ALBERT

Description: Disease- or treatment-associated chromatin conformation has yet to be illustrated. Here we first demonstrate that monocytic and erythroid leukemia cell lines have distinctly different chromatin conformation at the PU.1 locus: a looped, connected, RNA-polymerase-II-bound, active conformation in the former and a disconnected, inactive conformation in the latter. These conformations undergo opposite transformations, becoming more active in the erythroid leukemia line and less active in the monocytic leukemia line, in response to both DNA and histone hypomethylating drugs.To explore the underlying mechanisms we developed a novel method to analyze DNA modifications. We demonstrate that the erythroid leukemia line has a marked drug-responsive change in both hydroxymethyl-CpG and 5-meythyl-CpG at the promoter, whereas the monocytic leukemia line has a higher level bivalent histone/chromatin with co-localized H3K4me3 and H3K27me3 at the enhancer. Consequently, the erythroid leukemia line is more sensitive to DNA hypomethylation while the monocytic leukemia line is more sensitive to histone hypomethylation. Further studies on clinical leukemia samples confirm the findings, and demonstrate that the leukemic cells from the clinical samples have different chromatin conformations with much more bivalent chromatin and denser DNA/histone modifiers and are more sensitive to hypomethylating drugs, compared to normal controls. Different chromatin conformations dictate preferential drug responses and open new diagnostic and therapeutic avenues. Disclosures: No relevant conflicts of interest to declare.

Description: Normal hematopoiesis is controlled by a well-connected genetic network composed of several transcription factors (TFs) including PU.1 and GATA1. It has been postulated that both transcription factors and epigenetic modifiers work collaboratively to regulate hematopoietic stem cell differentiation and lineage specification as well as leukemogenesis. However, it is unclear about how the interplay between genetic network and epigenetic regulatory modifiers regulates locus-specific chromatin modifications and gene expression in normal hematopoiesis and hematologic malignancies such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Drugs targeting epigenetic modifiers including DNA methyltransferases (DNMTs), histone methyltransferases (HMTs) and histone deacetylases (HDACs) have been shown to be effective in a small portion of patients with MDS/AML, but the mechanisms underlying the efficacy and selectivity of different epigenetic modifying drugs are unknown. In this study, we performed growth-inhibition experiments with several epigenetic modifying drugs in multiple AML cell lines and identified two distinct lineage/differentiation-associated growth-inhibition patterns. Monocytic leukemia cells, but not erythroid leukemia cells, were sensitive to H3K4 HMT inhibitors, whereas both erythroid and monocytic leukemia cells were hypersensitive to DNMT and H3K27 HMT inhibitors. Importantly, co-immunoprecipitation experiments demonstrated lineage-specific interactions between the lineage-determining TFs (PU.1/SPI1 and GATA1) and the DNA/histone modifiers (DNMT1, DNMT3A/3B, TET2 and EZH2). Specifically, SPI1/PU.1 interacts with DNMT1 and EZH2, while GATA1 interacts with TET2 and DNMT3A/3B in MDS-derived erythroid leukaemia. In monocytic leukemia, SPI1/PU.1 interacts with TET2. Epigenetic modifying drugs such as azacytidine and 3-deazaneplanocin efficiently disrupted the interactions between the lineage-determining TFs and the DNA/histone modifiers without changing the expression of these proteins. We developed a new method, crosslink-assisted DNA modification immunoprecipitation assay (CDMIA), to simultaneously measure 5-methylcytosine (5-mC) and hydroxymethylcytosine (5-hmC). CDMIAs revealed significant drug-responsive changes in 5-mC/5-hmC at the promoters of differentiation/lineage-controlling genes such as PU.1/SPI1, but not at the global 5-mC/5-hmC. Sequential-ChIP and chromatin conformation capture (3C) showed that PU.1/SPI1 recruited polymerase II (pol-II) and the DNA/histone modifying complexes to PU.1/SPI1 toform distinct chromatin structures in a lineage-specific manner. We have selected azacytidine-resistant clones and established azacytidine-resistant cell lines from the previously azacytine-sensitive erythroid and monocytic leukemia cells. Strikingly, azacytine at the same concentrations failed to disrupt the interactions between the lineage-determining transcription factors and the DNA/histone modifiers in these drug-resistant leukemia cells. Genome-wide sequencing revealed novel mutations in TET2, TET3, DNMT3L and PU.1/SP1 that were confirmed by Sanger sequencing. These mutations correlated with the altered interactions between PU.1/SPI1 and the DNA/histone modifying complexes and predicted the responses to epigenetic modifying drugs. Examination of clinical specimens from patients with MDS/AML confirmed the presence of distinct lineage/differentiation-specific chromatin structure with a high-level recruitment of DNA/histone modifiers. Our genome-wide epigenetic analysis demonstrates the statistically significant enrichment of the SPI1/PU.1, TP53 and MYB DNA-binding motifs in hyper-H3K27 trimethylated DNA sequences in erythroid-predominant MDS. These results demonstrate the presence of locus-specific, drug-sensitive chromatin structures in MDS/AML subtypes. Our data revealed a novel epigenetic modifying drug action model that involves selective disruption of the disease-specific interactions between the lineage-determining factors and DNA/histone modifiers. Such drug action models may provide new insights into the mechanisms underlying the efficacy and selectivity of epigenetic modifying drugs. Disclosures Larson: Novartis: Consultancy, Research Funding; Pfizer: Consultancy; Ariad: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy.

