Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.

Genetic alterations activating NOTCH1 signaling and T cell transcription factors, coupled with inactivation of the INK4/ARF tumor suppressors are hallmarks of T-ALL, but detailed genome-wide sequencing of large T-ALL cohorts has not been performed. Using integrated genomic analysis of 264 T-ALL cases, we identify 106 putative driver genes, half of which were not previously described in childhood T-ALL (e.g. CCND3, CTCF, MYB, SMARCA4, ZFP36L2 and MYCN). We described new mechanisms of coding and non-coding alteration, and identify 10 recurrently altered pathways, with associations between mutated genes and pathways, and stage or subtype of T-ALL. For example, NRAS/FLT3 mutations were associated with immature T-ALL, JAK3/STAT5B mutations in HOX1 deregulated ALL, PTPN2 mutations in TLX1 T-ALL, and PIK3R1/PTEN mutations in TAL1 ALL, suggesting that different signaling pathways have distinct roles according to maturational stage. This genomic landscape provides a logical framework for the development of faithful genetic models and new therapeutic approaches.

To more comprehensively assess the pathogenic contribution of the PTEN-PI3K-AKT pathway to T-cell acute lymphoblastic leukemia (T-ALL), we examined diagnostic DNA samples from children with T-ALL using array comparative genomic hybridization and sequence analysis. Alterations of PTEN, PI3K, or AKT were identified in 47.7% of 44 cases.There was a striking clustering of PTEN mutations in exon 7 in 12 cases, all of which were predicted to truncate the C2 domain without disrupting the phosphatase domain of PTEN. Induction chemotherapy failed to induce remission in 3 of the 4 patients whose lymphoblasts harbored PTEN deletions at the time of diagnosis, compared with none of the 12 patients with mutations of PTEN exon 7 (P ‫؍‬ .007), suggesting that PTEN deletion has more adverse therapeutic consequences than mutational disruptions that preserve the phosphatase domain. These findings add significant support to the rationale for the development of therapies targeting the PTEN-PI3K-AKT pathway in T-ALL. IntroductionDespite recent improvements in therapy, approximately 25% of children and 50% to 70% of adults with T-cell acute lymphoblastic leukemia (T-ALL) develop treatment-resistant disease, 1,2 which carries a dire prognosis. 3 Molecularly targeted agents hold considerable promise for the treatment of T-ALL, although limits in our current understanding of the key pathways that drive T-ALL pathogenesis restrict our ability to use these agents effectively.PTEN is a negative regulator of oncogenic PI3K-AKT signaling, 4 and recent studies have demonstrated the inactivation of PTEN in human T-ALL cell lines and primary samples. [5][6][7][8] Furthermore, the inactivation of PTEN has been shown to play a prominent role in resistance to NOTCH inhibition in T-ALL cell lines, an effect that appears to be mediated by AKT. 7 The activation of PI3K-AKT signaling can also occur by mutation of PI3K or AKT genes, which have not previously been assessed in T-ALL. Finally, the spectrum of PTEN mutations has not been extensively analyzed in clinical samples of primary T-ALL. Here we investigated the frequency and prognostic implications of PTEN, PI3K, and AKT abnormalities in childhood T-ALL, using array comparative genomic hybridization (CGH), fluorescence in situ hybridization (FISH), and sequence analysis.

Academia and small business research units are poised to play an increasing role in drug discovery, with drug repurposing as one of the major areas of activity. Here we summarize project status for a number of drugs or classes of drugs: raltegravir, cyclobenzaprine, benzbromarone, mometasone furoate, astemizole, R-naproxen, ketorolac, tolfenamic acid, phenothiazines, methylergonovine maleate and beta-adrenergic receptor drugs, respectively. Based on this multi-year, multi-project experience we discuss strengths and weaknesses of academic-based drug repurposing research. Translational, target and disease foci are strategic advantages fostered by close proximity and frequent interactions between basic and clinical scientists, which often result in discovering new modes of action for approved drugs. On the other hand, lack of integration with pharmaceutical sciences and toxicology, lack of appropriate intellectual coverage and issues related to dosing and safety may lead to significant drawbacks. The development of a more streamlined regulatory process world-wide, and the development of pre-competitive knowledge transfer systems such as a global healthcare database focused on regulatory and scientific information for drugs world-wide, are among the ideas proposed to improve the process of academic drug discovery and repurposing, and to overcome the “valley of death” by bridging basic to clinical sciences.

