binding at RUNX1/CTCF-binding sites. In addition, CTCF knockdown caused increased differentiation. Azacitidine exposure caused major changes in CTCF occupancy in AML patient cells, partly by restoring a CTCF-binding pattern similar to NBM. We conclude that AML displays an aberrant increase in CTCF occupancy that targets key genes for AML development and impacts gene expression.

TNF receptor–associated factors (TRAFs) are multifunctional adaptor proteins involved in temporal and spatial coordination of signals necessary for normal immune function. Here, we report that TRAF3, a TRAF family member with a key role in Toll-like and TNF family receptor signaling and suppressor of lymphomagenesis, is post-translationally modified by the small ubiquitin-related modifier (SUMO). Through yeast two-hybrid and co-immunoprecipitation assays we have identified Ubc9, the SUMO conjugating enzyme, as a novel TRAF3-interacting protein. We show that Ubc9-dependent SUMOylation of TRAF3 modulates optimal association with the CD40 receptor, thereby influencing TRAF3 degradation and non-canonical NF-κB activation upon CD40 triggering. Collectively, our findings describe a novel post-translational modification of a TRAF family member and reveal a link between SUMOylation and TRAF-mediated signal transduction.

Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA associated with the promotion of several solid cancers. As part of the FANTOM6 project, we aimed to define its role in acute myeloid leukemia (AML) and myelopoiesis, since it remains largely uninvestigated. We show that NEAT1 expression increases during myelopoiesis, especially in monocytes. NEAT1 expression is elevated in AML compared to normal bone marrow (NBM), especially in AML with inv(16)and t(8;21). In addition, NEAT1 expression correlates positively with ASXL1, KRAS and NRAS mutations, but negatively with TP53 mutant AML. Higher NEAT1 expression is associated with better overall survival in AML, independent of other known risk factors. Knockdown of NEAT1 in AML cells induces monocytic differentiation and upregulated gene expression of genes involved in glucose metabolism. By investigating genome-wide RNA and DNA interactions using RADICL-sequencing, we show that NEAT1 binds to the RUNX2 locus that is associated with differentiation, metabolism, and glucose uptake. The results suggest that the lncRNA NEAT1 has a role in myelopoiesis, AML and is implicated in glycolysis.

Acute Myeloid Leukemia (AML) is the most common myeloid leukemia in adults. Although substantial progress has been made in recent years, the long-term prognosis for patients remains poor which is mainly due to the dated treatments that consist of cytotoxic drugs with low specificity. AML is a clonal disease with multiple co-existing clones in each patient. Often, patients that initially respond to treatment may develop resistance due to lingering leukemic stem cells (LSC), or sub-clones that survive the treatment and cause a relapse. Therefore, novel therapeutic strategies are needed to fully eradicate all leukemic cells. AML has a strong epigenetic component meaning mutations in genes encoding epigenetic regulators are frequently acquired during early AML development, and are present in the initiating clones. Thus, targeting the epigenetic machinery may offer a new avenue for AML treatment. Among the newer epigenetic drugs are BET inhibitors, which bind reversibly to bromodomains of BRD proteins and prevent protein-protein interactions with acetylated histones and transcriptions factors. One of the most promising BET inhibitors is OTX015, which has already been in Phase II clinical trials for AML in the U.S. (Braun & Gardin, Expert Opinion on Investigational Drugs, 2017). We aim to analyze the heterogeneous response to OTX015 in AML, and normal stem/progenitor, cells in order to dissect the BET-inhibitor response. The main focus is the specific transcriptional signatures at promoters and enhancers as enhancers, and especially super-enhancers, have previously been shown to be sensitive to BET-inhibitors (Loven et al, Cell, 2013). To this effect, we have established a protocol that allowed for the transcriptional profiling of single cells from AML patients that were at different differentiation stages, using FACS- sorting. The patients were obtained from the Swedish Acute Leukemia Registry. To decrease population heterogeneity, the project focused on distinct subgroups of AML that previously has been shown to be sensitive for BET inhibitors. The different isolated AML, and normal progenitor populations, were exposed to OTX015 for 48hrs, and processed with both bulk transcriptional profiling of the general cell population response, and single cell profiling to analyze cell heterogeneity, and single cell response. For the transcriptional profiling, we utilized a unique technique called Cap Analysis of Gene Expression (CAGE), a powerful 5' start profiling technology, that allows for the identification of the transcription start site at base pair resolution, and determination of enhancer activity based on enhancer RNA expression. The single cell profiling was performed using C1 CAGE, which is a single-cell implementation CAGE (Kouno et al, bioRxiv 330845, 2018).We envision that the heterogenic transcriptional drug response, on the single-cell level, in AML and normal stem/progenitor cells will lead to the identification of key genes and pathways involved in the differential drug response. Additionally, the application of CAGE technology will lead to discovery of specific transcriptional signatures at promoters and enhancers that may be predictive of drug resistance. Clinical significance: Leukemic cell heterogeneity remains the main problem in AML, as chemotherapy often fails to completely eradicate all AML sub-clones including LSC, leading to relapses and high mortality of the disease. This study will shed light to the unique features of AML cell heterogeneity and how their drug response differs, not only between AML cells, but also between AML cells and their normal counterparts, on the single-cell level, based on the response to OTX015. The significance will be two-fold: the in-depth characterization of the features in AML populations and normal cells, and the potential this study will provide for novel, more targeted, combination treatments in AML. Disclosures No relevant conflicts of interest to declare.