ABSTRACT:Acute myeloid leukemia (AML) with rearrangement of the mixed lineage leukemia gene expresses MLL-AF9 fusion protein, a transcription factor that impairs differentiation and drives expansion of leukemic cells. In this work, the zinc finger protein "growth factor independent 1" together with the histone methyltransferase LSD1 is revealed to occupy the promoter and regulate the expression of the lncRNA ELDR (EGFR [epidermal growth factor receptor] long non-coding downstream RNA) in the rearranged Mixed Lineage Leukemia (MLL) (MLL-r) AML cell line THP-1. Forced ELDR overexpression enhanced the growth inhibition of an Lysine-Specific Demethylase 1 inhibitor (LSD1i)/all-trans retinoic acid (ATRA) combination treatment and reduced the capacity of these cells to generate leukemia in xenografts, leading to a longer leukemia-free survival. ELDR is found to bind the clamp protein Proliferating Cell Nuclear Antigen (PCNA) and the MCM5 helicases causing defects of DNA replication fork progression. Moreover, AML cells overexpressing ELDR had reduced chromatin accessibility and transcription at α-satellite repeats in centromeres. In addition, ELDR RNA was detected close to MLL-AF9 at centromeres suggesting that it impedes leukemic progression preferentially of MLL-r AML by interfering with both DNA replication and centromeric transcription. Our findings reveal novel functions of the lncRNA ELDR in DNA replication and centromere biology when expressed at high levels in AML cells with MLL rearrangements. These discoveries could provide rationale for future strategies to treat MLL-r AML, which has a poor prognosis in children and adults. Delivery of the ELDR RNA could potentially be used as an adjunct to LSD1i/ATRA treatment or other currently used chemotherapeutic drugs to develop novel therapies for these AML subtypes.

Genetic interactions are typically studied by looking at the phenotype that results from disruption of pairs of genes, as well as from higher order combinations of perturbations. Systematically interrogating all pairwise combinations provides insights into how genes are organized into pathways and complexes to sustain cellular homeostasis and how interacting genes respond to stressors and external signals. Genetic interactions have been studied extensively in yeast, due, in part, to the availability of a systematic collection of gene knockouts, and the development of Synthetic Genetic Array (SGA) technology. In contrast, such approaches are more challenging in human cells and therefore comparable data for human cells is scarce. This study introduces an innovative approach to functionally characterize genetic interactions in human cells through CRISPR/Cas9 screens using a pooled genome-wide knockout library in NALM6 cells. By combining a single guide RNA (sgRNA) targeting the gene of interest (aka the query) in cells already infected with an inducible genome-wide sgRNA pool, it is possible to achieve near saturation of genome-wide double knockouts. We conducted 26 of these screens, which we term “gene by genome-wide” knockout screens. This approach can be rapidly performed, in part, because it bypasses the need to generate genotyped isogenic knockout clones. Data from these screens identified both expected and novel synthetic lethal and synthetic rescue interactions, demonstrating that this strategy is effective for large-scale genetic research in human cells. Additionally, we show that these GBGW screens can be combined with chemical perturbation to reveal new synthetic interactions that are not apparent without drug treatment. Finally, we show that cDNA overexpression can be incorporated with genome-wide knockouts to systematically explore gain-of-function scenarios. The complete dataset is accessible on the ChemoGenix website (URL: ). ### Competing Interest Statement The authors have declared no competing interest. Fonds de Recherche du Québec - Santé, https://ror.org/02eqrsj93 Canadian Institutes of Health Research, https://ror.org/01gavpb45, PJT-173443, PJT-191684, PJT-190250, Tier 1 Canada Research Chair in Translational Genomics, FDN-167277, Tier 1 Canada Research Chair in Regulation of mRNA Translation and Metabolism Natural Sciences and Engineering Research Council of Canada, RGPIN-2022-04206, RGPIN-2020-04947 Cancer Research Society, https://ror.org/00t38a349, 1281387

Targeted therapeutics for high-risk cancers remain an unmet medical need. Here we report the results of a large-scale screen of over 11,000 molecules for their ability to inhibit the survival and growth in vitro of human leukemic cells from multiple sources including patient samples, de novo generated human leukemia models, and established human leukemic cell lines. The responses of cells from de novo models were most similar to those of patient samples, both of which showed striking differences from the cell-line responses. Analysis of differences in subtype-specific therapeutic vulnerabilities made possible by the scale of this screen enabled the identification of new specific modulators of apoptosis, while also highlighting the complex polypharmacology of anti-leukemic small molecules such as shikonin. These findings introduce a new platform for uncovering new therapeutic options for high-risk human leukemia, in addition to reinforcing the importance of the test sample choice for effective drug discovery.

