MLL-rearranged Infant Acute Lymphoblastic Leukemia Research Articles

Selective Inhibition of Class II HDAC Isoforms 4 and 5 Provides a Promising Therapeutic Intervention for MLL-Rearranged Acute Lymphoblastic Leukemia in Infants

▪MLL-rearranged acute lymphoblastic leukemia (ALL) is characterized by deregulation of the epigenome and shows susceptibility towards epigenetic perturbators such as histone deacetylase (HDAC) inhibitors. Hence, HDACs represent attractive drug targets and a variety of small molecule HDAC inhibitors have been developed and evaluated for the treatment of hematological malignancies. However, most broad-spectrum inhibitors, which simultaneously target the majority of human HDAC isoforms, often induce toxicity, especially in combination with other therapeutic agents. Therefore, selective inhibition of only one or two HDAC isoforms may represent a better alternative, provided that disease-specific dependency on specific HDACs has been identified.We examined the effects of shRNA-mediated knock-down of the class II HDACs (i.e. HDAC4, HDAC5, HDAC6, HDAC7 and HDAC9) in the MLL-rearranged ALL cell lines SEM and ALL-PO. Except for HDAC9, loss of expression (both on the mRNA and protein level) of all HDACs led to strong reductions in viable cells (0.70 to 0.19-fold; p=0.02-0.0016) in both models due to apoptosis, cell cycle arrest, or a combination thereof.Next, we evaluated the in vitro efficacy of a variety of class II HDAC-specific inhibitors on a panel of MLL-rearranged ALL (n=5) using 4-day viability MTT assays. This revealed that the selective HDAC4/5 inhibitor LMK-235 was able to recapitulate the loss-of-function phenotype of HDAC4 and HDAC5. Dose response curves showed complete growth inhibition in MLL-rearranged ALL cell lines (n=5), as well as in primary MLL-rearranged infant ALL patient samples (n=4), with IC 50 values of ~100 nM and 40-100 nM, respectively. Importantly, at these concentrations, LMK-235 hardly affected whole bone marrow samples derived from healthy individuals (n=2), for which IC 50 values were ~1 µM.To further explore the potential of class II HDAC inhibitor-based therapeutic strategies, we performed a combinatorial drug screen to identify compounds that synergize with LMK-235. For this, a compound library (comprising >200 unique agents) was screened in the absence and presence of varying concentrations of LMK235 in the MLL-rearranged cell line models SEM and ALL-PO. This, and subsequent validation experiments in additional cell line models, revealed that Venetoclax (BCL2 inhibitor), Trametinib (MEK/ERK inhibitor), Ponatinib (multi-tyrosine kinase inhibitor) and Omipalisib (a PI3K/mTOR inhibitor) strongly synergized with LMK-235. Average ZIP synergy scores ranged from 10-30, with peak ZIP scores up to 40. Importantly, synergistic effects were consistent over all concentration combinations tested. The addition of 50-100 nM LMK-235 strongly reduced IC 50 values for Omipalisib, Ponatinib and Venetoclax (0.27-fold p=0.003, 0.11-fold p=0.0005, 0.75-fold p=0.0004, respectively) in both models.In preparation to assess the in vivo efficacy of LMK-235 in patient-derived xenograft (PDX) mouse models of MLL-rearranged infant ALL, pharmacokinetic/pharmacodynamic (PK/PD) analysis was performed in immunodeficient NSG mice (n=5). For this, mice were treated with 20 mg/kg of LMK-235, daily administered via intraperitoneal injections for a total of 29 days. While none of the mice showed signs of toxicity or weight loss, LMK-235 plasma levels were stably maintained at concentrations that are highly effective against MLL-rearranged ALL cells in vitro.Taken together, these data demonstrate that various class II HDAC isoforms are targetable vulnerabilities in MLL-rearranged ALL and that pharmaceutical inhibition of HDAC4/5 by LMK-235 represents an attractive therapeutic option. Moreover, high levels of synergy observed between this HDAC inhibitor and various agents belonging to drug classes already reported to be effective against MLL-rearranged ALL, warrants pre-clinical evaluation in vivo. Currently, the assessment of the in vivo efficacy of LMK-235 monotherapy in MLL-rearranged infant ALL PDX models is in progress, after which promising synergistic HDAC inhibitor-based drug combinations will be evaluated. To determine the additional therapeutic value, the efficacy of LMK-235 and promising synergistic combinations will be evaluated in the background of conventional combination chemotherapy, where PDX models will receive a mouse-adapted version of induction therapy currently applied for treatment of MLL-rearranged infant ALL patients. DisclosuresNo relevant conflicts of interest to declare.

Identification and characterization of relapse-initiating cells in MLL-rearranged infant ALL by single-cell transcriptomics

Infants with MLL-rearranged infant acute lymphoblastic leukemia (MLL-r iALL) undergo intense therapy to counter a highly aggressive malignancy with survival rates of only 30–40%. The majority of patients initially show therapy response, but in two-thirds of cases the leukemia returns, typically during treatment. The glucocorticoid drug prednisone is established as a major player in the treatment of leukemia and the in vivo response to prednisone monotreatment is currently the best indicator of risk for MLL-r iALL. We used two different single-cell RNA sequencing technologies to analyze the expression of a prednisone-dependent signature, derived from an independent study, in diagnostic bone marrow and peripheral blood biopsies. This allowed us to classify individual leukemic cells as either resistant or sensitive to treatment and show that quantification of these two groups can be used to better predict the occurrence of future relapse in individual patients. This work also sheds light on the nature of the therapy-resistant subpopulation of relapse-initiating cells. Leukemic cells associated with high relapse risk are characterized by basal activation of glucocorticoid response, smaller size, and a quiescent gene expression program with cell stemness properties. These results improve current risk stratification and elucidate leukemic therapy-resistant subpopulations at diagnosis.

Irinotecan Induces Disease Remission in Xenograft Mouse Models of Pediatric MLL-Rearranged Acute Lymphoblastic Leukemia.

Acute lymphoblastic leukemia (ALL) in infants (<1 year of age) remains one of the most aggressive types of childhood hematologic malignancy. The majority (~80%) of infant ALL cases are characterized by chromosomal translocations involving the MLL (or KMT2A) gene, which confer highly dismal prognoses on current combination chemotherapeutic regimens. Hence, more adequate therapeutic strategies are urgently needed. To expedite clinical transition of potentially effective therapeutics, we here applied a drug repurposing approach by performing in vitro drug screens of (mostly) clinically approved drugs on a variety of human ALL cell line models. Out of 3685 compounds tested, the alkaloid drug Camptothecin (CPT) and its derivatives 10-Hydroxycamtothecin (10-HCPT) and 7-Ethyl-10-hydroxycamtothecin (SN-38: the active metabolite of the drug Irinotecan) appeared most effective at very low nanomolar concentrations in all ALL cell lines, including models of MLL-rearranged ALL (n = 3). Although the observed in vitro anti-leukemic effects of Camptothecin and its derivatives certainly were not specific to MLL-rearranged ALL, we decided to further focus on this highly aggressive type of leukemia. Given that Irinotecan (the pro-drug of SN-38) has been increasingly used for the treatment of various pediatric solid tumors, we specifically chose this agent for further pre-clinical evaluation in pediatric MLL-rearranged ALL. Interestingly, shortly after engraftment, Irinotecan completely blocked leukemia expansion in mouse xenografts of a pediatric MLL-rearranged ALL cell line, as well as in two patient-derived xenograft (PDX) models of MLL-rearranged infant ALL. Also, from a more clinically relevant perspective, Irinotecan monotherapy was able to induce sustainable disease remissions in MLL-rearranged ALL xenotransplanted mice burdened with advanced leukemia. Taken together, our data demonstrate that Irinotecan exerts highly potent anti-leukemia effects against pediatric MLL-rearranged ALL, and likely against other, more favorable subtypes of childhood ALL as well.

