Search

Acute megakaryoblastic leukemia (AMKL) represents ∼10% of pediatric acute myeloid leukemia cases and typically affects young children (

Leukemia is a complex genetic disease caused by errors in differentiation, growth, and apoptosis of hematopoietic cells in either lymphoid or myeloid lineages. Large-scale genomic characterization of thousands of leukemia patients has produced a tremendous amount of data that have enabled a better understanding of the differences between adult and pediatric patients. For instance, although phenotypically similar, pediatric and adult myeloid leukemia patients differ in their mutational profiles, typically involving either chromosomal translocations or recurrent single-base-pair mutations, respectively. To elucidate the molecular mechanisms underlying the biology of this cancer, continual efforts have been made to develop more contextually and biologically relevant experimental models. Leukemic cell lines, for example, provide an inexpensive and tractable model but often fail to recapitulate critical aspects of tumor biology. Likewise, murine leukemia models of leukemia have been highly informative but also do not entirely reproduce the human disease. More recent advances in the development of patient-derived xenografts (PDXs) or human models of leukemias are poised to provide a more comprehensive, and biologically relevant, approach to directly assess the impact of the in vivo environment on human samples. In this review, the advantages and limitations of the various current models used to functionally define the genetic requirements of leukemogenesis are discussed.

Over 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.

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 hypomethyl - ation 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.

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.

The advent of large scale genomic sequencing technologies significantly improved the molecular classification of acute megakaryoblastic leukaemia (AMKL). AMKL represents a subset (∼10%) of high fatality pediatric acute myeloid leukemia (AML). Recurrent and mutually exclusive chimeric gene fusions associated with pediatric AMKL are found in 60%-70% of cases and include RBM15-MKL1, CBFA2T3-GLIS2, NUP98-KDM5A and MLL rearrangements. In addition, another 4% of AMKL harbor NUP98 rearrangements (NUP98r), with yet undetermined fusion partners. We report a novel NUP98-BPTF fusion in an infant presenting with primary refractory AMKL. In this NUP98r, the C-terminal chromatin recognition modules of BPTF, a core subunit of the NURF (nucleosome remodeling factor) ATP-dependent chromatin-remodeling complex, are fused to the N-terminal moiety of NUP98, creating an in frame NUP98-BPTF fusion, with structural homology to NUP98-KDM5A. The leukemic blasts expressed two NUP98-BPTF splicing variants, containing one or two tandemly spaced PHD chromatin reader domains. Our study also identified an unreported wild type BPTF splicing variant encoding for 2 PHD domains, detected both in normal cord blood CD34+ cells and in leukemic blasts, as with the fly BPTF homolog, Nurf301. Disease course was marked by rapid progression and primary chemoresistance, with ultimately significant tumor burden reduction following treatment with a clofarabine containing regimen. In sum, we report 2 novel NUP98-BPTF fusion isoforms that contribute to refine the NUP98r subgroup of pediatric AMKL. Multicenter clinical trials are critically required to determine the frequency of this fusion in AMKL patients and explore innovative treatment strategies for a disease still plagued with poor outcomes.

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. High-throughput screens of human AML LSCs are not performed due to technical issues such as low LSC frequency within primary samples, an inability to purify LSCs, and the difficulty maintaining and expanding primary patient samples and LSCs in vitro. We were able to optimize conditions for a 4-week in vitro large-scale expansion (>600 million bulk) of the primary human AML sample 8227 (OCI-AML-8227), functionally validated to be enriched for LSCs in long-term xenotransplant assays (Eppert et al., 2011). These optimized conditions enabled the isolation and maintenance of the LSC-containing fraction for a chemical screen. We isolated the CD34+ LSC-containing fraction (>90% purity) and performed a high-throughput screen of 11,166 chemical molecules using a CellTiter Glo assay followed by a counter screen against normal CD34+ cord blood (CB) hematopoietic stem and progenitor cells. From this HT screen, a total of 61 hits had >70% inhibition on CD34+ 8227 cells and We then performed dose response assays for each candidate compounds and confirmed 35 potent anti-LSC compounds with IC 50 < 1 μM. This refined the types of compounds to including anti-apoptotic inhibitors, GSK inhibitors, protease inhibitors, metabolism inhibitors, HDAC inhibitors, BET inhibitors, nucleic acid synthesis inhibitors, cell cycle inhibitors and Wnt/β-catenin inhibitors. This is interesting as some of the classes of these compounds (inhibitors of GSK, BET, nucleic acid synthesis, Wnt/β-catenin and metabolism) have been shown to target bulk and leukemic stem cells in AML in vitro and in vivo. We now aim to examine LSC eradication in a panel of genetically defined primary AMLs confirmed through in vitro and in vivo assays. Our goal is to be able to understand and establish the molecular mechanisms and biomarkers on primary functional LSCs. Disclosures No relevant conflicts of interest to declare.

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.

The development of biosensor arrays able to detect specific protein interactions is highly needed to precisely dissect fundamental biological systems and to broaden the scope of biomarker detection, especially to refine diagnostics of subtyped diseases such as cancer. Graphene-based field-effect transistor sensors (GFETs) are a promising emerging technology for such biomolecular sensing applications: their atomically-thin surface provides label-free sensitivity to biomolecules via direct electrostatic interactions, and their small footprint enables compact, rapid and parallelized assays. The selectivity of GFET sensors, however, requires functionalization of the graphene surface with a layer of bio-recognition species (“probe molecules”). In this presentation, we will describe our recent progress in immobilizing proteins as probe molecules on graphene field-effect transistors, specifically (1) monoclonal antibodies against a biomarker specific to MLL-translocated acute myeloid leukemia and (2) small Ras GTPase proteins regulated by various effector proteins. First, we will describe our GFET sensor design, based on on-chip arrays of GFETs made from CVD-grown graphene, mounted with a multi-channel delivery flow-cell enabling parallel assays on sub-ensembles of sensors. We will then present our investigation of protein immobilization on graphene. We found that antibodies and small proteins can spontaneously adhere to the graphene surface, but this adhesion is partially reversible under solution flow. To create stable anchor groups at the graphene surface which can then capture the protein probes, we propose to use covalent chemistry on the graphene surface. In particular, we developed a protocol based on electrochemically-driven aryldiazonium chemistry to increase the rate of formation and the density of anchor groups on the graphene surface. Using time-resolved electrical measurements, we observed a specific electrical signal associated with the irreversible immobilization of protein probes on the graphene surface. Finally, we will discuss the use of such protein-functionalized GFETs for the detection of specific probe-target interactions, for applications in fundamental biophysics and cancer diagnostics.

