1 Potent Efficacy of Combined PI3K/mTOR and JAK or ABL ...

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Potent Efficacy of Combined PI3K/mTOR and JAK or ABL Inhibition in Murine Xenograft Models of Ph-like Acute Lymphoblastic Leukemia Sarah K Tasian MD,1,2 David T Teachey MD,1,2 Yong Li,1 Feng Shen,1 Richard C Harvey PhD,4 I-Ming Chen DVM MS,4 Theresa Ryan,1 Tiffaney L Vincent,1 Cheryl L Willman MD,4 Alexander E Perl MD MS,2,3 Stephen P Hunger MD,1,2 Mignon L Loh MD,5,6 Martin Carroll MD,2,3 Stephan A Grupp MD PhD1,2

1 Department of Pediatrics, Division of Oncology, Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA 2 University of Pennsylvania Perelman School of Medicine 3 Department of Medicine, Division of Hematology, Abramson Cancer Center, University of Pennsylvania; Philadelphia, PA 4 Department of Pathology, University of New Mexico: Albuquerque, NM 5 Department of Pediatrics, Division of Hematology/Oncology, University of California, San Francisco Benioff Children’s Hospital and School of Medicine; San Francisco, CA 6 Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA. Corresponding author: Sarah K Tasian, MD 3501 Civic Center Boulevard, CTRB 3010 Philadelphia, Pennsylvania 19104 Phone: 215.590.5476 Fax: 215.590.3770 Email: [email protected] Short title: PI3K inhibition in Ph-like ALL Abstract word count: 232 Text word count: 3988 Number of figures/tables: 5 Number of supplemental figures: 5 Number of references: 60 Scientific category: Lymphoid Neoplasia Presented in part at the American Society of Hematology 2015 annual meeting (New Orleans, LA) and the International Society of Paediatric Oncology 2014 annual meeting (Toronto, ON)

Blood First Edition Paper, prepublished online October 24, 2016; DOI 10.1182/blood-2016-05-707653

Copyright © 2016 American Society of Hematology

For personal use only.on February 5, 2018. by guest www.bloodjournal.orgFrom

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KEY POINTS

1. PI3K/mTOR inhibition potently inhibited leukemia proliferation and signal

transduction in vivo in human Ph-like ALL xenograft models.

2. Combined PI3K/mTOR and JAK or ABL inhibition was superior to monotherapy in

CRLF2/JAK-mutant and ABL/PDGFR-mutant Ph-like ALL models.




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ABSTRACT

Philadelphia chromosome-like B-cell lymphoblastic leukemia (BCR-ABL1-like or

Ph-like ALL) is associated with activated JAK/STAT, SRC/ABL, and/or PI3K/Akt/mTOR

signaling and poor clinical outcomes. Inhibitors of PI3K pathway signaling (PI3Ki) have

been minimally investigated in Ph-like ALL to date. We hypothesized that targeted

inhibition of PI3Kα, PI3Kδ, PI3K/mTOR, or TORC1/TORC2 would decrease leukemia

proliferation and abrogate aberrant kinase signaling. We further hypothesized that

combined PI3K pathway and JAK inhibition or PI3K pathway and SRC/ABL inhibition

would have superior efficacy compared to inhibitor monotherapy. We treated ten

childhood ALL patient-derived xenograft models harboring various Ph-like genomic

alterations with four discrete PI3K pathway protein inhibitors and observed marked

leukemia reduction and in vivo signaling inhibition in all models. Treatment with the dual

PI3K/mTOR inhibitor gedatolisib resulted in near-eradication of ALL in CRLF2/JAK-

mutant models (n=7) with mean 92.2% (range 86.0-99.4%) reduction versus vehicle

controls (p<0.0001) and in prolonged animal survival. Gedatolisib also inhibited ALL

proliferation in ABL/PDGFR-mutant models (n=3) with mean 66.9% (range 42.0-87.6%)

reduction versus vehicle (p<0.0001). Combined gedatolisib and ruxolitinib treatment of

CRLF2/JAK-mutant models more effectively inhibited ALL proliferation than either

inhibitor alone (p<0.001) and further enhanced survival. Similarly, superior efficacy of

combined gedatolisib and dasatinib was observed in ABL/PDGFR-mutant models

(p<0.001). Overall, PI3K/mTOR inhibition potently decreased ALL burden in vivo, and

anti-leukemia activity was further enhanced with combination inhibitor therapy. Clinical

trials testing combinations of kinase inhibitors in patients with Ph-like ALL are indicated.




