BACKGROUND Philadelphia chromosome–like acute lymphoblastic leukemia (Ph-like ALL) is characterized by a gene-expression profile similar to that of BCR–ABL1–positive ALL, alterations of lymphoid transcription factor genes, and a poor outcome. The frequency and spectrum of genetic alterations in Ph-like ALL and its responsiveness to tyrosine kinase inhibition are undefined, especially in adolescents and adults. METHODS We performed genomic profiling of 1725 patients with precursor B-cell ALL and detailed genomic analysis of 154 patients with Ph-like ALL. We examined the functional effects of fusion proteins and the efficacy of tyrosine kinase inhibitors in mouse pre-B cells and xenografts of human Ph-like ALL. RESULTS Ph-like ALL increased in frequency from 10% among children with standard-risk ALL to 27% among young adults with ALL and was associated with a poor outcome. Kinase-activating alterations were identified in 91% of patients with Ph-like ALL; rearrangements involving ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK2, NTRK3, PDGFRB, PTK2B, TSLP, or TYK2 and sequence mutations involving FLT3, IL7R, or SH2B3 were most common. Expression of ABL1, ABL2, CSF1R, JAK2, and PDGFRB fusions resulted in cytokine-independent proliferation and activation of phosphorylated STAT5. Cell lines and human leukemic cells expressing ABL1, ABL2, CSF1R, and PDGFRB fusions were sensitive in vitro to dasatinib, EPOR and JAK2 rearrangements were sensitive to ruxolitinib, and the ETV6–NTRK3 fusion was sensitive to crizotinib. CONCLUSIONS Ph-like ALL was found to be characterized by a range of genomic alterations that activate a limited number of signaling pathways, all of which may be amenable to inhibition with approved tyrosine kinase inhibitors. Trials identifying Ph-like ALL are needed to assess whether adding tyrosine kinase inhibitors to current therapy will improve the survival of patients with this type of leukemia. (Funded by the American Lebanese Syrian Associated Charities and others.)

Pediatric acute lymphoblastic leukemia (ALL) is a heterogeneous disease consisting of distinct clinical and biological subtypes that are characterized by specific chromosomal abnormalities or gene mutations. Mutation of genes encoding tyrosine kinases is uncommon in ALL, with the exception of Philadelphia chromosomepositive ALL, where the t(9,22)(q34;q11) translocation encodes the constitutively active BCR-ABL1 tyrosine kinase. We recently identified a poor prognostic subgroup of pediatric BCR-ABL1-negative ALL patients characterized by deletion of IKZF1 (encoding the lymphoid transcription factor IKAROS) and a gene expression signature similar to BCR-ABL1-positive ALL, raising the possibility of activated tyrosine kinase signaling within this leukemia subtype. Here, we report activating mutations in the Janus kinases JAK1 (n ‫؍‬ 3), JAK2 (n ‫؍‬ 16), and JAK3 (n ‫؍‬ 1) in 20 (10.7%) of 187 BCR-ABL1-negative, high-risk pediatric ALL cases. The JAK1 and JAK2 mutations involved highly conserved residues in the kinase and pseudokinase domains and resulted in constitutive JAK-STAT activation and growth factor independence of Ba/F3-EpoR cells. The presence of JAK mutations was significantly associated with alteration of IKZF1 (70% of all JAK-mutated cases and 87.5% of cases with JAK2 mutations; P ‫؍‬ 0.001) and deletion of CDKN2A/B (70% of all JAK-mutated cases and 68.9% of JAK2-mutated cases). The JAK-mutated cases had a gene expression signature similar to BCR-ABL1 pediatric ALL, and they had a poor outcome. These results suggest that inhibition of JAK signaling is a logical target for therapeutic intervention in JAK mutated ALL. IKAROS ͉ kinase ͉ mutationA cute lymphoblastic leukemia (ALL) is the most common pediatric cancer, and despite high overall cure rates (1), ALL remains the second leading cause of cancer death in children. To improve outcome, it is necessary to identify highrisk patients at the time of diagnosis and then tailor therapy toward the genetic lesions driving their leukemia.Recent genome-wide analyses have identified common genetic alterations in childhood ALL that contribute to leukemogenesis (2, 3). To identify genetic lesions predictive of poor outcome in childhood ALL, we recently performed genomewide analysis of DNA copy number alterations, transcriptional profiling, and gene resequencing in a cohort of 221 children with B progenitor ALL predicted to be at high risk for relapse based on age and presentation leukocyte count (4). These patients were treated on the Children's Oncology Group P9906 trial by using an augmented reinduction/reconsolidation strategy (''Berlin-Frankfurt-Münster'' regimen) (5, 6). This cohort excluded patients with known good (ETV6-RUNX1 or trisomies 4 and 10) or very poor (hypodiploid, BCR-ABL1) risk sentinel genetic lesions, and it represents Ϸ12% of noninfant B precursor ALL cases (Table S1). Alteration of the lymphoid transcription factor IKZF1 (IKAROS) was associated with poor outcome and a leukemic cell gene expression signature highly similar to that of BCR-ABL1...