Acute myeloid leukemias (AMLs) result from a series of genetic events occurring in a stem or progenitor hematopoietic cell that gives rise to their clonal expansion and an impaired capacity to differentiate. To circumvent the genetic heterogeneity of AML patient cohorts, we have developed a model system, driven by the MLL-AF9 (MA9) oncogene, to generate multiple human leukemias using progenitor cells from a single healthy donor. Through stepwise RNA-sequencing data generated using this model and AML patients, we have identified consistent changes associated with MA9-driven leukemogenesis and demonstrate that no recurrent secondary mutations are required. We identify 39 biomarkers whose high expression level is specific to this genetic subtype of AML and validate that many of these have diagnostic utility. We further examined one biomarker, the receptor tyrosine kinase (RTK) RET, and show through shRNA knockdowns that its expression is essential for in vivo and in vitro growth of MA9-AML. These results highlight the value of novel human models of AML derived from single donors using specific oncogenic fusions to understand their biology and to uncover potential therapeutic targets.

Umbilical cord blood (CB)-derived hematopoietic stem cells (HSCs) are essential in many life saving regenerative therapies, but their low number in CB units has significantly restricted their clinical use despite the advantages they provide during transplantation1. Select small molecules that enhance hematopoietic stem and progenitor cell (HSPC) expansion in culture have been identified2,3, however, in many cases their mechanisms of action or the nature of the pathways they impinge on are poorly understood. A greater understanding of the molecular pathways that underpin the unique human HSC self-renewal program will facilitate the development of targeted strategies that expand these critical cell types for regenerative therapies. Whereas transcription factor networks have been shown to influence the self-renewal and lineage decisions of human HSCs4,5, the post-transcriptional mechanisms guiding HSC fate have not been closely investigated. Here we show that overexpression of the RNA-binding protein (RBP) Musashi-2 (MSI2) induces multiple pro-self-renewal phenotypes, including a 17-fold increase in short-term repopulating cells and a net 23-fold ex vivo expansion of long-term repopulating HSCs. By performing a global analysis of MSI2-RNA interactions, we determined that MSI2 directly attenuates aryl hydrocarbon receptor (AHR) signaling through post-transcriptional downregulation of canonical AHR pathway components in CB HSPCs. Our study provides new mechanistic insight into RBP-controlled RNA networks that underlie the self-renewal process and give evidence that manipulating such networks ex vivo can provide a novel means to enhance the regenerative potential of human HSCs.

Field-effect transistor devices based on functionalized graphene (G-FETs) are a promising technology for biomolecular sensing applications due to the several advantages they present, including the label-free detection of biomolecules with direct electrical read-out, real-time detection and multiplexing capability. The development of highly selective and sensitive sensors for protein biomarkers is especially desirable to open novel technological avenues for the early detection and monitoring of biomarkers associated with cancer diseases. In this presentation, I’ll describe our recent progress on the design and development of a label-free immunosensor based on antibody-modified graphene field-effect transistors for protein biomarker detection. Specifically, monoclonal antibodies were selected to target a protein biomarker specific to MLL translocated acute myeloid leukemia and we tested approaches for their immobilization on graphene. We found that the antibodies can spontaneously adhere to the graphene surface but this adhesion is partially reversible under solution flow. In order to stabilize the immobilization of antibodies, we developed a protocol based on electrochemically-driven chemistry to form stable covalent anchor groups at the graphene surface which can then capture antibodies. We optimized the rate of formation of anchor groups at the surface in order to maximize the density of anchor groups while maintaining high electrical currents in the graphene. We were then able to record a specific electrical signature showing irreversible immobilization of antibodies on the graphene surface, thus allowing further optimization of target detection. Employing a combination of microfluidics and real-time electrical measurements, we then investigated the response of the sensors to non-specific interactions with graphene as well as their response to specific antibody-antigen interactions in phosphate buffer solution. Finally, the sensors response to different concentrations of target protein was characterized to assess their performance parameters.

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.

Next generation DNA sequencing has provided significant insights into the genetic determinants of acute myeloid leukemia (AML). Large scale sequencing studies of AML patient cohorts have revealed a remarkable level of genetic heterogeneity between patients who nevertheless have the same disease phenotype. As a solution to the problem of extensive genetic diversity between patients, we have modified a previously published model system in order to generate multiple human leukemias from CD34+ cord blood cells from a single healthy donor. A human MLL-AF9 (MA9) fusion gene is retrovirally introduced into the donor cells which are then cultured for 30 days before being transplanted into immunocompromised (NSG) mice that subsequently develop either AML or acute B-cell lymphoblastic leukemia (B-ALL) after ~24 weeks. We have now generated 22 leukemias from 4 single donors and have performed RNA-seq on the samples during their step-wise leukemic transformation (i.e. CD34+ cells, CD34+ cells with MA9, and the resulting leukemias). We have compared these data to RNA-seq data we have generated for several pediatric AML patients with MA9 translocations, as well as normal blood cells and other tissues. This analysis has revealed 39 candidate genes with an expression pattern highly specific for MA9 AMLs. Interestingly, we can find no evidence for secondary mutations acquired by the human leukemias in our model system, suggesting the human MA9 translocation is sufficient to generate leukemias in this context. To understand the epigenetic impact of the MA9 fusion gene, we have examined the DNA methylation changes at each stage in our model system using a capture survey approach (e.g. Human Methyl-Seq; Agilent) and used this same approach for several primary patient samples with MLL translocations. These data have been correlated with gene expression changes within the model system and have revealed a number of specific changes with relevance for the process of transformation. Lastly, functional assessment of specific candidate genes through shRNA knock-down experiments has shown that at least some of these candidate genes, which are known oncogenes in other tumor types, are essential for MA9 AML. In summary, the combination of RNA-seq data from patient and single donor model AMLs has highlighted consistent genetic changes associated with this AML sub-group, and has also revealed novel potential therapeutic targets. Citation Format: Frederic Barabe, Magalie Celton, Audrey Forest, Anne Bergeron, Radia Johnson, Laurine Gil, Angélique Bellemare-Pelletier, Sonia Cellot, Josee Hebert, Etienne Gagnon, Brian T. Wilhelm. Integrated genetic and epigenetic analysis of model and patient acute myeloid leukemias. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-14.

