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Background: Leukemia is the most common type of childhood cancer. Although the prognosis for many pediatric leukemias has improved, leukemias associated with the t(10;11) CALM-AF10 translocation remain difficult to treat. CALM-AF10 leukemias account for ~5-10% of childhood T-cell acute lymphoblastic leukemia (T-ALL)as well as a subset of acute myeloid leukemia (AML). CALM-AF10 leukemias exhibit increased expression of proleukemic HOXA genes, but relatively little is known about the cellular mechanisms that drive CALM-AF10 leukemogenesis. Our laboratory has demonstrated that the CALM protein contains a nuclear export signal (NES) that is critical for CALM-AF10-dependent leukemogenesis. The NES interacts with the CRM1/XPO1 nuclear export receptor, which shuttles proteins from the nucleus to the cytoplasm through the nuclear pore complex. We have shown that transcriptional activation of HOXA genes by CALM-AF10 is dependent on its interaction with CRM1. Importantly, CRM1 does not contain a recognized DNA binding domain, and it is not currently understood how the CALM-AF10/CRM1 complex interacts with regulatory regions of HOXA genes. To identify proteins that mediate the interaction between the CALM-AF10/CRM1 complex and DNA, we took advantage of a proximity-based labeling approach using BioID2, a second-generation biotin ligase. When fused to a protein of interest and in the presence of biotin, BioID2 biotinylates proteins in close proximity to the ligase. These biotinylated proteins can then be identified by mass spectrometry (MS). Methods: We prepared an expression plasmid in which BioID2 was cloned in-frame with CALM-AF10. Human Embryonic Kidney 293 (HEK293) cells were transiently transfected with BioID2-CALM-AF10 and grown in the presence or absence of biotin. MS was performed to identify candidate interacting proteins. We validated direct interactions of candidate proteins with CALM-AF10 using co-immunoprecipitation experiments in HEK293 cells transfected with a CALM-AF10 plasmid. We confirmed that candidate proteins are present in murine CALM-AF10 leukemia cells via Western blotting. In order to efficiently knockout (KO) candidate proteins, we have generated a human U937 cell line (which harbors a t(10;11) CALM-AF10 translocation) with a stable incorporated Cas9. To assess whether KO of EPS15, DVL2 or CTTN affects HOXA5 expression, we performed RT-qPCR in U937-Cas9 cells lines with confirmed KO. Results: We carried out three independent transfections/MS experiments, which identified 71, 95 and 61 proteins, respectively. Of the proteins identified, 12 candidates were common to all three experiments . Importantly, we identified Disruptor Of Telomeric silencing 1-Like (DOT1L), a protein known to interact with AF10, and Nuclear pore complex protein 214 (NUP214), a protein that interacts with CRM1 and that is involved in leukemogenic translocations. We chose EPS15, DVL2 and CTTN for further study, as each of these proteins plays a role in leukemogenesis. We performed initial validation of direct interactions via co-immunoprecipitation and found that all three proteins co-precipitate with CALM-AF10. Western blotting showed that all three proteins are expressed in a murine CALM-AF10 leukemia cell line. We effectively knocked out EPS15 protein expression in U937 cells, and showed that HOXA5 expression is reduced in the setting of EPS15 knockout. Conclusion: We used biotin ligase-dependent proximity-based labeling to identify candidate proteins that potentially interact with the CALM-AF10 fusion protein. Our identification of DOT1L validates the approach, since DOT1L is known to interact with CALM-AF10. We have started to investigate three candidate proteins - EPS15, DVL2 and CTTN - all of which are involved in leukemogenic transformation. We have shown that EPS15, DVL2 and CTTN are expressed in murine CALM-AF10 leukemia cells and directly interact with the CALM-AF10 fusion protein. Knockout of EPS15 in U937 cells results in decreased HOXA5 expression, suggesting the importance of EPS15 in CALM-AF10 leukemogenesis. Evaluation of the roles of these proteins in leukemogenesis may lead to identification of novel pathways involved in CALM-AF10 leukemogenesis. Disclosures No relevant conflicts of interest to declare.

Background : The CALM-AF10 translocation is found in 5-10% of T-cell acute lymphoblastic leukemias (T-ALL), and a subset of acute myeloid leukemias (AML). CALM-AF10 leukemias are characterized by elevated expression of proleukemic HOXA genes. Since HOXA genes are difficult to target, we hypothesized that identification of non-HOXA CALM-AF10 effector genes could potentially yield novel therapeutic targets. To discover novel CALM-AF10-regulated genes, we took advantage of our prior observation that the nuclear export factor CRM1/XPO1 tethers CALM-AF10 to HOXA genes by interacting with a nuclear export signal within CALM. Using microarrays, we identified a set of genes that showed decreased expression in response to the CRM1 inhibitor Leptomycin B (LMB), similar to Hoxa genes, in murine CALM-AF10 leukemia cells. Then using RNA-sequencing, we discovered a set of genes increased in murine hematopoietic stem cells transduced with CALM-AF10. There were 11 genes that were both decreased in response to LMB and increased in response to CALM-AF10, which included the Hoxa gene cluster, as well as Six1. We demonstrated that CALM-AF10 increases Six1 expression and localizes to the Six1 locus, as it does the Hoxa genes. SIX1, like the Hoxa genes, is a homeobox gene that is associated with embryogenesis and is quiescent post-embryologically. In addition, SIX1 and its cofactor EYA2 are overexpressed in numerous solid tumors, and an inhibitor of the SIX1/EYA2 complex (Compound 8430) has recently been described. While there is evidence of a role for SIX1 in solid tumors, its role in leukemias has not been explored. Objective : Evaluate the effect of a SIX1/EYA2 complex inhibitor on leukemia cell proliferation. Design/Methods : SIX1 gene and protein expression were assessed in CALM-AF10, Jurkat (T-ALL) and NOMO1 (AML) leukemia cell lines via Western Blot and RT-qPCR. CALM-AF10 leukemias were