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INTRODUCTION

B-cell acute lymphoblastic leukemia (B-ALL), the most common childhood

cancer, is caused by somatic genetic mutations that result in aberrant arrest of normal

lymphoid maturation, dysregulated cellular proliferation, and evasion of programmed cell

death.1-3 Increased understanding of the biologic heterogeneity of childhood ALL has led

to modern risk stratification, which incorporates the critical contributions of genetic

subgroups and induction chemotherapy responses to deliver appropriately intensive

therapy to achieve cure.4-6 Unfortunately, approximately 15% of children with ALL have

recurrent disease, and relapsed ALL remains a leading cause of pediatric cancer

mortality.7 Adults with ALL fare even more poorly with >50% relapse rates and 20-40%

overall survival.8,9

Genomic profiling of high-risk (HR) ALL cases has identified the Philadelphia

chromosome-like subtype of B-ALL (Ph-like ALL), which comprises 10-20% of HR B-ALL

in children and adolescents and nearly 30% in young adults.10-15 Ph-like ALL is defined

by lack of BCR-ABL1 fusion (as in Ph+ ALL), but has a kinase-activated gene

expression signature similar to that of Ph+ ALL, frequent deletion of IKZF1, and

mutations in other kinase and cytokine receptor signaling pathway genes.12-14,16-18

Rearrangements of cytokine receptor-like factor 2 (CRLF2) occur in approximately 50%

of Ph-like ALL cases and result in CRLF2 overexpression.19-21 Half of CRLF2-rearranged

ALLs have concomitant alterations in Janus kinase (JAK) pathway-associated genes,

including JAK1 and JAK2, and a small number of these cases also harbor interleukin-7

receptor alpha (IL7RA) mutations.22-24 JAK2 point mutations are the most frequent co-

existing genetic abnormality in CRLF2-rearranged ALL and also occur in non-Ph-like

ALL, including trisomy 21-associated B-ALL and T-ALL.25,26 Genomic rearrangements of

Abelson kinase 1 and Abelson kinase 2 (ABL1 and ABL2), colony stimulating factor-1

receptor (CSF1R), platelet-derived growth factor receptor-beta (PDGFRB), JAK2,




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erythropoietin receptor (EPOR), and other genes account for an additional 30-40% of

Ph-like ALL and also drive constitutive kinase signaling.12-14,26,27 Patients with Ph-like

ALL often have high rates of minimal residual disease (MRD) at the end of induction

chemotherapy with some patients experiencing overt induction failure.14,21,28

Retrospective analyses of high-risk children and adolescents and young adults (AYAs)

with Ph-like ALL demonstrate greatly increased risk of treatment failure and poor overall

survival (OS) regardless of underlying Ph-like genomic alterations.10,13,14 New therapies

are indicated for these patients.

All Ph-like ALL-associated mutations identified to date activate kinase signaling,

particularly of CRLF2-, JAK-, ABL-, and PDGFRB-associated pathways. Biochemical

sequelae of these mutations have been primarily studied to date in the most common

CRLF2-rearranged subset of Ph-like ALL with the goal of identifying potential signal

transduction inhibitor (i) therapies, but perturbed intracellular signaling mechanisms of

these genomic alterations remain incompletely characterized. Others and we previously

reported constitutive and/or cytokine-inducible JAK/signal transduction activator of

transcription (JAK/STAT) and phosphatidylinositol 3-kinase/protein kinase B/mammalian

target of rapamycin (PI3K/Akt/mTOR) signaling in CRLF2-rearranged ALL.29,30 We

further observed robust inhibition of constitutively activated signal transduction with JAK

or mTOR inhibition in vitro and in vivo.24,31-33 More recent studies focused upon non-

CRLF2-rearranged Ph-like ALL cases have demonstrated in vitro and in vivo efficacy of

other kinase inhibitors, including anecdotal clinical responses in children and adults with

Ph-like ALL harboring ABL1, ABL2, or PDGFRB rearrangements and fusion proteins

(“ABL class” rearrangements) treated with imatinib or dasatinib.14,34,35

While preclinical32,36 and early clinical studies of JAK inhibition in CRLF2/JAK-

mutant and SRC/ABL inhibition in ABL/PDGFR-mutant Ph-like ALL are ongoing

(NCT02723994, NCT02883049), therapeutic disruption of aberrant PI3K pathway




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signaling has been minimally investigated. Clinical efficacy of the mTORi rapamycin and

its analogues has proven suboptimal in various cancers, at least in part due to

upregulation of Akt signaling, a known sequela of mTORi monotherapy and a common

resistance mechanism.37 Newer-generation kinase inhibitors that target multiple PI3K

pathway signaling proteins or that selectively inhibit PI3K isoforms may have superior

anti-leukemia cytotoxicity, as well as avoid compensatory upregulation of salvage

signaling pathways.38,39 Such “next generation” PI3K pathway inhibitors (PI3Ki) have

been minimally evaluated in ALL to date.39 Furthermore, the efficacy of simultaneously

targeting multiple oncogenic signaling networks in Ph-like ALL has not been

investigated, such as combination therapy with PI3Ki and JAKi.