Using next-generation sequencing of primary acute myeloid leukemia (AML) specimens, we identified to our knowledge the first unifying genetic network common to the two subgroups of KMT2A (MLL)-rearranged leukemia, namely having MLL fusions or partial tandem duplications. Within this network, we experimentally confirmed upregulation of the gene with the most subtype-specific increase in expression, LOC100289656, and identified cryptic MLL fusions, including a new MLL-ENAH fusion. We also identified a subset of MLL fusion specimens carrying mutations in SPI1 accompanied by inactivation of its transcriptional network, as well as frequent RAS pathway mutations, which sensitized the leukemias to synthetic lethal interactions between MEK and receptor tyrosine kinase inhibitors. This transcriptomics-based characterization and chemical interrogation of human MLL-rearranged AML was a valuable approach for identifying complementary features that define this disease.

Acute myeloid leukemias (AMLs) with translocations of the mixed lineage leukemia (MLL/KMT2A) gene are common in young patients and are generally associated with poor clinical outcomes. The molecular biology of MLL fusion genes remains incompletely characterized and is complicated by the fact that more than 100 different partner genes have been identified in fusions with MLL. The continuously growing list of MLL fusions also represents a clinical challenge with respect to identification of novel fusions and tracking of the fusions to monitor progression of the disease after treatment. Recently, we have developed a novel single-donor model leukemia system that permits the development of human AML from normal cord blood cells. Gene expression analysis of this model and of MLL-AML patient samples has identified a number of candidate biomarker genes with highly biased expression on leukemic cells. Here, we present data demonstrating the potential clinical utility of several of these candidate genes for identifying known and novel MLL fusions.

The development of next-generation sequencing technologies has had a profound impact on the field of cancer genomics. With the enormous quantities of data being generated from tumor samples, researchers have had to rapidly adapt tools or develop new ones to analyse the raw data to maximize its value. While much of this effort has been focused on improving specific algorithms to get faster and more precise results, the accessibility of the final data for the research community remains a significant problem. Large amounts of data exist but are not easily available to researchers who lack the resources and experience to download and reanalyze them. In this article, we focus on RNA-seq analysis in the context of cancer genomics and discuss the bioinformatic tools available to explore these data. We also highlight the importance of developing new and more intuitive tools to provide easier access to public data and discuss the related issues of data sharing and patient privacy.

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.

Acute myeloid leukemias (AML) comprise a genetically diverse group of human hematologic malignancies with a generally poor prognosis and modes of pathogenesis that have been difficult to investigate. Historic evidence and more recent findings have identified hematopoietic stem cell programs as major targets of mutations that predispose to and/or initiate a multistep process of transformation. However, details of the changes involved and how they interact in emerging human leukemic cells have been particularly challenging to characterize. This is due to an emerging appreciation of the heterogeneity in events that impact the differentiation processes of normal human hematopoietic cells, as well as difficulties in recreating the full leukemogenic alterations in the actual human cells affected, to avoid discrepancies inherent in studying model organisms. Here we describe several models of de novo human leukemogenesis that illustrate their power and the novel results they can generate. These include our recent discovery of a novel “latent” leukemic state that can be obtained in MYC-transduced human cord blood cells regenerating a normal spectrum of lymphoid and myeloid progeny in transplanted immunodeficient mice, but that can then be rapidly activated to an aggressive form of AML by in vivo exposure to a single human growth factor. These findings portend the future utility of de novo human leukemogenesis models as new platforms for elucidating shared molecular mechanisms responsible for different stages of human leukemogenesis that may be initiated by different mutations or exposure to different microenvironmental conditions. The flexibility and consistency of these models also make them attractive for identifying and testing new treatment strategies targeting mechanisms required for disease manifestation.

Genome-wide transcriptome profiling has enabled non-supervised classification of tumours, revealing different sub-groups characterized by specific gene expression features. However, the biological significance of these subtypes remains for the most part unclear. We describe herein an interactive platform, Minimum Spanning Trees Inferred Clustering (MiSTIC), that integrates the direct visualization and comparison of the gene correlation structure between datasets, the analysis of the molecular causes underlying co-variations in gene expression in cancer samples, and the clinical annotation of tumour sets defined by the combined expression of selected biomarkers. We have used MiSTIC to highlight the roles of specific transcription factors in breast cancer subtype specification, to compare the aspects of tumour heterogeneity targeted by different prognostic signatures, and to highlight biomarker interactions in AML. A version of MiSTIC preloaded with datasets described herein can be accessed through a public web server (http://mistic.iric.ca); in addition, the MiSTIC software package can be obtained (github.com/iric-soft/MiSTIC) for local use with personalized datasets.

Background Cancer genomics projects are producing ever-increasing amounts of rich and diverse data from patient samples. The ability to easily visualize this data in an integrated an intuitive way is currently limited by the current software available. As a result, users typically must use several different tools to view the different data types for their cohort, making it difficult to have a simple unified view of their data. Results Here we present Cascade, a novel web based tool for the intuitive 3D visualization of RNA-seq data from cancer genomics experiments. The Cascade viewer allows multiple data types (e.g. mutation, gene expression, alternative splicing frequency) to be simultaneously displayed, allowing a simplified view of the data in a way that is tuneable based on user specified parameters. The main webpage of Cascade provides a primary view of user data which is overlaid onto known biological pathways that are either predefined or added by users. A space-saving menu for data selection and parameter adjustment allows users to access an underlying MySQL database and customize the features presented in the main view. Conclusions There is currently a pressing need for new software tools to allow researchers to easily explore large cancer genomics datasets and generate hypotheses. Cascade represents a simple yet intuitive interface for data visualization that is both scalable and customizable. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2389-8) contains supplementary material, which is available to authorized users.