derived from murine models in our lab, Jurkat and NOMO1 cell lines were obtained from ATCC. The effect of compound 8430 - an inhibitor of the Six1/Eya2 interaction - on cell proliferation was evaluated using Cell-Titer-Glo Assays and liquid culture proliferation assays. In addition, we used the the CRM1 Nuclear Export Inhibitor KPT-330 alone and in combination with 8430 in these cell lines. SynergyFinder2 (https://synergyfinder.fimm.fi/) was used to assess synergy of 8430 and KPT-330. δ-score is a calculated value that indicates synergistic drug interaction, with a higher δ-score indicative of a synergistic effect of the drugs. Results : SIX1 gene and protein expression are increased in CALM-AF10 leukemia cell lines and Jurkat T-ALL cells, but not NOMO1 cells. Compound 8430 decreases cell proliferation in CALM-AF10 leukemias and Jurkat leukemia cell lines, however it did not affect the AML line NOMO1. Correspondingly, liquid cultures showed that 8430 alone slowed the proliferation of CALM-AF10 leukemia and the Jurkat cells, but not NOMO1 cells. The addition of KPT-330 to 8430 was synergistic in CALM-AF10 leukemia cells with a KPT-330 dose of 60 nM and multiple dose levels of 8430 (δ-scores 17-19) while in the Jurkat leukemia cells a dose of 30 nM of KPT-330 was synergistic at multiple dose levels of 8430 (δ-score 6-8) (Figure 1). Conclusions : The SIX1 homeobox gene is highly expressed during development, and its expression is silenced post-embryogenesis. Through an initial unbiased screen, we discovered that Six1 may play a role in CALM-AF10 leukemogenesis. We have determined that Six1 expression is upregulated in the presence of CALM-AF10. A role for Six1 in CALM-AF10 leukemogenesis is further supported by the ability of a SIX1/EYA2 inhibitor to slow the proliferation of CALM-AF10 leukemia cells. Importantly, based on our observation that 8430 slows proliferation of Jurkat cells, SIX1 inhibition may be relevant in other leukemias. Finally, our demonstration that 8430 synergizes with KPT-330, a Nuclear Export Inhibitor, suggests the possibility of a novel therapeutic approach for CALM-AF10 and other leukemias. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Introduction: While advances in front-line conventional chemotherapy have increased the likelihood of attaining remission in pediatric AML, relapse rates remain high (25-35%), and novel therapies are needed (Zhang, Savage et al. 2019). The clinical and molecular heterogeneity of AML makes it complex to study and creates challenges for the development of novel therapies (Bolouri, Farrar et al. 2018). It is important to identify cells and pathways underlying relapse to facilitate development of novel therapies. Single-cell RNA Sequencing (scRNA-Seq) allows in-depth analysis of the heterogeneous AML landscape to provide a detailed view of the tumor microenvironment, revealing populations of blasts and immune cells which may be relevant to relapse or complete remission. Methods: We analyzed ~36,500 cells from 14 pediatric AML bone marrow samples in our institutional biorepository, spanning different AML subtypes and 3 healthy children to generate a comprehensive scRNA-Seq landscape of immature AML-associated blasts and microenvironment cells. Samples collected at the time of diagnosis (Dx), end of induction (EOI), and relapse (Rel) were used to generate scRNA-Seq data using a droplet-based barcoding technique (Panigrahy, Gartung et al. 2019). After normalization of scRNA-Seq data, the cell clusters were identified using principal component analysis and Uniform Manifold Approximation and Projection (UMAP) approach (Becht et al, 2018). Differential expression, pathways and systems biology analysis between relapsed and remission patients reveal differences for specific cell clusters (Panigrahy, Gartung et al. 2019). To determine the clinical outcome association of our AML blast specific markers, survival analysis was performed on AML TARGET data (https://ocg.cancer.gov/programs/target) using cox proportional hazard survival approach. To characterize AML blast cells with high accuracy, we used support vector machine (SVM), an Artificial Intelligence based feature extraction and model development approach (Bhasin, Ndebele et al. 2016). Results:ScRNA-Seq analysis of paired Dx and EOI samples using UMAP identified three blast cell clusters with significant gene expression differences among different patients, indicating heterogeneity of AML blast cells (Fig 1a, b). Comparative analysis of the three Dx enriched blast cell clusters with other cells identified a "core blast cell signature" with overexpression of genes like AZU1, CLEC11A, FLT3, and NREP (Fig 1c). These core AML-blast genes were linked to significant activation of the Wnt/Ca2+, Phospholipase C, and integrin signaling pathways (Z score >2 and P-value The scRNA-Seq of AML specific blast cells from relapsed and remission samples exhibited a different clustering pattern indicating different transcriptome landscapes. Relapse-associated AML cell clusters expressed high levels of AZU1, S100A4, LGALS1, and GRK2 genes (Fig 2a). Analysis of the non-AML tumor microenvironment demonstrated enrichment of T/NK in relapsed samples, with differential expression of T cell regulatory/activation genes (Fig 2b, c). ScRNA-Seq showed enrichment of monocyte/macrophage cell clusters in remission samples with distinct relapse- and remission-specific clusters. Remission associated macrophage/monocyte clusters showed overexpression of S100A10, FTH1, CST3 and IFITM2 genes (Fig 2d). Similarly, enrichment of T cell and monocyte/macrophage clusters was observed in relapse and remission samples respectively during EOI. Conclusions: Using single cell transcriptomics we developed a novel potential gene signature to characterize heterogenous AML blast populations with high sensitivity. These genes and the pathways they regulate implicate potential therapeutic targets in pediatric AML. Single cell transcriptome analysis also enabled identification of cell clusters with modulated gene expression at both Dx and EOI that may be useful in predicting relapse/remission. Disclosures Bhasin: Canomiiks Inc: Current equity holder in private company, Other: Co-Founder.