Using patient-derived xenograft (PDX) models of childhood Ph-like ALL, we

demonstrate the in vivo therapeutic efficacy of and pharmacodynamic signaling inhibition

by four clinically promising PI3K pathway inhibitors with particularly potent efficacy of the

dual PI3K/mTORi gedatolisib. We further demonstrate augmented leukemia cytotoxicity

in vivo with combined gedatolisib and ruxolitinib (JAK1/2i) treatment of CRLF2/JAK-

mutant Ph-like ALL and with gedatolisib and dasatinib (SRC/ABLi) treatment of

ABL/PDGFR-mutant Ph-like ALL. These data provide compelling rationale for testing

combinations of kinase inhibitors without or with multi-agent cytotoxic chemotherapy in

children and adults with Ph-like ALL.

METHODS

Ph-like ALL specimens

Viably cryopreserved leukemia cells from children and AYAs with de novo Ph-like

ALL (n=8) were obtained from the Children’s Oncology Group (COG) for

xenotransplantation studies as described.12,14,32 Additional specimens from patients with

multiply relapsed Ph-like ALL (n=2) were obtained from the Children’s Hospital of




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Philadelphia (CHOP) and University of California, San Francisco leukemia

biorepositories under approved institutional research protocols after obtainment of

written informed consent in accordance with the Declaration of Helsinki (Table 1). Ph-like

genomic alterations were identified by polymerase chain reaction and Sanger

sequencing and/or fluorescence in situ hybridization (FISH) assays as described.21,40,41

RNA from primary and corresponding xenografted leukemia specimens were also

assessed for an activated kinase Ph-like ALL gene expression signature using a 15-

gene low density microarray (LDA) classifier as described.40

Patient-derived xenograft models

Studies to date have largely focused upon studying the most common Ph-like

ALL subset harboring CRLF2 rearrangements. However, Ph-like ALL is now known to be

highly genetically diverse with a variety of mutations that induce kinase

hyperactivation.14 In these studies, we thus assessed the efficacy of PI3K pathway

inhibition in patient-derived xenograft (PDX) models of CRLF2-rearranged, JAK1-mutant,

JAK2-rearranged, ABL1-rearranged, and PDGFRB-rearranged Ph-like ALL (Table 1).

Individual PDX models were established in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ

(NSG) mice as described.32,42 To assess initial ALL engraftment and during therapeutic

efficacy analyses, peripheral venous blood or splenocyte suspensions from vehicle or

PI3Ki-treated mice were erythrocyte-lysed, Fc-blocked, and stained with mouse anti-

human CD10-PE-Cy7, CD19-PE, and CD45-APC antibodies (eBioscience). Specimens

were analyzed on an Accuri C6 flow cytometer (BD Biosciences) with CountBright

absolute counting beads (ThermoFisher) for quantification of human leukemia cells as

described.32

Experimental randomization to treatment with vehicle or PI3Ki commenced when

all mice demonstrated ≥5% ALL in peripheral blood. Animals were sacrificed humanely




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at planned study endpoint or if ill-appearing in accordance with the Panel on Euthanasia

of the American Veterinary Medical Association’s guidelines. Animal studies were

conducted under a CHOP Institutional Animal Use and Care Committee (IACUC)-

approved protocol.

In vivo therapeutic efficacy studies

For each of the PDX models, cohorts of 5 engrafted mice were randomized to

daily treatment with vehicle (0.5% hydroxypropyl methylcellulose/0.2% Tween-80 in

water via oral gavage), vehicle (0.3% lactic acid in 5% dextrose in water [D5W]

intraperitoneally), PI3Kαi BYL719 (50 mg/kg/dose via oral gavage), PI3Kδi idelalisib

(formerly CAL-101; 50 mg/kg/dose via oral gavage), PI3K/mTORi gedatolisib (formerly

PKI-587 or PF-05212384; 10 mg/kg intraperitoneally), or TORC1/2i AZD2014 (10 mg/kg

intraperitoneally).

For combination studies in CRLF2/JAK-mutant ALL models, animals were

treated as above with vehicle, gedatolisib, ruxolitinib (2 g/kg ruxolitinib-infused rodent

chow continuously provided), or simultaneous gedatolisib and ruxolitinib. For

combination studies in ABL/PDGFR-mutant ALL models, animals were treated with

vehicle, gedatolisib, dasatinib (10 mg/kg/dose twice daily via oral gavage), or

simultaneous gedatolisib and dasatinib. Studies were terminated and all mice sacrificed

after 28 days of treatment or sooner if ill-appearing. Spleens and bone marrow were

harvested as described for quantification of human ALL and for cryopreservation for

future studies.32

Survival analyses were conducted in some PDX models with vehicle, gedatolisib,

ruxolitinib, dasatinib, combined gedatolisib and ruxolitinib, or combined gedatolisib and

dasatinib treatment (n = 5 mice/cohort) as above for up to 120 days to assess potential

longer-term therapeutic efficacy of inhibitor therapies.




