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The congenital bone marrow failure syndrome Diamond-Blackfan anemia (DBA) is typically associated with variants in ribosomal protein (RP) genes impairing erythroid cell development. Here we report multiple individuals with biallelic HEATR3 variants exhibiting bone marrow failure, short stature, facial and acromelic dysmorphic features, and intellectual disability. These variants destabilize a protein whose yeast homolog is known to synchronize the nuclear import of RPs uL5 (RPL11) and uL18 (RPL5), which are both critical for producing ribosomal subunits and for stabilizing the p53 tumor suppressor when ribosome biogenesis is compromised. Expression of HEATR3 variants or repression of HEATR3 expression in primary cells, cell lines of various origins, and yeast models impairs growth, differentiation, pre-ribosomal RNA processing, and ribosomal subunit formation reminiscent of DBA models of large subunit RP gene variants. Consistent with a role of HEATR3 in RP import, HEATR3-depleted cells or patient-derived fibroblasts display reduced nuclear accumulation of uL18. Hematopoietic progenitor cells expressing HEATR3 variants or small-hairpin RNAs knocking down HEATR3 synthesis reveal abnormal acceleration of erythrocyte maturation coupled to severe proliferation defects that are independent of p53 activation. Our study uncovers a new pathophysiological mechanism leading to DBA driven by biallelic HEATR3 variants and the destabilization of a nuclear import protein important for ribosome biogenesis. ispartof: Blood vol:139 issue:21 pages:3111-3126 ispartof: location:United States status: Published online

Acute lymphoblastic leukemia (ALL) is characterized by the presence of chromosomal changes, including numerical changes, translocations, and deletions, which are often associated with additional single-nucleotide mutations. In this study, we used single cell-targeted DNA sequencing to evaluate the clonal heterogeneity of B-ALL at diagnosis and during chemotherapy treatment. We designed a custom DNA amplicon library targeting mutational hotspot regions (in 110 genes) present in ALL, and we measured the presence of mutations and small insertions/deletions (indels) in bone marrow or blood samples from 12 B-ALL patients, with a median of 7973 cells per sample. Nine of the 12 cases showed at least 1 subclonal mutation, of which cases with PAX5 alterations or high hyperdiploidy (with intermediate to good prognosis) showed a high number of subclones (1 to 7) at diagnosis, defined by a variety of mutations in the JAK/STAT, RAS, or FLT3 signaling pathways. Cases with RAS pathway mutations had multiple mutations in FLT3, NRAS, KRAS, or BRAF in various clones. For those cases where we detected multiple mutational clones at diagnosis, we also studied blood samples during the first weeks of chemotherapy treatment. The leukemia clones disappeared during treatment with various kinetics, and few cells with mutations were easily detectable, even at low frequency (2 subclones at diagnosis and that even very rare mutant cells can be detected at diagnosis or during treatment by single cell-targeted DNA sequencing. ispartof: HEMASPHERE vol:6 issue:4 ispartof: location:United States status: published

The R98S mutation in ribosomal protein L10 (RPL10 R98S) affects 8% of pediatric T-cell acute lymphoblastic leukemia (T-ALL) cases, and was previously described to impair cellular proliferation. The current study reveals that RPL10 R98S cells accumulate reactive oxygen species which promotes mitochondrial dysfunction and reduced ATP levels, causing the proliferation defect. RPL10 R98S mutant leukemia cells can survive high oxidative stress levels via a specific increase of IRES-mediated translation of the anti-apoptotic factor B-cell lymphoma 2 (BCL-2), mediating BCL-2 protein overexpression. RPL10 R98S selective sensitivity to the clinically available Bcl-2 inhibitor Venetoclax (ABT-199) was supported by suppression of splenomegaly and the absence of human leukemia cells in the blood of T-ALL xenografted mice. These results shed new light on the oncogenic function of ribosomal mutations in cancer, provide a novel mechanism for BCL-2 upregulation in leukemia, and highlight BCL-2 inhibition as a novel therapeutic opportunity in RPL10 R98S defective T-ALL.

Background T cell acute lymphoblastic leukemia (T-ALL) is a high-risk subtype that comprises 10–15% of childhood and 20–25% of adult ALL cases. Over 70% of T-ALL patients harbor activating mutations in the NOTCH1 signaling pathway and are predicted to be sensitive to gamma-secretase inhibitors. We have recently demonstrated that selective inhibition of PSEN1-containing gamma-secretase complexes can overcome the dose-limiting toxicity associated with broad gamma-secretase inhibitors. In this study, we developed combination treatment strategies with the PSEN1-selective gamma-secretase inhibitor MRK-560 and other targeted agents (kinase inhibitors ruxolitinib and imatinib; XPO-1 inhibitor KPT-8602/eltanexor) for the treatment of T-ALL. Methods We treated T-ALL cell lines in vitro and T-ALL patient-derived xenograft (PDX) models in vivo with MRK-560 alone or in combination with other targeted inhibitors (ruxolitinib, imatinib or KPT-8602/eltanexor). We determined effects on proliferation of the cell lines and leukemia development and survival in the PDX models. Results All NOTCH1-signaling-dependent T-ALL cell lines were sensitive to MRK-560 and its combination with ruxolitinib or imatinib in JAK1- or ABL1-dependent cell lines synergistically inhibited leukemia proliferation. We also observed strong synergy between MRK-560 and KPT-8602 (eltanexor) in all NOTCH1-dependent T-ALL cell lines. Such synergy was also observed in vivo in a variety of T-ALL PDX models with NOTCH1 or FBXW7 mutations. Combination treatment significantly reduced leukemic infiltration in vivo and resulted in a survival benefit when compared to single treatment groups. We did not observe weight loss or goblet cell hyperplasia in single drug or combination treated mice when compared to control. Conclusions These data demonstrate that the antileukemic effect of PSEN1-selective gamma-secretase inhibition can be synergistically enhanced by the addition of other targeted inhibitors. The combination of MRK-560 with KPT-8602 is a highly effective treatment combination, which circumvents the need for the identification of additional mutations and provides a clear survival benefit in vivo. These promising preclinical data warrant further development of combination treatment strategies for T-ALL based on PSEN1-selective gamma-secretase inhibition.

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive leukemia that is most frequent in children and is characterized by the presence of few chromosomal rearrangements and 10 to 20 somatic mutations in protein-coding regions at diagnosis. The majority of T-ALL cases harbor activating mutations in NOTCH1 together with mutations in genes implicated in kinase signaling, transcriptional regulation, or protein translation. To obtain more insight in the level of clonal heterogeneity at diagnosis and during treatment, we used single-cell targeted DNA sequencing with the Tapestri platform. We designed a custom ALL panel and obtained accurate single-nucleotide variant and small insertion-deletion mutation calling for 305 amplicons covering 110 genes in about 4400 cells per sample and time point. A total of 108 188 cells were analyzed for 25 samples of 8 T-ALL patients. We typically observed a major clone at diagnosis (>35% of the cells) accompanied by several minor clones of which some were less than 1% of the total number of cells. Four patients had >2 NOTCH1 mutations, some of which present in minor clones, indicating a strong pressure to acquire NOTCH1 mutations in developing T-ALL cells. By analyzing longitudinal samples, we detected the presence and clonal nature of residual leukemic cells and clones with a minor presence at diagnosis that evolved to clinically relevant major clones at later disease stages. Therefore, single-cell DNA amplicon sequencing is a sensitive assay to detect clonal architecture and evolution in T-ALL. ispartof: BLOOD vol:137 issue:6 pages:801-811 ispartof: location:United States status: published

Acute leukemias (ALs) of ambiguous lineage are a heterogeneous group of high-risk leukemias characterized by coexpression of myeloid and lymphoid markers. In this study, we identified a distinct subgroup of immature acute leukemias characterized by a broadly variable phenotype, covering acute myeloid leukemia (AML, M0 or M1), T/myeloid mixed-phenotype acute leukemia (T/M MPAL), and early T-cell precursor acute lymphoblastic leukemia (ETP-ALL). Rearrangements at 14q32/BCL11B are the cytogenetic hallmark of this entity. In our screening of 915 hematological malignancies, there were 202 AML and 333 T-cell acute lymphoblastic leukemias (T-ALL: 58, ETP; 178, non-ETP; 8, T/M MPAL; 89, not otherwise specified). We identified 20 cases of immature leukemias (4% of AML and 3.6% of T-ALL), harboring 4 types of 14q32/BCL11B translocations: t(2,14)(q22.3;q32) (n = 7), t(6;14)(q25.3;q32) (n = 9), t(7;14)(q21.2;q32) (n = 2), and t(8;14)(q24.2;q32) (n = 2). The t(2;14) produced a ZEB2-BCL11B fusion transcript, whereas the other 3 rearrangements displaced transcriptionally active enhancer sequences close to BCL11B without producing fusion genes. All translocations resulted in the activation of BCL11B, a regulator of T-cell differentiation associated with transcriptional corepressor complexes in mammalian cells. The expression of BCL11B behaved as a disease biomarker that was present at diagnosis, but not in remission. Deregulation of BCL11B co-occurred with variants at FLT3 and at epigenetic modulators, most frequently the DNMT3A, TET2, and/or WT1 genes. Transcriptome analysis identified a specific expression signature, with significant downregulation of BCL11B targets, and clearly separating BCL11B AL from AML, T-ALL, and ETP-ALL. Remarkably, an ex vivo drug-sensitivity profile identified a panel of compounds with effective antileukemic activity.

