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Spleen tyrosine kinase (SYK) is a non-receptor tyrosine kinase that mediates integrin and Fc receptor signaling in myeloid cells. SYK has been implicated as an oncogenic driver in acute myeloid leukemia (AML) with aberrant expression of HOXA9 and MEIS1 and cooperates with FLT3 internal tandem duplication to drive leukemogenesis. The oral SYK inhibitor entospletinib (ENTO) has demonstrated clinical activity in HOXA9/MEIS1 driven AML and is currently being investigated in a phase 3 trial of previously untreated patients with nucleophosmin1-mutated (NPM1 mut) AML. Lanraplenib (LANRA) is a next generation oral SYK inhibitor with potency and selectivity comparable to ENTO. In healthy volunteers and patients with autoimmune disease, LANRA has shown pharmacokinetic properties that compare favorably with ENTO. To support the clinical development of LANRA for the treatment of AML, ex vivo treatment of patient-derived AML cells was used to compare its activity to that of ENTO, both as a single-agent and in combination with other AML therapies. First, ENTO and LANRA single-agent activities were evaluated in peripheral blood-derived blasts from 15 AML patients, representing different mutational backgrounds including NPM1, FLT3, PTPN11, and NRAS mutations. AML cells were seeded into 96 well plates and treated with ENTO and LANRA for 6 days. Comparable effects on viability were observed across the 15 models with the 2 compounds, and in 11 of the models, the half maximal inhibitory concentration (IC 50) values were within 2-fold of each other. ENTO had a slightly lower IC 50 value than LANRA in the FLT3-mutated models possibly due to the direct FLT3 inhibitory activity of ENTO. Next, we tested the activity of ENTO and LANRA ex vivo in bone marrow-derived AML blasts from 29 AML patients representing diverse mutational backgrounds, including NPM1, IDH1, FLT3, and RAS mutations as well as MLL rearrangements. The models were treated for 9 days with either ENTO or LANRA, and viability was assessed using Annexin V and 7-aminoactinomycin D staining. Again, ENTO and LANRA showed comparable effects on cell viability with no significant differences between the compounds when compared across the different mutational backgrounds. Both studies suggest the potential for anti-leukemic activity in several different genetically defined subsets of AML. Matrix combination assays were performed by combining ENTO or LANRA with either cytarabine (NPM1 mut), gilteritinib (FLT3 mut), or trametinib (RAS mut) with cell viability and death assessed after a 3-day incubation period. Increased cell death in an additive manner was observed in all combinations tested, with results for ENTO and LANRA being similar, indicating the utility of both compounds in combinatorial treatment paradigms. These results support the clinical evaluation of LANRA in genetically defined subsets of AML. A phase 1b/2 study of LANRA in combination with the selective FLT3 inhibitor gilteritinib, in patients with relapsed or refractory FLT3 mut AML is planned for the end of this year. Disclosures Day: Cyteir Therapeutics: Current equity holder in publicly-traded company, Ended employment in the past 24 months; Kronos Bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Heckman: Novartis: Research Funding; Orion Pharma: Research Funding; Celgene/BMS: Research Funding; Oncopeptides: Consultancy, Research Funding; Kronos Bio, Inc.: Research Funding. Schinzel: Kronos Bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Obholzer: Kronos Bio, Inc.: Current Employment, Current equity holder in publicly-traded company, Current holder of individual stocks in a privately-held company, Current holder of stock options in a privately-held company. Lin: Kronos Bio, Inc.: Current Employment. Kumar: Kronos Bio, Inc.: Current Employment, Current equity holder in publicly-traded company. DiMartino: Kronos Bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Saffran: Kronos Bio, Inc.: Current Employment, Current equity holder in publicly-traded company.