Targeting Critical Kinases and Anti-Apoptotic Molecules Overcomes Steroid Resistance in Infant MLL-Rearranged Leukemia

Acute lymphoblastic leukemia (ALL) with rearrangement of the mixed-lineage leukemia (MLL) gene frequently affects infants and is associated with a poor prognosis. Standard treatment protocol for infant MLL-rearranged ALL (MLL-ALL) includes glucocorticoids (GCs). However, resistance to GCs remains a major problem. Therefore, it is important to find new treatment strategies that overcome GC resistance in MLL-ALL. To identify novel therapeutic targets to overcome GC resistance in MLL-ALL, we compared transcriptional profiles of normal cord blood CD34+CD38- hematopoietic stem and progenitor cells and GC-resistant infant MLL-ALL leukemia-initiating cells (LICs). We found enrichment of the Src family kinases (SFKs) and Fms-like tyrosine kinase 3 (FLT3) signaling pathways in the LICs. We hypothesized that activation of these kinases may contribute to GC resistance in MLL-ALL cells. Using our previously developed infant MLL-ALL patient-derived xenograft (PDX) models (Aoki et al., Blood, 2015), we recapitulated human GC-resistance in vivo, characterized by increased hCD45+ chimerism in the peripheral blood after treatment with dexamethasone (% peripheral blood human MLL-ALL at pre-treatment: 34.1±5.2% vs. post treatment 51.3±6.6%, n=26). In order to investigate if inhibition of SFKs and FLT3 can overcome GC-resistance, we treated the MLL-ALL PDX models with our previously developed FLT3-SFK multiple kinase inhibitor RK-20449 (Saito et al., Science Translational Medicine, 2013). Combination treatment with dexamethasone and RK-20449 successfully eliminated human MLL-ALL cells from the peripheral blood (dexamethasone alone: 47.2±7.2% vs. combination: 5.6±2.8% hCD45+ cells, p=6.91E-7), bone marrow (dexamethasone alone: 72.2±4.6% vs. combination: 19.5±4.8% hCD45+ cells, p=1.79E-10), and spleen (dexamethasone alone: 52.6±4.8% vs. combination: 11.7±3.5% hCD45+ cells, p=3.75E-9). In addition, combination treatment eliminated infiltrated MLL-ALL from kidney and liver of the MLL-ALL PDX models. Bcl-2 homology domain 3 (BH3) profiling demonstrated that MLL-ALL cells resistant to RK-20449 treatment were dependent on the anti-apoptotic Bcl-2 protein for their survival. Additional inhibition of Bcl-2 by ABT-199 led to complete elimination of MLL-ALL cells in vitro and in vivo in all MLL-ALL patient cases (Figure1). Taken together, in this study we demonstrated that inhibition of SFKs and FLT3 by RK-20449 overcomes GC-resistance in MLL-ALL. Further, we identified Bcl-2 dependence as a mechanism of treatment resistance in MLL-ALL. Therefore, we believe that the combined inhibition of kinase and anti-apoptotic pathways may lead to effective treatment options for highly resistant infant MLL-ALL. Aoki, et al., Identification of CD34+ and CD34- leukemia-initiating cells in MLL-rearranged human acute lymphoblastic leukemia. Blood, 2015: p. 967-980. Saito, Y., et al., A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo. Science Translational Medicine, 2013: p. 1-15. Disclosures No relevant conflicts of interest to declare.

3108 - Blockage of NG2 Antigen Synergizes in Vivo with VXL Treatment Resulting in a Delayed Relapse in a Nsg Mice-Based Preclinical Model for MLL-Rearranged BCP-ALL

MLL-rearranged (MLLr) infant B-cell precursor ALL (iMLLr-BCP-ALL) has a dismal prognosis and is associated with a pro-B/mixed phenotype, therapy refractoriness and frequent central nervous system (CNS) disease/relapse. Neuron-glial antigen 2 (NG2) is specifically expressed in MLLr leukemias and is clinically used because of its predictive value. However, its role in MLL-mediated leukemogenesis remains elusive. We previously reported in a large patient cohort that high expression of NG2 associates with poor outcome. Furthermore, we also showed that although NG2 is a malleable marker not enriching for leukemia-initiating cells, it is consistently upregulated in blasts infiltrating extramedullar hematopoietic sites and the CNS, suggesting a key role in migration. We here hypothesize that NG2 may be a therapeutic target for iMLLr-BCP-ALL. Here, we demonstrate that blocking of NG2 in vivo promotes the exit of MLLr BCP-ALL blasts from BM to PB, suggesting a role for the extracellular domain of NG2 in retaining MLLr blasts within the BM niche. When combined with standard ALL chemotherapy (Vincristine, Prednisone and L-Asp, VxL), anti-NG2 resulted in 3-fold decreased levels of minimal residual disease. Importantly, follow-up of mice in (near)-complete remission evidenced that anti-NG2 when combined with VXL significantly delayed mice relapse. Preliminary studies suggest that NG2+ blasts are more resistant than NG2- blast to Glucocorticoids. In addition, NG2 promoter has binding sites for GC receptors, and treatment with dexamethasone results in increased levels of NG2, likely reflecting a NG2-mediated mechanism to escape GC toxicity. Collectively, our data propose NG2 antigen as a therapeutic target in MLLr-B-ALL using either antibody-based or CAR T-cell-based immunotherapy.

Abstract 1925: High-throughput drug library screening identifies potent drugs and novel drug targets for high-risk acute leukemia in children

Abstract BACKGROUND: Acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) represent the most common types of cancer among children. Although the survival rates of pediatric ALL and AML have improved substantially over the last decades, the prognosis for some subgroups of pediatric leukemia remain poor. MLL-rearranged infant ALL, MLL-rearranged AML, and NUP98-rearranged AML, for instance, still have 5-year event-free survival rates of only ~40%. Evidently, these high-risk subtypes of childhood leukemia urgently require new treatment strategies in order to improve clinical outcome. AIM: Identification of effective therapeutic drugs for high-risk leukemia subtypes harboring a translocation in the MLL or NUP98 gene, by using a drug repurposing strategy involving high-throughput screening of &amp;gt; 4000 compounds. METHODS: Primary leukemic cells derived from six patients with either MLL-rearranged infant ALL, pediatric MLL-rearranged AML, or pediatric NUP98-rearranged AML at diagnosis, were screened using commercially available drug libraries comprising a total of 4165 compounds. Drug sensitivity was assessed after 4 days treatment with 10 nM, 100 nM and 1000 nM of the library compounds using MTT assays. Potential hits were subsequently validated using cytotoxicity assays with a more extensive range of drug concentrations. RESULTS: The results of our drug screens showed that the most effective drugs, by far, were found for MLL-rearranged infant ALL. For MLL-rearranged AML the number of identified potent drugs was considerably less; notably, all of these compounds identified overlapped with the effective agents also found for MLL-rearranged infant ALL. Remarkably, for NUP98-translocated AML, only a few potential drug hits were identified, suggesting that this type of leukemia might be extremely chemo-resistant. In addition to novel candidate compounds, we also found several agents either recently described to have strong anti-leukemic effects against MLL-rearranged leukemia, such as the BCL2 inhibitors Venetoclax (ABT199) and Navitoclax (ABT263), or the MDM2 inhibitor Idasanutlin (RG7388), as well as finding drugs currently being used in the treatment of MLL-rearranged acute leukemias. Taken together, these observations indicate that high-throughput drug screening on primary patient samples is indeed able to identify effective compounds, validating our experimental approach. Interestingly, while validating newly identified drug hits, we observed a remarkable pattern for compounds effective against MLL-rearranged acute leukemia: the top hits seem to either directly or indirectly associate with p53 activity, albeit from various angles. CONCLUSION: Our data suggests a potential role for p53 in MLL-rearranged acute leukemia, and indicates that targeting p53 may well become an important therapeutic strategy for these types of childhood leukemia. Citation Format: Priscilla Wander, Sandra S. Pinhanços, Bianca Koopmans, M. Emmy M. Dolman, Pauline Schneider, Patricia Garrido Castro, Luke Jones, Susan T.C.J.M. Arentsen-Peters, Mark Kerstjens, Jan Molenaar, Huib N. Caron, Rob Pieters, Michel C. Zwaan, Ronald W. Stam. High-throughput drug library screening identifies potent drugs and novel drug targets for high-risk acute leukemia in children [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1925.