The proliferation and survival of hematopoietic stem cells (HSCs) has to be strictly coordinated to ensure the timely production of all blood cells. Here we report that the splice factor and RNA binding protein hnRNP L (heterogeneous nuclear ribonucleoprotein L) is required for hematopoiesis, since its genetic ablation in mice reduces almost all blood cell lineages and causes premature death of the animals. In agreement with this, we observed that hnRNP L deficient HSCs lack both the ability to self-renew and foster hematopoietic differentiation in transplanted hosts. They also display mitochondrial dysfunction, elevated levels of γH2AX, are Annexin V positive and incorporate propidium iodide indicating that they undergo cell death. Lin-c-Kit+ fetal liver cells from hnRNP L deficient mice show high p53 protein levels and up-regulation of p53 target genes. In addition, cells lacking hnRNP L up-regulated the expression of the death receptors TrailR2 and CD95/Fas and show Caspase-3, Caspase-8 and Parp cleavage. Treatment with the pan-caspase inhibitor Z-VAD-fmk, but not the deletion of p53, restored cell survival in hnRNP L deficient cells. Our data suggest that hnRNP L is critical for the survival and functional integrity of HSCs by restricting the activation of caspase-dependent death receptor pathways.

High levels of glutathione peroxidase 3 (GPx3) expression correlate with adverse prognosis in acute myeloid leukemia, and enhance activity of long-term repopulating hematopoietic stem cells in mice., The determinants of normal and leukemic stem cell self-renewal remain poorly characterized. We report that expression of the reactive oxygen species (ROS) scavenger glutathione peroxidase 3 (GPx3) positively correlates with the frequency of leukemia stem cells (LSCs) in Hoxa9+Meis1-induced leukemias. Compared with a leukemia with a low frequency of LSCs, a leukemia with a high frequency of LSCs showed hypomethylation of the Gpx3 promoter region, and expressed high levels of Gpx3 and low levels of ROS. LSCs and normal hematopoietic stem cells (HSCs) engineered to express Gpx3 short hairpin RNA (shRNA) were much less competitive in vivo than control cells. However, progenitor cell proliferation and differentiation was not affected by Gpx3 shRNA. Consistent with this, HSCs overexpressing Gpx3 were significantly more competitive than control cells in long-term repopulation experiments, and overexpression of the self-renewal genes Prdm16 or Hoxb4 boosted Gpx3 expression. In human primary acute myeloid leukemia samples, GPX3 expression level directly correlated with adverse prognostic outcome, revealing a potential novel target for the eradication of LSCs.

The three-amino-acid loop extension (TALE) class homeodomain proteins MEIS1 and PKNOX1 (PREP1) share the ability to interact with PBX and HOX family members and bind similar DNA sequences but appear to play opposing roles in tumor development. Elevated levels of MEIS1 accelerate development of HOX- and MLL-induced leukemias, and this pro-tumorigenic property has been associated with transcriptional activity of MEIS1. In contrast, reduction of PKNOX1 levels has been linked with cancer development despite the absence of an identifiable transactivating domain. In this report, we show that a chimeric protein generated by fusion of the MEIS1 C-terminal region encompassing the transactivating domain with the full-length PKNOX1 (PKNOX1-MC) acquired the ability to accelerate the onset of Hoxa9-induced leukemia in the mouse bone marrow transduction/transplantation model. Gene expression profiling of primary bone marrow cells transduced with Hoxa9 plus Meis1, or Hoxa9 plus Pknox1-MC revealed perturbations in overlapping functional gene subsets implicated in DNA packaging, chromosome organization, and in cell cycle regulation. Together, results presented in this report suggest that the C-terminal domain of MEIS1 confers to PKNOX1 an ectopic transactivating function that promotes leukemogenesis by regulating expression of genes involved in chromatin accessibility and cell cycle progression.

Acute megakaryoblastic (CD41+CD61+) leukemia (AMKL) is a subset (10%) of pediatric acute myeloid leukemia (AML) that typically affects young children ( We engineered human models of AMKL through overexpression of NUP98-KDM5A (N5A) in cord blood (CB)-HSPC using lentiviral transduction (vector carrying GFP reporter gene). We generated multiple de novo N5A models, from distinct genetic backgrounds (independent CB units), to identify fusion-specific features. Adoptive transfer of the fusion oncogene-carrying cells (or N5A-cells) in immunodeficient (NSG) recipient mice led to AMKL development with a latency of 32-46 weeks (λ of 1/6 to 2/3, n=3 independent experiments). Mice presented clinically overt signs of disease with leukemic cell infiltration of multiple organs (bone marrow, liver, and spleen, as well as lung and kidney) and myelofibrosis. Leukemic blasts consisted of CD45loCD34-CD41+CD61+ cells, faithfully phenocopying human AMKL. In addition, N5A overexpression led to the development of acute erythroid leukemia (AEL) (CD34-CD117+CD36+) and B-ALL (CD34+CD38+CD19+CD10+), reflecting the clinical heterogeneity of leukemia associated with NUP98 fusions and suggesting distinct cells of origin for each entity. While N5A harboring B-ALL have not yet been reported, the fusion is now emerging as a recurrent genetic aberration in AEL. Transcriptomic studies of flow-sorted GFP+ xenograft cells closely matched that of N5A pediatric samples, and showed upregulation of HOXA/B cluster genes, as compared to control HSPC. A hematopoietic stem cell signature was detected by gene set enrichment analysis (GSEA) for N5A AMKL, as well as novel cell surface markers, including p-selectin (SELP) and CD96. Thus far, cooperating mutations were not identified, suggesting that the N5A fusion is a potent oncogene. In addition, using optimized culture conditions to promote HSPC expansion, leukemic cell lines were generated. N5A-cells displayed maturation block and increased cell proliferation compared to controls, as assessed by cytology, serial tracking of increasing CD34+GFP+ cell fractions, and lack of a c-KIThi differentiated mast cell population. After 3 weeks in vitro, when control-transduced cells normally begin to die off, an immature cell population emerged from the N5A-cells and this population was sustained for >140 days. This was observed by day 25 of culture in 66% (2/3) to 92% (11/12) of the wells (n=3 expts). Progenitor frequency was markedly increased in N5A-cells (on average 1:3 vs 1:200 in CTL, at day 88 of culture; n=3 expts). These N5A engineered cell lines can be efficiently transduced with shRNA carrying lentiviral vectors and thus provide suitable substrates for chemical and genetic screening approaches. We have optimized a strategy to engineer human cell lines and xenograft models of high-fatality NUP98-KDM5A driven leukemia, identifying specific leukemia-activated genes and novel cell surface biomarkers for AMKL. These studies unraveled the unappreciated multilineage leukemic potential of N5A, indicating that engineered leukemia can be exploited to unravel novel disease subtypes, which is especially relevant for cryptic mutations such as N5A fusions. The generated cell lines pave the way to genetic- or chemical-based functional screens to identify promising drug targets. Citation Format: Sophie Cardin, Melanie Bilodeau, Louise Laramee, Loubna Jouan, Mathieu Roussy, R. Keith Humphries, Josee Hebert, Brian T. Wilhelm, Sonia Cellot. Human models of multilineage leukemia induced by NUP98-KDM5A chimeric fusion oncogene [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr A19.