High fatality pediatric acute myeloid leukemia (AML) remains a therapeutic challenge due to the lack of tailored treatments adapted to the genetic and cellular heterogeneity of the disease and the long-term toxicity of standard therapies (Hara, 2023; Mercher, 2019). Our group has previously developed synthetic and patient-derived xenograft (PDX) models of high-fatality acute megakaryoblastic leukemia (AMKL) and demonstrated that BCL-XL is a therapeutic vulnerability of NUP98-rearranged (NUP98r) and CBFA2T3::GLIS2 subgroups using in vitro and in vivo pharmacological inhibition approaches (e.g. BH3 mimetic navitoclax targeting pro-survival proteins BCL-XL/BCL-2/BCL-W and BCL-XL proteolysis targeting chimera DT2216) (Cardin 2019; Gress, 2024). Navitoclax or DT2216 combined with the standard of care drug cytarabine further reduced leukemic burden in xenograft models of AMKL (Gress, 2024). Using high throughput pharmacological screening, we delineated subtype-specific sensitivities to BH3 mimetics (navitoclax, venetoclax targeting BCL-2) in other types of adverse-risk leukemia, including a Down syndrome (DS)-AMKL PDX model (trisomy 21/T21), NUP98r AML and KMT2A-rearranged (KMT2Ar) AML (Safa-Tahar-Henni, 2024, in press). To build on these discoveries, we are now investigating additional adverse-risk AML subgroups, including those with TP53 gene alterations (TP53-AML). While TP53 alterations are common in hematological diseases and are recognized as a distinct entity in various risk classification systems for adult AML, this stratification remains neglected in pediatric populations (Döhner, 2022; Arber, 2022). Further research is needed to fully understand the implications of TP53 alterations in pediatric AML and to develop targeted therapeutic strategies for this subgroup. Among 122 pediatric AML patients in our provincial cohort (2012-2024), 10 (8%) harbored a TP53 alteration at diagnosis or at relapse. Four TP53-AML PDX models harboring different TP53 alterations alongside various genomic alterations (T21, KMT2Ar (n=2), PICALM::MLLT10) were successfully generated with SGM3 immunodeficient mice. Leukemia can sustain serial rounds of transplantation in recipient mice (up to four rounds tested) with latencies ranging from 2.9 to 38.1 weeks. Leukemic blasts infiltrated bone marrow (hCD45 = 11.5-99.7%) and spleen (hCD45 = 4-95%) as assessed by flow cytometry, along with spleen weights measurements (73-506 mg). Furthermore, we confirmed that leukemic blasts immunophenotypically recapitulate AML, demonstrating expression of primitive and myeloid lineage markers such as hCD45+, CD34+/-, CD117+ and CD33+. Phenotypic and molecular characterization using exome and transcriptome sequencing alongside comparative genomic hybridization (CGH) of blasts confirmed that our models accurately recapitulate the disease. To identify potential therapeutic vulnerabilities, we validated compounds of interest (e.g. BH-3 mimetics) using dose-response curve analyses where IC50 values were determined using a CellTiterGlo viability assay. We identified navitoclax, an inducer of apoptosis with broad affinity to BCL-2, BCL-XL and BCL-W (IC50 = 0.016-0.202μM) to be a promising therapeutic agent in all 4 PDX models. BCL-2 inhibition using venetoclax was also identified as a therapeutic vulnerability in 3 of the models (IC50 = 0.009-0.083 μM), excluding T21 (IC50 > 10μM), despite detectable intracellular BCL-2 protein levels. In vivo validation studies to confirm anti-leukemic activity are in progress. In line with these findings, a salvage therapeutic regimen including venetoclax was used as a bridge-to-transplant strategy in a case of primary refractory PICALM::MLLT10 AML. Overall, these results underscore the importance of assessing susceptibility to BH3 mimetics in adverse-risk pediatric AML, including those with TP53 alterations, in the context of functional precision medicine strategies.

Acute megakaryoblastic leukemia (AMKL) is a rare, developmentally restricted, and highly lethal cancer of early childhood. The paucity and hypocellularity (due to myelofibrosis) of primary patient samples hamper the discovery of cell- and genotypespecific treatments. AMKL is driven by mutually exclusive chimeric fusion oncogenes in two-thirds of the cases, with CBFA2T3::GLIS2 (CG2) and NUP98 fusions (NUP98r) representing the highest-fatality subgroups. We established CD34+ cord blood-derived CG2 models (n = 6) that sustain serial transplantation and recapitulate human leukemia regarding immunophenotype, leukemia-initiating cell frequencies, comutational landscape, and gene expression signature, with distinct upregulation of the prosurvival factor B-cell lymphoma 2 (BCL2). Cell membrane proteomic analyses highlighted CG2 surface markers preferentially expressed on leukemic cells compared with CD34+ cells (eg, NCAM1 and CD151). AMKL differentiation block in the mega-erythroid progenitor space was confirmed by single-cell profiling. Although CG2 cells were rather resistant to BCL2 genetic knockdown or selective pharmacological inhibition with venetoclax, they were vulnerable to strategies that target the megakaryocytic prosurvival factor BCL-XL (BCL2L1), including in vitro and in vivo treatment with BCL2/BCL-XL/BCL-W inhibitor navitoclax and DT2216, a selective BCL-XL proteolysis-targeting chimera degrader developed to limit thrombocytopenia in patients. NUP98r AMKL were also sensitive to BCL-XL inhibition but not the NUP98r monocytic leukemia, pointing to a lineage-specific dependency. Navitoclax or DT2216 treatment in combination with low-dose cytarabine further reduced leukemic burden in mice. This work extends the cellular and molecular diversity set of human AMKL models and uncovers BCL-XL as a therapeutic vulnerability in CG2 and NUP98r AMKL.