Description: Introduction FLT3 is a receptor tyrosine kinase that plays a role in hematopoietic stem/progenitor cell proliferation and survival and is frequently found to be mutated in patients with acute myeloid leukemia (AML). Mutations that lead to constitutive activation of FLT3 (such as internal tandem duplications of the juxtamembrane domain or point mutations involving the kinase domain) are associated with a poor prognosis. This poor prognosis is in part due to an increased relapse rate after allogeneic hematopoietic cell transplant (HCT). Several compounds that inhibit the activity of FLT3 in vitro, including ASP2215, midostaurin and quizartinib, are now being studied in clinical trials for the treatment of AML. Inhibition of the formation of phospho-FLT3 has been correlated with clinical anti-leukemia effects and remissions. Methods In this pilot study we use immunohistochemistry to measure the levels of activated FLT3 in bone marrow biopsies of patients prior to and during treatment inclinical trials at our institution to determine the efficacy of these FLT3 inhibitors and correlate it with patient outcomes. Results The different FLT3 compounds tested had a heterogenous effect on activated FLT3 levels. In some patients, ASP2215 caused a decrease in levels of activated FLT3 (indicated by brown nuclear staining), which corresponded to a decrease in leukemic blasts (Fig 1). Other patients, however, showed similar amounts of activated FLT3 both before and after treatment, which corresponded with no significant change in leukemic blasts. (Fig 2). Other FLT3 inhibitors also showed differences in their effects. Midostaurin reduced activated FLT3 levels, which correlated with a positive clinical response. In contrast, one patient receiving quizartinibshowed little to no decrease in activated FLT3 levels, despite remaining in clinical remission. This suggests that this FLT3 inhibitor may have alternative targets, such as the tyrosine kinases AXL or LTK. Conclusions The heterogeneity in the responses to ASP2215, midostaurin, and quizartinib suggests that there may be other targets for these compounds that are not currently accounted for in the clinical studies. Immunohistochemicalmeasurements of activated FLT3 in bone marrow sections before and after treatment with FLT3 inhibitors was not predictive for clinical response. Figure 1. Activated FLT3 levels in patient responsive to ASP2215; pre-treatment (A) and post-treatment (B) Figure 1. Activated FLT3 levels in patient responsive to ASP2215; pre-treatment (A) and post-treatment (B) Figure 2. Activated FLT3 levels in patient not responsive to ASP2215; pre-treatment (A) and post-treatment (B) Figure 2. Activated FLT3 levels in patient not responsive to ASP2215; pre-treatment (A) and post-treatment (B) Disclosures Larson: Pfizer: Consultancy; Ariad: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy.

Description: Key Points Ten cases of an indolent T-cell lymphoproliferative disease of the gastrointestinal tract are reported. It is important to recognize this condition because it can be mistaken for aggressive T-cell lymphoma, which may lead to unnecessary therapy.

Description: Key Points Loss of 1 copy of Ctnnb1 (encoding β-catenin) in an Apc-haploinsufficient microenvironment prevents the development of MDS. Modulation of WNT signaling in the niche using pyrvinium inhibits the development of MDS in Apc-haploinsufficient mice.