Background: Spleen tyrosine kinase (SYK) is a component of both lymphoid and myeloid cell signaling pathways and has been implicated in the pathogenesis of a subset of acute myeloid leukemia (AML) defined by dysregulated expression of the HOXA9 and MEIS1 transcription factors. Entospletinib (ENTO) is an oral, selective SYK inhibitor that is acceptably tolerated when administered with intensive induction and consolidation in newly diagnosed AML patients. In a phase 2 study, following induction with cytarabine and daunorubicin (7+3) plus ENTO, higher rates of complete response (CR) or CR with incomplete hematologic recovery (CRi) were observed in patients with rearrangements of the KMT2A (MLL) gene (MLL-r) and mutations of the nucleophosmin 1 (NPM1) gene, both of which are associated with aberrant expression of HOXA9 and MEIS1, as compared to patients without these mutations. In an exploratory analysis, patients with HOXA9/MEIS1 expression levels above the median experienced superior overall survival (OS) as compared to patients with expression levels below the median. In the AGILITY trial, we hypothesize that the addition of ENTO to intensive induction/consolidation in newly diagnosed patients with NPM1-mutated AML will improve the rate of CR without evidence of measurable residual disease (MRD-negative CR) post-induction and duration of event-free survival (EFS). Methods: AGILITY will be a global, multi-center, double-blind, placebo-controlled trial of ENTO in combination with cytarabine plus daunorubicin or idarubicin induction (7+3) and age-adjusted high-dose cytarabine (HiDAC) consolidation in newly diagnosed AML patients aged 18-75 years who are candidates for intensive induction and harbor a documented NPM1 mutation based on local or central mutation testing. Patients with co-mutated FLT3 (internal tandem duplication or tyrosine kinase domain) and for whom midostaurin with 7+3 is indicated are excluded. Patients will be stratified based on age ( An independent data-monitoring committee will monitor emerging safety and efficacy data from this trial on an ongoing basis. Disclosures Byrd: Vincerx Pharmaceuticals: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Novartis, Trillium, Astellas, AstraZeneca, Pharmacyclics, Syndax: Consultancy, Honoraria; Newave: Membership on an entity's Board of Directors or advisory committees. Cortes: Bristol Myers Squibb, Daiichi Sankyo, Jazz Pharmaceuticals, Astellas, Novartis, Pfizer, Takeda, BioPath Holdings, Incyte: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Bio-Path Holdings, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy, Research Funding; Takeda: Consultancy, Research Funding; Sun Pharma: Consultancy, Research Funding. Minden: Astellas: Consultancy. Oellerich: Roche: Consultancy; Gilead: Research Funding; Kronos Bio, Inc.: Consultancy; Merck KGaA: Consultancy, Research Funding. Stein: Syros Pharmaceuticals, Inc.: Consultancy; Daiichi Sankyo: Consultancy; PinotBio: Consultancy; Celgene: Consultancy; Bristol Myers Squibb: Consultancy; Jazz Pharmaceuticals: Consultancy; Foghorn Therapeutics: Consultancy; Blueprint Medicines: Consultancy; Gilead Sciences, Inc.: Consultancy; Abbvie: Consultancy; Janssen Pharmaceuticals: Consultancy; Genentech: Consultancy; Syndax Pharmaceuticals: Consultancy; Agios Pharmaceuticals, Inc: Consultancy; Novartis: Consultancy; Astellas: Consultancy. Elder: PharPoint Research, Inc.: Current Employment. Kumar: Kronos Bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Bray: Kronos Bio, Inc.: Consultancy. DiMartino: Kronos Bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Stock: Pfizer: Consultancy, Honoraria, Research Funding; amgen: Honoraria; agios: Honoraria; jazz: Honoraria; kura: Honoraria; kite: Honoraria; morphosys: Honoraria; servier: Honoraria; syndax: Consultancy, Honoraria; Pluristeem: Consultancy, Honoraria. OffLabel Disclosure: Entospletinib is an investigational therapy