Abstract Acute megakaryoblastic leukemia (AMKL) is a rare, developmentally restricted, and highly lethal cancer of early childhood. The paucity and hypocellularity (due to myelofibrosis) of primary patient samples hamper the discovery of cell- and genotype-specific treatments. AMKL is driven by mutually exclusive chimeric fusion oncogenes in two-thirds of the cases, with CBFA2T3::GLIS2 (CG2) and NUP98 fusions (NUP98r) representing the highest-fatality subgroups. We established CD34+ cord blood–derived CG2 models (n = 6) that sustain serial transplantation and recapitulate human leukemia regarding immunophenotype, leukemia-initiating cell frequencies, comutational landscape, and gene expression signature, with distinct upregulation of the prosurvival factor B-cell lymphoma 2 (BCL2). Cell membrane proteomic analyses highlighted CG2 surface markers preferentially expressed on leukemic cells compared with CD34+ cells (eg, NCAM1 and CD151). AMKL differentiation block in the mega-erythroid progenitor space was confirmed by single-cell profiling. Although CG2 cells were rather resistant to BCL2 genetic knockdown or selective pharmacological inhibition with venetoclax, they were vulnerable to strategies that target the megakaryocytic prosurvival factor BCL-XL (BCL2L1), including in vitro and in vivo treatment with BCL2/BCL-XL/BCL-W inhibitor navitoclax and DT2216, a selective BCL-XL proteolysis-targeting chimera degrader developed to limit thrombocytopenia in patients. NUP98r AMKL were also sensitive to BCL-XL inhibition but not the NUP98r monocytic leukemia, pointing to a lineage-specific dependency. Navitoclax or DT2216 treatment in combination with low-dose cytarabine further reduced leukemic burden in mice. This work extends the cellular and molecular diversity set of human AMKL models and uncovers BCL-XL as a therapeutic vulnerability in CG2 and NUP98r AMKL.

Acute myeloid leukemia (AML) is a genetically heterogeneous hematologic malignancy for which the mutational profile of the leukemic cells is the most important prognostic factor for disease-free survival and overall survival. The failure of chemotherapy to completely eradicate the leukemic clones is the most common cause of death in AML. The genetic events that can contribute to chemoresistance are therefore important factors for the clinical outcome, but the relative importance of these events on chemoresistance and persistence of leukemia stem cells (LSC) remains poorly defined. MLL rearranged AMLs account for 5-10% of all AMLs and the RAS pathway is the most frequently mutated pathway in this sub-group of AMLs. The goal of this project is to study the role and biology of RAS pathway mutations in clonal evolution in human MLL-rearranged AML. Methods We have previously shown that human cord blood CD34+ cells transduced with a retrovirus encoding the MLL-AF9 fusion gene with an EGFP maker generate human AML when injected into immunodeficient NSG-SGM3 mice. Using a similar experimental design, we added a second hit to the CD34 transduced cells before their injection into NSG-SGM3 mice. MLL-AF9 cells were electroporated with Cas9 enzyme for the control and with Cas9 enzyme plus a single guide RNA (sgRNA) designed to induce the KRAS G13D or the NRAS G12D mutation. Mice were sacrificed when they showed sign of disease and the bone marrow and spleen were collected and analyzed. Kaplan-Meier curves, flow cytometry analyses, RNA and exome sequencing and secondary transplantation were performed on the samples. Results Mice injected with MLL-AF9 + KRAS G13D got sick around day 80 after injection and around day 60 for MLL-AF9 NRAS G12D, whereas it took ~150 days for control mice (MLL-AF9 KRAS WT) to get sick (fig 1). In multiple experiment, the latency was roughly cut by half by the KRAS G13D and NRAS G12D mutations. The cell surface phenotype and morphology were not significantly different between MLL-AF9 WT and MLL-AF9 KRAS/NRAS mutated. The variant allele frequency (VAF) for the KRAS mutation invariably increased from the day of injection to the day of sacrifice, where the percentages varied between 20-40%, which is typically observed in AML patients. In contrast, the VAF for NRAS mutated cells was lower (3-9%) but seems to be very aggressive into mice. We performed limiting dilution analyses in secondary mice to quantify the LSC frequencies in MLL-AF9 WT and KRAS G13D / NRAS G12D leukemia. The average frequencies of control MLL-AF9 AMLs were between 1/510 000 to 1/1 450 000, while MLL-AF9+KRAS G13D AMLs frequencies were >1/45 000 and 1/7 800 for MLL-AF9+NRAS G12D AMLs, demonstrating that these 2 mutations increase the LSC frequency by >20-100 fold in our modelled MLL-AF9 AML. Using transcriptome analyses, we looked at the gene expression changes induced by the KRAS G13D mutation in comparison to MLL-AF9 leukemias. These experiments are in progress for the NRAS G13D mutation. Many more genes were overexpressed in MLL-AF9 KRAS G13D vs MLL-AF9 KRAS WT than down regulated. Genes from the hedgehog (Hh) pathway such as Patched1 (PTCH1) and Smoothened (SMO) were amongst the genes the most differentially overexpressed by the KRAS mutation. It is particularly interesting because they have been shown important in stem cell biology and could explain the increase in LSC. Some SMO inhibitors have been tested in clinical trial and Glasdegib is FDA approved in combination with low dose cytarabine in elderly patients. Its effect on MLL leukemias or on KRAS mutated AMLs has not been tested/reported in a clinical study. Experiments are currently in progress to test the effect of Glasgebib on engraftment of MLL-AF9 KRAS mutated cells in our experimental setting. Single cell RNA sequencing data on the three conditions will be presented at the meeting. Given the success of generating these two point mutations, we are currently generating more RAS pathway mutations, including other KRAS mutations, PNTP11 and NF1 mutations. Conclusion These experiments showed: 1) It is possible to induce 2 oncogenic hits in human primary cells and get leukemia in vivo; 2) the KRAS G13D and NRAS G12D mutations shorten the latency of the disease and 3) increase the LSC frequency in secondary mice; 4) a possible involvement of the Hh pathway on stemness/LSC in RAS mutated cells; 5) our experimental approach is robust and very promising to decipher the RAS pathway in human MLL leukemias.