The R98S mutation in ribosomal protein L10 (RPL10 R98S) affects 8% of pediatric T-cell acute lymphoblastic leukemia (T-ALL) cases, and was previously described to impair cellular proliferation. The current study reveals that RPL10 R98S cells accumulate reactive oxygen species which promotes mitochondrial dysfunction and reduced ATP levels, causing the proliferation defect. RPL10 R98S mutant leukemia cells can survive high oxidative stress levels via a specific increase of IRES-mediated translation of the anti-apoptotic factor B-cell lymphoma 2 (BCL-2), mediating BCL-2 protein overexpression. RPL10 R98S selective sensitivity to the clinically available Bcl-2 inhibitor Venetoclax (ABT-199) was supported by suppression of splenomegaly and the absence of human leukemia cells in the blood of T-ALL xenografted mice. These results shed new light on the oncogenic function of ribosomal mutations in cancer, provide a novel mechanism for BCL-2 upregulation in leukemia, and highlight BCL-2 inhibition as a novel therapeutic opportunity in RPL10 R98S defective T-ALL. ispartof: LEUKEMIA vol:33 issue:2 pages:319-332 ispartof: location:England status: published

Postnatal hematopoietic stem (and progenitor) cells (HS(P)Cs) are especially vulnerable to oxidative stress, leading to early hematopoietic senescence and/or malignant transformation. Elevated intracellular reactive oxygen species (ROS) can, among others, oxidize nucleotides, and thus can result in genotoxicity and mutagenesis if left unrepaired. Oxidized bases, as well as other spontaneous single base modifications, are recognized and repaired by the base excision repair (BER) pathway. Hence, the BER pathway is crucial to maintain genome integrity. In contrast to other DNA repair pathways however, the role of BER in maintaining HSPC functionality remains enigmatic, chiefly because knockout (KO) of BER genes is in many cases embryonic lethal. BER is a complex multi-step repair process. After initial removal and excision of the damaged base, the apurinic/apyrimidinic (AP) site is processed by the AP endonuclease (APEX1) enzyme. At this point, the BER pathway branches into 2 sub-pathways, namely the short-patch (SP-BER; wherein DNA polymerase beta (Polβ), Ligase III (Lig3) together with X-ray repair cross-complementing protein 1 (Xrcc1) are active) and the long-patch BER (LP-BER; wherein Lig1, Flap Structure-Specific Endonuclease 1 (Fen1), and sometimes Polβ are active) for the repair synthesis and the gap filling steps. In this study we wished to address the role of BER in adult hematopoiesis. Therefore, we used CRISPR-Cas9 to KO different BER genes in adult bone marrow (BM) HS(P)Cs, including two genes common to the BER (sub-)pathway(s) (Apex1 and Polβ) as well as one gene in the SP-BER (Xrcc1) and one gene in the LP-BER (Lig1) pathway. The effect thereof was evaluated on HS(P)C repopulation in vivo as well as on HS(P)C expansion during long-term in vitro culture (using the culture medium described by Wilkinson et al., Nature 2019). All CRISPR-Cas9 experiments were validated using a second sgRNA targeting the selected BER genes. Lig1-KO caused in vivo HSPC dysfunction: at 20 weeks post-transplantation, significantly less Lig1 KO cells were observed in the committed progenitor (HPC) and lineage committed (Lin +) BM compartments. By contrast, KO of Xrcc1 had only minor effects on HS(P)C repopulation, but we observed increased HSC expansion and myeloid biased differentiation in some recipient mice, which might correspond to clonal hematopoiesis and is consistent with the finding of XRCC1 loss-of-function mutation in myelodysplastic patients (Joshi et al, Ann Hematol 2016). Knockout of Polβ did not affect hematopoiesis in vivo or in vitro. The most severe phenotype was observed when we knocked out Apex1, as Apex1-KO HS(P)Cs failed to repopulate irradiated recipient mice. Already after 2 weeks, significantly less Apex1 deficient cells were detected in the different blood lineages and nearly no CRISPR-Cas9 KO cells could be detected from 4 weeks onwards. This was confirmed in vitro, where reduced expansion of Apex1 KO BM cells was observed. APEX1 has two major functional activities, namely its nuclease activity, involved in BER, and its redox activity (also called Ref-1 function) important in reducing oxidized transcription factors and therefore implicated in transcriptional regulation. However, little is known regarding the nuclease and Ref-1 function(s) in primary adult hematopoietic cells. We therefore cultured BM HS(P)Cs for 1 week in the continuous presence of 2 distinct chemicals blocking the APEX1 nucleases, or 2 different chemicals inhibiting specifically the Ref-1 function. We demonstrated that both APEX1 functions are essential for hematopoiesis, even if the 2 functions appear to support the survival, expansion and maintenance of HS(P)Cs through different mechanisms. While the Ref-1 function was essential for proliferation (as both Ref-1 inhibitors cause cell cycle arrest) of all the lineages (including the Lin + cells), both inhibitors of the nuclease function affected more the expansion/survival of the less committed HS(P)Cs without leading to any cell cycle arrest. In conclusion, this study demonstrates for the first time the important role of BER genes in adult hematopoiesis, often deregulated in cancer, including hematopoietic malignancies. We observed a particularly severe phenotype upon loss of Apex1 in adult HSPCs, and ongoing studies (such as RNA sequencing analysis) should provide novel insights in underlying mechanisms of APEX1 deficiencies in HS(P)Cs. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy caused by the accumulation of genomic lesions that affect the development of T-cells. Since many years, it has been established that deregulated expression of transcription factors, impairment of the CDKN2A/2B cell cycle regulators and hyperactive NOTCH1 signaling play prominent roles in the pathogenesis of this leukemia. In the past decade, systematic screening of T-ALL genomes by high resolution copy number arrays and next- generation sequencing technologies has revealed that T-cell progenitors accumulate additional mutations affecting JAK/STAT signaling, protein translation and epigenetic control, providing novel attractive targets for therapy. In this review, we provide an update on our knowledge on T-ALL pathogenesis, on the opportunities for the introduction of targeted therapy and on the challenges that are still ahead. ispartof: Blood vol:129 issue:9 pages:1113-1123 ispartof: location:United States status: published

Acute lymphoblastic leukemia (ALL) is a prevalent hematopoietic malignancy that requires urgent medical intervention to prevent inferior outcome. ALL is characterized by recurrent structural rearrangements, whole chromosome copy number changes and microdeletions of prognostic value. Currently an extensive panel of tests is required, including karyotype, FISH, whole genome arrays, Multiple Ligation-dependent Probe Amplification (MLPA) and PCR-based diagnostic methods. Testing is thus costly, laborious and time-consuming and due to the large number of tests required cascade testing is often performed resulting in lengthy turn-around-times (TAT). This does not conform to treatment protocols that require rapid results to stratify patients into different treatment arms and to identify those who may benefit from "targeted" therapies, such as the Ph-like ALLs. It is therefore interesting to examine new technologies which can simultaneously detect numerical and structural abnormalities in one assay. Such approaches have not yet been extensively introduced into routine diagnostics but implementation would not only be beneficial in reducing TAT but would simplify the analytical pathways and theoretically increase the diagnostic yield. One such novel technology is genome imaging of ultra-long linear molecules, enzymatically labeled at specific sequence motifs. The Saphyr genome imaging device (Bionano Genomics) detects numerical and structural variants (>500bp) with a TAT of less than one week. The aim of the current study is to assess whether implementation of this technology could (partially) replace current analytical strategies. Ten diagnostic T- and 10 diagnostic B-ALL cases were included in this series. All samples were analyzed with the Rare Variant Pipeline (RVP) and filters were set to detect chromosomal aberrations of greater than 5 Mb. For deletions, the limit of detection was set at 500 bp but only regions encompassing clinically relevant loci were investigated. There was an overall excellent concordance between the results: Bionano results were concordant with MLPA, a technique routinely used for rapid detection of key CNAs.All but one recurrent translocations identified by routine strategies were correctly identified by Bionano which failed to detect a STIL-TAL1 rearrangement in one of the two cases with this abnormality. Bionano further identified: A t(5;11) TCF7-SPI1 in a case with a failed karyotype (subsequently confirmed by another method) (Figure 1).A t(12;22) ZNF384-EP300 fusion in a case with a normal karyotype. This recurrent rare fusion was confirmed by FISH. In general there was an excellent concordance of whole/partial chromosome gains and losses and for hyperdiploidy (observed in 3 B-ALLs in this series). Moreover, Bionano identified also hyperdiploidy in a case with a normal karyotype. Interestingly, FISH analysis of the same case suggested the presence of a hypodiploid clone. This demonstrates the limitation of DNA based techniques to accurately determine ploidy when allele information is not available. There were some discrepancies between the results of cytogenetics and Bionano: Bionano could not identify the presence of multiple clones, a common limitation for DNA based techniques.Bionano did not confirm some abnormalities identified by karyotype. Chromosome analysis of ALL samples is notoriously difficult due to low chromosome resolution explaining some of these differences. Some of the discrepant abnormalities were often marked as uncertain or were present only in a subclone ( Overall our data demonstrate that genome imaging is a promising technique to identify structural and numerical abnormalities in ALL. Bionano provided an informative result in each case and results were concordant with other results in the majority of cases. However this study also highlighted a few limitations. Further studies are underway to understand why the STIL-TAL1 was overlooked and to determine whether some of the additional variants identified by Bionano represent true rearrangements or technical artefacts. Disclosures No relevant conflicts of interest to declare.