It is believed that hemopoietic stem cells (HSC), which colonize the fetal liver (FL) rapidly, expand to establish a supply of HSCs adequate for maintenance of hemopoiesis throughout life. Accordingly, FL HSCs are actively cycling as opposed to their predominantly quiescent bone marrow counterparts, suggesting that the FL microenvironment provides unique signals that support HSC proliferation and self-renewal. We now report the generation and characterization of mice with a mutant allele of Baf250a lacking exons 2 and 3. Baf250aE2E3/E2E3 mice are viable until E19.5, but do not survive beyond birth. Most interestingly, FL HSC numbers are markedly higher in these mice than in control littermates, thus raising the possibility that Baf250a determines the HSC pool size in vivo. Limit dilution experiments indicate that the activity of Baf250aE2E3/E2E3 HSC is equivalent to that of the wild-type counterparts. The Baf250aE2E3/E2E3 FL-derived stroma, in contrast, exhibits a hemopoiesis-supporting potential superior to the developmentally matched controls. To our knowledge, this demonstration is the first that a mechanism operating in a cell nonautonomous manner canexpand the pool size of the fetal HSC populations.

The cytotoxic activity of mouse natural killer cells is regulated in part through cell surface molecules belonging to the Ly49 multigene family. In mice, the genomic sequence of the Ly49 gene cluster has been examined in detail and this analysis provided a model of the expansion of this multigene family. In the present study, we have analyzed a 1.8-Mb region of the draft rat genome revealing surprising differences in size and gene content between the mouse and the rat Ly49 clusters. The rat cluster contains at least 36 Ly49 genes, including pseudogenes, while dot-plot analysis of the cluster reveals an equidistant spacing of genes, suggesting that duplication of genes in the cluster occurred through a mechanism similar to that in the mouse. Phylogenetic analysis of the predicted rat genes reveals a number of distinct gene clusters and indicates that the majority of gene duplication events occurred after the divergence of mice and rats. Thus, the rodent Ly49 locus is subject to extremely rapid gene amplification and diversification.

The Ly49 family of natural killer (NK) receptors is encoded by a highly polymorphic multigene family in the mouse and is also present in multiple copies in the rat. However, this gene exists as a single copy in primates and is mutated to non-function in humans. We recently showed that the cow also likely has only one Ly49 gene, but it is unclear what the Ly49 gene content is for other mammals. We have now isolated Ly49 cDNAs from the domestic cat, dog and pig and show that the corresponding gene appears to be single copy in these three species. The open reading frame is intact in all the genes and the putative proteins contain an immune tyrosine-based inhibition motif (ITIM), suggesting a role as an inhibitory receptor. In contrast to the other mammals, several Ly49-like genes appear to exist in the horse, indicating that amplification of this locus has occurred in a non-rodent lineage. Finally, phylogenetic analysis suggests that the rodent Ly49 genes have evolved more rapidly than their counterparts in mammals where the gene has remained as a single copy.

NK cells in adult mice express two families of MHC class I-specific receptors, namely, Ly49 and CD94/NKG2. Co-expression of these receptors in various combinations generates diverse receptor repertoires. The expression of individual receptors is mostly stochastic and independent of each other. NK cells acquire the receptors as they develop from progenitors in the bone marrow in adult mice. In vivo as well as in vitro studies have shown that the acquisition of the receptors is ordered and regulated by the host MHC class I. Developing NK cells first acquire CD94/NKG2 and subsequently various Ly49 receptors in an ordered manner. Unlike adult NK cells, most fetal and neonatal NK cells express CD94/NKG2 but not Ly49. During the first several weeks after birth, NK cells expressing various Ly49 receptors slowly accumulate, while CD94/NKG2+ NK cells decrease to approximately 50% of the population. The acquisition of NK receptors following hematopoietic stem cell transplantation is also a slow and apparently preprogrammed process, mimicking the ontogeny, regardless of whether stem cells from fetal liver or adult bone marrow are used as donors. The regulation of the transcription of individual receptor genes is rather complex, since two promoters have been identified for the genes encoding Ly49 and CD94.

The cytotoxic activity of murine natural killer cells is controlled in part through the action of genes belonging to the Ly49 family. Members of this multigene family are found in a region on mouse chromosome 6 termed the natural killer gene complex. Using data available through public databases, we performed sequence analysis of a 620-kb region in C57Bl/6 (B6) mice that contains the Ly49 genes. The contiguous genomic sequence has allowed us to describe the complete B6 Ly49 gene repertoire, which includes two recently described genes as well as three partial genes. We have shown that the genes in the cluster have evolved through a series of large duplication events involving units of one or more genes and we have attempted to characterize the nature of the duplication end points. Finally, we have used information regarding gene sequence relationships and insertion of repetitive elements to construct a model for the evolution of the gene cluster. Our study illustrates that the Ly49 cluster represents an example of a rapidly evolving gene family, and continued analysis of this region in other strains will undoubtedly provide further insight into mechanisms for generating genomic diversity.