Background : The CALM-AF10 translocation is found 5-10% of T-cell acute lymphoblastic leukemias (T-ALL), and a subset of acute myeloid leukemias (AML). CALM-AF10 leukemias are characterized by elevated expression of proleukemic HOXA genes. Since HOXA genes are difficult to target, we hypothesized that identification of non-HOXA CALM-AF10 effector genes could potentially yield novel therapeutic targets. To discover novel CALM-AF10-regulated genes, we took advantage of our prior observation that the nuclear export factor CRM1/XPO1 tethers CALM-AF10 to HOXA genes by interacting with a nuclear export signal within CALM. Using microarrays, we identified a set of genes that showed decreased expression in response to the CRM1 inhibitor, Leptomycin B (LMB), similar to Hoxa genes, in murine CALM-AF10 leukemia cells. Then using RNA-sequencing, we discovered a set of genes increased in murine hematopoietic stem cells transduced with CALM-AF10. There were 11 genes that were both decreased in response to LMB and increased in response to CALM-AF10, which included the Hoxa gene cluster, as well as Six1. Similar to HOXA genes, SIX1 is a homeobox gene that is associated with embryogenesis and is quiescent post-embryologically. Additionally, SIX1 and its cofactor EYA2 have been found to be overexpressed in numerous solid tumors, and inhibitor of the SIX1/EYA2 complex has recently been described. While there is evidence of a role for SIX1 in solid tumors, its role in leukemias has not been explored. Objective: To evaluate the role of SIX1 in CALM-AF10 leukemias. Design/Methods: RT-qPCR and Chromatin Immunoprecipitation (ChIP) were performed using bone marrow progenitors transduced with CALM-AF10 or an empty vector, with and without LMB. Methylcellulose colony assays assessed the ability of SIX1 to enhance self-renewal of hematopoietic progenitors. An inhibitor of the Six1/Eya2 interaction (compound 8430) was used to evaluate cell proliferation. Downstream targets of Six1 were evaluated using RT-qPCR in CALM-AF10 cells treated with Six1/Eya2 inhibitor (8430). Results: RT-qPCR confirmed overexpression of SIX1 in CALM-AF10 leukemia cells, and showed decreased SIX1 expression in the presence of LMB. Furthermore, ChIP revealed that CALM-AF10 binds to the SIX1 gene locus. Overexpression of SIX1 in fetal liver progenitors was sufficient to increase self-renewal potential. The 8430 Six1/Eya2 inhibitor slowed cell growth in CALM-AF10 cells compared to cells treated with DMSO alone. Finally, downstream targets such as Slc2a1, Cdk2, and Cyclina2 were decreased in 8430-treated CALM-AF10 leukemia cells. Conclusions: The SIX1 homeobox gene is highly expressed during embryogenesis, and its expression is silenced post-embryogenesis. Through an initial unbiased screen, we discovered that Six1 may play a role in CALM-AF10 leukemogenesis. We have determined that Six1 expression is upregulated in the presence of CALM-AF10. Further, we have shown a potential oncogenic role for Six1, as it was able to increase the self-renewal potential of hematopoietic progenitors. The role of Six1 in CALM-AF10 leukemia is further supported by the ability of a SIX1/EYA2 inhibitor to slow the growth of CALM-AF10 leukemia cells and decrease the expression of downstream targets of SIX1. These observations suggest that Six1 plays a pathogenic role in leukemogenesis, and may be a novel therapeutic target in CALM-AF10 leukemias. Disclosures No relevant conflicts of interest to declare.

Background: Leukemia is the most common type of childhood cancer. Although the prognosis for many pediatric leukemias has improved, leukemias associated with the t(10;11) CALM-AF10 translocation remain difficult to treat. CALM-AF10 leukemias account for ~5-10% of childhood T-cell acute lymphoid leukemia (T-ALL) as well as a subset of acute myeloid leukemia (AML). CALM-AF10 leukemias exhibit increased expression of proleukemic HOXA genes, but relatively little is known about the cellular mechanisms that drive CALM-AF10 leukemogenesis. Our laboratory has demonstrated that the CALM protein contains a nuclear export signal (NES) that is critical for CALM-AF10-dependent leukemogenesis. The NES interacts with the CRM1/XPO1 nuclear export receptor, which shuttles proteins from the nucleus to the cytoplasm through the nuclear pore complex. We have shown that transcriptional activation of HOXA genes by CALM-AF10 is critically dependent on its interaction with CRM1. Importantly, CRM1 does not contain a recognized DNA binding domain, and it is not currently understood how the CALM-AF10/CRM1 complex interacts with regulatory regions of HOXAgenes. In order to identify proteins that mediate the interaction between the CALM-AF10/CRM1 complex and DNA, we took advantage of a proximity-based labeling approach using BioID2, a second-generation biotin ligase. When fused to a protein of interest and in the presence of biotin, BioID2 biotinylates proteins in close proximity to the ligase. These biotinylated proteins can then be identified by mass spectrometry (MS). Methods: We prepared an expression plasmid in which BioID2 was cloned in-frame with CALM-AF10. We then transiently transfected Human Embryonic Kidney 293 (HEK293) cells with the BioID2-CALM-AF10 plasmid, grew them in the presence or absence of biotin, and performed streptavidin-pulldown followed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to identify candidate interacting proteins. Proteins were considered candidates if they had a peptide spectrum match (PSM) score > 10 and at least a two-fold greater PSM score versus negative control. We validated direct interactions of candidate proteins with CALM-AF10 by performing co-immunoprecipitation experiments. Results: We first confirmed that the addition of BioID2 to CALM-AF10 does not affect the transcriptional activation of HOXA genes or CALM-AF10 mediated immortalization of hematopoietic stem cells. We carried out three independent transfections/LC-MS/MS experiments, which identified 71, 95 and 61 proteins, respectively. Of the proteins identified, 11 candidates were common to all three experiments.Of particular interest, we identified Disruptor Of Telomeric silencing 1-Like (DOT1L), a protein known to interact with AF10, and Nuclear pore complex protein 214 (NUP214), a protein that has been identified in leukemogenic translocations. The nine additional candidate proteins included: EPS15, DVL2, DVL3, and DDX3X -all known to play a role in leukemogenesis. We performed initial validation of direct interactions via co-immunoprecipitation and found that Epidermal Growth Factor Receptor Substrate 15(EPS15) co-precipitates with CALM-AF10. Conclusion: We used biotin ligase-dependent proximity-based labeling to identify candidate proteins that potentially interact with the CALM-AF10 fusion protein. Our identification of DOT1L validates the approach, since DOT1L is known to interact with CALM-AF10. We have started to investigate other candidate proteins, focusing on known translocation partners in various leukemias. Our screen identified EPS15, a protein involved in receptor-mediated endocytosis of epidermal growth factor and a known translocation partner for MLL/KMT2A. KMT2A-EPS15 translocations (t(1;11)(p32;q23)) have been identified in both AML and ALL, and KMT2A-EPS15 is among the eight most common KMT2A rearrangements. We have shown that EPS15 co-immunoprecipitates with CALM-AF10, suggesting that EPS15 may also play a role in CALM-AF10 leukemogenesis. Further evaluation of this interaction is underway, and may lead to identification of novel pathways involved in CALM-AF10 leukemogenesis. Disclosures No relevant conflicts of interest to declare.