Supplemental Digital Content is available in the text. ispartof: Hemasphere vol:2 issue:2 ispartof: location:United States status: published

Next-generation sequencing has provided a detailed overview of the various genomic lesions implicated in the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL). Typically, 10-20 protein-altering lesions are found in T-ALL cells at diagnosis. However, it is currently unclear in which order these mutations are acquired and in which progenitor cells this is initiated. To address these questions, we used targeted single-cell sequencing of total bone marrow cells and CD34+CD38- multipotent progenitor cells for four T-ALL cases. Hierarchical clustering detected a dominant leukemia cluster at diagnosis, accompanied by a few smaller clusters harboring only a fraction of the mutations. We developed a graph-based algorithm to determine the order of mutation acquisition. Two of the four patients had an early event in a known oncogene (MED12, STAT5B) among various pre-leukemic events. Intermediate events included loss of 9p21 (CDKN2A/B) and acquisition of fusion genes, while NOTCH1 mutations were typically late events. Analysis of CD34+CD38- cells and myeloid progenitors revealed that in half of the cases somatic mutations were detectable in multipotent progenitor cells. We demonstrate that targeted single-cell sequencing can elucidate the order of mutation acquisition in T-ALL and that T-ALL development can start in a multipotent progenitor cell. ispartof: LEUKEMIA vol:32 issue:6 pages:1358-1369 ispartof: location:England status: published

Acute lymphoblastic leukemia (ALL), which is the most common cancer in children, shows extensive genetic intra-tumoral heterogeneity. This heterogeneity might be the underlying reason for an incomplete response to treatment and for the development of relapse. In order to envision the clinical implementation of a refined risk-category strategy based on ALL subclonal composition, it is essential to first generate a reference single-cell map and accumulate evidence on how the subclonal composition affects the response to treatment. For that, we performed large-scale and integrative single-cell genome and transcriptome profiling of pediatric samples at diagnosis, during drug treatment and in case of relapse. We used the 10x Genomics platform for single-cell RNA-sequencing analysis (around 4000 cells per sample) and the Tapestri Platform (Mission Bio) for targeted single-cell DNA-sequencing (around 5000 cells per sample) of the most mutated genomic regions in ALL. For the later, we developed a custom panel that covers 305 ALL mutational hotspots across 110 genes. We have determined a reference single-cell map of the cellular (based on the gene expression profile) and the clonal composition (based on the co-occurrence of mutations at each individual cell) for pediatric ALL at diagnosis (8 T-ALL and 10 B-ALL patients). We have also reconstructed the tumor phylogeny highlighting the order of mutational acquisition and the most likely pattern of evolution. Moreover, we have studied how T-ALL evolves during drug treatment at single-cell resolution in 4 patients, unraveling which are the most sensitive clones to the therapy, which are the most resistant ones and when relapse clones originated. Single-cell RNA-sequencing also provided information on how normal hematopoiesis recovers during chemotherapy treatment. The results show that ALL is typically composed by a major clone and 5-10 smaller clones that have different sensitivities to the therapy. We have been able to detect minor clones ( Disclosures Maertens: Gilead Sciences: Other: Grants, personal fees and non-financial support; Cidara: Other: Personal fees and non-financial support; Amplyx: Other: Personal fees and non-financial support; F2G: Other: Personal fees and non-financial support; Merck: Other: Personal fees and non-financial support; Pfizer: Other: Grant and personal fees; Astellas Pharma: Other: Personal fees and non-financial support.

ispartof: HEMASPHERE vol:3 issue:6 ispartof: location:United States status: published

Ribosomopathies are rare diseases caused by mutations in proteins constituting the ribosome (ribosomal proteins) or factors involved in ribosome production (ribosome biogenesis factors). With the exception of 5q-syndrome, which is an acquired disease, most established ribosomopathies are congenital

Cancer studies have historically focused on changes in the transcriptome of tumor cells to reveal the molecular pathways responsible for cellular transformation. In the last 20 years, however, it has become clear that deregulation of translation also plays a crucial role in cancer development and progression. Major players in cancer biology, such as the PI3K pathway, tumor suppressor protein p53 and MYC, can deregulate expression of components of the translation machinery and can influence the spectrum of mRNAs which are most efficiently translated in the cell. In addition, somatic lesions affecting ribosome biogenesis, translation initiation and elongation factors have been described in a wide variety of human cancers.1 The cancer promoting action of such lesions is supported by the observation that patients with congenital mutations in ribosomal proteins or ribosome biogenesis factors develop ribosomopathies, diseases with specific pathological characteristics that often lead to an increased risk of developing hematopoietic malignancies and solid tumors.2 T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy caused by accumulation of multiple co-operating oncogenic lesions in developing T cells. It has been well-established that prominent roles in T-ALL pathogenesis are played by: i) ectopic expression of oncogenic transcription factors such as TAL1, TLX1 and TLX3; ii) deregulation of the CDKN2A and CDKN2B cell cycle regulators; iii) constitutive activation of NOTCH1 signaling; and iv) hyperactivation of cytokine signaling by defects, e.g. in IL7R and JAK kinases.3,4 Recent next generation sequencing based screens in T-ALL have further expanded the spectrum of defects involved in the pathogenesis of this disease. First, it became clear that epigenetic regulators like PHF6, SUZ12, EZH2, TET1 and KDM6A are also involved in T-ALL pathogenesis.5 Second, defects in essential components of the translation machinery have been revealed. We described mutations affecting the ribosomal proteins L5/uL18 (RPL5/uL18) and L10/uL16 (RPL10/uL16) in 10% of pediatric TALL patients.6 In addition, ribosomal protein L22/eL22 (RPL22/eL22) is inactivated in another 10% of T-ALLs7 and rare mutations in the ribosomal protein L11/uL5 (RPL11/uL5) gene were found in relapsed T-ALL patients (Figure 1).8 The oncogenic capacity of ribosomal protein defects in T-ALL is illustrated by the observation that loss of one copy of RPL22/eL22 accelerates tumor formation in a mouse model of T-cell lymphoma.7 Whereas acquiring mutations in ribosomal proteins is the most direct way to influence generation and function of mature ribosomes in a cell, other mutations in T-ALL may also affect these processes. For example, up to 40% of all T-ALL cases carry loss-of-function defects in the PHF6 gene.9 While the exact role of PHF6 in T-ALL is not yet understood, it has been proposed that it functions as an epigenetic regulator. PHF6 localizes in the nucleolus, inhibits rRNA synthesis, and its inter-actors, identified by mass spectrometry, include several ribosomal proteins.10,11 These observations suggest a role for PHF6 in ribosome biogenesis, and loss of PHF6 function in T-ALL could thus represent an alternative way to interfere with proper formation of ribosomes (Figure 1). Figure 1. Mutations that impair maturation of the translation machinery in T-ALL. Mutations in ribosomal proteins and defective PHF6 function may impair formation of mature ribosomes (ribosome biogenesis) in T-ALL. Note that ribosome biogenesis defects have only ... Besides the identification of mutations in ribosomal proteins, there are additional indications for an essential role of translational deregulation in T-ALL. Translation of most cellular mRNAs depends on a cap structure in the 5′ part of the mRNA (cap-dependent translation). However, for other mRNAs, translation is initiated by alternative structures such as an internal ribosomal entry site (cap-independent translation). It was shown that T-ALL development in mice can be accelerated by overexpression of eIF4A and eIF4E, two proteins that are part of the protein complex that initiates cap-dependent translation downstream of mTORC1.12,13 The strict dependence of T-ALL cells on cap-dependent translation is further supported by the observations that silvestrol, a drug inhibiting eIF4A, can impair proliferation of mouse and human T-ALL leukemia cells, both in vitro and in vivo,12 and that interference with eIF4E by shRNA knockdown or administration of the eIF4E inhibitor 4EGI-1 reduces the viability of T-ALL blasts in vitro.13 As far as we are aware, no specific genetic lesions in eIF4A, eIF4E or other components of the protein complex supporting cap-dependent translation have been described in T-ALL, suggesting that the role of other (known) genetic lesions in T-ALL in driving cap-dependent translation has been underestimated. An obvious candidate is the NOTCH1 pathway which is hyperactivated in 60% of T-ALL cases by mutations in the NOTCH1 receptor itself and/or by inactivation of its ubiquiting ligase FBXW7.3 Whereas hyperactive NOTCH1 signaling most likely drives T-cell transformation by influencing several pathways, NOTCH1 hyperactivates the PI3K-AKT-mTORC1 pathway and may thus support cap-dependent translation. Indeed, NOTCH1 activity in TALL cells leads to HES1 mediated downregulation of PTEN, a critical negative regulator of the PI3K pathway. Moreover, NOTCH1 can activate AKT via the LCK tyrosine kinase in T cells. Furthermore, numerous signaling molecules upstream of PI3K, including the interleukin 7 receptor alpha chain (IL7RA) and the pre-T-cell receptor alpha (PTCRA), are up-regulated upon activation of NOTCH1 signaling in T-ALL lymphoblasts.14 In addition to impairing degradation of NOTCH1, FBXW7 deletion may further enhance cap-dependent translation by directly stabilizing mTOR, another known substrate of FBXW7.15 Inactivation of the PTEN tumor suppressor, an event occurring in 20% of T-ALLs, is another way for T-ALL cells to hyperactivate the PI3K-AKT-mTORC1 axis. Finally, hyperactivation of receptor tyrosine kinases can also stimulate mTORC1 activity and cap-dependent translation (Figure 2). Interestingly, whereas constitutive activation of the receptor tyrosine kinase TRK leads to increased mTORC1 signaling in lymphoid cells, pre-leukemic cells with hyperactive TRK tend to acquire activating mutations in NOTCH1 and loss of PTEN. This leads to T-ALL during clonal evolution, resulting in even stronger activation of mTORC1 and more pronounced dependence on cap-dependent translation.13 Figure 2. T-ALL cells depend on cap-dependent translation. Several molecular lesions in T-ALL (PTEN or FBXW7 inactivation, NOTCH1 or RTK hyperactivation) promote cap-dependent translation in T-ALL cells, resulting in more efficient translation of T-ALL promoting ... How the defects in the translation machinery or cap-dependent translation described above drive T-ALL is the next important question. The Wendel laboratory recently showed that inhibition of eIF4A function with the drug silvestrol in T-ALL cells impairs the translation of components essential for T-ALL pathogenesis, such as NOTCH1, MYC, RUNX1 and BCL11B, suggesting that cells with hyperactive cap-dependent translation may shift towards a T-ALL-promoting translation program (Figure 2).12 It is not clear at this point if the defects in the ribosome are acting via a similar mechanism or one that is completely different. Whereas the RPL10/uL16 mutations impair ribosome biogenesis and translational fidelity,6,16 a thorough characterization of the effects of these ribosomal defects on the cellular translation profile in T-ALL has still not been made. Moreover, it remains to be established whether these defects are promoting leukemia by altering the translational profile of the ribosome (Figure 1) or by affecting translation-independent extra-ribosomal functions that have been assigned to these proteins. Is the occurrence of defects in the ribosome and in the regulation of translation a specific characteristic of T-ALL? As far as we are aware, residue R98 in RPL10/uL16, a strong mutational hotspot in T-ALL, is not targeted by mutations in other cancer types, including other acute leukemias such as B-ALL or AML. At this point, we do not understand the reason for the unique occurrence of this mutation in T-ALL. In contrast, RPL22/eL22 and RPL5/uL18 were identified in the pan-cancer project as genes that are recurrently mutated in various cancer types. The dependence on cap-dependent translation is also not unique for T-ALL cells. Silvestrol and 4EGI-1 were shown to have therapeutic effects in xenograft models for various leukemias and solid tumors.17–19 It still needs to be determined, however, if this addiction to cap-dependent translation drives cell type specific translation programs in different tumor types. In conclusion, in addition to the extensive list of defective processes and molecular aberrations already known in TALL, a central role of defective translation machinery and regulation was recently revealed in this disease. These findings offer novel opportunities for T-ALL therapy. Current treatment regimens consist of intensive schemes of chemotherapy and are associated with a multitude of long-term side-effects, while failing to induce long-term remission in 25% of pediatric and 50% of adult patients. For patients with one or several lesions driving cap-dependent translation, such as PTEN, NOTCH1 or FBXW7 mutations, drugs like 4EGI-1 or silvestrol could be considered. In contrast to what one might expect, off-target toxicity of these compounds seems limited. 4EGI-1 shows no toxicity on human CD34+ cells,20 and numerous studies showing therapeutic effects of these drugs in in vivo application in mouse tumor xenografts support the concept that there is a therapeutic window for treatment in humans.