Acute myeloid leukemia (AML) occurs when hematopoietic progenitor cells acquire genetic defects blocking the regulation of normal growth and differentiation. Although recurrent translocations have been identified in AML, almost half of adult AML patients present with a normal karyotype (NK-AML). While cell line models exist to study AML, they frequently have abnormal/unstable karyotypes, while primary cells from NK-AML patients are difficult to maintain in vitro. Here we provide a thorough molecular characterization of a recently established cell line, CG-SH, which has normal cytogenetics, representing a useful new model for NK-AML. Using high-throughput DNA sequencing, we first defined the genetic background of this cell line. In addition to identifying potentially deleterious SNVs in genes relevant to AML, we also found insertions in both GATA2 and EZH2, two genes previously linked to AML. We further characterized the growth of this model system in vitro with a cytokine mix that promotes faster cell growth. We assessed gene expression changes after the addition of cytokines to the culture media and found differential expression in genes implicated in proliferation, apoptosis and differentiation. Our results provide a detailed molecular characterization of genetic defects in this cell line derived from an NK-AML patient.

The GATA2 gene encodes a zinc-finger transcription factor that acts as a master regulator of normal hematopoiesis. Mutations in GATA2 have been implicated in the development of myelodysplastic syndrome and acute myeloid leukemia (AML). Using RNA sequencing we now report that GATA2 is either mutated with a functional consequence, or expressed at low levels in the majority of normal karyotype AML (NK-AML). We also show that low-GATA2-expressing specimens (GATA2(low)) exhibit allele-specific expression (ASE) (skewing) in more than half of AML patients examined. We demonstrate that the hypermethylation of the silenced allele can be reversed by exposure to demethylating agents, which also restores biallelic expression of GATA2. We show that GATA2(low) AML lack the prototypical R882 mutation in DNMT3A frequently observed in NK-AML patients and that The Cancer Genome Atlas AML specimens with DNMT3A R882 mutations are characterized by CpG hypomethylation of GATA2. Finally, we validate that several known missense single-nucleotide polymorphisms in GATA2 are actually loss-of-function variants, which, when combined with ASE, represent the equivalent of homozygous GATA2 mutations. From a broader perspective, this work suggests for the first time that determinants of ASE likely have a key role in human leukemia.

Murine natural killer (NK) cells express two families of MHC class I-specific receptors, namely the Ly49 family and CD94/NKG2 heterodimers. Stochastic co-expression of these receptors generates diverse receptor repertoires in adult NK-cell populations, whereas fetal NK cells have much more limited receptor diversity as they mostly express CD94/NKG2A but not Ly49. These receptors are also expressed on CD8-T cells and NK1.1+ T cells and regulate their functions, but their expression pattern on NK cells is significantly different from those on T cells. Thus, expression of Ly49 and CD94/NKG2 is developmentally regulated. NK cells acquire the Ly49 family of receptors in an orderly manner as they differentiate from bone marrow progenitors in vitro. Similarly, acquisition of CD94 and NKG2 by NK cells as they differentiate from embryonic stem cells is also orderly To gain insight into the mechanisms regulating Ly49 expression, potential regulatory regions of several Ly49 genes have been examined. Ly49 genes with different expression patterns have remarkably similar sequences in the putative regulatory regions. Finally, a functional Ly49 gene has been identified in baboon, and primate comparisons suggest that functional extinction of the Ly49 gene in the human lineage seems to have been a relatively recent event.

Despite numerous studies on the function of Ly49 natural killer cell receptors in the mouse, relatively little is known about how these genes are regulated at the transcriptional level. In the present study, we sequenced and compared 800 bp of the promoter region of nine Ly49 genes from C57B1/6 mice. This comparison showed that there is a high degree of sequence identity between the genes, and also revealed a region which is conserved between the mouse genes and the human Ly49L gene, indicating a potential core promoter region. This analysis also found that Ly49B and H differ from the other genes in having long interspersed repetitive sequence in their promoter region which suggests a gene conversion or rearrangement involving these two genes. In addition, we performed 5' rapid amplification of cDNA ends on four Ly49 genes to localize transcriptional start sites. These experiments showed that the transcriptional initiation sites are heterogeneous for all of the genes examined, and that a large majority of Ly49G transcripts originate from the second exon as well as its first intron. Although potential TATA boxes have been previously identified for some of the genes, we did not find evidence that a majority of transcripts initiate at the expected distance downstream of these boxes. Our data suggest that differences in the location of transcriptional start sites contribute to the observed complexity in receptor repertoire patterns.

Histone methylation is a dynamic and reversible process proposed to directly impact on stem cell fate. The Jumonji (JmjC) domain-containing family of demethylases comprises 27 members that target mono-, di-, and trimethylated lysine residues of histone (or nonhistone) proteins. To evaluate their role in regulation of hematopoietic stem cell (HSC) behavior, we performed an in vivo RNAi-based functional screen and demonstrated that Jarid1b and Jhdm1f play opposing roles in regulation of HSC activity. Decrease in Jarid1b levels correlated with an in vitro expansion of HSCs with preserved long-term in vivo lymphomyeloid differentiation potential. Through RNA sequencing analysis, Jarid1b knockdown was associated with increased expression levels of several HSC regulators (Hoxa7, Hoxa9, Hoxa10, Hes1, Gata2) and reduced levels of differentiation-associated genes. shRNA against Jhdmlf, in contrast, impaired hematopoietic reconstitution of bone marrow cells. Together, our studies identified Jarid1b as a negative regulator of HSC activity and Jhdmlf as a positive regulator of HSC activity.

Transforming growth factor-β (TGF-β) maintains self-tolerance through a constitutive inhibitory effect on T-cell reactivity. In most physiological situations, the tolerogenic effects of TGF-β depend on the canonical signaling molecule Smad3. To characterize how TGF-β/Smad3 signaling contributes to maintenance of T-cell tolerance, we characterized the transcriptional landscape downstream of TGF-β/Smad3 signaling in resting or activated CD4 T cells. We report that in the presence of TGF-β, Smad3 modulates the expression of >400 transcripts. Notably, we identified 40 transcripts whose expression showed Smad3 dependence in both resting and activated cells. This 'signature' confirmed the non-redundant role of Smad3 in TGF-β biology and identified both known and putative immunoregulatory genes. Moreover, we provide genomic and functional evidence that the TGF-β/Smad3 pathway regulates T-cell activation and metabolism. In particular, we show that TGF-β/Smad3 signaling dampens the effect of CD28 stimulation on T-cell growth and proliferation. The impact of TGF-β/Smad3 signals on T-cell activation was similar to that of the mTOR inhibitor Rapamycin. Considering the importance of co-stimulation on the outcome of T-cell activation, we propose that TGF-β-Smad3 signaling may maintain T-cell tolerance by suppressing co-stimulation-dependent mobilization of anabolic pathways.