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Vehicle reagents were obtained from Sigma-Aldrich. BYL719, idelalisib, and

AZD2014 were purchased from Active Biochem. Gedatolisib and ruxolitinib were

provided by Pfizer and Incyte, respectively. Dasatinib was purchased from LC Labs.

Pharmacodynamic assessment of signal transduction inhibition

For measurements of in vivo signaling inhibition, additional PDX mice (n=3-4

animals/treatment) were administered vehicle or inhibitors as above for 72 hours, then

sacrificed at one hour following final inhibitor dose for leukemia cell-specific phosphoflow

cytometry analysis as described.32 Fixed and permeabilized splenocytes from vehicle-

and PI3Ki-treated animals were Fc-blocked and stained with mouse anti-human CD10-

PE-Cy7, CD19-APC-Cy7, and/or TSLPR-PE antibodies (BD Biosciences or

eBioscience). Cells were also stained with rabbit anti-human antibodies against

phosphorylated (p) 4EBP1T37/46 or pAktS473 (Cell Signaling Technologies; CST) with

secondary Pacific Blue-conjugated IgG H+L (Invitrogen/Life Technologies) and with

pS6S240/244-Ax488 (CST), pERKT202/Y204-Ax647 (BD Biosciences), or pSTAT5Y694-Ax647

(BD Biosciences). Data were compensated, acquired, and analyzed on an LSRII flow

cytometer (BD Biosciences) as described.29,32 Phosphosignaling data were gated and

measured using fluorescence-minus-one (FMO) controls for each phosphoprotein

fluorophore.43 Immunoblotting of splenic lysates from end-study animals (after 3 or 4

weeks of treatment) for phosphorylated pSTAT5Y694, pS6S240/244, 4EBP1T37/46,

corresponding total proteins, and β-actin (all antibodies from CST) was performed as

described for the combination inhibitor experiments.32 For experiments with dasatinib

treatment, immunoblotting was also performed for total and pCrkLY207 (CST), a

downstream effector of ABL-mediated signaling.44,45




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Statistical analyses

For therapeutic efficacy studies, mean human ALL cell numbers in peripheral

blood of inhibitor- and vehicle-treated animals for each xenograft model were calculated

at each measured time point. Kaplan-Meier curves for survival analyses were compared

using the log-rank test. Human ALL cell number in murine spleens (efficacy studies) and

phosphoflow cytometry data for each phosphoprotein (pharmacodynamic studies) were

compared via ANOVA with Dunnett’s or Tukey’s post-test for multiple comparisons. All

statistical analyses were conducted using Prism version 6.0h for Mac (GraphPad).

RESULTS

Genetic Characterization of Ph-like ALL PDX models

LDA data confirmed the Ph-like signature in relevant PDX models (n=9 Ph-like,

n=1 non-Ph-like), which were concordant with gene expression signature patterns of

primary ALL specimens from which PDX models were derived (Supplemental Figure 1).

Known Ph-like driver lesions (e.g., CRLF2 rearrangements, JAK1 and JAK2 point

mutations, ABL1 or PDGFRB fusions) were also identified in all xenografted leukemias

by FISH and RT-PCR or PCR with Sanger sequencing, confirming genetic fidelity of

studied models (not shown).

PI3K pathway inhibitors robustly inhibit leukemia proliferation in Ph-like ALL

Based upon our prior studies demonstrating aberrant PI3K pathway signaling in

CRLF2-rearranged ALL and in vitro signaling inhibition with kinase inhibitors,29,32 we

hypothesized that “next generation” PI3Ki could robustly inhibit in vivo leukemia

proliferation and oncogenic signal transduction. We tested four clinically-available,

selective inhibitors of PI3K pathway proteins to identify the most potent therapeutic

approach(es) of targeting activated PI3K signaling in Ph-like ALL. In therapeutic efficacy




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analyses, engrafted mice were treated daily with vehicle or PI3Ki for 2-4 weeks

depending upon the rapidity of leukemia progression in control animals. We assessed

tumor burden in peripheral blood during treatment (line graphs) and in spleens at the

conclusion of treatment (column graphs; Figure 1). In total, ten PDX models representing

genetically diverse subsets of Ph-like ALL were studied. Importantly, all PI3Ki-treated

models demonstrated inhibition of ALL proliferation in blood and spleens in comparison

to vehicle-treated control animals (Figure 1 and representative flow cytometry data in

Supplemental Figure 2). Inhibitor treatment appeared well-tolerated with normal physical

appearance and stability of weight in animals during studies (Supplemental Figure 3).

Therapeutic responses varied modestly among PDX models for each PI3Ki tested

depending upon the underlying genomic alteration(s) and the disease status of the

primary ALL specimen engrafted (de novo versus relapse).