The NUP214-ABL1 fusion protein is a constitutively active protein tyrosine kinase that is found in 6% of patients with T-cell acute lymphoblastic leukemia and that promotes proliferation and survival of T-lymphoblasts. Although NUP214-ABL1 is sensitive to ABL1 kinase inhibitors, development of resistance to these compounds is a major clinical problem, underlining the need for additional drug targets in the sparsely studied NUP214-ABL1 signaling network. In this work, we identify and validate the SRC family kinase LCK as a protein whose activity is absolutely required for the proliferation and survival of T-cell acute lymphoblastic leukemia cells that depend on NUP214-ABL1 activity. These findings underscore the potential of SRC kinase inhibitors and of the dual ABL/SRC kinase inhibitors dasatinib and bosutinib for treating of NUP214-ABL1 positive T-cell acute lymphoblastic leukemia. In addition, we used mass spectrometry to identify protein interaction partners of NUP214-ABL1. Our results strongly support that the signaling network of NUP214-ABL1 is distinct from that previously reported for BCR-ABL1. Moreover, we identify three NUP214-ABL1 interacting proteins, MAD2L1, NUP155, and SMC4, as strictly required for the proliferation and survival of NUP214-ABL1 positive T-cell acute lymphoblastic leukemia cells. In conclusion, this work identifies LCK, MAD2L1, NUP155 and SMC4 as four new potential drug targets in NUP214-ABL1 positive T-cell acute lymphoblastic leukemia. ispartof: Haematologica vol:99 issue:1 pages:85-93 ispartof: location:Italy status: published

Adult T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic tumor associated with poor outcome. In this study, we analyzed the prognostic relevance of genetic alterations, immunophenotypic markers, and microarray gene expression signatures in a panel of 53 adult T-ALL patients treated in the Eastern Cooperative Oncology Group E2993 clinical trial. An early immature gene expression signature, the absence of bi-allelic TCRG deletion, CD13 surface expression, heterozygous deletions of the short arm of chromosome 17, and mutations in IDH1/IDH2 and DNMT3A genes are associated with poor prognosis in this series. In contrast, expression of CD8 or CD62L, homozygous deletion of CDKN2A/CDKN2B, NOTCH1 and/or FBXW7 mutations, and mutations or deletions in the BCL11B tumor suppressor gene were associated with improved overall survival. Importantly, the prognostic relevance of CD13 expression and homozygous CDKN2A/CDKN2B deletions was restricted to cortical and mature T-ALLs. Conversely, mutations in IDH1/IDH2 and DNMT3A were specifically associated with poor outcome in early immature adult T-ALLs. This trial was registered at www.clinicaltrials.gov as #NCT00002514.

Diamond-Blackfan anaemia (DBA) is an inherited disease characterized by pure erythroid aplasia that has been tagged as a 'ribosomopathy'. We report a multi-centre study focused on the analysis of rRNA processing of 53 Italian DBA patients using capillary electrophoresis analysis of rRNA maturation of the 40S and 60S ribosomal subunits. The ratio of 28S/18S rRNA was higher in patients with mutated ribosomal proteins (RPs) of the small ribosomal subunit. In contrast, patients with mutated RPs of the large ribosomal subunit (RPLs) had a lower 28S/18S ratio. The assay reported here would be amenable for development as a diagnostic tool.

Oncogenic activating mutations in NOTCH1 occur in more than 50% of T-cell acute lymphoblastic leukemias (T-ALLs). In the present study, we describe a novel mechanism of NOTCH1 activation in T-ALL in which a deletion removing the 5′ portion of NOTCH1 abolishes the negative regulatory control of the extracellular domain and leads to constitutively active NOTCH1 signaling. Polypeptides translated from truncated transcripts encoded by the NOTCH1 deletion allele retain the transmembrane domain of the receptor and are constitutively cleaved by the γ-secretase complex, resulting in high levels of NOTCH1 signaling that can be effectively blocked by γ-secretase inhibitors. Our results expand the spectrum of oncogenic lesions activating NOTCH1 signaling in human T-ALL.

ispartof: HemaSphere vol:2 issue:5 ispartof: location:United States status: published

Background Activating NOTCH1 mutations are common in T-cell acute lymphoblastic leukemia. Inhibition of NOTCH1 signaling with γ-secretase inhibitors causes cell cycle block, but only after treatment for several days. We further documented the effects of γ-secretase inhibitor treatment on T-cell acute lymphoblastic leukemia cell lines and tested whether combining γ-secretase inhibitors with other anti-cancer drugs offers a therapeutic advantage. Design and Methods The effect of γ-secretase inhibitor treatment and combinations of γ-secretase inhibitors with chemotherapy or glucocorticoids was assessed on T-cell acute lymphoblastic leukemia cell lines. We sequenced NOTCH1 in T-cell acute lymphoblastic leukemia cases with ABL1 fusions and tested combinations of γ-secretase inhibitors and the ABL1 inhibitor imatinib in a T-cell acute lymphoblastic leukemia cell line. Results γ-secretase inhibitor treatment for 5–7 days reversibly inhibited cell proliferation, caused cell cycle block in sensitive T-cell acute lymphoblastic leukemia cell lines, and caused differentiation of some T-cell acute lymphoblastic leukemia cell lines. Treatment for 14 days or longer was required to induce significant apoptosis. The cytotoxic effects of the chemotherapeutic agent vincristine were not significantly enhanced by addition of γ-secretase inhibitors to T-cell acute lymphoblastic leukemia cell lines, but γ-secretase inhibitor treatment sensitized cells to the effect of dexamethasone. NOTCH1 mutations were identified in all T-cell acute lymphoblastic leukemia patients with ABL1 fusions and in a T-cell acute lymphoblastic leukemia cell line expressing NUP214-ABL1 . In this cell line, the anti-proliferative effect of imatinib was increased by pre-treatment with γ-secretase inhibitors. Conclusions Short-term treatment of T-cell acute lymphoblastic leukemia cell lines with γ-secretase inhibitors had limited effects on cell proliferation and survival. Combinations of γ-secretase inhibitors with other drugs may be required to obtain efficient therapeutic effects in T-cell acute lymphoblastic leukemia, and not all combinations may be useful.

Ribosomopathies are largely congenital diseases linked to defects in ribosomal proteins or biogenesis factors. Some of these disorders are characterized by hypoproliferative phenotypes such as bone marrow failure and anemia early in life, followed by elevated cancer risks later in life. This transition from hypo- to hyperproliferation presents an intriguing paradox in the field of hematology known as "Dameshek's riddle." Recent cancer sequencing studies also revealed somatically acquired mutations and deletions in ribosomal proteins in T-cell acute lymphoblastic leukemia and solid tumors, further extending the list of ribosomopathies and strengthening the association between ribosomal defects and oncogenesis. In this perspective, we summarize and comment on recent findings in the field of ribosomopathies. We explain how ribosomopathies may provide clues to help explain Dameshek's paradox and highlight some of the open questions and challenges in the field. ispartof: Blood vol:125 issue:9 pages:1377-82 ispartof: location:United States status: published

International audience; Recently, we and others described a new chromosomal rearrangement, that is, inv(7)(p15q34) and t(7;7)(p15;q34) involving the T-cell receptor beta (TCRbeta) (7q34) and the HOXA gene locus (7p15) in 5% of T-cell acute lymphoblastic leukemia (T-ALL) patients leading to transcriptional activation of especially HOXA10. To further address the clinical, immunophenotypical and molecular genetic findings of this chromosomal aberration, we studied 330 additional T-ALLs. This revealed TCRbeta-HOXA rearrangements in five additional patients, which brings the total to 14 cases in 424 patients (3.3%). Real-time quantitative PCR analysis for HOXA10 gene expression was performed in 170 T-ALL patients and detected HOXA10 overexpression in 25.2% of cases including all the cases with a TCRbeta-HOXA rearrangement (8.2%). In contrast, expression of the short HOXA10 transcript, HOXA10b, was almost exclusively found in the TCRbeta-HOXA rearranged cases, suggesting a specific role for the HOXA10b short transcript in TCRbeta-HOXA-mediated oncogenesis. Other molecular and/or cytogenetic aberrations frequently found in subtypes of T-ALL (SIL-TAL1, CALM-AF10, HOX11, HOX11L2) were not detected in the TCRbeta-HOXA rearranged cases except for deletion 9p21 and NOTCH1 activating mutations, which were present in 64 and 67%, respectively. In conclusion, this study defines TCRbeta-HOXA rearranged T-ALLs as a distinct cytogenetic subgroup by clinical, immunophenotypical and molecular genetic characteristics.