Methyltransferases are enzymes fundamental to a wide range of normal biological activities that can become dysregulated during oncogenesis. For instance, the recent description of the methyltransferase-like (METTL) family of enzymes, has demonstrated the importance of the N6-adenosine-methyltransferase (m6A) modification in transcripts in the context of malignant transformation. Because of their importance, numerous METTL family members have been biochemically characterized to identify their cellular substrates, however some members such as METTL7B, recently renamed TMT1B and which is the subject of this review, remain enigmatic. First identified in the stacked Golgi, TMT1B is also localized to the endoplasmic reticulum as well as lipid droplets and has been reported as being upregulated in a wide range of cancer types including lung cancer, gliomas, and leukemia. Interestingly, despite evidence that TMT1B might act on protein substrates, it has also been shown to act on small molecule alkyl thiol substrates such as hydrogen sulfide, and its loss has been found to affect cellular proliferation and migration. Here we review the current evidence for TMT1B's activity, localization, and potential biological role in the context of both normal and cancerous cell types.

Acute myeloid leukemia (AML) is an aggressive form of blood cancer. Despite the use of cytotoxic standard-of-care drugs, patients often succumb to the disease partially due to the inability of medically unfit patients to withstand the cytotoxic treatments, regrowth from minimal residual disease and the chemo-resistant nature of leukemic stem cells (LSCs). Hence, novel therapies should focus on targeting the unique biology of LSCs to eliminate and avoid reoccurrence. To overcome challenges inherent of screening rare LSCs in vitro such as culturing and expanding, we optimized the conditions for a 4-week in vitro large-scale expansion (>600 million bulk) and enrichment of the CD34+ LSC-containing fraction (>90% purity) for a primary human AML sample (OCI-AML-8227), functionally validated to be enriched for LSCs in long-term xenotransplant assays (Eppert et al., 2011). Next, we performed a high-throughput screen of 11,140 chemical molecules in 3 stages. First, the viability of AML CD34+ cells and healthy cord blood (CB) CD34+ cells was read out at 1-2 doses using a CellTiter-Glo® Luminescent assay. 61 compounds had >70% inhibition of 8227 CD34+ cells and <30% inhibition on CB CD34+ cells. Next, we determined the dose response and refined the hits to 33 potent compounds with LC50 < 1 μM, including novel compounds and classes previously shown to target bulk and leukemic stem cells in AML. We are now presenting the follow up hits identified from the third stage of validation where we determined the LC 50 specifically in the CD34- (blast) and CD34+CD38- (LSC-enriched) OCI-AML-8227 populations using flow cytometry. We identified 25 novel anti-LSC compounds with high efficacy against CD34+CD38- AML cells (LC 50 < 500 nM). Venetoclax was among the top hits, a compound that revolutionized treatment for poor prognosis AML patients due to its anti-LSC activities, providing internal validation of the screen. We then tested these candidates in a second LSC-enriched model with poor prognosis, OCI-AML-20, to ensure the response of compounds on LSCs is not exclusive to OCI-AML-8227 and to investigate the influence of the microenvironment on drug efficiency. A total of 5 hits have significant responses (>50% reduction in LSC enriched populations) and nontoxic to stroma. Furthermore, we refined our top candidates to 7 compounds based on their efficiencies in the two LSC-enriched models (OCI-AML-20 and 8227) and low toxicity on stroma. To gain insights on their mechanisms of action in LSCs, the two models were treated with the 7 candidates and cytarabine as a control for 3 days and apoptosis was measured by flow cytometry. Out of 7 candidates, 5 induced apoptosis in the LSC-enriched fractions, suggesting elimination of LSCs through apoptosis. The remaining compounds may eliminate LSCs through different mechanisms. From these results, we focused on the three leading compounds and validated them for toxicity on CD34+ hematopoetic stem and progenitor cord blood cells (HSPCs) vs CD34+CD38- (LSC-enriched) OCI-AML-8227 by flow cytometry. Although slight toxicity was observed in HSPCs at higher doses, the LC 50 for the stem cell vs LSC-enriched populations differ by ~6-40-fold, indicating that a significantly lower concentration can be used to eradicate LSCs while sparing HSPCs (LC 50 for CD34+ population CB vs 8227; Compound A: 1558 nM vs 83 nM, Compound B: >2000 nM vs 305 nM and Compound C: 612 nM vs 16 nM, respectively). To functionally validate if HSPCs proliferation and differentiation was impaired and if leukemic progenitors were eradicated, a colony forming unit assay was performed for 12 days after 6 days of treatment. Candidates were found to eliminate leukemic progenitors by 50% or more, reducing leukemia initiating potential and having minimal or no impact on CB progenitor functionality. Overall, compound A is a potential candidate to move forward due to its ability to target and eliminate LSCs through apoptosis in two LSC-enriched models, its low toxicity on stroma and normal cord blood cells. This candidate is classified as an indole, a class shown by Pabst et al., 2014 to reduce CD34+CD15- AML cells in a drug screen for aryl hydrocarbon modulators, suggesting a potential mechanism for LSC elimination through apoptosis. We now aim to examine LSC eradication in a panel of genetically defined primary AMLs to be able to determine the broad applicability of this compound and translate the preliminary results for clinical use.