Motivation: The growth of next-generation sequencing (NGS) has not only dramatically accelerated the pace of research in the field of genomics, but it has also opened the door to personalized medicine and diagnostics. The resulting flood of data has led to the rapid development of large numbers of bioinformatic tools for data analysis, creating a challenging situation for researchers when choosing and configuring a variety of software for their analysis, and for other researchers trying to replicate their analysis. As NGS technology continues to expand from the research environment into clinical laboratories, the challenges associated with data analysis have the potential to slow the adoption of this technology. Results: Here we discuss the potential of virtual machines (VMs) to be used as a method for sharing entire installations of NGS software (bioinformatic ‘pipelines’). VMs are created by programs designed to allow multiple operating systems to co-exist on a single physical machine, and they can be made following the object-oriented paradigm of encapsulating data and methods together. This allows NGS data to be distributed within a VM, along with the pre-configured software for its analysis. Although VMs have historically suffered from poor performance relative to native operating systems, we present benchmarking results demonstrating that this reduced performance can now be minimized. We further discuss the many potential benefits of VMs as a solution for NGS analysis and describe several published examples. Lastly, we consider the benefits of VMs in facilitating the introduction of NGS technology into the clinical environment. Contact: brian.wilhelm@umontreal.ca

Upon muscle injury, the high mobility group box 1 (HMGB1) protein is upregulated and secreted to initiate reparative responses. Here we show that HMGB1 controls myogenesis both in vitro and in vivo during development and after adult muscle injury. HMGB1 expression in muscle cells is regulated at the translational level: the miRNA miR-1192 inhibits HMGB1 translation and the RNA-binding protein HuR promotes it. HuR binds to a cis-element, HuR binding sites (HuRBS), located in the 3'UTR of the HMGB1 transcript, and at the same time miR-1192 is recruited to an adjacent seed element. The binding of HuR to the HuRBS prevents the recruitment of Argonaute 2 (Ago2), overriding miR-1192-mediated translation inhibition. Depleting HuR reduces myoblast fusion and silencing miR-1192 re-establishes the fusion potential of HuR-depleted cells. We propose that HuR promotes the commitment of myoblasts to myogenesis by enhancing the translation of HMGB1 and suppressing the translation inhibition mediated by miR-1192.

Pediatric acute megakaryoblastic leukemia (AMKL) accounts for 10% of childhood acute myeloid leukemia (AML) cases and remains a high fatality cancer. CBFA2T3-GLIS2, NUP98-KDM5A, RBM15-MKL1 and MLL gene rearrangements are recurrent aberrations that are mutually exclusive and found at similar frequencies in half the cases of pediatric AMKL. The recently identified CBFA2T3-GLIS2 and NUP98-KDM5A chimeric oncogenes are associated with inferior outcomes (overall survival, OS: ~30%) compared to patients harboring the RBM15-MKL1 gene fusion (OS ~70%). To investigate NUP98-KDM5A driven leukemogenesis, human cell lines and mouse models were engineered using overexpression of the chimeric oncogene in CD34+cord blood (CB) stem/progenitor cells. To this end, the cDNA of the NUP98-KDM5A fusion, consisting of the 5' portion of the nuclear pore protein nucleoporin 98 (NUP98) gene fused to the 3' portion of the histone lysine demethylase 5A (KDM5A) encoding gene, was cloned into a MNDU lentiviral vector carrying a GFP reporter gene. Using optimized culture conditions, 10,000 freshly isolated CB-CD34+ (day 0) cells were seeded in multiple wells in vitro and transduced with either NUP98-KDM5A or control (CTL) vectors. Initial gene transfer rates were 8.2 ± 0.95% (expt.1, n=3) and 22.9 ± 4.16% (expt.2, n=12) for NUP98-KDM5A and 48 ± 0.04% (expt.1, n=3) and 76.9 ± 6.36% (expt.2, n=4) for CTL conditions. Overexpression (OE) of NUP98-KDM5A led to maturation block and increased cell proliferation in vitro as compared to CTL, as assessed by cytological examination of cells, serial tracking of increasing CD34+GFP+ cell fractions and lack of a c-KIThi differentiated mast cell population. This was observed by day 25 of culture in 66% of the wells in a first experiment (2/3), and in 92% (11/12) of the wells in a confirmatory study. An overriding NUP98-KDM5A CD34+GFP+ immature cell population was present by day 42 of culture (up to 94% of cells), while CD34+GFP+cells were significantly decreased in the CTL conditions (0.3 to 8%), where mast cells predominated. Cell lines were maintained in culture for 180 days in the first experiment (day 145 in ongoing expt.2) and aliquoted at regular intervals for immunophenotypic assessment, ARN/DNA extraction, cryopreservation, and cytogenetics studies. Clonogenic activity was markedly increased in NUP98-KDM5A-OE cells (colony forming cell frequency of 1:3 vs 1:200 in CTL, at day 88 of culture). Transcriptomic profiling of selected cell lines closely matched that of NUP98-KDM5A bearing pediatric AMKL samples. Notably, there was an up-regulation of HOXA and HOXB gene clusters, as well as other transcription factors, epigenetic regulators, cell surface receptors and kinases. No additional driver mutations were detected in the cell lines or patient samples (n=2). Epigenetic characterisation of 2 cell lines is ongoing (H3K4, H3K9, H3K27 and H3K79 methylation status) as the chimeric oncogene encodes for the C-terminal portion of a H3K4 histone demethylase (KDM5A). Xenotransplantation of 75% of day 7 cells in immunodeficient mice resulted in the development of overt AMKL in 1 of 3 mice after 32 weeks. Recipient mouse bones were white and brittle, and the marrow cavity infiltrated by 30% hCD45loCD61+GFP+ leukemic blasts, with typical megakaryoblastic morphology. The leukemic blasts were also detected in blood (5%), and in enlarged spleen (0.2%). Secondary transplantation of isolated AMKL cells (from bone marrow and spleen) was performed, along with expression profiling by RNA sequencing. In an ongoing confirmatory experiment, 4 out of 12 mice displayed hCD45+NUP98-KDM5A-GFP+ cells (0.1, 0.2, 0.5, and 1.4%) in blood at 16 weeks, while 1 out of 4 CTL mice displayed 0.4% hCD45+-GFP+ engraftment at the same time point. Analysis of lentiviral integration patterns of genomic DNA of both cell lines and xenografts by southern blot is ongoing to determine clonality. Overexpression of the NUP98-KDM5A chimeric oncogene in cord blood CD34+ cells can thus be used to engineer human cell lines and xenograft models to study this poor prognostic subgroup of pediatric AMKL. By crossing expression profiles of patient samples, cell lines and xenograft models, a list of potential NUP98-KDM5A direct targets was elaborated. The engineered cell lines pave the way to genetic and chemical screens, to identify leukemia specific functional dependencies and drug targets, to ultimately improve patient outcome. Disclosures No relevant conflicts of interest to declare.