The BCR-ABL1 fusion kinase is frequently associated with chronic myeloid leukemia and B-cell acute lymphoblastic leukemia but is rare in T-cell acute lymphoblastic leukemia (T-ALL). We recently identified NUP214-ABL1 as a variant ABL1 fusion gene in 6% of T-ALL patients. Here we describe the identification of another ABL1 fusion, EML1-ABL1, in a T-ALL patient with a cryptic t(9;14)(q34;q32) associated with deletion of CDKN2A (p16) and expression of TLX1 (HOX11). Echinoderm microtubule-associated protein-like 1-Abelson 1 (EML1-ABL1) is a constitutively phosphorylated tyrosine kinase that transforms Ba/F3 cells to growth factor-independent growth through activation of survival and proliferation pathways, including extracellular signal-related kinase 1/2 (Erk1/2), signal transducers and activators of transcription 5 (Stat5), and Lyn kinase. Deletion of the coiled-coil domain of EML1 abrogated the transforming properties of the fusion kinase. EML1-ABL1 and breakpoint cluster region (BCR)-ABL1 were equally sensitive to the tyrosine kinase inhibitor imatinib. These data further demonstrate the involvement of ABL1 fusions in the pathogenesis of T-ALL and identify EML1-ABL1 as a novel therapeutic target of imatinib. (Blood. 2005;105:4849-4852)

The mutational landscape of T-cell acute lymphoblastic leukemias (T-ALL) has been intensively studied over the past decades and we now have an extensive list of genetic defects that can occur in these tumors.[1][1] Central to T-ALL pathogenesis is the NOTCH1 signaling cascade which is hyperactivated

Inhibition of the BCR-ABL1 tyro-sine kinase with selective small molecule tyrosine kinase inhibitors such as imatinib, nilotinib or dasatinib has revolutionized the treatment of chronic myeloid leukemia (CML).[1][1],[2][2],[3][3] These drugs target the ATP-binding pocket of the ABL1 kinase domain

The protein tyrosine phosphatase CD45, encoded by the PTPRC gene, is well known as a regulator of B- and T-cell receptor signaling. In addition, CD45 negatively regulates JAK family kinases downstream of cytokine receptors. Here, we report the presence of CD45 inactivating mutations in T-cell acute lymphoblastic leukemia. Loss-of-function mutations of CD45 were detected in combination with activating mutations in IL-7R, JAK1, or LCK, and down-regulation of CD45 expression caused increased signaling downstream of these oncoproteins. Furthermore, we demonstrate that down-regulation of CD45 expression sensitizes T cells to cytokine stimulation, as observed by increased JAK/STAT signaling, whereas overexpression of CD45 decreases cytokine-induced signaling. Taken together, our data identify a tumor suppressor role for CD45 in T-cell acute lymphoblastic leukemia.

To the editor: Recent data indicate that NOTCH1 mutations significantly increase the risk of CLL progression toward Richter syndrome (RS) and chemoresistance,[1][1],[2][2] and that activation of NOTCH1 at time of CLL diagnosis is an independent prognostic factor of poor survival.[1][1],[3][3] We

With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted mutations with a large independent validation set obtained by capillary re-sequencing. We found that the combination of two mapping algorithms, namely BWA-SW and SSAHA2, coupled with the variant calling algorithm Atlas-SNP2 yields the highest sensitivity (95%) and the highest specificity (93%). Next, we applied this analysis pipeline to identify mutations in a set of 58 cancer genes, in a panel of 18 T-ALL cell lines and 15 T-ALL patient samples. We confirmed mutations in known T-ALL drivers, including PHF6, NF1, FBXW7, NOTCH1, KRAS, NRAS, PIK3CA, and PTEN. Interestingly, we also found mutations in several cancer genes that had not been linked to T-ALL before, including JAK3. Finally, we re-sequenced a small set of 39 candidate genes and identified recurrent mutations in TET1, SPRY3 and SPRY4. In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations. ispartof: PLoS One vol:7 issue:6 ispartof: location:United States status: published

T-cell acute lymphoblastic leukemia (T-ALL) is a malignancy of T-cell precursors that mainly occurs in children and adolescents. A variety of oncogenic events that are involved in the pathogenesis of T-ALL have been identified, including NOTCH1 and PTEN mutations, overexpression of TAL1 , LYL1 and

Chromosomal region 1p22 is deleted in ~20% of multiple myeloma patients, suggesting the presence of an unidentified tumor suppressor gene in this region. Using high resolution copy number arrays, we delimit a 58 kb minimal deleted region on 1p22.1 encompassing two genes: ectopic viral integration site 5 (EVI5) and ribosomal protein L5 (RPL5). Although mutations in 1p22 genes are rare in multiple myeloma, the tumor suppressor role of EVI5 and RPL5 may be supported by the fact that these genes show the highest frequency of mutations predicted to impair protein function on 1p22. Interestingly, inactivation of RPL5 was also recently described in T-cell acute lymphoblastic leukemia (T-ALL) and glioblastoma. We found that 1p22 deleted patients have significantly lower levels of EVI5 and RPL5 mRNA expression (59% and 71% residual expression respectively; p Interestingly, RPL5 but not EVI5 mRNA expression levels were significantly lower in multiple myeloma patients responding to bortezomib compared to patients that are not responding (68% residual RPL5 expression in responders versus non-responders). The clinical relevance of these findings is illustrated by the observation that PFS of newly diagnosed patients with low RPL5 expression was significantly longer when they were treated on a bortezomib containing protocol (median PFS bortezomib protocol 29.8 months versus 18.7 months for non-bortezomib, p=0.03, data phase III HOVON-65/ GMMG-HD4 trial). In contrast, PFS of RPL5 high patients was not influenced by bortezomib. These associations between RPL5 expression level and bortezomib response were confirmed when performing the same analyses on the PFS data from relapse patients in the APEX trial. For low EVI5 expressing patients, there was a non-significant trend towards benefit from bortezomib which was not present in the EVI5 high cases. Taken together, these data suggest that RPL5 expression levels are a better biomarker for bortezomib response than 1p22 deletion. In conclusion, we provide genetic data that narrow down the list of candidate tumor suppressors on 1p22 to EVI5 and RPL5. Although the exact role of these genes in suppressing multiple myeloma disease progression remains to be determined, we identify low RPL5 expression levels in multiple myeloma as a novel, clinically relevant biomarker associated with initial response and survival benefit upon treatment with bortezomib. Disclosures Mulligan: Millennium Pharmaceuticals, Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Employment. Delforge:Amgen: Honoraria; Novartis: Honoraria; Celgene Corporation: Honoraria; Janssen: Honoraria. Sonneveld:Janssen-Cilag, Celgene, Onyx, Karyopharm: Honoraria, Research Funding; novartis: Honoraria.

Abstract 1492 Aberrant activation of the PI3K/Akt signaling pathway is a frequent event in cancer including various types of leukemia. Consequently, much emphasis has been placed on developing inhibitors that target this pathway. However, this would require an in depth knowledge of the role that specific class I PI3K isoforms (α, β, γ, δ)play in the pathogenesis of a particular hematological malignancy. For instance, PI3Kδ has been shown to be essential for the growth and survival of tumors derived from B cells such as chronic lymphocytic leukemia (CLL). Such knowledge has lead to development of the selective inhibitor GS-1101 (CAL-101) that has shown significant efficacy in clinical trials. Although PI3Kγ plays an important role in modulating the immune function of T cells, its role in leukemogenesis and tumor cell survival is poorly defined. Thus, it is unclear whether an inhibitor that also targets PI3Kγ would be of any benefit in hematological malignancies. T cell acute lymphoblastic leukemia (T-ALL) is an aggressive cancer resulting from clonal proliferation of T lymphoid precursors. Previous reports suggest that hyperactivation of the PI3K/Akt signaling pathway is a common feature of this disease with the majority of cases due to the loss of function of the tumor suppressor PTEN. However, it remains to be determined whether any particular class I PI3K isoform predominates in T-ALL pathogenesis. We now report that in the absence of PTEN-mediated regulation in T cell progenitors that PI3Kγ can promote leukemogenesis even in the absence of its delta counterpart. However, inactivation of both isoforms was necessary for the suppression of tumor development in animals (< 20% dead at 220 days as compare to >85% for controls), suggesting that PI3Kα and/or PI3Kβ cannot adequately compensate for a deficiency in their γ/δ counterparts. The importance of PI3Kγ in tumor progression was established by the inability of the PI3Kδ selective inhibitor IC87114 to reduce tumor burden in mice (Fig. 1A). In contrast, treatment of PI3Kγ deficient tumors with the same inhibitor dramatically reduced disease in affected tissues (Fig. 1B). Based on these observations we developed an inhibitor, designated CAL-130, which targets both PI3Kγ and PI3Kδ in an attempt to exploit the addiction of PTEN null T-ALL tumors to both isoforms. IC50 values of this compound were 1.3 nM and 6.1 nM for p110δ and p110γ catalytic domains, respectively, as compared to 115 nM and 56 nM for p110α and p110β. Importantly, this small molecule does not inhibit additional intracellular signaling pathways (>300 kinases tested) that are critical for general cell function and survival. Oral administration of this compound to diseased mice (blast counts > 50 million/ml) for 7 days reduced tumor burden and extended median survival of treated animals to 45 day as compared 7.5 days for the control group (P Disclosures: Kashishian: Gilead Sciences: Employment. Lannutti:Gilead Sciences Inc: Employment.