Pbx1 is the product of a proto-oncogene originally discovered at the site of chromosomal translocations in acute leukemias. It binds DNA as a complex with a broad subset of homeodomain proteins, but its contributions to hematopoiesis have not been established. This paper reports that Pbx1 is expressed in hematopoietic progenitors during murine embryonic development and that its absence results in severe anemia and embryonic lethality at embryonic day 15 (E15) or E16. Definitive myeloerythroid lineages are present inPbx1−/−fetal livers, but the total numbers of colony-forming cells are substantially reduced. Fetal liver hypoplasia reflects quantitative as well as qualitative defects in the most primitive multilineage progenitors and their lineage-restricted progeny. Hematopoietic stem cells from Pbx1−/−embryos have reduced colony-forming activity and are unable to establish multilineage hematopoiesis in competitive reconstitution experiments. Common myeloid progenitors (CMPs), the earliest known myeloerythroid-restricted progenitors, are markedly depleted inPbx1−/−embryos at E14 and display clonogenic defects in erythroid colony formation. Comparative cell-cycle indexes suggest that these defects result largely from insufficient proliferation. Megakaryocyte- and erythrocyte-committed progenitors are also reduced in number and show decreased erythroid colony-forming potential. Taken together, these data indicate that Pbx1 is essential for the function of hematopoietic progenitors with erythropoietic potential and that its loss creates a proliferative constriction at the level of the CMP. Thus, Pbx1 is required for the maintenance, but not the initiation, of definitive hematopoiesis and contributes to the mitotic amplifications of progenitor subsets through which mature erythrocytes are generated.

The t(11;19)(q23;p13.1) chromosomal translocation in acute myeloid leukemias fuses the gene encoding transcriptional elongation factor ELL to the MLL gene with consequent expression of an MLL-ELL chimeric protein. To identify potential mechanisms of leukemogenesis by MLL-ELL, its transcriptional and oncogenic properties were investigated. Fusion with MLL preserves the transcriptional elongation activity of ELL but relocalizes it from a diffuse nuclear distribution to the nuclear bodies characteristic of MLL. Using a serial replating assay, it was demonstrated that the MLL-ELL chimeric protein is capable of immortalizing clonogenic myeloid progenitors in vitro after its retroviral transduction into primary murine hematopoietic cells. However, a structure–function analysis indicates that the elongation domain is not essential for myeloid transformation because mutants lacking elongation activity retain a potent ability to immortalize myeloid progenitors. Rather, the highly conserved carboxyl terminal R4 domain is both a necessary and a sufficient contribution from ELL for the immortalizing activity associated with MLL-ELL. The R4 domain demonstrates potent transcriptional activation properties and is required for transactivation of a HoxA7 promoter by MLL-ELL in a transient transcriptional assay. These data indicate that neoplastic transformation by the MLL-ELL fusion protein is likely to result from aberrant transcriptional activation of MLLtarget genes. Thus, in spite of the extensive diversity of MLL fusion partners, these data, in conjunction with previous studies of MLL-ENL, suggest that conversion of MLL to a constitutive transcriptional activator may be a general model for its oncogenic conversion in myeloid leukemias.

The t(11;19)(q23;p13.1) chromosomal translocation in acute myeloid leukemias fuses the gene encoding transcriptional elongation factor ELL to the MLL gene with consequent expression of an MLL-ELL chimeric protein. To identify potential mechanisms of leukemogenesis by MLL-ELL, its transcriptional and oncogenic properties were investigated. Fusion with MLL preserves the transcriptional elongation activity of ELL but relocalizes it from a diffuse nuclear distribution to the nuclear bodies characteristic of MLL. Using a serial replating assay, it was demonstrated that the MLL-ELL chimeric protein is capable of immortalizing clonogenic myeloid progenitors in vitro after its retroviral transduction into primary murine hematopoietic cells. However, a structure–function analysis indicates that the elongation domain is not essential for myeloid transformation because mutants lacking elongation activity retain a potent ability to immortalize myeloid progenitors. Rather, the highly conserved carboxyl terminal R4 domain is both a necessary and a sufficient contribution from ELL for the immortalizing activity associated with MLL-ELL. The R4 domain demonstrates potent transcriptional activation properties and is required for transactivation of a HoxA7 promoter by MLL-ELL in a transient transcriptional assay. These data indicate that neoplastic transformation by the MLL-ELL fusion protein is likely to result from aberrant transcriptional activation of MLLtarget genes. Thus, in spite of the extensive diversity of MLL fusion partners, these data, in conjunction with previous studies of MLL-ENL, suggest that conversion of MLL to a constitutive transcriptional activator may be a general model for its oncogenic conversion in myeloid leukemias.