A rare subtype of acute myeloid leukemia (AML) is acute megakaryoblastic leukemia (AMKL). Recurrent and mutually exclusive oncogenic fusions are detected in AMKL and are considered the transforming event in this disease. AMKL usually affects children below 3 years of age and is associated with less than 40% cure rates. In addition, the development of genotype tailored therapies is urgently needed in AMKL but greatly limited by the paucity of primary sample material. Our research group has established synthetic human models of high-fatality pediatric AMKL, driven by distinct oncogenic fusions, which phenocopy the disease in a patho-physiological context in mice. Inducers of mitochondria-mediated apoptosis, so called BH3 mimetics, recently entered the therapeutic arena in pediatric leukemia with promising results. Therefore, we set out to investigate the potential of Venetoclax (inhibitor of BCL-2) and Navitoclax (inhibitor of BCL-2, BCL-XL and BCL-W) as novel therapeutic options as a bridge to curative bone marrow transplantation in this high-fatality infant leukemia. Our research demonstrates that genetic and pharmacological inhibition of the pro-survival BCL-2 family member BCL-XL results in significant induction of apoptosis in our models of AMKL. In contrast, inhibition of BCL-2 does not induce apoptosis in our models, which is currently the most investigated BCL-family member in the clinic for other subtypes of AML (Venetoclax). In addition, Navitoclax showed promising in vivo activity with a significant decrease in infiltrating leukemic cells in bone-marrow and spleen after drug treatment in comparison to vehicle-only controls. In summary, this project will bring mechanistic insight into the role of apoptotic pathways in AMKL and greatly accelerate the identification of novel therapeutic options in high-fatality infant AML. A rare subtype of acute myeloid leukemia (AML) is acute megakaryoblastic leukemia (AMKL). Recurrent and mutually exclusive oncogenic fusions are detected in AMKL and are considered the transforming event in this disease. AMKL usually affects children below 3 years of age and is associated with less than 40% cure rates. In addition, the development of genotype tailored therapies is urgently needed in AMKL but greatly limited by the paucity of primary sample material. Our research group has established synthetic human models of high-fatality pediatric AMKL, driven by distinct oncogenic fusions, which phenocopy the disease in a patho-physiological context in mice. Inducers of mitochondria-mediated apoptosis, so called BH3 mimetics, recently entered the therapeutic arena in pediatric leukemia with promising results. Therefore, we set out to investigate the potential of Venetoclax (inhibitor of BCL-2) and Navitoclax (inhibitor of BCL-2, BCL-XL and BCL-W) as novel therapeutic options as a bridge to curative bone marrow transplantation in this high-fatality infant leukemia. Our research demonstrates that genetic and pharmacological inhibition of the pro-survival BCL-2 family member BCL-XL results in significant induction of apoptosis in our models of AMKL. In contrast, inhibition of BCL-2 does not induce apoptosis in our models, which is currently the most investigated BCL-family member in the clinic for other subtypes of AML (Venetoclax). In addition, Navitoclax showed promising in vivo activity with a significant decrease in infiltrating leukemic cells in bone-marrow and spleen after drug treatment in comparison to vehicle-only controls. In summary, this project will bring mechanistic insight into the role of apoptotic pathways in AMKL and greatly accelerate the identification of novel therapeutic options in high-fatality infant AML.

Acute myeloid leukemia (AML) is an aggressive form of blood cancer defined by the uncontrolled proliferation and clonal expansion of immature myeloblast cells in the blood and bone marrow, leading to hematopoietic failure. Despite the use of aggressive and cytotoxic standard-of-care drugs, patients often relapse and succumb to the disease partially due to the inability of medically unfit patients to withstand the cytotoxic treatments, regrowth from minimal residual disease and the chemo-resistant nature of leukemic stem cells (LSCs) which can remain in a quiescent state and reside in a protective bone marrow niche. Hence, novel therapies targeting unique leukemic stem cell biology are highly needed to eliminate and avoid reoccurrence.