Abstract 471 T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy associated with the activation of oncogenic transcription factors. Thus, 5% to 10% of pediatric and up to 30% of adult T-ALL patients show aberrant expression of the TLX1 transcription factor oncogene. Aberrant expression of TLX1 in Lck-TLX1 transgenics induces transformation of T-cell progenitors and the development of clonal T-cell lymphoblastic tumors with over 80% penetrance and a latency of 29 weeks. The prolonged latency before T-ALL development in TLX1 transgenic mice and the clonal nature of these tumors suggested the presence of cooperating mutations involved in the pathogenesis of these leukemias. Array Comparative Genomic Hybridization (aCGH) analysis identified several recurring chromosomal alterations in these tumors including three heterozygous deletions on chromosome 12, with a common deleted region containing only the Bcl11b gene. Moreover, DNA sequence analysis of Bcl11b showed the presence of Bcl11b mutations in 4/15 (27%) mouse TLX1 induced T-ALLs, which together with the 3 Bcl11b deletions identified in our aCGH analysis brings the prevalence of Bcl11b alterations in mouse TLX1 induced tumors to 7/15 (47%). Notably, mutation analysis of Bcl11b in a panel of 21 non TLX1-transgenic mouse T-ALL tumors failed to detect any Bcl11b mutations (P Bcl11b encodes a zinc finger transcription factor with a critical role in the differentiation and survival of T-cell progenitors in the thymus. Given the similarities between our mouse model of TLX1-induced leukemia and human T-ALL, we hypothesized that BCL11B alterations could also be implicated in the pathogenesis of human T-ALL. Most notably, aCGH analysis of human T-ALL samples showed the presence of focal heterozygous deletions encompassing the BCL11B locus in 2/69 (3%) T-ALL cases. In addition, mutation analysis of BCL11B in human T-ALL demonstrated the presence of somatic truncating frameshift mutations and somatic missense point mutations in 9/71 (13%) cases analyzed. Interestingly, all 6 BCL11B missense mutations involved zinc finger domains. One sample showed compound heterozygous BCL11B mutations while the remaining cases harbored heterozygous BCL11B lesions. Finally, expression analysis of TLX1 or TLX3 in 8 T-ALLs harboring mutations or deletions in BCL11B with RNA available showed aberrant expression of these transcription factor oncogenes in 5/8 (63%) [TLX1 (4/8); TLX3 (1/8)] of these samples. The identification of a high prevalence of Bcl11b mutations and deletions in TLX1-induced tumors suggested a specific genetic interaction between these two genes in T-cell transformation. We contemplated two alternative scenarios. First, TLX1 could induce partial inactivation of BCL11B in T-cell transformation, an effect that would be reinforced by secondary genetic alterations in the BCL11B locus during tumor progression. Alternatively, BCL11B mutations and TLX1 overexpression could operate in parallel pathways that contribute to distinct but complementary aspects of tumor development. To test if BCL11B could be a direct transcriptional target of TLX1 in T-ALL, we analyzed the binding of TLX1 to the BCL11B promoter via chromatin immunoprecipitation analysis in ALL-SIL, a T-ALL cell line expressing high levels of TLX1 as result of the t(10;14)(q24;q11.2) translocation. This analysis revealed that indeed TLX1 binds to the BCL11B promoter. Moreover, siRNA knockdown of TLX1 in this cell line resulted in transcriptional upregulation of BCL11B, indicating that BCL11B is a direct transcriptional target downregulated by TLX1 in T-ALL. The model that emerges from these results is that the TLX1 oncogene directly downregulates the BCL11B tumor suppressor gene, and that the oncogenic effects of this transcriptional regulatory axis can be fixed and reinforced by secondary deletions and mutations in the BCL11B locus acquired during tumor progression. Altogether, these results highlight the power of integrated genomic analysis of human and mouse leukemias, identify a TLX1-BCL11B transcriptional regulatory axis in the pathogenesis of T-ALL and define BCL11B as a tumor suppressor gene recurrently deleted and mutated in 16% of human T-ALL patients. Disclosures: No relevant conflicts of interest to declare.

Abstract 141 Introduction: T-cell lymphoblastic leukemia (T-ALL) arises from clonal expansion of a lymphoid progenitor that has undergone stepwise alteration at distinct stages of differentiation. It is suggested that a set of cooperative mutations that affect different pathways are required before thymocytes become fully malignant. Despite major improvements in our understanding of the molecular genetics of T-ALL, the underlying mechanisms that lead to the abnormal proliferation and enhanced survival of the leukemic cells remain largely unknown. Results: Array CGH analysis revealed an acquired homozygous microdeletion at chromosome 18p11 in 6 % of T-ALL cases. The deleted region was only 125 kb in size and restricted to the PTPN2 (protein tyrosine phosphatase, non-receptor type 2) locus. PTPN2 encodes an intracellular non-transmembrane tyrosine-specific phosphatase that functions as a negative regulator of a variety of signaling proteins including several members of the janus kinase (JAK) and of signal transducer and activator of transcription (STAT) families, growth factor receptors and SRC family kinases. Homozygous deletion of PTPN2 was specifically found in cases with aberrant expression of the TLX1 transcription factor, with two cases also harboring the NUP214-ABL1 fusion. Analysis of additional TLX1 positive cases by quantitative PCR identified loss of one copy of PTPN2 in 5 out of 20 cases. No mutations were detected in the coding region of PTPN2. To determine the effect of loss of PTPN2 in T-cells, we downregulated the expression of PTPN2 using RNAi technology. siRNA mediated knock-down of PTPN2 affected activation of JAK1 associated cytokine receptors implicated in T-cell development. Ligand stimulation of IL7 and interferon gamma receptor resulted in an augmented and prolonged phosphorylation of JAK1 as well as downstream targets STAT1 and STAT5 in T-ALL cell lines with knock-down of PTPN2. In addition, knock- down of Ptpn2 sensitized the pro B-cell line Ba/F3 to transformation by wild type JAK1 confirming a clear relationship between loss of PTPN2 and JAK1 activation. Knock-down of PTPN2 expression also provided a proliferative advantage and reduced sensitivity to kinase inhibitors in lymphoblastic leukemia cell lines HSB-2 and ALL-SIL. Conclusion: In conclusion, our data provide genetic and functional evidence for a tumor suppressor role of PTPN2 in T-ALL and warrant testing of JAK inhibitors for the treatment of this specific subset of T-ALLs as well as further analysis of a potential negative impact of loss of PTPN2 on responsiveness to anti-cancer treatments. Disclosures: Ferrando: Merck, Pfizer: Research Funding.

Abstract 676 T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy associated with the activation of transcription factor oncogenes. TLX1/HOX11 was originally isolated from the recurrent t(10;14)(q24;q11) translocation and is aberrantly expressed in 5% to 10% of pediatric and up to 30% of adult T-ALL. The TLX3/HOX11L2 oncogene is closely related to TLX1 and is activated by the cryptic t(5;14)(q35;q32) chromosomal translocation in 25% of pediatric T-ALLs. TLX1 and TLX3 positive T-ALLs have a distinct gene expression profile resembling that of thymocytes blocked at the early double-positive stage of development, suggesting that aberrant expression of TLX1 and TLX3 interferes with critical transcriptional regulatory networks that control cell proliferation, differentiation and survival during T-cell development. However, the identity of such oncogenic pathways and the mechanisms through which they operate are still largely unknown. Here we used an integrated systems biology approach to elucidate the transcriptional regulatory networks controlled by aberrant expression of TLX1 and TLX3 in T-ALL. Towards this goal, we performed gene expression profiling studies and ChIP-on-chip analysis of TLX1 and TLX3 direct target genes in leukemic lymphoblasts. ChIP-on-chip analysis of TLX1 direct target genes identified 5,550 promoters bound by TLX1 in ALL-SIL T-ALL cells with a significance cutoff of P 75% overlap with the TLX3 ChIP-on-chip target genes (P Disclosures: No relevant conflicts of interest to declare.

Abstract 42 Although BCR-ABL kinase inhibitors (TKIs) have revolutionized treatment of CML, they do not eradicate disease and treatment resistance can emerge. We recently identified Placental Growth Factor (PlGF) as an additional pathogenic factor in murine BCR-ABL1+ leukemia. PlGF induces proliferation of bone marrow stromal cells and of BCR-ABL1+ cell lines. PlGF is upregulated in blood (PB) and bone marrow (BM) of mice with BCR-ABL1+ leukemia and it's inhibition by a monoclonal antibody (αPlGF) significantly prolongs survival of mice bearing BCR-ABL1-unmutated and -T315I mutant blast crisis (BC) CML (Loges et al., Blood 2008; 112: abstract 1094). Now, we have further characterized the role of PlGF in disease progression, the mechanism of action of αPlGF and validated PlGF as novel target in human CML. We first quantified PB and BM PlGF protein levels at different time points after inoculation of BCR-ABL1 transduced BM cells and found significantly increasing PlGF levels upon disease progression. In line with those data, PB and BM PlGF protein levels correlated with numbers of GFP-marked leukemia cells (r=0.81; p=7-fold more PlGF than leukemia cells (p=0.003), which corroborates our preclinical data and extends the concept that PlGF is primarily produced by stromal cells in CML patients. In summary inhibition of PlGF may serve as a new candidate to be targeted in combination therapies or in TKI refractory CML. Disclosures: Carmeliet: Thrombogenics: Research Funding.

Abstract 142 T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy associated with the activation of transcription factor oncogenes. TLX1/HOX11 was originally isolated from the recurrent t(10;14)(q24;q11) in T-ALL and is aberrantly expressed in 5% to 10% of pediatric and up to 30% of adult T-ALL cases. Tlx1 plays an important role during embryonic development and acts as a master transcriptional regulator necessary for the genesis of the spleen. TLX1 positive T-ALLs have a distinct gene expression profile resembling that of thymocytes blocked at the early double positive stage of development. This observation supports the hypothesis that aberrant expression of TLX1 contributes to the pathogenesis of T-ALL by interfering with critical transcriptional regulatory networks involved in cell proliferation, differentiation and survival during T-cell development. However, the identity of such oncogenic pathways and the mechanisms though which they operate are still largely unknown. In order to gain further insight into the mechanisms of transformation induced by TLX1, we generated a transgenic model of TLX1 induced T-ALL. In this model, a human TLX1 cDNA was expressed in developing thymocytes under the control of the proximal LCK promoter. TLX1 transgenic mice displayed a specific defect in T-cell development characterized by reduced thymic size and cellularity with increased apoptosis and a differentiation arrest at the CD4/CD8 double negative, CD25/CD44 double positive stage of differentiation (DN2 thymocytes). Long term follow up revealed that TLX1 transgenic mice develop tumors with a median latency of 29 weeks. TLX1 induced leukemias are characterized by increased thymic size and diffuse infiltration of bone marrow, spleen and peripheral organs by lymphoblasts expressing T-cell markers. Analysis of TCRβ expression and transplantation into isogenic recipients demonstrated that TLX1 tumors are clonal and transplantable. Microarray gene expression profiling of mouse and human T-ALLs showed that tumors from TLX1 transgenic mice have a gene expression signature that is highly related to that of human T-ALLs with aberrant expression of TLX1. Moreover, ChIP-on-chip analysis of promoters bound by TLX1 showed this genetic program is dominated by the downregulation of TLX1 direct target genes. Mutation profiling of T-cell oncogenes and array CGH analysis in mouse TLX1 tumors demonstrated the presence of cooperative mutations including Pten deletions, activating mutations in Notch1 and loss of Bcl11b. Strikingly, SKY analysis and array CGH revealed that 80% of TLX1 induced tumors had numerical chromosomal abnormalities including a high frequency of trisomy 15. Analysis of gene expression of ChIP-on-chip TLX1 direct target genes in double negative thymocytes from preleukemic mice showed downregulation of genes primarily involved in the control of chromosomal segregation during mitosis such as Bub1, Brca2, Chek1, Kntc1, Kif23, CenpE and Plk1. These data suggest that aberrant TLX1 expression directly promotes aneuploidy and contributes to T-cell transformation by interfering with the expression of genes responsible for chromosomal segregation during mitosis. Importantly, T-cell lymphoblasts from TLX1 transgenic mice failed to undergo a mitotic cell cycle arrest after treatment with taxol, a cell cycle inhibitor that interferes with microtubule remodeling during mitosis. Strikingly, karyotype analysis of a series of 59 pediatric T-ALLs demonstrated a high frequency of chromosomal gains and losses in TLX1 and TLX3 positive human T-cell tumors compared with other genetic subgroups of T-ALL (P Disclosures: Ferrando: Merck, Pfizer: Research Funding.