Abstract 3187: Pediatric Preclinical Testing Consortium evaluation of the menin inhibitor, VTP-50469, against xenograft models of MLL-rearranged infant acute lymphoblastic leukemia

Abstract Introduction: Rearrangements involving the MLL (mixed lineage leukemia, KMT2A) gene (MLLr) occur broadly in acute leukemia, in ~80% of infant acute lymphoblastic leukemia (ALL) cases, and are associated with poor outcome. Menin is a ubiquitously expressed nuclear protein, and the MLLr-menin interaction is the key impetus for transformation of MLLr-expressing cells. VTP-50469 is a potent, orally available, small molecule inhibitor of the MLL-menin interaction with pM binding affinity for menin. Therefore, it was of interest to test the in vivo efficacy of VTP-50469 against preclinical models of infant MLLr-ALL. Methods: Infant MLLr-ALL patient-derived xenografts (PDXs) grew in an orthotopic manner in NSG mice. Engraftment and response to treatment were assessed by enumeration of the % human leukemic blasts in the murine peripheral blood (%huCD45+). Treatment commenced when the median %huCD45+ exceeded 1%, and mice received VTP-50469 (120 mg/kg by oral gavage twice daily x 28) or vehicle. An event was defined as the %huCD45+ &amp;gt;25% or leukemia-related morbidity. The Kaplan-Meier method was used to compare event-free survival (EFS) between treated (T) and control (C) groups. Stringent objective response measures were assigned to each mouse and reported as group medians (Houghton et al, Pediatr. Blood Cancer, 2007;49:928-40). Leukemia infiltration into the femoral bone marrow was also assessed at Day 28 following treatment initiation. VTP-50469 was provided by Vitae Pharmaceuticals. Results: VTP-50469 was well tolerated, with maximum average weight losses of 1.6-6.4% across treatment groups compared to 0-2.0% in vehicle control treated groups. VTP-50469 induced significant differences in EFS distribution compared to control in 6 of 6 (100%) of the evaluable MLLr-ALL PDXs. VTP-50469 T-C values in MLLr-ALL PDXs ranged from 1.2 to 100 days (T/C 1.3-21.1), and Maintained Complete Responses (MCRs) were observed in 5 of 6 PDXs. Two of 8 mice engrafted with an MLLr-ALL harboring the MLL-AFF1 (t4;11) translocation had not reached event &amp;gt;230 days following treatment initiation. A significant reduction (P&amp;lt;0.001) in bone marrow infiltration at Day 28 was observed in 2 of 4 evaluable MLLr-ALL PDXs. VTP-50469 at 30 mg/kg (4-fold lower than its maximum tolerated dose) also elicited MCRs in 8 of 8 mice engrafted with an MLL-AFF1 PDX. The on-target activity of VTP-50469 was verified by its lack of efficacy against an ALL PDX harboring the BCR-ABL1 translocation. Conclusions: VTP-50469 exerted profound in vivo efficacy against ALL PDXs derived from infants harboring MLL-AFF1, MLL-GAS7, and MLL-ENL translocations, and significantly reduced leukemia infiltration in the bone marrow. VTP-50469 was also effective across a broad dose range, indicating that it may represent a novel treatment for MLLr leukemia. (Supported by NCI Grants CA199222 &amp; CA199000) Citation Format: Richard B. Lock, Kathryn Evans, Tara Pritchard, Stephen W. Erickson, Yuelong Guo, David A. Claremon, Gerard M. McGeehan, Beverly A. Teicher, Malcolm A. Smith. Pediatric Preclinical Testing Consortium evaluation of the menin inhibitor, VTP-50469, against xenograft models of MLL-rearranged infant acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3187.

Differential Expression of Adhesion Molecule Receptors May Influence Bone Marrow Microenvironment-Mediated Protection of Leukemia-Initiating Cells (LICs) in Infant MLL-rearranged (MLL-R) Acute Lymphoblastic Leukemia (ALL)