Background: The NUP98 and NUP214 nucleoporins (NUPs) are recurrently fused to heterologous proteins in leukemia. The resulting chimeric oncoproteins retain the NUP phenylalanine-glycine (FG) repeat motifs that mediate interaction with the nuclear export receptor Crm1. NUP fusion leukemias are characterized by HOXA gene upregulation; however, their molecular pathogenesis remains poorly understood. To investigate the role of Crm1 in mediating the leukemogenic properties of NUP chimeric proteins, we studied the SQSTM1-NUP214 fusion. Methods: We synthesized a SQSTM1-NUP214 fusion protein which retains only a short C-terminal portion of NUP214 containing FG motifs that mediate interaction with Crm1, and then introduced point mutations targeting these FG motifs (SQSTM1-NUP214FGmut). We compared the activity of these two fusion proteins using co-immunoprecipitation with CRM1, methylcellulose colony assays, murine transplantation, RT-qPCR, and chromatin immunoprecipitation. Results: We found that the ability of the SQSTM1-NUP214FGmut protein to interact with Crm1 was reduced by more than 50% compared with SQSTM1-NUP214. Further, mutation of FG motifs affected transforming potential: while SQSTM1-NUP214 conferred robust colony formation to transduced hematopoietic progenitors in a serial replating assay, the effect of SQSTM1-NUP214FGmut was greatly diminished. Moreover, SQSTM1-NUP214 caused myeloid leukemia in all transplanted mice (6/6), whereas none of the SQSTM1-NUP214FGmut reconstituted mice developed leukemia (0/7). These oncogenic effects coincided with the ability of SQSTM1-NUP214 and SQSTM1-NUP214FGmut to upregulate the expression of Hoxa and Meis1 genes in hematopoietic progenitors. Indeed, chromatin immunoprecipitation assays demonstrated that impairing the interaction of SQSTM1-NUP214 with Crm1 reduced binding of the fusion protein to Hoxa and Meis1 loci. Conclusions: These findings highlight the importance of Crm1 in mediating the leukemogenic properties of SQSTM1-NUP214, and suggest a conserved role of Crm1 in recruiting oncoproteins to their effector genes. Disclosures No relevant conflicts of interest to declare.

Background: The CALM-AF10 translocation is detected in ~10% of T-cell acute lymphoblastic leukemias (T-ALLs), and in some acute myeloid leukemias (AMLs). CALM-AF10 leukemias are characterized by high expression of proleukemic HOXA genes, which serve a critical role in hematopoiesis. We hypothesized that identification of novel CALM-AF10 effector genes may yield new therapeutic targets in this difficult to treat leukemia. We took advantage of our prior observation that the nuclear export factor CRM1/XPO1 tethers CALM-AF10 to HOXA genes by interacting with a nuclear export signal (NES) in CALM. Using next generation sequencing, we determined that, SIX1, similar to HOXA genes, is increased in CALM-AF10 leukemias and decreased in response to CRM1 inhibition with Leptomycin B (LMB). Design/Methods: RT-qPCR and Chromatin Immunoprecipitation were performed using both bone marrow progenitors and murine embryonic fibroblasts (MEFs) transduced with CALM-AF10 or an empty vector, with and without LMB. The ability of SIX1 to enhance self-renewal of hematopoietic progenitors was examined by measuring the colony-forming ability of transduced fetal liver hematopoietic progenitor cells. CRISPR-Cas9 was used to silence SIX1 in Human Embryonic Kidney 293 (HEK293) cells. Results: RT-qPCR confirmed overexpression of SIX1 in both CALM-AF10 transduced MEFs and CALM-AF10 leukemias, with decreased SIX1 expression observed in the presence of LMB. ChIP analysis showed that CALM-AF10 binds to the SIX1 gene locus. Overexpression of SIX1 in fetal liver cells was sufficient to increase the self-renewal potential of colony-forming progenitors. SIX1 was successfully knocked out in HEK293 cells without a significant effect on HEK293 proliferation. Conclusions: The SIX1 homeobox gene is highly expressed during development and its expression is silenced post-embryogenesis. Increased SIX1 expression has been reported in numerous solid tumors. We have determined that SIX1 is upregulated in CALM-AF10 leukemias, and increases the self-renewal potential of hematopoietic progenitors. Using CRISPR-Cas9 to silence SIX1, we have demonstrated that SIX1 is not essential for cell survival, and that its inhibition may impair CALM-AF10 leukemia cell proliferation. Thus, SIX1 may play a pathogenic role in leukemogenesis and is a potential therapeutic target in CALM-AF10 leukemias. Disclosures No relevant conflicts of interest to declare.