Treatment with the PI3K/mTORi gedatolisib was remarkably efficacious in all

tested models with mean reduction in splenic ALL cell counts of 91.8% (range 82.5-

99.4%) in comparison to vehicle-treated mice (p<0.0001 for all models). Treatment with

the PI3Kαi BYL719, PI3Kδi idelalisib, or TORC1/TORC2i AZD2014 inhibited ALL

proliferation with mean leukemia reductions of 55.0% (range 27.5-72.6%), 38.1% (range

13.9-53.1%), and 52.8% (range 20.1-88.7%), respectively, versus vehicle controls.

Leukemia inhibition by the two isoform-selective PI3K inhibitors, BYL719 and idelalisib,

were generally similar with greater responses to BYL719 in some models (Figure 1).

Therapeutic responses to AZD2014 were greater in the two tested relapsed ALL models

(ALL121, ALL4364) in which high basal p4EBP1 activation was observed in the

pharmacodynamic studies reported below. Overall, these data suggest that Ph-like ALL

requires PI3K pathway signaling activation for survival in vivo and demonstrate potent

efficacy of the PI3K/mTORi gedatolisib in suppressing ALL cell growth.




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Pharmacodynamic inhibition of signaling proteins

We next addressed the question of whether PI3Ki could abrogate constitutive

PI3K pathway signaling in vivo and whether compensatory upregulation of alternative

pathways occurs after drug administration (Figure 2A). Long-term treatment of human

cancer cells with kinase inhibitors can lead to selection for alternative signaling

activation.39,46 Engrafted PDX mice were treated with vehicle or PI3Ki for 72 hours, then

sacrificed for immediate quantification of target protein phosphorylation. We first defined

basal activation of PI3K pathway phosphoproteins, pERK, and pSTAT5 by leukemia cell-

specific phosphoflow cytometry measurements and displayed data as the percentage of

cells in each positive FMO phosphoprotein gate (Figure 2B). Overall, constitutive

activation of pSTAT5, pS6, and pERK was observed in most models regardless of

underlying Ph-like genetic alteration(s). Basal activation of pAktS473 and p4EBP1 was

more heterogeneous across models (Figure 2C).

We then compared leukemia signaling in PI3Ki-treated animals to vehicle-treated

controls to assess potential in vivo phosphoprotein inhibition (Figure 3 and Supplemental

Figure 5). Treatment with the PI3Kα and PI3Kδ isoform-selective inhibitors BYL719 and

idelalisib resulted in significant inhibition of pS6 in 6/10 and 7/10 PDX models,

respectively (p<0.05 for each). Both PI3Ki also decreased p4EBP1 (1/10 models for

BYL719, 3/10 for idelalisib), pAkt (2/10 models for each inhibitor), and pERK (3/10

models for each inhibitor), suggesting potent inhibition of downstream mTORC1

signaling and potential crosstalk with or direct inhibition of the Ras/MAPK/ERK pathway

(Figure 3). The PI3K/mTORi gedatolisib also potently inhibited pS6 and p4EBP1 in vivo

in 8 of 10 models versus vehicle controls, as well as decreased pAktS473 (3/10 models)

and pERK (1 model) (p<0.05 for each; Figure 3). Importantly, minimal upregulation of

pAktS473 was observed in BYL719-, idelalisib-, or gedatolisib-treated animals (Figure 3),

suggesting generally effective blockade of potential TORC2-mediated feedback




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signaling loops that may reactivate proximal PI3K pathway signaling. Similarly, treatment

with the TORC1/TORC2i AZD2014 significantly inhibited pS6 and p4EBP1 in 6 of 10

models (p<0.05). Surprisingly, minimal inhibition of the TORC2 phosphoprotein pAktS473

was observed in AZD2014-treated animals (1/10 models), although many PDX models

did not have basal pAktS473 activation (Figure 2C).

Consistent with our earlier studies,32 we observed marked constitutive pSTAT5

activation in all tested CRLF2/JAK-mutant or ABL/PDGFR-mutant Ph-like ALL PDX

models (Figure 2C). Perhaps surprisingly, in vivo inhibition of pSTAT5 occurred with

BYL719 (1 model), idelalisib (2 models), gedatolisib (2 models), and AZD2014 (1 model)

treatment (Figure 3). These data suggest potential off-target effects of PI3K pathway

inhibitors in these models and/or possible interconnection of PI3K/Akt/mTOR and

JAK/STAT signaling networks previously described in Ph-like ALL.29,30,32

Three conclusions can be drawn from these experiments. First, the remarkable

efficacy of gedatolisib treatment correlates with inhibition of pS6 and p4EBP1 in Ph-like

ALL models. Second, minimal upregulation of AktS473 occurs after PI3K pathway

inhibition with tested agents. Third, a complex interplay of signaling pathway regulation

apparently occurs after in vivo administration of PI3K pathway inhibitors, which may be

difficult to assess fully at a single optimized pharmacodynamic time point in these

preclinical models.