Background: Compared to older children with ALL who achieve a minimal residual disease (MRD)-negative remission, infants with ALL who achieve an MRD-negative remission have a significantly higher rate of relapse. This suggests that, despite the achievement of MRD negativity, a very small amount of leukemia cells persist and contribute to disease relapse in infant ALL; LICs are likely to represent this persistent population of cells. Previously, we demonstrated that infant MLL-R ALL derive significantly more protection from co-culture with bone marrow (BM) stromal cells than non-MLL-R ALL. Therefore, protection by the BM microenvironment may contribute to LIC persistence in infant MLL-R ALL. We hypothesized that infant MLL-R ALL LICs have increased interactions with the BM microenvironment, through increased surface expression of adhesion molecule receptors. We also hypothesized that co-culture with normal BM stroma would protect LICs from spontaneous and chemotherapy-induced apoptosis, and AMD3100 (plerixafor) would decrease stromal protection through inhibition of CXCR4-CXCL12 signaling.Methods/Results: We analyzed 9 viably cryopreserved diagnostic samples collected from infants with MLL-R ALL (n=4 MLL-AF4, n=5 MLL-ENL). Using flow cytometry, we identified 2 phenotypically-defined LIC subpopulations, CD34+CD38+CD19+ and CD34-CD19+ (Aoki et al 2015), within the bulk leukemic blast population (CD45+). Consistent with previous findings, 34+38+19+ LICs were predominant in MLL-AF4 samples, while 34-19+ LICs were predominant in MLL-ENLsamples. Next, we measured surface expression of the adhesion molecule receptors CXCR4, CD49d (VLA-4), CXCR7, and CXCR3 (quantified as mean fluorescence intensity, MFI). Overall, surface expression of CXCR4, CD49d, CXCR7, and CXCR3 was higher in the 34+38+19+ LICs, compared to 34-19+ LICs (e.g., CXCR4 MFI 142 in 34+38+19+ vs. 76 in 34-19+, p=0.02).Next, samples were treated with dose ranges (0-30 µM) of AraC or etoposide (Etop) and cultured for 48 hours in 3 conditions: 1) off stroma, 2) on stroma, or 3) on stroma with the CXCR4 inhibitor AMD3100 (10 μM). Stromal cells were cultured from a healthy BM donor. In vehicle control-treated 34+38+19+ LICs, stromal co-culture led to increased surface expression of CD49d (avg 64% increase, p=0.03) and CXCR7 (avg 67% increase, p=0.02). Conversely, in vehicle control-treated 34-19+ LICs, stromal co-culture did not affect surface expression of the measured adhesion molecule receptors. In all 3 culture conditions, surface expression of CXCR4, CD49d, and CXCR7 was significantly higher in 34+38+19+ LICs compared to 34-19+ LICs (p≤0.01).We then measured apoptosis by flow cytometry and Annexin V binding. In the absence of chemotherapy, stromal co-culture significantly protected 34+38+19+ LICs from spontaneous apoptosis (p<0.001), but not 34-19+ LICs (p=0.16). Treatment with AMD3100 decreased stromal protection from spontaneous apoptosis in 34+38+19+ LICs (p<0.05), but not 34-19+ LICs (p=0.13). Notably, 34-19+ LICs were more resistant to spontaneous apoptosis even when cultured without stromal support (avg Annexin V-negative fraction 76.5% in 34-19+ vs. 62.8% in 34+38+19+, p=0.005). In spite of differences in stromal-mediated protection from spontaneous apoptosis, stromal co-culture protected both LIC populations from AraC- or Etop-induced apoptosis (p<0.001 for 34+38+19+, p<0.01 for 34-19+). Also, 34-19+ LICs were more resistant to Etop than 34+38+19+ LICs in the presence (p<0.001) or absence (p<0.01) of stroma. Finally, AMD3100 decreased stromal protection from AraC- or Etop-induced apoptosis (p<0.001 for 34+38+19+, p<0.05 for 34-19+).Conclusions: Our results suggest that the two immunophenotypically distinct LIC populations in infant MLL-R ALL may rely differently on the BM microenvironment. Higher surface expression of adhesion molecule receptors may explain why 34+38+19+ LICs derive more benefit from stromal co-culture, while lower surface expression of adhesion molecule receptors may explain decreased reliance on stroma by 34-19+ LICs. There may also be differences in chemotherapy resistance between the LIC populations. Despite these differences, CXCR4 inhibition enhanced chemosensitivity in both LIC populations. These results support the development of new therapeutic strategies that target leukemia-stroma interactions to improve outcomes for infants with MLL-R ALL. DisclosuresNo relevant conflicts of interest to declare.

Interaction with the DNA Binding Domain of MLL and a Small Molecular Drug Induces Proteolysis of MLL-Fusion Proteins and Ablates Leukemic Stem Cell Activity

IntroductionLeukemias harbouring 11q23 abnormalities causing mixed-lineage leukaemia gene (MLL) rearrangements are associated with poor clinical outcomes. Despite being an aggressive leukaemia, the MLL rearranged infant ALL has among the lowest mutation rates reported for any cancer. This means that to improve survival for patients with this aggressive leukaemia we need drugs that target the abnormal proteins produced by the MLL fusion gene or that interact with the abnormal MLL fusion protein to shut down the cellular machinery that drives these leukemias. Indeed, targeting MLL fusion dependent gene pathways has become a major focus.Our previous studies have shown that inhibition of MLL-fusions, in a conditional mouse model of MLL-ENL driven acute myeloid leukaemia, resulted in a block in self-renewal of the leukemic cells and ablated the leukaemia in the mice. This led us to hypothesise that if, we could achieve pharmacological inactivation of the MLL fusion proteins, we could achieve improved clinical outcomes. To achieve this, we set out a drug screening programme in acute leukaemia with the aim to discover drugs that can inactivate MLL-fusion oncoproteins.ResultsOur drug discovery pipeline screened clinical approved drugs for their ability to inhibit the function of the MLL fusion protein. This lead to the discovery of a drug that interacts with the DNA binding domain within the MLL fusion protein. This interaction destabilises the MLL fusion protein so that the fusion protein gets degraded within 24 hours of addition of the drug. So far, we have shown that we can inhibit and induce the degradation of MLL-AF9, MLL-AF6 and MLL-AF4 (and WT MLL) in the human MLL rearranged cell lines (THP-1, SHI-I and MV4-11), in primary immortalized cells in which the MLL-AF9 is overexpressed from a lentiviral backbone and in patient derived leukemic samples.Inactivation/degradation of the MLL fusion protein should shut down the cellular machinery that drives these leukemias. It is well established that MLL-fusions lead to abhorrent upregulation of its target genes HOXA9, MEIS1 and c-MYB. Treatment of MLL rearranged cells resulted in the downregulation of these MLL-fusion target genes within 24hrs of addition of the drug. Furthermore, Gene Set Enrichment Analysis of drug treated MLL-AF9 cells showed strong negative enrichment to various published MLL fusion target gene sets. Inactivation of MLL fusion protein should also result in block in self-renewal as we have previously shown in our conditional mouse model. Indeed, Gene Set Enrichment Analysis showed negative enrichment to published Leukemic Stem Cell gene set. To analyse the impact of drug treatment on self-renewal, we used a well-established self-renewal assay, whereby self-renewal is assessed by their ability to form colonies derived from single cells in methylcellulose. While treatment had no significant impact on the colony formation of CD34 positive cord blood progenitors, the drug was able to block the colony formation ability of MLL rearranged cell lines while only slowing a slight reduction in in the colony numbers of non MLL rearranged cell lines.ConclusionOverall, the data indicates that we may have discovered a new targeted treatment for MLL rearranged leukemia, which shows excellent clinical properties. We have successfully generated Patient Derived Xenografts (PDX) models and we are currently testing this drug to verify its effectiveness in the treatment on PDX. We will include this data in our presentation. DisclosuresNo relevant conflicts of interest to declare.

Network-based expression analysis reveals key genes related to glucocorticoid resistance in infant acute lymphoblastic leukemia.

Despite vast improvements that have been made in the treatment of children with acute lymphoblastic leukemia (ALL), the majority of infant ALL patients (~80%, < 1year of age) that carry a chromosomal translocation involving the mixed lineage leukemia (MLL) gene shows a poor response to chemotherapeutic drugs, especially glucocorticoids (GCs), which are essential components of all current treatment regimens. Although addressed in several studies, the mechanism(s) underlying this phenomenon have remained largely unknown. A major drawback of most previous studies is their primary focus on individual genes, thereby neglectingthe putative significance of inter-gene correlations. Here, we aimed at studying GC resistance in MLL-rearranged infant ALL patients by inferring an associated module of genes using co-expression network analysis. The implications of newly identified candidate genes with associations to other well-known relevant genes from the same module, or with associations to known transcription factor or microRNA interactions, were substantiated using literature data. A weighted gene co-expression network was constructed to identify gene modules associated with GC resistance in MLL-rearranged infant ALL patients. Significant gene ontology (GO) terms and signaling pathways enriched in relevant modules were used to provide guidance towards which module(s) consisted of promising candidates suitable for further analysis. Through gene co-expression network analysis a novel set of genes (module) related to GC-resistance was identified. The presence in this module of the S100 and ANXA genes, both well-known biomarkers for GC resistance in MLL-rearranged infant ALL, supports its validity. Subsequent gene set net correlation analyses of the novel module provided further support for its validity by showing that the S100 and ANXA genes act as 'hub' genes with potentially major regulatory roles in GC sensitivity, but having lost this role in the GC resistant phenotype. The detected module implicates new genes as being candidates for further analysis through associations with known GC resistance-related genes. From our data we conclude that available systems biology approaches can be employed to detect new candidate genes that may provide further insights into drug resistance of MLL-rearranged infant ALL cases. Such approaches complement conventional gene-wise approaches by taking putative functional interactions between genes into account.