Acute megakaryoblastic leukemia (AMKL) is a rare subtype of pediatric acute myeloid leukemia (AML) with dismal survival prognosis in children below 3 years of age (<40% of cure rates). In two thirds of cases, recurrent and mutually exclusive oncogenic fusions are detected, such as CBFA2T3-GLIS2 (CG2) or NUP98 rearrangements (e.g. NUP98-KDM5A), which are considered the transformative event in this disease. The development of genotype tailored therapies is urgently needed in AMKL but greatly limited by the paucity of primary sample material, which is among other things attributed to myelofibrosis and the rarity of primary patients. Therefore, our research group has engineered synthetic human models of high-fatality pediatric AMKL with different oncogenic fusions that faithfully phenocopy the disease in a patho-physiological context. In recent years, inducers of mitochondria-mediated apoptosis, so called BH3 mimetics, entered the therapeutic arena in adult AML and pediatric leukemia with promising results. The molecules emphasized on are Venetoclax (a specific inhibitor of BCL2) and Navitoclax (broader affinity to BCL2, BCL-XL and BCL-W). Even though we see promising results in other leukemia, these agents were so far not investigated as potential therapies in pediatric high-fatality AMKL. To first overcome the paucity of patient material for research, we generated synthetic models of high-risk AMKL by transducing cord-blood derived hematopoietic stem and progenitor cells (HSPC) with lentiviral particles carrying the CBFA2T3-GLIS2 oncogenic fusion, followed by xenotransplantation into NSG mice. This approach generated leukemia with a latency between 9.9 and 36.1 weeks in primary mice which are able to sustain serial rounds of transplantation in recipient mice (up to 5 rounds tested). Furthermore, leukemic blasts immunophenotypically recapitulate AMKL, demonstrating expression of megakaryopoietic markers such as CD41, CD61 and CD56 that are even maintained after in vitro culture of 6 days and subsequent transplantation. Furthermore, we derived a CG2 specific gene expression signature from transcriptomic profiling of our models as well as patient samples that showed high expression of NCAM1, BMP2, ERG and low GATA1 levels, as reported for CG2 leukemia. Remarkedly, one of the specific up regulated genes in our signature for CG2 was pro-survival factor BCL2. In addition, our models are located in the megakaryocytic-erythroid differentiation space, as assessed by single cell RNAseq, and similar to their healthy counterparts of the megakaryopoietic lineage they demonstrated high expression of BCL-XL on RNA and protein level, in contrast to AML samples. Based on the aberrant expression of BCL2 in our synthetic leukemia models and lineage related expression of BCL-XL, we set out to test Venetoclax and Navitoclax in the context of AMKL. We identified Navitoclax (inhibitor of BCL2, BCL-XL and BCL-W) as a therapeutic vulnerability in our models of AMKL (CG2 and NUP98 rearranged), whereas our cells demonstrated resistance to treatment with Venetoclax. We further investigated the molecular mechanism and showed that shRNA mediated knock-down or inhibition of BCL-XL, by either Navitoclax or the BCL-XL specific proteasomal degrader DT2216, results in significant induction of apoptosis in our models of AMKL. On the contrary, genetic or pharmacological inhibition of BCL2 did not induce apoptosis in our synthetic models of AMKL, even at doses as high as 10µM. Furthermore, a genotype matched leukemic model of NUP98-KDM5A, which was presenting as monocytic (CD68+LYZ+) AML instead of AMKL, was resistant to either treatment with Venetoclax or Navitoclax whereas ML2, a MLL rearranged AML cell line, showed increased sensitivity to both Venetoclax and Navitoclax treatment. Moreover, in vivo treatment of a xenografted CG2 AMKL model with Navitoclax reduced leukemic burden in mice in bone-marrow and spleen in comparison to vehicle treated controls. In conclusion, we generated a model of rare CG2 pediatric high-fatality leukemia that faithfully mimics the patient situation and allows biomass generation for large scale multi-omic approaches. Furthermore, we demonstrate a lineage- and genotype specific targetable dependency of pediatric AMKL towards inhibition of BCL-XL but not BCL2, that could be transferred to the clinic as a novel therapeutic option in high-risk infant leukemia.

ABSTRACTOver the last two decades, molecular biology has been changed by the introduction of high-throughput technologies. Data sharing requirements have prompted the establishment of persistent data archives. A standardized approach for recording and managing these data was first proposed in the Minimal Information About a Microarray Experiment (MIAME) guidelines. The Minimal Information about a high throughput nucleotide Sequencing Experiment (MINSEQE) proposal was introduced in 2008 as a logical extension of the guidelines to next-generation sequencing (NGS) technologies used for transcriptome analysis.We present a historical snapshot of the data-sharing situation focusing on transcriptomics data from both microarray and RNA-sequencing experiments published between 2009 and 2013, a period during which RNA-seq studies became increasingly popular for transcriptome analysis. We assess how much data from RNA-seq based experiments is actually available in persistent data archives, compared to data derived from microarray based experiments, and evaluate how these types of data differ. Based on this analysis, we provide recommendations to improve RNA-seq data availability, reusability, and reproducibility.