Ly49-mediated recognition of MHC-I molecules on host cells is considered vital for natural killer (NK)–cell regulation and education; however, gene-deficient animal models are lacking because of the difficulty in deleting this large multigene family. Here, we describe NK gene complex knockdown (NKCKD) mice that lack expression of Ly49 and related MHC-I receptors on most NK cells. NKCKD NK cells exhibit defective killing of MHC-I–deficient, but otherwise normal, target cells, resulting in defective rejection by NKCKD mice of transplants from various types of MHC-I–deficient mice. Self–MHC-I immunosurveillance by NK cells in NKCKD mice can be rescued by self–MHC-I–specific Ly49 transgenes. Although NKCKD mice display defective recognition of MHC-I–deficient tumor cells, resulting in decreased in vivo tumor cell clearance, NKG2D- or antibody-dependent cell-mediated cytotoxicity–induced tumor cell cytotoxicity and cytokine production induced by activation receptors was efficient in Ly49-deficient NK cells, suggesting MHC-I education of NK cells is a single facet regulating their total potential. These results provide direct genetic evidence that Ly49 expression is necessary for NK-cell education to self–MHC-I molecules and that the absence of these receptors leads to loss of MHC-I–dependent “missing-self” immunosurveillance by NK cells.

The regulation of posttranscriptional modifications of pre-mRNA by alternative splicing is important for cellular function, development, and immunity. The receptor tyrosine phosphatase CD45, which is expressed on all hematopoietic cells, is known for its role in the development and activation of T cells. CD45 is known to be alternatively spliced, a process that is partially regulated by heterogeneous nuclear ribonucleoprotein (hnRNP) L. To investigate the role of hnRNP L further, we have generated conditional hnRNP L knockout mice and found that LckCre-mediated deletion of hnRNP L results in a decreased thymic cellularity caused by a partial block at the transition stage between double-negative 4 and double-positive cells. In addition, hnRNP L−/− thymocytes express aberrant levels of the CD45RA splice isoforms and show high levels of phosphorylated Lck at the activator tyrosine Y394, but lack phosphorylation of the inhibitory tyrosine Y505. This indicated an increased basal Lck activity and correlated with higher proliferation rates of double-negative 4 cells in hnRNP L−/− mice. Deletion of hnRNP L also blocked the migration and egress of single-positive thymocytes to peripheral lymphoid organs in response to sphingosine-1-phosphate and the chemokines CCL21 and CXCL12 very likely as a result of aberrant splicing of genes encoding GTPase regulators and proteins affecting cytoskeletal organization. Our results indicate that hnRNP L regulates T cell differentiation and migration by regulating pre-TCR and chemokine receptor signaling.

In this study, we show the high frequency of spontaneous γδ T-cell leukemia (T-ALL) occurrence in mice with biallelic deletion of enhancer of zeste homolog 2 (Ezh2). Tumor cells show little residual H3K27 trimethylation marks compared with controls. EZH2 is a component of the PRC2 Polycomb group protein complex, which is associated with DNA methyltransferases. Using next-generation sequencing, we identify alteration in gene expression levels of EZH2 and acquired mutations in PRC2-associated genes (DNMT3A and JARID2) in human adult T-ALL. Together, these studies document that deregulation of EZH2 and associated genes leads to the development of mouse, and likely human, T-ALL.

The molecular mechanisms regulating self-renewal of leukemia stem cells remain poorly understood. Here we report the generation of 2 closely related leukemias created through the retroviral overexpression of Meis1 and Hoxa9. Despite their apparent common origin, these clonal leukemias exhibit enormous differences in stem cell frequency (from 1 in 1.4, FLA2; to 1 in 347, FLB1), suggesting that one of these leukemias undergoes nearly unlimited self-renewal divisions. Using next-generation RNA-sequencing, we characterized the transcriptomes of these phenotypically similar, but biologically distinct, leukemias, identifying hundreds of differentially expressed genes and a large number of structural differences (eg, alternative splicing and promoter usage). Focusing on ligand-receptor pairs, we observed high expression levels of Sdf1-Cxcr4; Jagged2-Notch2/1; Osm-Gp130; Scf-cKit; and Bmp15-Tgfb1/2. Interestingly, the integrin beta 2-like gene (Itgb2l) is both highly expressed and differentially expressed between our 2 leukemias (∼ 14-fold higher in FLA2 than FLB1). In addition, gene ontology analysis indicated G-protein-coupled receptor had a much higher proportion of differential expression (22%) compared with other classes (∼ 5%), suggesting a potential role regulating subtle changes in cellular behavior. These results provide the first comprehensive transcriptome analysis of a leukemia stem cell and document an unexpected level of transcriptome variation between phenotypically similar leukemic cells.

Next-generation sequencing technologies are revolutionizing genomics research. It is now possible to generate gigabase pairs of DNA sequence within a week without time-consuming cloning or massive infrastructure. This technology has recently been applied to the development of 'RNA-seq' techniques for sequencing cDNA from various organisms, with the goal of characterizing entire transcriptomes. These methods provide unprecedented resolution and depth of data, enabling simultaneous quantification of gene expression, discovery of novel transcripts and exons, and measurement of splicing efficiency. We present here a validated protocol for nonstrand-specific transcriptome sequencing via RNA-seq, describing the library preparation process and outlining the bioinformatic analysis procedure. While sample preparation and sequencing take a fairly short period of time (1-2 weeks), the downstream analysis is by far the most challenging and time-consuming aspect and can take weeks to months, depending on the experimental objectives.