Superior anti-leukemia efficacy of combination signal transduction inhibitor treatment

Given the potent, but incomplete, therapeutic efficacy and pharmacodynamic

effects of PI3K/mTORi monotherapy in Ph-like ALL models, we further assessed the

potential for enhanced efficacy of gedatolisib when co-administered with ruxolitinib

(CRLF2/JAK-mutant models; Figure 4A) or dasatinib (ABL1/PDGFRB-mutant models;

Figure 4B). Indeed, combined inhibitor therapy resulted in superior inhibition of ALL




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proliferation in murine spleens than was observed with inhibitors alone with near-

complete eradication of leukemia in most models (orange asterisks in Figures 4A-4B;

Figure 4C). Furthermore, greater in vivo inhibition of JAK/STAT, PI3K, and/or ABL

pathway signaling phosphoproteins was also observed with combination inhibitor

treatment, as shown by immunoblotting of splenic lysates from vehicle- and inhibitor-

treated animals after 3-4 weeks of treatment (Figure 4D). Combination inhibitor therapy

also appeared well-tolerated with stability of animal weights in most PDX models during

treatment (Supplemental Figure 4). Taken together, these data demonstrate enhanced

anti-leukemia efficacy of simultaneous inhibition of multiple signaling nodes in Ph-like

ALL and provide strong preclinical rationale to advance such treatment approaches to

clinical testing.

Survival benefit of inhibitor treatment

Given the robust potency of gedatolisib monotherapy and enhanced signaling

inhibition when combined with ruxolitinib or dasatinib, we next queried whether inhibitor

treatment of established leukemia could confer a survival benefit. To address this

question, we conducted longer-term survival analyses of vehicle, gedatolisib

monotherapy, and combination inhibitor treatment in four PDX ALL models (2

CRLF2/JAK, 2 ABL/PDGFR). Mice were first injected with human ALL cells and

monitored for engraftment. Once ≥5% leukemia was detected in peripheral blood, daily

treatment with vehicle or inhibitor(s) was commenced, and animals were followed by

weekly peripheral blood analysis as above.

As anticipated, gedatolisib monotherapy significantly prolonged survival versus

vehicle controls in all tested models (Figure 5; p<0.05 for each). Similar survival benefit

was also observed with ruxolitinib monotherapy treatment (Figure 5A; ALL121 and

JH331 models) and with dasatinib monotherapy treatment (Figure 5B; NH011 and PHL3




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models). Enhanced survival was further observed with combined gedatolisib and

ruxolitinib or gedatolisib and dasatinib treatment for up to 120 days. When possible,

spleens from expiring animals were analyzed by flow cytometry, which confirmed

presence of residual or recurrent human leukemia. These studies thus further

demonstrate superior efficacy of combination kinase inhibitor approaches in Ph-like ALL.

DISCUSSION PI3K/Akt/mTOR Signal Transduction in Human Leukemias

PI3K pathway proteins play a central, highly complex role in the metabolic

regulation and survival of cancer cells. Constitutive activation of PI3K/Akt/mTOR

signaling occurs frequently in a variety of human cancers and likely contributes to

avoidance of normal apoptotic death mechanisms following cellular injury.47,48

Dysregulated PI3K/Akt/mTOR signaling has also been associated with resistance to

cytotoxic chemotherapy.49,50 However, the specific role and necessity of PI3K pathway

signaling in B-precursor ALL remains inadequately characterized.39

We previously observed constitutive PI3K/Akt/mTOR activation in childhood Ph-

like ALL and signaling inhibition with in vitro treatment of primary leukemia cells with

PI3K pathway inhibitors.29 We also previously demonstrated in vivo efficacy of

rapamycin treatment in some Ph-like ALL xenograft models also used in the current

study (JH331, JH612, NH362, NL482A, JL491), although therapeutic responses to

rapamycin were incomplete and did not appear to correlate with pharmacodynamic

inhibition of TORC1 phosphoproteins.32 In the current studies, we demonstrate that

treatment with the PI3K/mTORi gedatolisib profoundly inhibited in vivo Ph-like ALL

proliferation. Furthermore, extended gedatolisib treatment was well-tolerated in PDX

models and significantly prolonged animal survival. Treatment with BYL719 and




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idelalisib reduced ALL burden by approximately half of that in vehicle-treated animals in

most models. The comparable efficacy of both PI3Kαi and PI3Kδi is perhaps surprising,

as B-cell lymphoid malignancies are not generally PI3KCA mutation-driven and have

higher expression of PI3Kδ.38,51 However, PI3Kα dependence of Ras-driven myeloid

leukemias and therapeutic activity of BYL719 in AML cell line xenograft models was

recently reported, providing additional rationale for further study of PI3Kαi in human

leukemias.52

Although development of PI3Ki resistance or upregulation of alternate signaling

pathways are plausible potential explanations for incomplete therapeutic efficacy, the

partial treatment responses we observed with BYL719 and idelalisib during relatively

short-duration animal experiments likely reflect at least in part known solubility issues for

oral gavage and poor pharmacokinetic properties of PI3K isoform-selective inhibitors in

mice.38,51,53 Similarly, the TORC1/TORC2i AZD2014 moderately inhibited leukemia

proliferation in CRLF2/JAK-mutant ALL PDX models, particularly in two aggressive

relapsed ALL models (ALL121, ALL4364), which may correlate with basal activation of

pAktS473. Interestingly, no appreciable reduction in leukemia burden was observed with