The t(10;11) chromosomal translocation gives rise to the CALM-AF10 fusion gene and is found in patients with aggressive and difficult-to-treat hematopoietic malignancies. CALM-AF10-driven leukemias are characterized by HOXA gene up-regulation and a global reduction in H3K79 methylation. DOT1L, the H3K79 methyltransferase, interacts with the octapeptide/leucine zipper domain of AF10, and this region has been shown to be necessary and sufficient for CALM-AF10-mediated transformation. However, the precise role of CALM in leukemogenesis remains unclear. Here, we show that CALM contains a nuclear export signal (NES) that mediates cytoplasmic localization of CALM-AF10 and is necessary for CALM-AF10-dependent transformation. Fusions of the CALM NES (NES(CALM)-AF10) or NES motifs from heterologous proteins (ABL1, Rev, PKIA, APC) in-frame with AF10 are sufficient to immortalize murine hematopoietic progenitors in vitro. The CALM NES is essential for CALM-AF10-dependent Hoxa gene up-regulation and aberrant H3K79 methylation, possibly by mislocalization of DOT1L. Finally, we observed that CALM-AF10 leukemia cells are selectively sensitive to inhibition of nuclear export by Leptomycin B. These findings uncover a novel mechanism of leukemogenesis mediated by the nuclear export pathway and support further investigation of the utility of nuclear export inhibitors as therapeutic agents for patients with CALM-AF10 leukemias.

WHIM syndrome is a rare, autosomal dominant, immunodeficiency disorder so-named because it is characterized by warts, hypogammaglobulinemia, infections, and myelokathexis (defective neutrophil egress from the BM). Gain-of-function mutations that truncate the C-terminus of the chemokine receptor CXCR4 by 10-19 amino acids cause WHIM syndrome. We have identified a family with autosomal dominant inheritance of WHIM syndrome that is caused by a missense mutation in CXCR4, E343K (1027G → A). This mutation is also located in the C-terminal domain, a region responsible for negative regulation of the receptor. Accordingly, like CXCR4R334X, the most common truncation mutation in WHIM syndrome, CXCR4E343K mediated approximately 2-fold increased signaling in calcium flux and chemotaxis assays relative to wild-type CXCR4; however, CXCR4E343K had a reduced effect on blocking normal receptor down-regulation from the cell surface. Therefore, in addition to truncating mutations in the C-terminal domain of CXCR4, WHIM syndrome may be caused by a single charge-changing amino acid substitution in this domain, E343K, that results in increased receptor signaling.

HOXA genes are effectors of oncogenic transformation that are frequently upregulated in myeloid and T-cell acute leukemias. Chromosomal translocation-derived oncoproteins, including MLL fusions, NUP (NUP98 or NUP214) fusions or CALM-AF10, bind to HOXA genes and result in their overexpression. We have previously demonstrated that a CRM1-dependent Nuclear Export Signal (NES) within CALM is essential for CALM-AF10’s ability to upregulate HOXA genes and cause leukemia in mice. Interfering with the CRM1/CALM-AF10 interaction by either genetic or pharmacologic inhibition abolishes CALM-AF10’s ability to bind to and activate HOXA gene expression. Furthermore, we showed that CRM1 binds to HOXA loci, suggesting that CRM1 recruits CALM-AF10 to its target genes. To explore whether CRM1 is also involved in the upregulation of Hoxa genes associated with MLL- and NUP98-fusion genes, we measured Hoxa transcript levels in murine leukemia cells treated with the CRM1 inhibitor Leptomycin B (LMB). LMB is a small molecule that covalently binds to the NES binding domain of CRM1 and blocks its ability to interact with NES partner proteins. We found that treatment of MLL-AF10, MLL-ENL, NUP98-HOXA9 or NUP98-AF10 leukemia cells with LMB (1 nM, 2 hours) causes a 50% reduction of Hoxa7, Hoxa9, Hoxa10 and Hoxa11 levels, similar to what is observed in CALM-AF10 leukemia cells. This suggests that in addition to its ability to interact with CALM-AF10, CRM1 may also participate in the transcriptional activation of Hoxa genes caused by MLL- or NUP98-fusion proteins. To demonstrate the importance of the CRM1/CALM interaction in CALM-AF10-dependent oncogenesis, we studied the biological activity of an artificial CRM1-AF10 fusion protein. Using a murine bone marrow clonogenic progenitor replating assay, we found that while native CRM1 overexpression did not result in transformation, the CRM1-AF10 fusion significantly increased the self-renewal of clonogenic progenitors. This effect was even more pronounced when CRM1 was fused to the MLL partner ENL: transduction with a CRM1-ENL fusion gene caused the immortalization of clonogenic bone marrow progenitors. Both CRM1-AF10- and CRM1-ENL-transduced progenitors displayed overexpression of Hoxa genes. To investigate the leukemogenic potential of CRM1-AF10in vivo, we transplanted mice with retrovirally transduced bone marrow progenitors and found that CRM1-AF10 induces myeloid neoplasms with a low penetrance and long latency (after more than a year of observation, 5 of 15 mice developed myeloid neoplasms between 160 and 220 days). These primary CRM1-AF10 leukemias could be transplanted to secondary recipients and cause myeloid leukemias with a shorter latency. Experiments to determine the leukemogenic potential of CRM1-ENLin vivo are ongoing. In contrast to CRM1-AF10, CRM1-ENL-transduced progenitors displayed a marked proliferative advantage in all transplanted mice (assessed by the elevation in the percentage of GFP-expressing CRM1-ENL-transduced cells in the peripheral blood over time); mice transplanted 74 days ago will be followed to determine survival curves. In summary, our results demonstrate that CRM1 regulates the expression of Hoxa genes in mouse leukemia cells, and alteration of CRM1’s activity can drive murine leukemogenesis. This has implications for understanding the mechanisms of HOXA deregulation in human leukemias induced by various fusion oncoproteins. It is noteworthy that in addition to interacting directly with CALM-AF10 through the NES, CRM1 physiologically interacts with NUP98 and NUP214 to facilitate transport through the nuclear pore. Our data also suggest that the anti-tumor effects of CRM1 inhibitors (Selective Inhibitors of Nuclear Export, SINEs) currently undergoing clinical trials, could be mediated, at least in part, by their ability to block the transcriptional activation of tumor-promoting genes by CRM1. Disclosures No relevant conflicts of interest to declare.