Hematopoietic clones with leukemogenic mutations arise in healthy people as they age, but progression to acute myeloid leukemia (AML) is rare. Recent evidence suggests that the microenvironment may play an important role in modulating human AML population dynamics. To investigate this concept further, we examined the combined and separate effects of an oncogene (c-MYC) and exposure to interleukin-3 (IL-3), granulocyte-macrophage colony-stimulating factor (GM-CSF), and stem cell factor (SCF) on the experimental genesis of a human AML in xenografted immunodeficient mice. Initial experiments showed that normal human CD34+ blood cells transduced with a lentiviral MYC vector and then transplanted into immunodeficient mice produced a hierarchically organized, rapidly fatal, and serially transplantable blast population, phenotypically and transcriptionally similar to human AML cells, but only in mice producing IL-3, GM-CSF, and SCF transgenically or in regular mice in which the cells were exposed to IL-3 or GM-CSF delivered using a cotransduction strategy. In their absence, the MYC+ human cells produced a normal repertoire of lymphoid and myeloid progeny in transplanted mice for many months, but, on transfer to secondary mice producing the human cytokines, the MYC+ cells rapidly generated AML. Indistinguishable diseases were also obtained efficiently from both primitive (CD34+CD38-) and late granulocyte-macrophage progenitor (GMP) cells. These findings underscore the critical role that these cytokines can play in activating a malignant state in normally differentiating human hematopoietic cells in which MYC expression has been deregulated. They also introduce a robust experimental model of human leukemogenesis to further elucidate key mechanisms involved and test strategies to suppress them.

Chromosomal translocations involving the KMT2A gene are among the most common genetic alterations found in pediatric acute myeloid leukemias although the molecular mechanisms that initiate the disease remain incompletely defined. To elucidate these initiating events we used a human model system of acute myeloid leukemia driven by the KMT2A-MLLT3 (KM3) fusion. More specifically, we investigated changes in DNA methylation, histone modifications, and chromatin accessibility at each stage of our model system and correlated these with expression changes. We observed the development of a pronounced hypomethylation phenotype in the early stages of leukemic transformation after KM3 addition along with loss of expression of stem-cell-associated genes and skewed expression of other genes, such as S100A8/9, implicated in leukemogenesis. In addition, early increases in the expression of the lysine demethylase KDM4B was functionally linked to these expression changes as well as other key transcription factors. Remarkably, our ATAC-sequencing data showed that there were relatively few leukemia-specific changes and that the vast majority corresponded to open chromatin regions and transcription factor clusters previously observed in other cell types. Integration of the gene expression and epigenetic changes revealed that the adenylate cyclase gene ADCY9 is an essential gene in KM3-acute myeloid leukemia, and suggested the potential for autocrine signaling through the chemokine receptor CCR1 and CCL23 ligand. Collectively, our results suggest that KM3 induces subtle changes in the epigenome while co-opting the normal transcriptional machinery to drive leukemogenesis.

Infant acute lymphoblastic leukemias (ALL) are rare hematological malignancies occurring in children younger than 1 year of age, most frequently associated with KMT2A rearrangements (KMT2A-r). The smaller subset without KMT2A-r, which represents 20% of infant ALL cases, is poorly characterized. Here we report two cases of chemotherapy-sensitive non-KMT2A-r infant ALL. Transcriptome analyses revealed identical ACIN1-NUTM1 gene fusions in both cases, derived from cryptic chromosomal rearrangements undetected by standard cytogenetic approaches. Two isoforms of the gene fusion, joining exons 3 or 4 of ACIN1 to exon 3 of NUTM1, were identified. Both fusion transcripts contained the functional DNA-binding SAP (SAF-A/B, Acinus, and PIAS) domain of ACIN1 and most of NUTM1. The detection of the ACIN1-NUTM1 fusion by RT-PCR allowed the molecular monitoring of minimal residual disease in a clinical setting. Based on publicly available genomic datasets and literature review, we predict that NUTM1 gene fusions are recurrent events in infant ALL. As such, we propose two clinically relevant assays to screen for NUTM1 rearrangements in bone marrow cells, independent of the fusion partner: NUMT1 immunohistochemistry and NUTM1 RNA expression. In sum, our study identifies ACIN1-NUTM1 as a recurrent and possibly cryptic fusion in non-KMT2A-r infant ALL, provides clinical tools to screen for NUTM1-rearranged leukemia and contributes to the refinement of this new subgroup.