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AALL0434 established that ABFM with C-MTX was superior to ABFM plus HDMTX for T-ALL in approximately 90% of patients who received CRT, with later timing for those receiving HDMTX.

High-throughput sequencing (HTS) of lymphoid receptor genes is an emerging technology that can comprehensively assess the diversity of the immune system. Here, we applied HTS to the diagnosis of T-lineage acute lymphoblastic leukemia/lymphoma. Using 43 paired patient samples, we then assessed minimal residual disease (MRD) at day 29 after treatment. The variable regions of TCRB and TCRG were sequenced using an Illumina HiSeq platform after performance of multiplexed polymerase chain reaction, which targeted all potential V-J rearrangement combinations. Pretreatment samples were used to define clonal T cell receptor (TCR) complementarity-determining region 3 (CDR3) sequences, and paired posttreatment samples were evaluated for MRD. Abnormal T lymphoblast identification by multiparametric flow cytometry was concurrently performed for comparison. We found that TCRB and TCRG HTS not only identified clonality at diagnosis in most cases (31 of 43 for TCRB and 27 of 43 for TCRG) but also detected subsequent MRD. As expected, HTS of TCRB and TCRG identified MRD that was not detected by flow cytometry in a subset of cases (25 of 35 HTS compared with 13 of 35, respectively), which highlights the potential of this technology to define lower detection thresholds for MRD that could affect clinical treatment decisions. Thus, next-generation sequencing of lymphoid receptor gene repertoire may improve clinical diagnosis and subsequent MRD monitoring of lymphoproliferative disorders.

The BCL11B transcription factor is required for normal T-cell development, and has recently been implicated in the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) induced by TLX overexpression or Atm deficiency. To comprehensively assess the contribution of BCL11B inactivation to human T-ALL, we performed DNA copy number and sequencing analyses of T-ALL diagnostic specimens, revealing monoallelic BCL11B deletions or missense mutations in 9% (n ‫؍‬ 10 of 117) of cases. Structural homology modeling revealed that several of the BCL11B mutations disrupted the structure of zinc finger domains required for this transcription factor to bind DNA. BCL11B haploinsufficiency occurred across each of the major molecular subtypes of T-ALL, including early T-cell precursor, HOXApositive, LEF1-inactivated, and TAL1-positive subtypes, which have differentiation arrest at diverse stages of thymocyte development. Our findings provide compelling evidence that BCL11B is a haploinsufficient tumor suppressor that collaborates with all major T-ALL oncogenic lesions in human thymocyte transformation. IntroductionT-cell acute lymphoblastic leukemia (T-ALL) can be subclassified into distinct molecular subtypes based on dominant oncogenic alterations that lead to differentiation arrest at specific stages of T-cell development. 1,2 These include the HOXA/MEIS1, TLX1/3, and TAL1-overexpressing subtypes, 2,3 the LEF1-inactivated subtype, 4 and the recently identified group of T-ALL cases with developmental arrest at very early stages of T-cell development defined by a characteristic early T-cell precursor (ETP) phenotype or by absence of biallelic TCR␥ deletions (ABD). 5,6 On the other hand, other T-ALL oncogenic alterations, such as deletions of CDKN2A or mutations of NOTCH1 and PTEN, occur across all T-ALL subtypes, 2,7 suggesting that they can contribute to thymocyte transformation at diverse stages of T-cell development.The BCL11B transcription factor plays key roles in normal T-cell development. In murine thymocytes, Bcl11b inactivation leads to developmental arrest at a DN2-DN3 stage, 8-10 acquisition of NK-like features, 8,11 and aberrant self-renewal activity. 10 In human T-ALL, BCL11B is involved in recurrent cryptic t(5;14)(q35; q32) translocations with the TLX3 locus, in which BCL11B gene regulatory elements drive aberrant overexpression of the TLX3 oncogene. [12][13][14][15] However, several lines of evidence suggest that BCL11B haploinsufficiency may also be an important pathogenetic consequence of this translocation. For example, we have recently identified monoallelic Bcl11b deletions in most T-ALLs arising in Atm-deficient mice, 16 and Bcl11b has been shown to suppress murine T-lymphoblastic malignancies induced by p53 haploinsufficiency, radiation, or the BCR-ABL oncogene. 17,18 Furthermore, recent work has also revealed monoallelic BCL11B lesions in TLX1-induced murine T-ALL, and in TLX1-or TLX3-overexpressing human T-ALL. 19 Here, we show results of array CGH and sequencing analyses in T-ALL, which reveal heter...