Abstract 1386 Background: The CALM-AF10 fusion protein arises from the t(10;11) chromosomal translocation and is found in 8–10% of T-cell acute lymphoblastic leukemias and a smaller percentage of acute myeloid leukemias; these hematopoietic malignancies are associated with a poor clinical outcome. The precise contributions of the Clathrin Assembly Lymphoid Myeloid leukemia (CALM) protein to leukemogenesis remain uncertain. CALM plays a role in clathrin-dependent endocytosis, which mediates the entry of growth factor receptors and nutrients into cells and is essential for the internalization of iron-bound transferrin. We have previously shown that Calm-deficient (Calm−/−) mouse fibroblasts derived from fit1 mice are iron deficient, and are more sensitive to treatment with iron chelators. Objective: Since CALM-AF10 leukemia cells are haploinsufficient for CALM, we hypothesize that reduced levels of CALM in CALM-AF10 leukemia cells cause a relative iron deficiency, and result in enhanced sensitivity to iron deprivation. Design/Methods: Fibroblasts and fetal liver hematopoietic progenitors (HP) were derived from Calm−/−, Calm+/− or Calm+/+ E14 embryos. The proliferation rates of non-immortalized fibroblasts were compared in the presence and absence of supplemental iron (ferric ammonium citrate (FAC)) or treatment with an iron chelator (deferoxamine (DFO)). Surface transferrin receptor expression was quantified by flow cytometry. Primary HP cells were cultured in the presence or absence of DFO and viable cell numbers were determined. To examine the anti-leukemic effect of iron deprivation in vivo, C57BL/6J-Tyrc-2J mice were fed a low-iron diet, transplanted with CALM-AF10-transduced Calm+/− leukemia cells and leukemia latency was determined. Results: Heterozygous Calm+/− fibroblasts exhibit CALM protein levels that are intermediate between their wildtype (Calm+/+) and deficient (Calm−/−) counterparts. Calm+/− cells display a slower rate of proliferation in vitro (50% reduction of viable cells) compared to their wildtype fibroblasts, and this growth deficiency can be corrected by iron supplementation with 50 mM FAC. The presence of reduced intracellular iron levels in Calm+/− fibroblasts was manifested by increased transferrin receptor expression relative to wildtype cells. In vitro, Calm+/− HP cells showed greater sensitivity to iron chelation by DFO (5 mM) than Calm+/+ controls: the relative number of viable cells in the presence of DFO was 20% lower in Calm+/− compared to Calm+/− HP cells. To assess the impact of iron deprivation in vivo, bone marrow cells from Calm+/−CALM-AF10 leukemic mice were injected into secondary recipient mice preconditioned by having received a low-iron diet for 8 weeks (n=9). The onset of leukemia in transplanted mice maintained on the iron-deficient diet was considerably delayed (median survival 93 days versus 63 days, p=0.013) relative to age- and gender-matched control mice fed a normal diet (n=9). Conclusions: We have shown that reduced CALM expression impairs iron import and consequently limits the rate of cell proliferation. Both in vitro and in vivo results suggest that CALM haploinsufficient CALM-AF10 leukemias are particularly sensitive to iron deprivation. This raises the possibility that iron chelation may be a previously unappreciated treatment option for patients with aggressive CALM-rearranged leukemias. We are currently studying the impact of iron chelation in murine CALM-AF10 in vivo leukemia models. Disclosures: No relevant conflicts of interest to declare.

Autoimmune lymphoproliferative syndrome (ALPS) is a rare disorder of abnormal lymphocyte survival caused by defective Fas-mediated apoptosis. Patients with ALPS develop lymphadenopathy, hepatosplenomegaly, and increased number of a T cell population normally found in low numbers in peripheral blood called double negative T cells (DNTs, T cell phenotype CD3+/4−/8−, TCRalpha/beta +). Patients frequently develop severe autoimmune disease, primarily manifested as autoimmune cytopenias. Some patients with ALPS need long-term treatment and these patients have limited therapeutic options. Sirolimus, an mTOR inhibitor, has been shown to induce apoptosis in normal and malignant lymphocytes. Because ALPS is caused by defective lymphocyte apoptosis, we hypothesized that sirolimus would be effective by inducing apoptosis in these abnormal cells, controlling the lymphoproliferation that is the hallmark of the disease. We previously tested this hypothesis using murine models of ALPS, and have now opened a phase I/II clinical trial testing sirolimus in patients with ALPS. Six children with ALPS (2 type IA; 4 type III) were started on treatment with sirolimus, targeting a serum trough level of 5–15ng/ml. 4 patients were treated for clinically significant autoimmune cytopenias that either failed standard therapies or in whom these therapies, including high dose corticosteroids, were not tolerated. The two other patients also had autoimmune cytopenias; however, the indication for treatment was autoimmune arthritis and colitis with steroid intolerance. Four of the patients had previously failed treatment with mycophenolate mofetil and not all six could tolerate corticosteroids. One patient had failed treatment with rituximab, methotrexate, cyclosporine, tacrolimus, anti-TNFalpha agents, and cyclophosphamide. Another patient had failed treatment with mercaptopurine and plaquenil. Five of 6 patients had complete resolution of autoimmune cytopenias and normalization of blood counts within 4 weeks of initiating therapy with sirolimus. One of six patients had persistent Grade 1 thrombocytopenia (plt count >100,000/mm3 but less than 150,000/mm3). Four patients had resolution of lymphadenopathy and splenomegaly (3 complete; 1 partial with a greater than 90% reduction). Patients have been treated for 3, 3, 4, 15, 26, and 36 months, respectively. The two patients with co-morbid autoimmune arthritis and colitis showed response in these symptoms as well. All six patients had a greater than 50% reduction in DNTs. Serial PET/CTs were performed on one patient that demonstrated a complete resolution of diffuse PET-avid disease after 3 months. No patient developed any significant toxicity. One patient had developed EBV reactivation while being treated with a combination of high dose steroids, mycophenolate mofetil, and plaquenil-the EBV load went to zero after conversion to sirolimus, which may represent the effect of an mTOR inhibitor on EBV-transformed B cells. We found sirolimus significantly reduced the lymphoproliferative state and improved autoimmunity in patients with ALPS who had failed other therapies. We will continue to test sirolimus in a clinical trial; however, based on the significant improvement we found with this series we would argue that sirolimus be considered as second line therapy for patients with steroid-refractory or steroid-intolerant disease.