The t(10;11)(p12;q23) chromosomal translocation in human acute myeloid leukemia results in the fusion of theMLL and AF10 genes. The latter codes for a novel leucine zipper protein, one of many MLL fusion partners of unknown function. In this report, we demonstrate that retroviral-mediated transduction of an MLL-AF10complementary DNA into primary murine myeloid progenitors enhanced their clonogenic potential in serial replating assays and led to their efficient immortalization at a primitive stage of myeloid differentiation. Furthermore, MLL-AF10–transduced cells rapidly induced acute myeloid leukemia in syngeneic or severe combined immunodeficiency recipient mice. Structure/function analysis showed that a highly conserved 82–amino acid portion of AF10, comprising 2 adjacent α-helical domains, was sufficient for immortalizing activity when fused to MLL. Neither helical domain alone mediated immortalization, and deletion of the 29–amino acid leucine zipper within this region completely abrogated transforming activity. Similarly, the minimal oncogenic domain of AF10 exhibited transcriptional activation properties when fused to the MLL or GAL4 DNA-binding domains, while neither helical domain alone did. However, transcriptional activation per se was not sufficient because a second activation domain of AF10 was neither required nor competent for transformation. The requirement for α-helical transcriptional effector domains is similar to the oncogenic contributions of unrelated MLL partners ENL and ELL, suggesting a general mechanism of myeloid leukemogenesis by a subset of MLL fusion proteins, possibly through specific recruitment of the transcriptional machinery.

The MLL gene is fused to over 30 different fusion partners by reciprocal translocations in human acute leukemias. Some fusion partners are associated almost exclusively with myeloid or lymphoid leukemias while others are found in both. The degree to which the fusion partner contributes to the lineage of the resulting leukemia remains a matter of controversy. Using a novel model system, we demonstrate that myeloid vs lymphoid differentiation of hematopoietic progenitors transformed by MLL-AF9 can be predictably driven by cytokine combinations in vitro and in vivo. The t(9;11)(p22;q23) MLL-AF9 fusion gene is commonly associated with M5 myeloid leukemia but approximately 5% of MLL-AF9 leukemia is B-lymphoid. Expression of MLL-AF9 in human CD34+ cells enables efficient modeling of acute myeloid, B-lymphoid and biphenotypic leukemia. The lineage of the resulting leukemia can be readily manipulated in vitro (by altering the growth factors) or in vivo (using B-lymphoid-biased NOD/SCID mice or myeloid-biased NOD/SCID that are transgenic for human SCF, GM-CSF and IL-3). The cytokines IL-3, IL-7 and FLT3L appear to exert the major effects on lineage fate determination in vitro. Through limiting dilution and clonality analyses, we find a complex relationship between different leukemia stem cell compartments, with some LSC demonstrating multipotentiality and others showing strict lineage commitment. Data indicate that these differences are primarily due to microenvironment effects, with the identity of the initial cell that is targeted by MLL-AF9 possibly playing a role. These results would argue against a deterministic role for the fusion partner in MLL leukemia. This human-based system should prove useful in addressing the mechanism of lineage promiscuity of MLL leukemias. It also affords us the unique ability to determine the susceptibility of the different LSC to standard chemotherapeutic compounds, in addition to identifying novel therapeutic strategies that may be effective in treating MLL leukemia.