Key Points• Targeting of CD123 via CAR-engineered T cells results in rejection of human AML and myeloablation in mouse models.Many patients with acute myeloid leukemia (AML) are incurable with chemotherapy and may benefit from novel approaches. One such approach involves the transfer of T cells engineered to express chimeric antigen receptors (CARs) for a specific cell-surface antigen. This strategy depends upon preferential expression of the target on tumor cells. To date, the lack of AML-specific surface markers has impeded development of such CARbased approaches. CD123, the transmembrane a chain of the interleukin-3 receptor, is expressed in the majority of AML cells but is also expressed in many normal hematopoietic cells. Here, we show that CD123 is a good target for AML-directed CAR therapy, because its expression increases over time in vivo even in initially CD123 dim populations, and that human CD123-redirected T cells (CART123) eradicate primary AML in immunodeficient mice. CART123 also eradicated normal human myelopoiesis, a surprising finding because anti-CD123 antibody-based strategies have been reportedly well tolerated. Because AML is likely preceded by clonal evolution in "preleukemic" hematopoietic stem cells, our observations support CART123 as a viable AML therapy, suggest that CART123-based myeloablation may be used as a novel conditioning regimen for hematopoietic cell transplantation, and raise concerns for the use of CART123 without such a rescue strategy. (Blood. 2014;123(15):2343-2354

CRLF2 rearrangements, JAK1/2 point mutations, and JAK2 fusion genes have been identified in Philadelphia chromosome (Ph)-like acute lymphoblastic leukemia (ALL), a recently described subtype of pediatric high-risk B-precursor ALL (B-ALL) which exhibits a gene expression profile similar to Ph-positive ALL and has a poor prognosis. Hyperactive JAK/STAT and PI3K/mammalian target of rapamycin (mTOR) signaling is common in this highrisk subset. We, therefore, investigated the efficacy of the JAK inhibitor ruxolitinib and the mTOR inhibitor rapamycin in xenograft models of 8 pediatric B-ALL cases with and without CRLF2 and JAK genomic lesions. Ruxolitinib treatment yielded significantly lower peripheral blast counts compared with vehicle (P < .05) in 6 of 8 human leukemia xenografts and lower splenic blast counts (P < . IntroductionSurvival rates for childhood B-precursor acute lymphoblastic leukemia (B-ALL) approach 90% with current combination chemotherapy regimens. 1 Intensification of chemotherapy regimens has largely been responsible for dramatic improvements in survival; however, recent modifications have yielded diminishing returns, particularly in a subset of leukemias that are relatively resistant to conventional cytotoxic chemotherapy. The identification of underlying genetic alterations in chemotherapy-resistant subtypes, particularly lesions that drive leukemogenesis and can be targeted with novel therapies, remains an urgent need.Genome-wide analyses and next-generation sequencing approaches have advanced our understanding of potential leukemogenic mutations in pediatric ALL. [2][3][4][5][6][7] Recently, these analyses identified a cohort of clinically high-risk pediatric B-precursor ALL with gene expression profiles similar to those of Philadelphia chromosome-positive ALL (Ph ϩ ALL, also termed BCR-ABL1-positive ALL). 2,4,8 This Ph-like cohort suffers high rates of relapse and mortality. The similarity to Ph ϩ ALL suggests that aberrant kinase activity may also drive this subset of ALL. Indeed, several lesions affecting kinase activity and cytokine signaling have recently been identified in Ph-like ALL. 9 Rearrangements in CRLF2 (cytokine receptor-like factor 2), leading to overexpression of this component of the heterodimeric cytokine receptor for thymic stromal lymphopoietin (TSLP), are present in up to 7% of childhood B-precursor ALL overall, 10-12 represent approximately half of Ph-like ALLs, 8 and are highly associated with point mutations in Janus kinase (JAK) family members. 11,13-15 Moreover, CRLF2 overexpression is an independent negative prognostic factor in high-risk pediatric B-ALL. 16 The frequency of genetic alterations in CRLF2 and JAK2 in high-risk B-ALL and Down syndrome-associated ALL 10,17 suggests that these lesions may be key events in leukemogenesis. Consistent with its role in early B-cell development, we have previously demonstrated that TSLP stimulates proliferation of precursor B-ALL cell lines. 18,19 Similarly, JAK signaling has been implicated in BCR-ABL1-mediated transform...