MEK inhibition is a promising therapeutic strategy for MLL-rearranged infant acute lymphoblastic leukemia patients carrying RAS mutations.

Acute lymphoblastic leukemia (ALL) in infants is an aggressive malignancy with a poor clinical outcome, and is characterized by translocations of the Mixed Lineage Leukemia (MLL) gene. Previously, we identified RAS mutations in 14-24% of infant ALL patients, and showed that the presence of a RAS mutation decreased the survival chances even further. We hypothesized that targeting the RAS signaling pathway could be a therapeutic strategy for RAS-mutant infant ALL patients. Here we show that the MEK inhibitors Trametinib, Selumetinib and MEK162 severely impair primary RAS-mutant MLL-rearranged infant ALL cells in vitro. While all RAS-mutant samples were sensitive to MEK inhibitors, we found both sensitive and resistant samples among RAS-wildtype cases. We confirmed enhanced RAS pathway signaling in RAS-mutant samples, but found no apparent downstream over-activation in the wildtype samples. However, we did confirm that MEK inhibitors reduced p-ERK levels, and induced apoptosis in the RAS-mutant MLL-rearranged ALL cells. Finally, we show that MEK inhibition synergistically enhances prednisolone sensitivity, both in RAS-mutant and RAS-wildtype cells. In conclusion, MEK inhibition represents a promising therapeutic strategy for MLL-rearranged ALL patients harboring RAS mutations, while patients without RAS mutations may benefit through prednisolone sensitization.

Systematic chemical and molecular profiling of MLL-rearranged infant acute lymphoblastic leukemia reveals efficacy of romidepsin

To address the poor prognosis of mixed lineage leukemia (MLL)-rearranged infant acute lymphoblastic leukemia (iALL), we generated a panel of cell lines from primary patient samples and investigated cytotoxic responses to contemporary and novel Food and Drug Administration-approved chemotherapeutics. To characterize representation of primary disease within cell lines, molecular features were compared using RNA-sequencing and cytogenetics. High-throughput screening revealed variable efficacy of currently used drugs, however identified consistent efficacy of three novel drug classes: proteasome inhibitors, histone deacetylase inhibitors and cyclin-dependent kinase inhibitors. Gene expression of drug targets was highly reproducible comparing iALL cell lines to matched primary specimens. Histone deacetylase inhibitors, including romidepsin (ROM), enhanced the activity of a key component of iALL therapy, cytarabine (ARAC) in vitro and combined administration of ROM and ARAC to xenografted mice further reduced leukemia burden. Molecular studies showed that ROM reduces expression of cytidine deaminase, an enzyme involved in ARAC deactivation, and enhances the DNA damage–response to ARAC. In conclusion, we present a valuable resource for drug discovery, including the first systematic analysis of transcriptome reproducibility in vitro, and have identified ROM as a promising therapeutic for MLL-rearranged iALL.

Constitutive Activation of FLT3 Is a Positive Prognostic Factor in Infants with MLL-Rearranged Acute Lymphoblastic Leukemia

Constitutive activation of the FMS-related tyrosine kinase-3 (FLT3) is a common feature of acute leukemias which can be caused by activating mutations or by high expression levels. Aberrant FLT3 downstream signaling is mediated via the RAS/MAPK, PI-3-Kinase/AKT, and STAT5 pathways leading to proliferation, survival, and therapy resistance. In MLL-rearranged acute lymphoblastic leukemia (ALL) activating FLT3 tyrosine kinase domain mutations (TKDs) affecting codons D835 and I836 are frequently identified (Armstrong et al., 2003; Taketani et al., 2004). In addition, MLL-rearranged ALLs are consistently characterized by an exceptionally high FLT3 expression (Armstrong et al., 2002) which has been shown to be associated with ligand independent signaling (Stam et al., 2005). However, the prognostic impact of a constitutive activation of FLT3 in this ALL subset remains controversial.Here, we report on the FLT3 mutational status and gene transcription levels in a large cohort of 95 infants and 72 children with MLL-rearranged ALL. Results obtained were further complemented by a high resolution melting (HRM) screen for common activating NRAS and KRAS mutations at codons 12, 13, and 61. All patients were enrolled in the multicenter trials ALL-BFM 86, 90, 95, 2000, and AIEOP-BFM ALL 2009 as well as Interfant-99 and Interfant-06.In infants, FLT3-TKD mutations were identified in 12/95 patients (12.6%) including one novel insertion/deletion involving codons D835 to S838. In only 2/95 patients (2.1%) an alteration in the juxtamembrane domain of FLT3 was detected. Of the 12 infants with mutation only 2 suffered from a relapse, 2-years cumulative incidence of relapse (CIR) 18%± 12%. In children, only one FLT3 aberration (FLT3-TKD D835 mutation) was detected (1/72, 1.4%). FLT3 transcript levels were analyzed by quantitative real-time PCR in 124 patients (69 infants and 55 children) with available RNA. When we separated the infant cohort into two groups according to the median RQ value, FLT3high and FLT3low, the CIR was significantly different (CIR 19%±7% vs. 66%± 9%, Gray p=0.0001). Of the 6 patients with low FLT3 transcription level, but with presence of a mutation, only one had a relapse. These results indicate that activating FLT3 mutations may compensate for the high relapse risk of patients with a low FLT3 expression. Accordingly, we could show that the CIR was significantly reduced for infants with a low FLT3activation (low transcription, no mutation 19%±7%) compared to those with a high FLT3 activation (high transcription or mutation 75%±9%, Gray p<0.0001, Figure 1). In multivariate analysis, the high prognostic impact of the FLT3 transcription level in infants was independent of age (< vs. ≥6 month), white blood cell count at diagnosis (WBC ≥ vs. <300000), or prednisone response (poor vs. good). This influence of the FLT3 expression could not be seen in children: CIR 13%±7% for low transcription vs. 12%±7% for high transcription.The only other known recurrent mutations in pediatric MLL-rearranged ALL are activating N- and KRAS mutations at codons 12, 13, and 61 (Liang et al., 2006; Andersson et al., 2015). As RAS signaling is considered as a putative downstream target of FLT3, we investigated the frequency of these mutations and their impact in the context of the prognostic value of FLT3 activation. We identified non-synonymous N/KRAS mutations in 21/95 (22.1%) infants and in 10/72 (13.9%) children. The presence of activating RAS mutations correlated with a higher rate of relapse and a lower probability of event-free survival (pEFS). For infants alone, constitutive activation of N/KRAS resulted in a lower pEFS (43%±6% wt vs. 11%±8%, p=0.01), but there were no significant differences in the CIR (40%±6% wt vs. 51±12%, p=0.40).In summary, we confirm that MLL-rearranged infant ALL represents a biologically distinctive entity with unique molecular genetic features. However, in contrast to published studies, we report that hyperactivation of FLT3 signaling is associated with a good prognosis in MLL-rearranged infant ALL. Our data has important implications for the design of rational therapies in MLL-rearranged ALL as the use of small molecule FLT3 inhibitors may be disadvantageous in some infants depending on FLT3 expression levels and FLT3 and RAS mutational status. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Identifying Subclonal Epigenetic Changes Driving Chemoresistance in Infant MLL-r Acute Lymphoblastic Leukemias