Background: Current evidence suggests that genetic and epigenetic abnormalities drive the development of human Acute Myeloid Leukemias (AMLs). However, whether these are sufficient to establish a permanent, self-sustaining AML population, and the potential role of shared perturbed downstream pathways is unknown. We hypothesized that a modest upregulated expression of MYC might play such a role given its commonly increased expression in many AML patients' cells. To test this hypothesis, we assessed the dynamics and types of cells produced in sublethally irradiated NOD-Rag1-/--IL2Rγc-/-(NRG) mice transgenically producing human IL3, GM-CSF and SCF (NRG-3GS mice) following their transplantation with freshly isolated subsets of normal CD34+ cord blood (CB) cells that were first lentivirally transduced with a human MYC cDNA. Results: FACS and Western blot analyses indicated this produced a 2 to 5-fold increase in MYC mRNA and protein levels in MYC-transduced CD34+ CB cells, and 21/22 NRG-3GS mice injected with ≥6,500 of these cells developed a fatal human AML population within 7 weeks. Histological analysis of their bone marrow and spleen cells showed both contained a prominent human CD123+CD33+CD15±CD34-CD14-CD19-CD3- blast population. Additional limiting dilution transplants showed that both the CD34+CD38- cells (enriched for hematopoietic stem cells) and the more differentiated CD34+ GMPs were similarly highly susceptible (at frequencies of 1/14 and 1/46, respectively) and, in both cases, generated progeny that could initiate serially transplantable leukemias with the same phenotypic and transcriptomic features. Comparison to normal CB cells indicated these most closely resembled GMPs, and comparison to pediatric AML patient samples indicated a similarity to myelomonocytic leukemias with enhanced MYC expression. Interestingly, 14 sublethally irradiated NRG mice (the parental strain not producing human 3GS) transplanted with matched aliquots of CD34+ MYC-transduced cells regenerated a normal spectrum of CD19+ lymphoid cells, CD14+ and CD15+ GM cells and readily detectable CD34+ cells for up to 32 weeks of follow-up with no evidence of leukemogenesis. However, transfer of these regenerated human cells into secondary NRG-3GS mice, even after this extended period, enabled their rapid production of a lethal human AML in all 5 mice tested. In contrast, matched aliquots transplanted into 5 NRG recipients produced declining grafts of normal cells. This finding was then exploited to determine which growth factors were responsible for activating the AML program by transplanting NRG mice with CD34+ CB cells transduced with MYC and just a single growth factor, or all 3 as a positive control. In this set of experiments, a lethal human AML was obtained when MYC was paired with human IL3 or GM-CSF (or all 3 together), but not with SCF (or no growth factors). Conclusion: We report here a new in vivo model of MYC-induced human myeloid leukemogenesis that produces a serially transplantable AML closely resembling human pediatric myelomonocytic leukemias with elevated MYC expression. The rapidity, consistency, and high frequency of this transformation process obtained by transducing late granulopoietic as well as early types of normal human CD34+ progenitor cells makes this system highly attractive for future mechanistic and therapeutic testing experiments. The discovery that MYC deregulation alone generates a stable "latent program" that can be rapidly activated by exposure to exogenous growth factors typical of inflammatory states also raises intriguing questions about the potential role of such events in the genesis of AML populations that arise in patients. Disclosures Beer: Karus therapeutics Ltd.: Employment.

Hematopoietic stem cells (HSC) are responsible for the on demand production of blood cells both in homeostasis and in response to stress.HSCs reside in specialized niches bone marrow (BM) niches, which regulate their function.These niches are dynamic entities with the capacity to sense and respond to specific requirements in blood production, but the mechanisms underlying this dynamic regulation remain unclear.Accumulating evidence indicate that HSCs are highly heterogeneous, and different BM niches have been proposed, potentially supporting different HSC subsets.We recently identified a subset of HSCs, which is molecularly and functionally primed for platelet replenishment.However, the role of the niche in the regulation of plateletbiased HSC function is still unknown.This work aims at investigating the role of the BM niche in the response of plateletbiased HSCs to thrombocytopenia.In response to platelet depletion platelet-biased HSCs are rapidly and selectively recruited into cell cycle, through a feedback mechanism to replenish platelet numbers and homeostasis.Using RNA-sequencing to analyze different BM niche cell populations and HSC subsets we identified IL-1 as a cytokine released upon platelet depletion and specifically sensed by niche LepR+ perivascular cells.Abrogation of IL-1 signaling specifically in LepR+ niche cells but not in hematopoietic cells impaired the platelet-biased HSC response to platelet depletion.This process was found to be dependent on platelet activation.This work uncovers a molecular mechanism involving the pro-inflammatory signal IL-1 and the niche perivascular cell compartment in the rapid activation of platelet biased HSCs to thrombocytopenia, highlighting a mechanism by which a distinct HSC subset senses and responds to the loss of the lineage it is intrinsically primed for.

Acute myeloid leukemia (AML) is a disease that results from the uncontrolled growth of primitive myeloid progenitor cells that are unable to undergo terminal differentiation. To better understand the genetic and epigenetic changes involved in leukemogenesis, we use a human model leukemia system where cord blood donor cells from a single donor are transduced with the human KMT2A-MLLT3 gene fusion to produce leukemias. We have generated multiple model leukemias and compared these to genetically matched pediatric AML patient samples that has allowed us to characterize the step-wise epigenetic and splicing changes that accompany leukemogenesis, allowing us to build an integrated view of this process. Our analysis of these data have revealed a number of candidate biomarker genes that are expressed in KMT2A translocated AMLs but not normal blood cells, some of which are important for leukemic growth. These candidate genes, which have validated diagnostic value, have also been used as targets for monoclonal antibody generation in order to assess their value as potential immunotherapeutics. Having established the value of this approach, we are now expanding our models to include additional oncogenic drivers in order to elucidate the differences in patient outcomes associated with the presence of specific fusions. Moreover, we have recently leveraged these model leukemias and matched patient samples to perform a high-throughput small molecule screen to identify novel therapeutic vulnerabilities and deconvolute the role of secondary mutations in pediatric patients. The establishment of this chemogenomic pipeline to generate, characterize, and then screen model leukemias will provide not only insight into the molecular mechanisms involved in this disease, but also how they can be rationally targeted to improve patient outcomes.