Philadelphia chromosome (Ph)-like acute lymphoblastic leukemia (ALL), also referred to as --like ALL, is a high-risk subset with a gene expression profile that shares significant overlap with that of Ph-positive (Ph) ALL and is suggestive of activated kinase signaling. Although Ph ALL is defined by - fusion, Ph-like ALL cases contain a variety of genomic alterations that activate kinase and cytokine receptor signaling. These alterations can be grouped into major subclasses that include ABL-class fusions involving ABL1, ABL2, CSF1R, and PDGFRB that phenocopy BCR-ABL1 and alterations of CRLF2, JAK2, and EPOR that activate JAK/STAT signaling. Additional genomic alterations in Ph-like ALL activate other kinases, including BLNK, DGKH, FGFR1, IL2RB, LYN, NTRK3, PDGFRA, PTK2B, TYK2, and the RAS signaling pathway. Recent studies have helped to define the genomic landscape of Ph-like ALL and how it varies across the age spectrum, associated clinical features and outcomes, and genetic risk factors. Preclinical studies and anecdotal reports show that targeted inhibitors of relevant signaling pathways are active in specific Ph-like ALL subsets, and precision medicine trials have been initiated for this high-risk ALL subset.

Adults and children with high-risk CRLF2-rearranged acute lymphoblastic leukemia (ALL) respond poorly to current cytotoxic chemotherapy and suffer unacceptably high rates of relapse, supporting the need to use alternative therapies. CRLF2 encodes the thymic stromal lymphopoietin (TSLP) receptor, which activates cell signaling in normal lymphocytes on binding its ligand, TSLP. We hypothesized that aberrant cell signaling occurs in CRLF2-rearranged ALL and can be targeted by signal transduction inhibitors of this pathway. In a large number of primary CRLF2-rearranged ALL samples, we observed increased basal levels of pJAK2, pSTAT5, and pS6. We thus characterized the biochemical sequelae of CRLF2

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• ETP-ALL, a high-risk subtype of T-ALL, is characterized by aberrant activation of the JAK/STAT signaling pathway.• The JAK1/2 inhibitor ruxolitinib demonstrates robust activity in patientderived xenograft models of ETP-ALL.Early T-cell precursor (ETP) acute lymphoblastic leukemia (ALL) is a recently described subtype of T-ALL characterized by a unique immunophenotype and genomic profile, as well as a high rate of induction failure. Frequent mutations in cytokine receptor and Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathways led us to hypothesize that ETP-ALL is dependent on JAK/STAT signaling. Here we demonstrate aberrant activation of the JAK/STAT pathway in ETP-ALL blasts relative to non-ETP T-ALL. Moreover, ETP-ALL showed hyperactivation of STAT5 in response to interleukin-7, an effect that was abrogated by the JAK1/2 inhibitor ruxolitinib. In vivo, ruxolitinib displayed activity in 6 of 6 patient-derived murine xenograft models of ETP-ALL, with profound single-agent efficacy in 5 models. Ruxolitinib treatment decreased peripheral blast counts relative to pretreatment levels and compared with control (P < .01) in 5 of 6 ETP-ALL xenografts, with marked reduction in mean splenic blast counts (P < .01) in 6 of 6 samples. Surprisingly, both JAK/STAT pathway activation and ruxolitinib efficacy were independent of the presence of JAK/STAT pathway mutations, raising the possibility that the therapeutic potential of ruxolitinib in ETP-ALL extends beyond those cases with JAK mutations. These findings establish the preclinical in vivo efficacy of ruxolitinib in ETP-ALL, a biologically distinct subtype for which novel therapies are needed. (Blood. 2015;125(11):1759-1767 Introduction Early T-cell precursor (ETP) acute lymphoblastic leukemia (ALL) was first described in 2009 as a subtype of T-ALL with a unique immunophenotype that includes expression of myeloid and early progenitor or stem cell markers in addition to T-cell lineage markers. 1Although overall survival for the majority of T-ALL cases has improved dramatically over the last 50 years, 2 largely due to intensification of chemotherapy regimens, many published studies suggest a large percentage of ETP-ALL cases have dismal outcomes.1,3-7 More recent studies suggest that children with ETP-ALL treated on contemporary protocols that intensify therapy based on minimal residual disease response may not fare as poorly as originally thought. 8,9 ETP-ALL, which represents ;10% to 15% of new T-ALL diagnoses in children 1,4,5 and ;10% to 30% in adults, 3,6 accounts for a disproportionate fraction of T-ALL induction failures (ie, failure to achieve a morphologic remission at the end of the first month of chemotherapy). Novel therapies with alternative mechanistic approaches are urgently needed for chemotherapy-refractory subgroups of ETP-ALL.In addition to an immunophenotype with myeloid/stem cell markers, ETP-ALL cases demonstrate a similar transcriptional and mutational landscape to myeloid leukemias and hematopoietic stem ce...