IntroductionThis study addresses the unsolved clinical problem of relapse in MLL-rearranged infant (<1 year old) acute lymphoblastic leukemia (ALL): 80% of infants with ALL harbor MLL rearrangements (MLL-r) and 66% of these will relapse and die with current treatment [5-year event free survival is 34%]. The typical pattern of failure in MLL-r ALL is successful remission induction (>90%) followed by early relapse (60-80%), suggesting rapid emergence of one or more chemoresistant subclones. Recently, whole genome sequencing of 47 MLL-r infant ALL cases showed a mean of only 1.3 non-silent mutations in the predominant leukemic clone (Andersson Nat. Gen. 2015;47:330-7). The critical barrier to progress in identifying novel, more effective therapies is this striking paucity of genomic changes that are found in addition to the MLL rearrangement. Therefore we hypothesized that epigenetic changes drive evolution of chemoresistant subclones and cause relapse.MethodsWe tested this hypothesis on two MLL-r infant ALL cases that had paired diagnosis-relapse (DX-RL) leukemic specimens using whole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq). We prepared WGBS and RNA-seq libraries and performed paired-end sequencing (2x100bp) using Illumina HiSeq 2500. Paired-end reads received a methylated (1) or unmethylated (0) calls at each contiguous CpG they cover producing a data set of four 0/1-state-long "epialleles" with 16 possible methylation state patterns ("0-0-0-0" to "1-1-1-1"). For each epiallele, we calculated the frequency of each of the 16 patterns at DX and RL. We developed analysis methods to align bisulfite-converted reads to the genome, call methylation states at CpGs within reads, assess subclonal "epiallele" frequency changes between DX and RL, map the genomic locations of epialleles to promoter regions of their corresponding gene isoforms, and quantify differential gene isoform expression between DX and RL.ResultsWGBS generated ~400 million paired-end reads per sample with 25X average coverage. After removing duplicates and repeats, we obtained methylation calls at ~15 million CpGs per case. RNA-seq generated RNA transcript quantification for ~47,000 isoforms from ~30,000 genes per sample. We extracted from the WGBS data paired-end reads that map uniquely to gene promoter regions and that cover at least 4 contiguous CpGs to a depth of at least 4X. In all, case A had 237,040 epialleles annotated to 11,484 gene promoters, and case B had 853,678 epialleles annotated to 14,717 gene promoters. By plotting the change in epiallele frequency between DX and RL, we were able to identify epiallele-defined subclones that were: not detectable at DX but present at RL ("emergent" at RL), present at DX but undetectable at RL ("driven extinct" at RL), and unchanged significantly between DX and RL ("founder") (Fig. 1). For example, in case A, we found 145 "1-1-1-1" epialleles that were at 0% frequency at DX and 66±17% (mean±st.dev.) frequency at RL (corresponding to 76±11% methylation increase at RL) that were associated with 29±77-fold decrease in expression of their associated gene isoform. 18 of these epialleles were: mapped to the promoter of IKZF1 (a known tumor-suppressor gene in ALL), present at 0% frequency at DX and 40±0.04% at RL, and associated with 8.5±10-fold decrease in IKZF1 isoforms expression. These results support the hypothesis that subclonal methylation changes associated with corresponding expression changes may drive chemoresistance and relapse.ConclusionsWe have developed analytic techniques to integrate WGBS and RNA-seq data for discovery of subclonal epigenetic changes that either emerge or are driven extinct under the selective pressure of chemotherapy treatment. Such data provide support for the hypothesis that chemoresistance in this disease may be driven by epigenetic mechanisms. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

A Case of Concordant Twins with Infant ALL and Discordant Clinical Outcome – Part I: the genetic basis – identification of DSC2 as a gene with prognostic impact in infant MLL-rearranged ALL

Infant acute lymphoblastic leukemia (ALL) is associated with an unfavorable prognosis due to a high proportion of early relapses. We report on a pair of monozygotic twin sisters diagnosed with ALL (MLL-ENL fusion) in early infancy. Despite good initial treatment responses in both twins, one sister developed very early relapse (Twin A) and succumbed to the disease. The other sister went into continuous complete remission (Twin B) and is alive after 9 years. We performed exome sequencing experiments to identify additional diverging mutations in the twins that may be connected to the different clinical outcomes. Results obtained were further complemented by sequencing analyses of xenografted twin leukemias from different disease time points providing insights into clonal evolution in this twin model of infant leukemia. Apart from an overall paucity of mutations, genetic alterations predicted to be relevant were detected only in leukemic cells of the survivor, Twin B. In particular, we show evidence for a heterozygous desmocollin 2 (DSC2) mutation which is absent in Twin A. Notably, high gene expression of DSC2 in a cohort of infant ALL patients harboring MLL-ENL and MLL-AF9 fusions conferred a poor prognosis characterized by a significantly increased relapse rate. Our data suggest that high levels of DSC2 expression in residual cells may be a pathogenic mechanism in relapsing infant ALL.

Identification of genes transcriptionally responsive to the loss of MLL fusions in MLL-rearranged acute lymphoblastic leukemia.

Introduction MLL-rearranged acute lymphoblastic leukemia (ALL) in infants (<1 year) is characterized by high relapse rates and a dismal prognosis. To facilitate the discovery of novel therapeutic targets, we here searched for genes directly influenced by the repression of various MLL fusions.MethodsFor this, we performed gene expression profiling after siRNA-mediated repression of MLL-AF4, MLL-ENL, and AF4-MLL in MLL-rearranged ALL cell line models. The obtained results were compared with various already established gene signatures including those consisting of known MLL-AF4 target genes, or those associated with primary MLL-rearranged infant ALL samples.ResultsGenes that were down-regulated in response to the repression of MLL-AF4 and MLL-ENL appeared characteristically expressed in primary MLL-rearranged infant ALL samples, and often represented known MLL-AF4 targets genes. Genes that were up-regulated in response to the repression of MLL-AF4 and MLL-ENL often represented genes typically silenced by promoter hypermethylation in MLL-rearranged infant ALL. Genes that were affected in response to the repression of AF4-MLL showed significant enrichment in gene expression profiles associated with AF4-MLL expressing t(4;11)+ infant ALL patient samples.ConclusionWe conclude that the here identified genes readily responsive to the loss of MLL fusion expression potentially represent attractive therapeutic targets and may provide additional insights in MLL-rearranged acute leukemias.