AZD2014 treatment in the tested BCR-JAK2 fusion model (NL482A) or ABL/PDGFR-

mutant models (NL432, NH011, PHL3) despite constitutive mTORC1 activation (pS6

and p4EBP1). However, minimal basal TORC2 signaling activation (pAktS473) was

detected in these four models. These data suggest biologic differences and signaling

dependencies among the genetically heterogeneous Ph-like ALL subgroups, as well as

highlight potential limitations of our pharmacodynamic assays with respect to

measurement of target inhibition of multiple phosphoproteins at a single time point in

animals treated with various inhibitors. Additional studies are indicated to assess such

response differences.




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As anticipated, we observed augmented anti-leukemic efficacy with simultaneous

targeting of two discrete oncogenic pathways in Ph-like ALL. Firstly, gedatolisib

monotherapy demonstrated markedly greater anti-leukemia efficacy in these studies in

comparison to prior studies testing single-agent ruxolitinib or dasatinib in Ph-like ALL

models.12,14,27,32 Interestingly, while highly effective in all tested models, gedatolisib more

potently inhibited ALL proliferation in CRLF2/JAK models than in ABL/PDFGR models,

highlighting potential differential signaling dependencies driven by underlying Ph-like

genetic alterations. In addition, combined gedatolisib and ruxolitinib or gedatolisib and

dasatinib treatment of CRLF2/JAK or ABL/PDGFR models, respectively, resulted in

superior therapeutic efficacy, pharmacodynamic phosphoprotein inhibition, and survival

benefit. Such dual pathway-targeting approaches may also minimize potential for

compensatory signaling upregulation that is a common mechanism of treatment

resistance.38,39

In pharmacodynamic studies, we observed few increased signaling sequelae in

animals treated with PI3Ki. It is plausible that dynamic signaling changes occur over a

longer treatment time period than 4 weeks or in other phosphoproteins than were

evaluated in our studies. However, use of next generation inhibitors that target proximal

PI3K pathway proteins or “vertically” inhibit multiple PI3K pathway nodes may more

potently shut down aberrant PI3K signaling in Ph-like ALL and perhaps ultimately evoke

superior therapeutic efficacy.

Our results are consistent with studies by Badura and colleagues, who assessed

effects of various PI3K pathway inhibitors incubated in vitro with primary BCR-ABL1-

rearranged and non-rearranged B-ALL cells.54 They also observed greatest anti-

proliferative and pro-apoptotic activity of dual PI3K/mTOR inhibition (BGT-226, BEZ-235)

in ALL cells versus pan-PI3K (BKM-120), mTOR (everolimus), or TORC1/TORC2 (Torin

1, PP242, KU-0063794) inhibition. Cytotoxic effects of the various inhibitors were similar




18

among Ph+ and non-Ph+ ALL specimens in their study, suggesting that PI3Ki efficacy

may not be restricted to specific ALL subsets. Similarly, Kharas et al. and Wong et al.

demonstrated potent in vitro cytotoxicity of PI3K/mTORi incubated with murine or human

ALL cell lines, as well as reduction in leukemia burden and prolonged survival in murine

and human ALL cell line-engrafted mice treated with PI3K/mTORi.55,56 We also observed

greatest phosphosignaling inhibition with PI3K/mTORi (gedatolisib) without upregulation

of pAktS473, suggesting potent blockade of the PI3K pathway and consistent with

preclinical data from Mallon et al.57

Unlike the Badura study, we did not observe appreciably increased TORC2-

mediated pAktS473 with PI3K isoform-selective or TORC1/TORC2 inhibitor treatment,

possibly due to differences in specific PI3Ki drugs tested and in vivo versus in vitro

systems analyzed. The lack of observed pS6 and p4EBP1 inhibition in a few PDX

models may also reflect characteristics of utilized phosphoantibody reagents,

mechanism(s) of action of each PI3Ki, and dynamic signaling networks evaluated in vivo

at a single time point. Although we did not specifically investigate selective Akt inhibition

given mixed preclinical and clinical data to date,50 our observed basal activation of pAkt

in some Ph-like ALL models and recent data demonstrating reversal of steroid

resistance in T-ALL with newer Akt inhibitors may warrant future study of these agents.58

We thus demonstrate that activated PI3K pathway signaling is prevalent in Ph-

like ALL and can be effectively targeted in vivo using clinically available kinase inhibitors.