Description: Background: BETs are evolutionarily conserved proteins that specifically bind to acetyl-lysines on histones and other proteins to recruit transcriptional machinery and influence gene expression (Shi and Vakoc. 2014 Mol Cell 54, 728-736). Small molecules that target BETs, such as JQ1 and I-BET, can effectively inhibit the growth of midline carcinoma cells that have a BRD4-NUT gene fusionas well as leukemia cells, such as AML, which have a diverse genetic background and do not have BRD4 rearrangements. DNA methyltransferase (DNMT) inhibitors, such as azacitidine (5-AZA) and decitabine, have been proven effective in some patients with hematologic malignancies including AML and MDS. However, the detailed mechanisms underlying the selectivity and resistance of these epigenetic-modifying drugs remain elusive. Our previous genome-wide epigenetic profiling data have demonstrated epigenetic inactivation of the SPI1/PU.1 pathway in cytogenetically normal MDS with erythroid predominance (Cheng et al. 2013 Leukemia 27, 1291-1300). This study aims to elucidate the role of chromatin structure in the regulation of response to epigenetic drugs in MDS and AML. Methods: Co-immunoprecipitation (co-IP) coupled with RNase/DNase digestion, super-resolution two-photon stimulated-emission depletion (STED) confocal microscopy, high-throughput sequencing and chromatin conformation capture (3C) were used. Results: Our data demonstrate that GATA1 and SPI1/PU.1, erythroid- vs. myeloid-determining transcription factors (TFs), selectively interact with specific sets of DNA/histone modifiers, such as TET2, DNMTs and EZH2, to form distinct lineage-specific, drug-responsive chromatin structures at specific gene loci. The interactions between the TFs, DNA/histone modifiers and chromatin structures are highly sensitive to RNase and DNase digestions, i.e., dependent on native chromatin environment. Our experiments show that hnRNPK, a conserved factor in the heterogeneous nuclear RNA-binding protein (hnRNP) complexes, directly interact with the lineage-determining TFs and DNA/histone modifiers as well as RNAs/DNAs to form distinct chromatin-structures in MDS/AML cells. Epigenetic drugs, such as 5-AZA, efficiently disrupt the hnRNPK-mediated chromatin structures in 5-AZA-sensitive MDS/AML cells, but not in 5-AZA-resistant MDS/AML cells. Our data demonstrate a marked (~4-6 fold) increase in BRD4, BRD2 and DNMT1 in the 5-AZA-resistant MDS/AML cell lines compared to the 5-AZA-sensitive MDS/AML cell lines. Strikingly, a massive amount of BRD4-associated RNA polymerase II (pol-II) is observed in the 5-AZA-resistant MDS/AML cells, but not in the 5-AZA-senstive MDS/AML, and there is approximately 70-80 fold increase in BRD4-associated pol-II, but not in BRD4-associated GATA1, in the 5-AZA-resistant cells compared to the 5-AZA-sensitive cells. Such BRD4-associated pol-II is almost exclusively in a processive pol-II complex that is associated with the phosphorylated C-terminal domain (S2p/S5p-CTD) of pol-II, and sensitive to JQ1. Furthermore, JQ1 significantly decreases the interactions between BRD4 and lineage-determining TFs GATA1 and SPI1/PU.1, in the 5-AZA-sensitive MDS/AML cells, but not in the 5-AZA-resistant MDS/AML cells. A very low concentration (0.01 uM) of JQ1 can re-sensitize the 5-AZA-resistant MDS/AML cell lines and completely reverse the drug resistance to 5-AZA, suggesting a BET-mediated 5-AZA-resistance in those cells. Genome-wide chromatin immunoprecipitation coupled with high-throughput sequencing has been carried out to map the BRD4-associated RNA pol-II at the genome-wide level in the 5-AZA resistant and sensitive MDS/AML cells. Our experiments using clinical specimens demonstrate a positive correlation between MDS/AML progression and increase in expression of hnRNPK, BRD2 and BRD4, confirming their importance and clinical relevance. Conclusion: Our study has revealed a novel drug resistance mechanism that operates through BET-mediated recruitment of an active pol-II complex and induction of drug-responsive chromatin structural changes in MDS/AML cells (Fig 1). Such BET-mediated changes in pol-II complexes and chromatin structure could become useful biomarkers to predict drug responses, leading to rational designs and actionable targets to reprogram therapeutic drug susceptibility for more effective therapy in MDS and AML. Disclosures No relevant conflicts of interest to declare.