POL5551, a Novel and Potent CXCR4 Antagonist, Enhances Sensitivity to Chemotherapy in an in Vivo Model of High-Risk (HR) Pediatric Acute Lymphoblastic Leukemia (ALL)

Background: Interaction between surface receptor CXCR4 (s-CXCR4) and chemokine SDF-1 (CXCL12) is critical in signaling between leukemic blasts and the bone marrow (BM) microenvironment. We previously demonstrated: 1) chemotherapy-induced upregulation of s-CXCR4 in acute myeloid leukemia (AML) and ALL enhances stromal protection from chemotherapy-induced apoptosis; 2) the FDA-approved CXCR4 inhibitor plerixafor reverses stromal protection and chemotherapy resistance both in vitro in stromal co-cultures of pre-B cell ALL cell lines and in vivo in xenografts of primary samples of infant MLL-rearranged (MLL-R) ALL; 3) the novel Protein Epitope Mimetic POL5551, a selective and potent antagonist of CXCR4, blocks the SDF-1-binding site of CXCR4, inhibits SDF-1-induced chemotaxis, and reverses stromal-mediated protection from chemotherapy in vitro in pre-B and T ALL cell lines. Here, we further characterize the effects of POL5551 (POL) on surface adhesion molecule expression in ALL, and its in vivo effects in a xenograft model of HR pediatric ALL.In Vitro Methods/Results: We have previously shown that POL inhibits 12G5 antibody binding to s-CXCR4 in ALL cell lines, suggesting an overlapping of the two binding sites. We sought to verify these results using primary samples of pediatric ALL. We treated 3 pre B and 3 T cell ALL primary samples with a dose range of POL and measured s-CXCR4 by FACS at multiple time points. POL inhibition of 12G5 binding was potent (average IC50 at 2 hours pre B 8.3 nM, T 1.4 nM), rapid (<1 hour) and sustained (>24 hours). Further, POL was significantly more potent at inhibiting 12G5 binding than plerixafor (average IC50 at 2 hours pre B 18.4 nM, T 8.4 nM). To further characterize POL’s effects in ALL, we treated 2 pre B and 2 T cell ALL cell lines with POL or vehicle control and then treated with SDF-1α or vehicle control. Treatment with POL inhibited SDF-1α-induced phosphorylation of ERK1/2 in a dose-dependent manner. In parallel, we measured POL-induced compensatory upregulation of the alternative surface adhesion molecules CXCR7 and VLA-4 (CD49d), and found that POL led to increased CXCR7 expression at early time points that began to decrease after 24 hours. We did not find a consistent effect of POL on CD49d surface expression.Xenograft Methods/Results: Infant MLL-R ALL primary samples (n=4) were transplanted into sublethally irradiated NSG mice. After 2 weeks, mice were treated on days 1-3 of 2 consecutive weeks with 1) vehicle control (C), 2) POL (5 mg/kg SC), 3) AraC (200 mg/kg IP), or 4) POL followed by AraC 4 hours later (POL+AraC). One week after treatment, cells were harvested from BM, spleen, and peripheral blood (PB). Leukemic blasts were defined as human CD19+ and CD45+. Overall leukemic burden (average % blasts in BM+spleen+PB) did not differ between mice treated with either C (56.2%) or POL (49.5%, p=0.12). However, treatment with AraC (36.7%, p=3E-07) or POL+AraC (26.3%, p=4E-15) significantly decreased total leukemic burden compared to C. Notably, POL+AraC significantly decreased total leukemic burden compared to AraC alone (p=0.001), demonstrating that POL increased overall sensitivity to AraC. When analyzed by organ-specific leukemic burden, POL+AraC resulted in decreased leukemic burden compared to AraC alone in BM (42.8 vs. 49.8%, p=0.27), spleen (16.9 vs. 30.8%, p=0.002), and PB (19.3 vs. 29.6%, p=0.008). Interestingly, AraC and POL+AraC led to significantly increased CXCR7 expression (blasts from BM p<0.01, spleen p<0.04, and PB p<0.03 vs. C) as well as a trend toward increased CD49d expression compared to C.Conclusions: POL5551 is a potent antagonist of s-CXCR4 in pediatric ALL cell lines and primary samples. Surface expression of adhesion molecules in ALL blasts is dynamic and affected by anti-leukemic therapy. Importantly, POL5551 enhances sensitivity to AraC in a xenograft model of infant MLL-R ALL, a HR subtype of pediatric ALL. Our findings support the continued development of BM microenvironment-targeted agents as a therapeutic strategy for pediatric ALL. DisclosuresRomagnoli:Polyphor Ltd.: Employment. Douglas:Polyphor Ltd.: Employment. Tuffin:Polyphor Ltd.: Employment. Zimmermann:Polyphor Ltd.: Employment.

MEK Inhibition Is a Promising Therapeutic Strategy for MLL-Rearranged Infant ALL Patients Carrying RAS Mutations

Background: Acute Lymphoblastic Leukemia (ALL) in infants is characterized by a high incidence (~80%) of chromosomal rearrangements of the Mixed Lineage Leukemia (MLL) gene, fusing the N-terminal portion of MLL to the C-terminal region of one of its translocation partner genes. MLL-rearranged infant ALL patients are challenged by a very poor prognosis (i.e. 30-40% 5-year EFS), hence the need for better risk stratification and improved therapeutic solutions is evident. We recently screened a relatively large cohort (n=109) infant ALL patients (all enrolled in INTERFANT treatment protocols) for the presence of KRAS and NRAS mutations and found that the incidence of such mutations ranges between 14-24%, depending on the type of MLL translocation. Moreover, these mutations were found to represent independent predictors of exceedingly poor prognosis; patients carrying RAS mutations essentially stand no chance in surviving their malignancy, as all RAS mutation-positive MLL-rearranged infant ALL patients deceased within 3 years from diagnosis.Aims: Here we aimed to identify a therapeutic strategy to improve the prognosis of MLL-rearranged infant ALL patients carrying RAS mutations.Methods: For this, 8 small molecule inhibitors against different RAS-pathway components were selected and initially tested for anti-leukemic activity against the MLL-rearranged ALL cell lines SEM and RS4;11 (RASwt) and KOPN8 (RASmut) using MTS cell viability assays. Next, primary MLL-rearranged infant ALL samples (n=20) all carrying MLL translocation t(4;11) (giving rise to the MLL-AF4 fusion protein) either with (n=6) or without (n=14) RAS mutations were exposed to these inhibitors in MTT cytotoxicity assays. In addition, we assessed the RAS activity in RAS mutated and wild-type MLL-rearranged infant ALL cells, and performed immunoblotting analysis of downstream MEK and ERK both in the absence and presence of the MEK inhibitors.Results: We found that the MEK inhibitors MEK162, Selumetinib and Trametinib effectively reduced the viability of KOPN8 cells (RASmut), whereas SEM and RS4;11 cells (RASwt) largely remained unaffected. In line with this, MLL-AF4+ infant ALL patient samples carrying RAS mutations were significantly more sensitive to these MEK inhibitors when compared with patients carrying wild-type RAS genes: LC50 values for MEK162 were 0.04 vs. 26.9 µM (p<0.01), for Selumetinib 0.04 and 23.7 µM (p<0.01), and for Trametinib 0.01 vs. 26.5 µM (p<0.01), respectively. Furthermore, the presence of RAS mutations in primary MLL-rearranged infant ALL samples was associated with significantly increased RAS activity, as determined by immunoprecipitation of GTP-bound RAS. Remarkably, however, enhanced RAS activation did not manifest itself in the form of increased phosphorylation of the downstream ERK protein, while a slight increase of MEK phosphorylation was observed. Yet, MEK inhibitor exposure in both KOPN8 and SEM cells resulted in nearly complete abrogation of ERK phosphorylation, without affecting total ERK protein levels, suggesting that the loss of ERK activation plays an important role in the observed anti-leukemic effects. Furthermore, MEK162 and Selumetinib seemed to induce accumulation of phosphorylated MEK, while MEK phosphorylation was hardly affected by Trametinib. Interestingly, a subgroup of patient samples (n=5) with wild-type RAS also showed sensitivity towards MEK inhibition, similar to the primary cells with RAS mutations. However, this observation could not be explained by increased RAS activation, nor by the phosphorylation levels of either MEK or ERK.Conclusions: Our data show that MEK inhibition represents a promising therapeutic approach for MLL-rearranged infant ALL patients carrying additional RAS mutations. Furthermore, the mechanism of action provoked by these MEK inhibitors seems to involve abrogation of ERK phosphorylation, but the initial level of ERK phosphorylation did not correlate with MEK inhibitor sensitivity, and has no predictive value. Currently we are in the process of testing the efficacy of the above mentioned MEK inhibitors in vivo using a xenograft mouse model, while further elucidation of the molecular mechanisms underlying the anti-leukemic effects of these inhibitors in MLL-rearranged ALL cells is in progress. DisclosuresNo relevant conflicts of interest to declare.