Background: Clathrin Assembly Lymphoid Myeloid leukemia (CALM) gene rearrangements, in which CALM is fused to MLL or AF10 genes, are found in aggressive leukemias and lymphomas. Expression of MLL-CALM or CALM-AF10 fusion proteins immortalizes murine hematopoietic cells in vitro, correlating with leukemogenesis in vivo. While disrupted MLL or AF10 activity contributes to transformation, perturbation of normal CALM function may also play a role. The native CALM protein is primarily cytoplasmic and functions in Clathrin-Dependent Endocytosis (CDE). We have previously shown that overexpression of CALM-containing fusion proteins in COS7 cells impairs CDE of both Transferrin (TF) and Epidermal Growth Factor (EGF). These initial observations were made using a qualitative (but time-consuming) visual assay of Texas Red (TR)-labeled TF or EGF. We confirmed these results using a semi-quantitative radioactive assay (with 131I-TF or EGF) that, while sensitive, lacked specificity for transfected cells. Here we describe the development of a flow cytometry-based assay of CDE that permits specific quantitation in cells transfected with CALM-containing proteins. We also measure downstream effects of perturbed CDE on growth factor signaling. Objectives: To validate a novel flow cytometry-based CDE assay; To identify CALM domains that play critical roles in CDE; To analyze kinetics of phosphorylation of JAK2, a downstream target of growth factor signaling, during perturbed CDE. Methods: COS7 cells transfected with GFP-tagged CALM-containing constructs were incubated at 4°C for 1h with AlexaFluor (AF) 633-TF or AF647-EGF to allow binding, followed by incubation at 25°C (5, 10, or 15 min) to permit internalization. Following acid buffer wash and fixing (1% formalin/PBS), internalized fluorescence was measured by flow cytometry. Geometric mean fluorescence intensities of GFP+/AF+ populations were normalized to respective 4°C controls. JAK2 phosphorylation was assessed by western blotting at various time intervals following GM-CSF stimulation of six different leukemia cell lines. Results: Overexpression of CALM-containing constructs in COS7 cells resulted in a reduced rate of TF or EGF internalization. Native CALM (N-CALM1–660) overexpression reduced the rate of TF and EGF internalization by 53%. The portion of CALM found in MLL-CALM fusions, CALM256–660, reduced TF and EGF internalization by 66% compared with controls. CALM436–583 overexpression reduced the rate of TF and EGF internalization by 43%. A series of CALM deletion constructs (CALM256–492, CALM256–502, CALM337–531, CALM593–660, and CALM601–660) did not perturb internalization of TF or EGF. Thus, the presence of a 52 amino acid (aa) region from CALM aa 531–583 was required to perturb internalization. Phosphorylation of JAK2 was prolonged in the setting of CALM-AF10 expression (U937 and P31/Fuji cells) compared with cell lines that do not express CALM-AF10 (HL60, K562, MonoMac6, THP1), likely as a consequence of perturbed CDE. Conclusions: We demonstrate that CALM-dependent perturbation of CDE in COS7 cells can be measured by a novel flow cytometry-based approach. Use of this rapid, quantitative assay narrows the specific region of CALM critical to CDE perturbation to 52 aa. We also show that signaling downstream of growth factors is enhanced during perturbed CDE in leukemia cell lines. These observations support an underappreciated role for CDE dysregulation in leukemogenic transformation.

Background: Clathrin Assembly Lymphoid Myeloid leukemia (CALM) gene rearrangements occur in a subset of aggressive leukemias and lymphomas, in which CALM is fused to the MLL or AF10 genes. Previous studies have shown that expression of MLL-CALM or CALM-AF10 fusion proteins immortalizes murine hematopoietic progenitor cells, an observation that often correlates with leukemogenesis in vivo. While disruption of MLL or AF10 activity contributes to malignant transformation, perturbation of normal CALM function may also play a role. Indeed, the identification of significant hematologic abnormalities in fit1 mice that harbor calm mutations suggests a role for CALM in normal hematopoiesis. The native CALM protein is primarily cytoplasmic and functions in Clathrin-Dependent Endocytosis (CDE). We have demonstrated that expression of native CALM or a CALM C-terminal domain in COS7 cells impairs endocytosis of both Transferrin and Epidermal Growth Factor (EGF). Since cell surface growth factor (GF) signaling may be downregulated by receptor internalization via CDE, we hypothesize that disruption of CDE by CALM-containing fusion proteins interferes with attenuation of GF signaling in hematopoietic cells; this results in sustained proliferation that contributes to leukemogenesis. Objectives: 1) To demonstrate that expression of CALM fusion proteins interferes with the endocytosis of hematopoietic GF; 2) To analyze the time course of phosphorylation of Janus kinases (JAK), downstream targets of GF signaling; 3) To determine whether cells expressing CALM-containing fusion proteins have a survival advantage. Methods: COS7 cells transfected with CALM-containing constructs, and hematopoietic cell lines that natively harbor CALM-AF10 translocations (U937, P31/Fuji) were incubated with 125I-EGF or 125I-GM-CSF, respectively, and the amount of internalized radioactivity was measured. To measure the functional significance of impaired endocytosis, the pattern of JAK phosphorylation in these cells was analyzed by Western blot. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was employed to measure cell proliferation rates. Results: Expression of CALM fusion proteins in COS7 cells was associated with a 40–50% reduction in the rate of EGF endocytosis when compared to control cells. Hematopoietic cell lines that natively harbor CALM-AF10 translocations (U937, P31/Fuji) exhibited reduced rates of GM-CSF endocytosis in comparison with hematopoietic cells lacking such translocations (HL60, K562). EGF treatment of CALM fusion-expressing COS7 cells resulted in increased and prolonged JAK1 phosphorylation. JAK2 phosphorylation was similarly affected in GM-CSF-treated hematopoietic cell lines that natively express CALM-AF10 fusion proteins. Finally, expression of MLL-CALM or CALM-AF10 proteins in COS7 cells was associated with a reduced serum requirement in vitro, showing increased proliferation in low serum relative to controls. Conclusion: We have demonstrated that CALM-dependent perturbation of endocytosis in hematopoietic cells is associated with increased GF signaling, as well as a proliferative advantage in low serum. These observations argue for a crucial and previously unappreciated role for CDE dysregulation in leukemogenic transformation.