Introduction of imatinib and second-generation BCR/ABL inhibitors has revolutionized treatment of patients with Philadelphia chromosome positive (Ph+) leukemia, but leukemia cells persist even in successfully treated patients, and some patients develop resistance and ultimately relapse. The reasons for these drawbacks are not entirely resolved, but besides BCR/ABL the host stroma potentially plays an important (independent) role. Placental Growth Factor (PlGF), a homologue of VEGF, was already proven to be abundantly secreted by stromal cells in solid tumors. Therefore, we investigated the role of PlGF, and the therapeutic potential of αPlGF, a monoclonal antibody against PlGF, which we recently reported to have a broad anti-tumoral potential in pre-clinical models of solid tumors (Fischer et al., Cell, 2007), in BCR/ABL+ lymphoid and myeloid leukemia. First, we studied expression of PlGF by 5 different human and murine BCR/ABL+ leukemia cell lines (Bv-173, BaF3, 32D, K562, KCL22) in vitro and found that neither of the cell lines secreted PlGF protein, but expressed its target receptor VEGFR-1. In contrast, primary murine adherent bone marrow stromal cells (BMDSC) expressed abundant amounts of PlGF protein (up to 105 pg/ml/105 cells), indicating a potential stroma-related function of PlGF. Second, we analyzed whether PlGF could induce proliferation and thereby revealed dose-dependent induction of proliferation by recombinant PlGF in all analyzed leukemia cell lines. This pro-proliferative effect of PlGF was nearly completely abrogated by both αPlGF and an extracellular anti-VEGFR-1 antibody, thus indicating that it is mediated primarily by VEGFR-1. Third, we studied potential paracrine interactions between BMDSCs and leukemia cells by performing co-culture experiments. Remarkably, coculture of BMDSC with leukemia cells significantly induced proliferation of both cell types. We hypothesized, that this induction of proliferation might be mediated by PlGF and indeed found its nearly complete abrogation upon addition of αPlGF to the co-cultures. Furthermore, BMDSCs significantly upregulated PlGF secretion (2.1 fold; N=3; P=0.005) when cultured in presence of leukemia cells. Thus, we conclude, that stromal derived PlGF promotes proliferation of leukemia cells in a paracrine fashion and at the same time acts as autocrine pro-proliferative signal for stromal cells. To test this hypothesis in vivo, we established 3 different murine models of BCR/ABL+ myeloid and lymphoid leukemia. Subsequently, we analyzed PlGF protein as present in blood and bone marrow of diseased mice in comparison to healthy mice, and detected no PlGF protein in the peripheral blood of healthy mice and low amounts of PlGF protein in their bone marrow. In contrast, leukemic mice showed PlGF protein (76.5 ± 18.4 pg / ml plasma; N=7) in their circulation at levels comparable to mice bearing solid tumors, and, interestingly more than 8.9 fold (N=7; P

Leukemias are often associated with aberrant tyrosine kinase activity that occurs as a result of chromosomal translocations. These mutations are able to confer a proliferative and survival advantage to leukemic cells, as well as cooperate with other mutations that impair cell differentiation, thus leading to the development of leukemia. NUP214-ABL1 is one such recently identified fusion gene that is generated by episomal amplification. The presence of the fusion was recently identified in approximately 6% of patients with T-cell acute lymphoblastic leukemia (T-ALL). By the use of a murine retroviral bone marrow transplantation model we have demonstrated that mice transplanted with NUP214-ABL1 transduced bone marrow cells developed either a myeloproliferative disorder (MPD) with a disease latency of 70 to 118 days or a T cell lymphoblastic leukemia with a disease latency of 115 to 124 days. The myeloproliferative phenotype was characterized by splenomagaly and leukocytosis, and analysis of the histopathology revealed extramedullary hematopoiesis in the liver, lung, kidney and Peyer’s patches, and an increase of peripheral blood neutrophils. Flow cytometry of single cell suspensions from spleen and bone marrow samples of mice with a myeloproliferative phenotype demonstrated an increase of Gr-1+/Mac-1+ cells (approximately 70%). Two of the mice that were transplanted with NUP214-ABL1 transduced bone marrow cells developed T cell lymphomas that were characterized by large thymomas, a phenotype that is consistent with other models of activated tyrosine kinases over long disease latencies. Histopathological analysis of the thymi revealed effacement of normal thymic architecture as well as T cell infiltrate into the surrounding skeletal muscle. In addition, flow cytometric analysis revealed a significant increase in the CD4+/CD8+ T cell population in the thymi of these animals. No disease was observed in secondary transplant recipients following 60 days of observation. In conclusion, these results indicate that NUP214-ABL1 is able to cause either a myeloproliferative disease or a T cell lymphoma over longer latencies in mice, the latter being similar to the phenotype observed in humans with expression of the NUP214-ABL1 fusion. These findings provide a useful model for future experiments to determine if there is a contribution of other mutations together with the NUP214-ABL1 fusion towards the development of a T-ALL phenotype in mice.

Background Molecular analysis of T-cell acute lymphoblastic leukemia (T-ALL) has provided evidence that a stepwise alteration of at least four specific pathways is required during transformation of thymocytes to leukemic T-cells. Genetic alterations in hematopoietic precursor cells lead to loss of cell cycle control, impaired differentiation, proliferation and survival advantages, and unlimited self-renewal capacity. These defects include inactivation of CDKN2A (P16) present in 96 % of the patients, deregulated expression of transcription factors, and mutation of NOTCH1 in 56% of patients. However, the molecular lesions leading to the proliferative and survival advantages of T-ALL cells are less well characterized, remaining unknown in 80 % of the T-ALLs. Aims Our aim was to set up a genome-wide analysis of T-ALL in order to detect cryptic deletions and amplifications, with a special focus on the 90 protein tyrosine kinase genes present in the human genome. Methods We used the array-CGH (micro-array comparative genomic hybridization) technology with slides containing genomic BAC probes spaced every 1 Mb over the human genome. An additional 480 probes were added covering the genomic locations of each of the 90 protein tyrosine kinases genes. A total of 27 T-ALL cases and 12 cell lines were included in the study. Results An interstitial deletion on chromosome 9p24 directly upstream of JAK2 was identified in one patient. The deletion was confirmed by FISH. Quantitative PCR (qPCR) analyses indicated that the deletion was 700 kb in size including exons 1–4 of JAK2. In two cell lines, deletions affecting ALK and ERBB4 were detected. Molecular analyses to characterize the possible presence of fusion transcripts involving tyrosine kinases are in progress. We did not detected other rearrangements involving tyrosine kinase genes in neither of the 26 other T-ALL cases nor in the 10 cell lines, indicating that cryptic deletions or amplifications involving tyrosine kinase genes are relatively rare in T-ALL. The most frequent aberration was the deletion of CDKN2A (16/27 cases and 9/12 cell lines) ranging from only one clone to almost the complete 9p arm. MYB duplication was found in two cases and 4 cell lines, and was confirmed by qPCR and FISH analysis. Two of the 4 cell lines had overexpression of MYB detected by qPCR, which can interfere with apoptosis enhancing the survival of the cells, as has been previously described. PTEN deletion was present in one case and one cell line. Other unbalanced aberrations of various size were detected: del (2p) in 5/12 cell lines, del (5q) in 1/27 samples and 4/12 cell lines, del(6q) in 3/27 samples and 2/12 cell lines, or del(9p) in 5/27 samples and 4/12 cell lines. Some of these rearrangements were not observed by standard cytogenetics. Strikingly, cell lines had significantly more chromosomal abnormalities than primary T-ALL cases. Conclusions We detected a novel cryptic rearrangement of JAK2 in one T-ALL case, and duplication of MYB in two T-ALL cases (2/27; 7.5%) and four cell lines (4/12; 33%). Our results suggest that cryptic deletions or amplifications involving tyrosine kinase genes are relatively rare in T-ALL.