Exome Sequencing Identifies Pxdn and DSP As Recurrently Mutated Genes in Infant ALL Patients Carrying a MLL-AF4 Translocation

Background and purpose: Acute lymphoblastic leukemia (ALL) in infants (<1 year of age) carrying MLL translocations represent a highly aggressive subtype of leukemia with an exceedingly poor prognosis. Although MLL rearrangements have been considered to be causative for this type of leukemia, recent studies using mouse models suggest that the expression of chimeric MLL fusion genes alone may not be sufficient to induce leukemia. In an attempt to identify additional mutations that synergize with MLLfusion genes in driving leukemogenesis, we performed exome-sequencing in primary infant ALL patient samples (n=13) carrying the t(4;11)-translocation, giving rise to the MLL-AF4 fusion protein.Materials and Methods: Bone marrow or peripheral blood samples from untreated infants diagnosed with t(4;11)+ ALL were collected at our laboratory as part of the international collaborative INTERFANT treatment protocols. Genomic DNA was extracted from ~5×106leukemic cells. Exome capture has been performed using the Sure Select Human All Exon v2 kit (Agilent Technologies). The samples were prepped for sequencing according to the TruSeq v3 protocol (Illumina) prior to sequencing on the Hiseq2000 with a v3 flowcell for 100bp = 7bp index (Illumina). The reads have been aligned against the human reference genome build 19 (hg19) using a BWA and NARWHAL based pipeline. Sequential filtering selected for single nucleotide variations (SNVs) in canonical splice sites, insertions/deletions (indels) providing frameshifts, indels involving regions conserved between species (phyloP >3), nonsense mutations and nonsynonymous missense mutations involving regions conserved between species. All known annotated single nucleotide polymorphisms according to dbSNP build 138 and an in-house database of 1354 sequenced exomes were excluded. Recurrent mutations were validated by Sanger sequencing on an extended infant ALL patient cohort (n=122).Results: The sequenced exomes had an average coverage depth of 102.5 reads per region or 109 per base. Exome sequencing revealed that, after filtering, t(4;11)+ infant ALL patients on average carried 71 variants (range 58-98, including rare germline variants and somatic mutations). To identify recurrent mutations we selected 23 genes in which two or more patients carried a mutation for further validation by Sanger sequencing. Although all 23 genes were successfully validated, no additional patients carrying these mutations were found. However, recurrent secondary mutations within the same functional region as the initial mutations were found in two genes: PXDN and DSP. The average incidences of the PXDN and DSP mutations amongst MLL-rearranged infant ALL patients were 32% and 20%, respectively. Interestingly, MLL-rearranged infant ALL patients carrying a PXDN mutation had a significantly (p=0.013) better prognosis compared with patients not carrying a PXDNmutation, with mean EFS rates of 6.4 vs. 3.2 years, respectively. Both gene products are involved in intracellular interactions, desmosome formation, extracellular matrix consolidation and phagocytosis and no prior associations with ALL have been made before.Conclusion: We identified 23 genes with two or more mutations in our initial exome sequencing cohort. None of these mutations were found in additional patients in our validation cohort. Despite an average of 71 variations per patient, no recurrent mutations were identified and our study provides evidence supporting previous observations that infant ALL has one of the lowest mutation rates observed in human cancer. However, we identified additional mutations within the same functional region as the initial mutation in DSP and PXDN. Interestingly, PXDN mutations show an association with a favorable prognosis in MLL-R patients. DisclosuresNo relevant conflicts of interest to declare.

HMGA2 As a Potential Molecular Target in MLL-AF4 Positive Infant Acute Lymphoblastic Leukemia

Leukemic cells of acute lymphoblastic leukemia (ALL) in infants are frequently characterised by chromosome translocations involving 11q23, resulting in the rearrangement of the mixed-lineage leukemia (MLL) gene and subsequent generation of MLL fusion gene. Among more than 50 genes which have been identified as the fusion partner of the MLL gene, fusion with AF4 is characteristically observed in infant ALL representing a hallmark of poor prognosis. Although recent progress of intensive chemotherapy with or without stem cell transplantation has improved its treatment outcome, the treatment is often accompanied by long-term side effects. Less toxic molecular targeting therapies are therefore necessary for infant ALL.We have previously reported that in infant ALL with MLL fusion gene, microRNA let-7b is significantly downregulated by DNA hypermethylation of its promoter region. The downregulation of let-7b is one of the consequences of oncogenic MLL fusion proteins contributing to leukemogenesis possibly through upregulation of let-7b-regulated target genes with oncogenic potential such as high mobility group AT-hook 2 (HMGA2). HMGA2 is a chromatin-remodelling factor, which alters chromatin architecture by binding to AT-rich regions in the DNA, either promoting or inhibiting the expression of its target genes. One of the targets of HMGA2 is CDKN2A gene which encodes 2 cell cycle regulators p16INK4A and p14ARF. This let-7b-HMGA2-CDKN2A axis regulates cellular growth and senescence of stem cells both in normal and pathological state such as cancer.We initially examined the expression of HMGA2 in leukemic cells obtained from 35 MLL-rearranged infant ALL patients (MLL-AF4, n = 26; MLL-AF9, n = 4; MLL-ENL, n = 5) using quantitative RT-PCR. As results, HMGA2 was highly expressed in most of the patients with MLL fusion gene, especially in MLL-AF4-positive cases, compared to those without the fusion. These results indicate that deregulation of let-7b-HMGA2 axis by MLL fusion may contribute to leukemogenesis and could be a possible target of molecular therapy against MLL-rearranged ALL.As let-7b is downregulated by promoter hypermethylation, demethylating agents such as 5-azacytidine could be applied to recover the expression of the gene in leukemic cells with MLL fusion gene. To test this possibility, leukemic cell lines with MLL-AF4 fusion gene were used. The administration of 5-azacytidine alone was able to restore the expression of suppressed let-7b as well as p16INK4A gene in the leukemic cells, but the effects was incomplete, showing persistent partial promoter methylation. In addition, the recovered expression disappeared when 5-azacytidine was removed. On the other hand, when HMGA2 inhibitor was combined with 5-azacytidine, the expression of let-7b was upregulated and sustained resulting in suppression of HMGA2 protein itself. This upregulation of let-7b and suppression of HMGA2 protein persisted even after the removal of 5-azacytidine, possibly through maintaining of the demethylating status by HMGA2 inhibitor. Inhibition of HMGA2 by either siRNA or HMGA2 inhibitor suppressed the growth of MLL-AF4-positive leukemic cells when analysed by MTT assay. The effects of HMGA2 inhibitor on cell growth inhibition became more prominent in combination with demethylating agent 5-azacytidine.Our results revealed the functional significance of let-7b and HMGA2 in controlling MLL-AF4-positive leukemic cell growth and the therapeutic potential of combining demethylating agent and the HMGA2 inhibitor in the treatment of MLL-AF4-positive ALL. DisclosuresNo relevant conflicts of interest to declare.