Description: Background: Activenuclear-cytoplasmic shuttling of proteins and RNAs, such as heterogeneous ribonucleoproteins (hnRNPs), is essential for the normal function and survival of eukaryotic cells and tumorigenesis (Dreyfuss et al. 1993 Annu Rev Biochem 62, 289; Gorlich and Mattaj 1996 Science 271, 1513). Up-regulation of exportin 1 (XPO1)/chromosomal maintenance 1 (CRM1), a member of the karyopherin-β family of nuclear export receptor proteins, has been implicated in solid and hematologic malignancies (Kau Kau et al. 2004).Selinexor (KPT-330) has been shown to be able block in vitro and in vivo XPO1/CRM1 functions and is currently in phase-II/IIb clinical trials for treatment of hematologic and solid tumors (Senapedis et al., 2014 Nat Rev Cancer 4, 106). However, the mechanisms underlying the selectivity and efficacy of selinexor are incompletely understood, and no biomarkers are currently available to predict clinical responses to selinexor in clinical settings. In this study, we focus on determining the effects of selinexor on the nuclear-cytoplasmic shuttling of hnRNPs, particularly hnRNPK and hnRNPA1, to elucidate the roles of the hnRNPs in the regulation of selectivity and efficacy of selinexor in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Method:We performed growth inhibition/killing assays, histopathologic evaluations, immunohistochemical studies, subcellular fraction western blotting, super-resolution stimulated emission depletion (STED) confocal microcopy and siRNA knockdown experiments. Results: Our in vitro experiments demonstrate a marked increase in XPO1/CRM1 protein and decrease in TP53 in our azacitidine-resistant MDS/AML cell lines compared to our azacitidine-sensitive MDS/AML cell lines. Selinexor treatment efficiently blocks export of hnRNP K from nuclei and increased nuclear accumulation of hnRNPK and inhibits MDS/AML cell growth, while the protein levels of XPO1/CRM1 and TP53 remain unchanged. Our experiments using clinical bone marrow specimens show no significant difference in the total protein level or nuclear accumulation of XPO1/CRM1 between the normal control and MDS or AML bone marrow specimens. In contrast, a strong positive correlation between MDS/AML disease progression and hnRNPK protein accumulation is observed in those clinical specimens. We have extended our experiments to clinical bone marrow specimens from a small cohort in a clinical trial for selinexor in AML at the University of Chicago (NCT02573363). In our small cohort, 5 patients responded to selinexor, 4 patients did not respond and 1 had a partial response. All 5 responders show a striking decrease in their bone marrow blast percentage from their pre-treatment marrows (average blast percentage 37.4%) to their post-treatment (average blast percentage 1.8%). Non-responders show no such difference in pre and post-treatment blast percentage (56.3 and 57.1%, respectively). Importantly, our experiments demonstrate a marked difference in the protein accumulation and subcellular localization of hnRNPK and hnRNPA1, another member of the hnRNP family, between selinexor-responder and selinexor-non-responder bone marrow specimens. Specifically, selinexor responders had much higher levels of hnRNPK and hnRNPA1 proteins in their pre-treatment bone marrows than non-responders, despite the fact that the latter had higher bone marrow blast percentages on average. There is markedly reduced accumulation of hnRNPK and hnRNPA1 in the post-selinexor treatment bone marrow specimens from the responders, but not the non-responders, suggesting these hnRNPs as key therapeutic targets for selinexor in MDS and AML. In contrast, no significant change in XPO1/CRM1 protein levels is observed in the selinexor-responder vs. selinexor-non-responder bone marrow specimens. Conclusion:Our data have revealed a novel drug-action mechanism by which selinexor impairs the nuclear-cytoplasmic shuttling of hnRNPK and hnRNPA1 in MDS and AML cells. Differential expression and localization of these hnRNPs in normal vs. MDS vs. AML cells may provide the rationale for the preferential killing of leukemia cells by selinexor. Our data also suggest the possibility to develop novel hnRNP-based biomarkers to predict the response to selinexor in clinical settings. Disclosures Liu: Karyopharm: Research Funding; BMS: Research Funding.