The t(9;11)(p22;q23) results in the creation of an MLL-AF9 fusion gene and is observed in 27% of 11q23 leukemias. t(9;11) is commonly associated with an M5 monocytic leukemia and patients harboring this translocation are included in the intermediate or poor cytogenetic risk groups, with an average 42% overall survival at five years. Using primary human hematopoietic progenitor cells, we have developed a system that closely mimics the MLL-AF9 associated disease observed in human acute myeloid leukemia (AML). Injection of MLL-AF9 expressing cells into sublethally-irradiated NOD/SCID mice produced an aggressive FAB-M5-like leukemia that infiltrated the spleen and liver and induced death with an average latency of 8 weeks. Serial transplantation of leukemic cells recapitulated the disease with a similar latency. MLL-AF9 expression conferred the ability to grow indefinitely in culture, promoted an accumulation of cells resembling monoblasts and was associated with an increase in telomerase activity. Mono- or oligoclonal outgrowth arose in vitro as well as in vivo. Numeric karyotypic changes or normal karyotypes, in the absence of structural rearrangements, additions or deletions were detected in cultured cells as well as samples from leukemic mice. Principal Component Analysis of genome-wide gene expression data from MLL-AF9 expressing cultured cells revealed a gene expression signature that closely mirrors that observed in MLL-rearranged leukemic cells from patient samples. Furthermore, training of a (linear) Support Vector Machine with gene expression data from patient samples resulted in the correct classification of all MLL-AF9-expressing cell cultures as MLL-rearranged leukemia. We conclude that expression of MLL-AF9 in a normal human hematopoietic progenitor is sufficient to recapitulate many key aspects of the clinical disease. This model will yield valuable insights into the molecular pathogenesis of MLL fusion driven leukemia and will serve as a powerful in vivo model for testing much needed novel therapeutic targets.

Translocations involving the MLL gene, primarily t(9;11) and t(10;11) together with rearrangements affecting the core binding factor (CBF) genes, t(8;21) and inv(16) comprise the most frequent cytogenetic abnormalities in acute myeloid leukemia (AML). Although all of these rearrangements generate chimeric transcription factors (MLL-AF9, MLL-AF10, AML1-ETO and CBFβ-MYH11) clinicopathologic features and transcriptional profiles clearly distinguish MLL-rearranged from CBF-rearranged AML. To understand how these distinct subgroups of AML arise, we have developed a model for studying the effects of MLL and CBF fusion proteins on the growth, survival and differentiation human myeloid progenitors in vitro. Using retroviral mediated gene transfer, we transduced CD34 selected normal human cord blood (CB) cells with vector (MIEG3) alone or with vectors expressing MLL-AF9, MLL-AF10 or AML1-ETO fusion genes. Whereas CB transduced with MIEG3 proliferated in liquid culture for 6 to 8 weeks, MLL-AF9, MLL-AF10 and AML1-ETO transduced cells have continued to proliferate continuously in culture for more than 16 weeks without any sign of crisis. At any point after transduction, CB expressing MLL-AF9 or MLL-AF10 exhibited a faster rate of growth as compared with AML1-ETO or MIEG3 transduced CB. This difference in growth rate was associated with a reduced frequency of spontaneous apoptosis by annexin staining in the MLL cultures, as compared with the AML1-ETO cultures, but no difference in the fraction of cells in S-phase. MLL-AF9 and MLL-AF10 transduced CB also exhibited evidence of early myeloid maturation arrest based on morphology and surface antigen expression. However, while AML1-ETO transduced cells continue to express CD34 throughout their time in culture, MLL cultures lose expression of this stem cell-associated antigen and acquire expression of c-Kit and CD33, neither of which is expressed in AML1-ETO cultures. Also, unlike AML1-ETO transduced cells, CB transduced with with MLL fusions retain serial clonogenicity for 3 or more rounds of plating in methylcellulose assays. We used quantitative realtime RT-PCR to measure expression of 3 genes that are differentially expressed in patients with MLL or CBF gene fusions based on published microarray data. While expression of SPARC increased over time in MIEG3 cultures or remained stable in CB transduced with AML1-ETO, it decreased to nearly undetectable levels in MLL-AF9 transduced cultures. In contrast, expression of both BMI-1 and HOXA9 increased in the MLL-AF9 cultures and decreased in the MIEG3 and AML1-ETO cultures. The transcriptional changes in our long-term cultures mirror the gene expression differences that have been observed in AML associated with MLL or CBF fusions and suggest that this will be a useful model to study how chimeric transcription factors contribute to myeloid leukemogenesis. Interestingly, CB transduced with a mutated MLL-AF10 (MA10ΔLZ) lacking the leucine zipper domain required for transformation of primary murine myeloid progenitors did not differ, in terms of growth or differentation, from MIEG3 transduced cells. This suggests that the effects of MLL-AF9 and MLL-AF10 on normal CB may reflect early events in myeloid leukemogenesis. The in vivo leukemogenic potential of MLL fusion transduced CB is currently being evaluated in NOD/SCID mice.