Background: MLL translocations are common in infant leukemias, and >50 distinct translocation partners have been described. We recently identified the CALM gene as a novel MLL partner in an infant with aggressive AML. Interestingly, CALM was first discovered as a translocation partner for AF10, which had previously been identified as an MLL fusion partner in aggressive leukemias and lymphomas. The native CALM protein exhibits predominantly cytoplasmic localization, and participates in clathrin-dependent endocytosis and intracellular vesicle transport. We have previously shown that expression of MLL-CALM immortalizes murine hematopoietic progenitors, and that fusion of the carboxy terminus of CALM to MLL alters MLL transcriptional activity. We hypothesize that CALM possesses a specific transcriptional activation domain (TAD) which modulates MLL transcriptional activity of HOX genes, thereby contributing to leukemogenesis. Objectives: 1) To determine whether native CALM localizes to the nucleus, 2) To delineate specific CALM domains which constitute the CALM TAD, and 3) To determine whether MLL-CALM activates transcription through the murine HOXA7 promoter. Methods: Human fibroblast cells were treated with Leptomycin B (an antifungal antibiotic which specifically inhibits nuclear export) and stained with an anti-CALM antibody. We prepared a set of expression vectors in which various portions of CALM are fused to a GAL4 DNA-binding domain. These vectors were co-transfected with a GAL4-luciferase reporter plasmid into COS7 cells, and luciferase activity was measured 48 hours after transient transfection. Luciferase assays were also performed using MSCV-MLL-CALM or MSCV-CALM plasmids co-transfected with a HOXA7 promoter-luciferase reporter construct. Results: After inhibition of nuclear export, native CALM localized to both the nucleus and cytoplasm. Significant luciferase activity was only observed with constructs containing distal CALM carboxy amino acids (aa 436–660). Mutation of an NR (Nuclear Receptor) Box motif (aa 510–514) did not affect CALM-dependent transcription. We found that two endocytosis-related NPF domains play opposite roles: deletion of NPF#1 (aa 437–439) dramatically reduced, while mutation of NPF#2 (aa 639–641) increased transcriptional activity. Expression constructs lacking GAL4 DNA binding domains had no effect on transcription, and GAL4 binding sites were required for luciferase activity in this system. Finally, MLL-CALM activated transcription of the murine HOXA7 promoter in comparison with native CALM or empty vector. Conclusions: We have confirmed that native CALM is able to localize to the nucleus, and we have begun to identify specific critical residues in the CALM TAD. The presence of a CALM TAD in MLL-CALM suggests that altered transcriptional regulation of MLL-dependent HOX genes may play an important role in MLL-CALM dependent transformation. Our observations raise the possibility that other MLL partners with native cytoplasmic localization may possess unrecognized transcriptional activity, and provide new insight into both MLL-CALM and CALM-AF10 mediated leukemogenesis.

Background: We recently identified a novel fusion protein, MLL-CALM, in an infant with fatal AML. Although disruption of normal MLL function clearly contributes to leukemogenesis, perturbed CALM function may also be important. The native CALM protein plays a key role in clathrin-dependent endocytosis (CDE) and intracellular vesicle transport. Interestingly, CALM was first described as a partner for the AF10 gene - itself an MLL partner - in aggressive leukemias and lymphomas. Recently, it was shown that mutations in calm are responsible for hematopoietic abnormalities in inbred fit1 mice. Taken together, these observations suggest an important role for CALM in both normal and malignant hematopoiesis. We hypothesize that disrupted CDE resulting from the presence of CALM-containing fusion proteins interferes with downregulation of growth factor signaling, thereby contributing to leukemogenesis. Objective: 1) To determine whether expression of MLL-CALM or CALM-AF10 interferes with endocytosis of transferrin (TF), 2) To analyze the importance of distinct CALM domains which affect endocytosis, and 3) To determine whether MLL-CALM expression reduces the IL-3 growth factor dependence of FL5.12 cells. Design/Methods: The relative ability of leukemia cell lines that harbor MLL and CALM translocations to endocytose AlexaFluor633-conjugated TF was assessed by flow cytometry. The degree of Texas Red (TR)-TF endocytosis in COS7 cells expressing GFP-tagged MLL-CALM and CALM-AF10 was quantitated using densitometry. CALM deletion constructs were prepared and endocytosis of Texas Red-TF was examined in COS-7 cells transfected with these plasmids. Finally, IL-3-dependent FL5.12 cells engineered to stably express MLL-CALM were grown in decreasing amounts of IL-3-containing WEHI conditioned medium and survival was determined. Results: U937 and P31/Fujioka cells (that harbor the CALM-AF10 translocation) showed reduced endocytosis of AF633-TF, but cells that lack CALM translocations (THP-1, K562, MonoMac6, HL-60) showed robust AF633-TF uptake. COS7 cells expressing MLL-CALM or CALM-AF10 showed 40–50% less endocytosis of TR-TF compared with untransfected cells or cells transfected with empty vector. CALM aa 484–620 appear to be important in inhibiting endocytosis. IL-3-dependent FL5.12 cells transfected with an MLL-CALM expression vector grew better in low concentrations of IL-3-containing WEHI conditioned media in comparison with FL5.12 cells transfected with empty vector. Conclusions: Expression of MLL-CALM or CALM-AF10 interferes with endocytosis, and MLL-CALM expression renders FL5.12 cells less dependent on exogenous IL-3. The ability of MLL-CALM and CALM-AF10 to interfere with CDE may result in sustained growth factor signaling and contribute to the development of aggressive hematopoietic malignancies.