Description: A del(5q) is frequently noted in MDS, AML, and therapy-related myeloid neoplasms (t-MN) following alkylating agent therapy. Mutation/loss of the TP53 is gene found in 80% of t-MNs with a del(5q). Recent studies suggest that TP53 mutations are found at a low frequency in hematopoietic stem/progenitor cells (HSPCs) in adults (Xie et al., Nat Med 20:1472, 2014; Genovese et al., NEJM 371:2477, 2014; Jaiswal et al., NEJM 371:2488, 2014), and chemotherapy confers a selective growth advantage to these rare clones (Wong et al., Nature 518:552, 2015). We previously established a mouse model for t-MN with a del(5q) and showed that haploinsufficiency of two del(5q) genes, Egr1 and Apc, cooperate with loss of function of the Trp53 (p53) gene to induce myeloid neoplasms in mice. Specifically, transplantation of Egr1+/-, Apcdel/+ bone marrow (BM) cells transduced with p53 shRNAs into wild type (WT) recipients resulted in the development of a transplantable AML, characterized by a complex karyotype and genetic instability, in 17% of mice. There is growing evidence that microenvironment perturbations play a major role in the malignant process; however, the effect of cytotoxic therapy on HSPCs as well as the BM niche is not well understood. Using our mouse model of t-MN with a del(5q), we explored the effects of ENU, an alkylating agent, on both HSPCs and the BM microenvironment by exposing both donor and recipient mice to ENU (Panel 1 in the figure). In mice transplanted with Egr1+/-, Apcdel/+, p53 shRNA HSPCs, exposure to ENU strikingly decreased survival (median survival: 200d vs. not reached) and increased the incidence of AML or MDS with multilineage dysplasia (73% vs. 17%). In the absence of p53 knockdown (i.e., control shRNA), mice survived longer (370d vs. 200d, P = 0.0014); however, 100% of mice developed MDS with dyserythropoiesis. None developed AML, suggesting that loss of p53 function is critical for leukemic transformation (Panel 2). Loss of both del(5q) genes, EGR1 and APC, was necessary to develop AML. Compared to mice transplanted with Egr1+/-, Apcdel/+, p53 shRNA HSPCs, mice transplanted with Egr1+/-, p53 shRNA HSPCs survived longer (369 d vs. 200 d, P = 0.0117) and only 40% of mice developed MDS with dysgranulopoiesis and/or dyserythropoiesis (Panel 3). None developed AML. Thus, severity of disease increases with loss of more than one del(5q) gene. Finally, to determine the separate effects of alklating agent therapy on HSPCs vs. the niche, we treated either the recipient or donor mice with ENU. Whereas ENU exposure to both donor and recipient resulted in a profound expansion of p53 shRNA+ cells and the development of MDS/AML in 73% of mice, ENU exposure of either donor or recipient led to only modest expansion of p53 shRNA+ cells and none of the mice developed MDS or AML. This suggests that the clonal expansion of cells with loss of multiple 5q genes and p53 is likely promoted by cytotoxic exposure to the cells themselves, as well as exposure to the surrounding niche cells. t-MN patients with a del(5q) typically present with trilineage dysplasia implicating all three hematopoietic cell lineages (erythroid, myeloid, and megakaryocytic) in the dysplastic process. Our mouse models shed light on some of the key genes on 5q, as well as the environmental exposure, that contributes to trilineage dysplasia in patients. Finally, our data suggests that t-MN is a "disease of the tissue", and the expansion of mutant HSPCs, e.g., with TP53 mutations, likely results from the combined effects of cytotoxic therapy on the hematopoietic cells themselves, as well as the BM microenvironment that supports hematopoiesis Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.

Description: Cell fate determination in the hematopoietic system involves the onset and resolution of mixed lineage patterns of gene expression. Molecular mechanisms underlying the concerted activation and repression of alternate lineage genes remain to be elucidated. We have proposed a gene regulatory network for macrophage development in which the transcription factors PU.1 and the Egr’s function in a feed forward loop to activate macrophage genes. In the network, the Egr’s counteract the neutrophil regulator Gfi-1 and also repress alternate lineage genes. Using mutant alleles of Egr-1 and Egr-2 we validate the model and demonstrate that the Egr’s are required for initiating but not maintaining the repression of neutrophil genes during macrophage differentiation. Employing a PU.1−/− progenitor cell line we show that PU.1 transiently binds to and activates both macrophage and neutrophil gene promoters thereby leading to the onset of mixed lineage gene activity. While inducing macrophage cell fate determination, PU.1 remains persistently bound to macrophage gene promoters aided by the Egr’s. Surprisingly, the Egr’s displace PU.1 from neutrophil gene promoters by interacting with a co-repressor Nab-2 thereby repressing the alternate lineage program. We propose that the Egr’s have evolved to molecularly discriminate distinct sets of target genes and delineate divergent patterns of gene activity.