Transcriptional repression by chimeric transcription factors is emerging as a common theme in leukemogenesis and as a therapeutic target for chromatin remodeling agents. We hypothesized that rearrangements involving the MLL gene result in the inappropriate silencing of growth and survival control genes subordinate to this positive epigenetic transcriptional regulator. To identify some of these genes, we used Significance Analysis of Microarrays (SAM), a supervised learning algorithm. We found significant gene expression differences between 13 patients with MLL translocations and 12 core binding factor (CBF) rearranged patients, 2 t(8;21), 10 INV16, from a Pediatric Oncology Group AML study (POG 9421). We also analyzed gene expression data from a published study of adult AML including 8 MLL rearranged patients, 11 with t(8;21) and 15 with INV16. SAM identified 10 genes, common to both datasets, that were significantly under-expressed in the MLL rearranged patients. One of the most significant genes was osteonectin, also known as secreted protein, acidic, rich in cysteine (SPARC). This gene encodes a matricellular glycoprotein with diverse functions in cell-matrix interactions. SPARC has been identified as a target of epigenetic silencing in pancreatic cancer and addition of exogenous SPARC to cancer cell lines induces growth arrest and apoptosis. To determine if leukemia cell lines could be used as a model to study the basis for SPARC silencing and its role in cell growth and survival we measured SPARC expression in AML cell lines with rearranged and germline MLL genes. By real-time quantitative reverse transcriptase PCR (Q-RT-PCR), the cell lines THP-1 (MLL-AF-9) and ML-2 (MLL-AF6) expressed SPARC mRNA levels 40 to 1000 fold lower than Kasumi-1 (t(8;21)) and KG1a. By Western blot, SPARC was easily detectable in Kasumi-1 and KG1a but undetectable in the MLL rearranged lines. Bisulfite sequencing revealed extensive methylation of CpG dinucleotides in the promoter region and first exon of SPARC in THP-1 and ML-2 but a complete lack of methylation in KG1a. Treatment with the DNA methyltransferase inhibitor 5-aza-2′deoxycytidine (DAC) restored SPARC expression to nearly normal levels in THP-1 cells by Q-RT-PCR and Western blot, suggesting that promoter methylation is critical to the silencing of this gene. To determine if SPARC was contributing to the growth inhibitory effect of DAC, cells were cultured in varying concentrations of exogenous purified SPARC. Concentrations of SPARC that reduced the growth of ML-2 and THP-1 by 30 to 40% had no effect on the growth of KG1a cells. We conclude that SPARC, a putative tumor suppressor that is epigenetically silenced in pancreatic cancer, is also silenced by promoter methylation in AML with MLL rearrangements. These studies suggest that SPARC expression may constitute a reliable pharmacodynamic endpoint for clinical studies of chromatin remodeling agents in patients with MLL rearranged AML. Whether SPARC is a direct target of MLL and how MLL rearrangements are related to SPARC silencing are the subject of future studies.