BCR-ABL1 is frequently associated with CML and B-ALL, but is rarely found in T-ALL. We recently identified two variant ABL1 fusions in T-ALL: NUP214-ABL1, associated with episomal amplification of ABL1 in 6% of T-ALL cases, and EML1-ABL1, associated with the cryptic translocation t(9;14)(q34;q32) in 1 patient. Similar to BCR-ABL1, NUP214-ABL1 and EML1-ABL1 are constitutively activated tyrosine kinases that transform the Ba/F3 cell line to interleukin-3 (IL3) independent growth. In the case of NUP214-ABL1, however, the Ba/F3 cells need a significantly longer period to obtain the same level of proliferation compared to BCR-ABL1 and EML1-ABL1 transformed cells. In mouse bone marrow transplantation experiments, BCR-ABL1 induced CML with a latency of 3 weeks, while with EML1-ABL1 the mice developed disease after several months, and for NUP214-ABL1 no leukemia developed within 12 months after transplantation. These data suggest that EML1-ABL1 and NUP214-ABL1 are weaker oncogenes compared to BCR-ABL1. To gain further insights in these differences, we generated a number of deletion constructs of BCR-ABL1, EML1-ABL1 and NUP214-ABL1 and assayed the respective proteins for autophosphorylation and for their ability to transform Ba/F3 cells. For BCR-ABL1, we observed that the coiled-coil domain is not strictly required for kinase activity and transformation of Ba/F3 cells, as reported previously. In contrast, the coiled-coil domain of EML1 is sufficient and required to generate a constitutively activated EML1-ABL1 fusion protein. In the case of NUP214-ABL1, the coiled-coil domains are required, but not sufficient to generate an activated NUP214-ABL1 fusion in Ba/F3 cells, and also deletion of the N-terminal and C-terminal regions of NUP214 results in a loss of activity of NUP214-ABL1. Additional experiments confirmed that EML1-ABL1 is activated through homodimerization, while the exact mechanism of activation of NUP214-ABL1 remains unclear. In contrast to BCR-ABL1 and EML1-ABL1, NUP214-ABL1 seems to have a lower kinase activity and lacks detectable phosphorylation of the activation loop of the kinase domain. NUP214-ABL1 interacts with the nuclear pore proteins NUP62, NUP88 and RanBP2, is partially localized at the nuclear envelope, and phosphorylates RanBP2. In conclusion, we describe significant differences between BCR-ABL1, EML1-ABL1 and NUP214-ABL1. For BCR-ABL1, the coiled-coil domain is sufficient for kinase activation, however BCR-ABL1 can also be activated by coiled-coil independent mechanisms. These mechanisms explain the high kinase activity and strong transforming capacity of BCR-ABL1. For EML1-ABL1, the coiled-coil domain is the only domain that can activate the kinase, probably explaining its weaker transforming capacity in mouse bone marrow transplantation models when compared to BCR-ABL1. NUP214-ABL1 is a very weak oncogene, the coiled-coil domains of NUP214 need to cooperate with other domains to activate NUP214-ABL1 adequately in Ba/F3 cells. These results may explain why NUP214-ABL1 is always amplified in T-ALL patients, and why NUP214-ABL1 is associated with T-ALL and not with CML.

Oncogenic NOTCH signaling is a major driver of T-cell transformation in T-cell acute lymphoblastic leukemia (T-ALL). However, clinical studies testing the efficacy of NOTCH1 inactivation with γ-secretase inhibitors (GSIs) have shown limited antileukemic activity for these drugs as single agents. Here we used an expression-based virtual screening approach and network perturbation analyses to identify and functionally characterize new highly active antileukemic drugs synergistic with NOTCH1 inhibition in T-ALL. Gene expression profiling studies have shown a prominent gene expression signature dominated by genes involved in growth and metabolism downstream of NOTCH1 in T-ALL. Notably, loss of the PTEN tumor suppressor gene confers resistance to GSI therapy and effectively rescues the gene expression signature induced by NOTCH1 inhibition in T-ALL. We hypothesized that drugs inducing transcriptional programs overlapping with those driven by NOTCH1 inhibition and antagonizing those resulting from PTEN loss could have synergistic antileukemic effects with GSIs in PTEN wild type and PTEN null leukemia cells. To address this question we generated gene expression signatures from Pten conditional-inducible knockout NOTCH1-driven leukemias in basal condition, upon NOTCH1 inhibition by GSI treatment and upon deletion of Pten. Connectivity Map (cMAP) analysis in this series identified 17 high scoring compounds as candidate antileukemic drugs (p To address the mechanisms mediating the antileukemic effects of withaferin A we performed a detailed analysis of the gene expression signatures induced by this drug in T-ALL lymphoblasts. These studies revealed a strong enrichment of downregulated genes involved in translation regulation in T-ALL cells upon treatment with withaferin A (p Disclosures Califano: Therasis Inc: Employment; Cancer Genetics Inc: Consultancy; Ipsen pharmaceuticals: Consultancy; Thermo Fischer Scientific: Consultancy.

T-cell acute lymphoblastic leukemia (T-ALL) is a malignancy of the lymphoblasts committed to the T-cell lineage. Despite the therapeutic improvements witnessed over the years, ∼25% of children and ∼50% of adults still show a poor long-term outcome. While many recurrent oncogenic lesions have been identified through the characterization of chromosomal aberrations and candidate gene sequencing, several observations indicate that additional genetic alterations, not evident by conventional cytogenetics, might influence leukemogenesis and treatment outcome. Improvement of our knowledge in the identification and characterization of new oncogenic genome variations is expected to lead to a better prognostic classification and should also allow the design of tailored therapeutic strategies. To get further insights into the molecular pathogenesis of T-ALL and to identify novel markers for risk stratification and treatment improvement, we performed whole transcriptome sequencing (RNA-seq) on 18 refractory T-ALL cases sampled at diagnosis (median age 37.5 years, range 11-55). A pool of normal thymus cells was used as negative control. Next generation sequencing libraries were constructed from the mRNA fraction, followed by paired-end sequencing on a HiSeq2000 (Illumina). Sequence reads were aligned to the reference genome and were processed to identify gene expression levels, gene fusion transcripts and single nucleotide variations (SNVs). We first determined accurate gene expression levels from the RNA-seq data and used them to classify patients into T-ALL subtypes. Next, we applied the deFuse algorithm to detect fusion transcripts. Fusion transcripts detected also in normal thymus cells were filtered out, as well as fusions involving ribosomal genes. After applying these filters, we obtained 407 fusion transcripts (average: 22.6/sample, range: 0-84) predominantly involving genes localized on the same chromosome and mostly generated by deletion (306/407). Novel candidate fusion transcripts were confirmed by RT-PCR and Sanger sequencing. The SET-NUP214 fusion was identified in 2 cases, as well as 2 novel fusion transcripts involving the T-cell receptor (TCR) genes and not detected by conventional cytogenetics: the first fusion resulted in a chromosomal rearrangement between HOXA-AS4 and TRBC2 (also accompanied by overexpression of the HOXA genes) and the second between TRAC and SOX8 (associated with SOX8 overexpression). Interestingly, we also found out-of-frame fusion transcripts leading to the potential inactivation of tumor suppressor genes, such as PTEN-FAS and MAST3-C19orf10. Finally, we performed SNV calling on our dataset. After removing the most common polymorphisms, we obtained 1,483 protein-altering SNVs (missense, nonsense mutations and mutations affecting splicing), ranging between 30 and 131 per sample, with 85 genes that contain a protein-altering mutation in at least 3 of the 18 samples (i.e. 16% of cohort). Members or modulators of NOTCH and JAK/STAT pathways were the most recurrently mutated, each accounting for ∼38% of cases. In particular, 7/18 samples showed previously reported lesions in the NOTCH1 (n=5) and FBXW7 (n=1) genes but also in novel candidates as NOTCH2 (n=1), NOTCH3 (n=1) and SPEN (n=1). Interestingly, 1 patient showed 2 different mutations in the exon 26 of NOTCH1, while in 2 samples NOTCH1 mutation was associated with mutations in NOTCH2 or NOTCH3. Similarly, the JAK/STAT pathway was affected in 7/18 samples, including JAK1 (n=2), JAK3 (n=5), TYK2 (n=1) but also the novel candidates STAT5A (n=2) and STAT6 (n=1). Four of the 5 JAK3-positive patients showed also a mutation in another gene of the same pathway, such as JAK1 (n=1), STAT5A (n=2) and STAT6 (n=1). Thus, mutational screening of both the NOTCH and JAK/STAT pathway shows that mutations can occur simultaneously and suggests that more than one lesion is required for leukemic transformation. In conclusion, RNA-seq appears as a promising tool to dissect the heterogeneity of T-ALL and to identify targets that might be useful for tailored therapeutic interventions. Further investigations are ongoing to determine the recurrence and specificity of these lesions, and their potential in inducing a refractory phenotype. Finally, in vitro experiments will be carried out to investigate the transforming capability of specific lesions and the targettability of the recurrently impaired pathways. Disclosures: No relevant conflicts of interest to declare.

The NOTCH pathway is a key regulator of developmental choices, differentiation and function throughout the hematopoietic system. An aberrant activation of this pathway may underlie leukemogenesis, as shown in T-ALL cases with the rare t(7;9)(q35;q34) targeting NOTCH1 or with mutation(s) of NOTCH1 found in approximately 50% of T-ALL cases. We report here evidence for NOTCH1 and NOTCH2 rearrangements in B-cell lymphoma. Involvement of NOTCH1 was identified by the presence of dic(9;14)(q34;q32) and trisomy 12 in a case of chronic lymphocytic leukemia (CLL) at the time of transformation, and by st(9;22)(q34;q11) accompanied by t(14;18)(q32;q21)/IGH-BCL2 and t(8;14)(q24;q32)/IGH-CMYC in a follicular lymphoma (FL). FISH analysis of dic(9;14) and t(9;22) demonstrated the respective involvement of the IGH and IGL loci, and mapped both 9q34 breakpoints to the 5′ end of NOTCH1. Western blot analysis with cleaved Notch1 (Val1744) antibody was performed in both cases and hyperactive NOTCH1 signaling was found in the first case only. This particular case displayed in addition a mutation in the PEST domain of NOTCH1. No mutations, neither in the PEST, nor in HD domain of NOTCH1 (2 domains frequently mutated in T-ALL) were found in the FL case. FISH analysis of 30 additional lymphoma cases documented by structural aberrations of 9q33q34 revealed a normal status of NOTCH1. NOTCH2 rearrangement was identified by FISH in 1 out of the 3 leukemia/lymphoma cases we could collect with t(1;14)(p13;q32). This particular CLL case showed a 3-way translocation, t(1;14;18)(p13;q32;q21), targeting also BCL2. So far, this patient did not show any clinical features of CLL transformation. We hypothesize that IG-translocations affecting NOTCH genes in B-cell malignancies contribute to the lymphomagenesis by deregulating the transcription of these genes resulting in an aberrant ligand-independent NOTCH signaling. Mutation in the PEST domain of NOTCH1 as found in one case with dic(9;14) may further contribute to the process by stabilization of the aberrant product. Further molecular and immunohistochemical investigations of these cases are in progress.