We report particularly potent efficacy of the PI3K/mTORi gedatolisib as monotherapy

and enhanced efficacy in combination with ruxolitinib or dasatinib in specific genetic

subsets of Ph-like ALL. Our pharmacodynamic assays also identified constitutive basal

activation of PI3K and JAK/STAT phosphoproteins in Ph-like ALL, which may be

informative biomarkers to guide precision medicine-focused clinical selection of specific

kinase inhibitors for individual leukemias. However, significant and/or dose-limiting




19

toxicities of various PI3K pathway inhibitors in adults with cancer have been reported, as

well as modest clinical activity of some inhibitor monotherapies.38,59,60 Careful evaluation

of the biochemical mechanisms and anti-leukemia efficacy of PI3K/mTORi and their

toxicity profiles, particularly in combination with JAKi or ABLi, is warranted to facilitate

rapid clinical translation of novel kinase inhibitor-based therapies for children and adults

with Ph-like ALL.




20

ACKNOWLEDGMENTS We thank Dr Miles Pufall (University of Iowa) and Dr David Fruman (University of

California, Irvine) for thoughtful discussions about this work and Dr Shannon Maude

(Children’s Hospital of Philadelphia) and Dr Elliot Stieglitz (University of California, San

Francisco) for assistance with experimental reagents. Support for these studies was

from a National Institutes of Health/National Cancer Institute (NIH/NCI) Mentored Career

Development Award K08CA184418 (SKT), an NIH/NCI Paul Calabresi Career

Development Award for Clinical Oncology award to the University of Pennsylvania

K12CA076931 (SKT), an NIH/National Center for Research Resources award to the

University of Pennsylvania Institute for Translational Medicine and Therapeutics

UL1RR024134 (SKT), Alex’s Lemonade Stand Foundation (ALSF) Young Investigator

and Center of Excellence awards (SKT), the Rally Foundation for Childhood Cancer

Research (SKT), and the Leukemia and Lymphoma Society Specialized Center of

Research Program (DTT and SAG). This work was also supported by grants to the

Children’s Oncology Group, specifically U10 CA98543 (Chair’s grant and supplement to

support the COG High Risk ALL TARGET Project), U10 CA98413 (Statistical Center),

and U24 CA114766 (specimen banking). SKT was an ALSF Scholar in Developmental

Therapeutics. DTT is supported by a Research Scholar Grant (RSG-14-022-01-CDD)

from the American Cancer Society. CLW is the Maurice and Marguerite Liberman

Distinguished Chair in Cancer Research� Professor of Pathology and Medicine. SPH is

the Jeffrey E. Perelman Distinguished Chair in the Department of Pediatrics. MLL is the

Deborah and Arthur Ablin Chair in Molecular Pediatric Oncology. MC is supported by

Veterans Administration Merit Award 1I01BX000918. SAG is the Yetta Deitch Novotny

Endowed Chair in Pediatric Oncology.




21

AUTHORSHIP CONTRIBUTIONS

SKT designed and directed research, performed research, analyzed data, and wrote the

manuscript. DTT and CLW provided key reagents and interpreted data. YL, FS, RCH,

TR, TLV, and I-MC performed research and analyzed and interpreted data. AEP, SPH,

MLL, MC, and SAG contributed to research design and data interpretation. SPH and MC

edited the manuscript. All authors critically reviewed the manuscript prior to submission.

CONFLICT OF INTEREST DISCLOSURES

SKT and MC have a research collaboration with Incyte Corporation without financial

support. RCH, I-MC, CLW, and SPH are co-inventors on US Patent No. 8,568,974 B2

“Identification of novel subgroups of high-risk pediatric precursor-B acute lymphoblastic

leukemia, outcome correlations and diagnostic and therapeutic methods related to

same.” This technology has not been licensed, and there is no income. The remaining

authors declare no relevant competing financial interests for this work.




22

TABLES

Table 1. Genomic characteristics of ALL specimens utilized for xenograft studies.

PDX = patient-derived xenograft, USI = unique specimen identifier for primary patient sample, D = de novo, R = relapse, n/a = not available. * Non-Ph-like by prediction analysis of microarrays

PDX USI Disease status

Ph-like ALL genomic lesions

CRLF2 JAK ABL class NH362 PALTWS D IGH@-CRLF2* JH331 PAMDKS D IGH@-CRLF2 JAK2R683G JH612 PAMDRM D IGH@-CRLF2 JAK2GPinsR683

ALL121 n/a R IGH@-CRLF2 JAK2R683G ALL4364 PAWAKV R P2RY8-CRLF2 JAK2R683G

JL491 PAKMVD D JAK1S646F NL482A PAKYEP D BCR-JAK2 NL432 PAKKCA D EBF1-PDGFRB NH011 PAKVKK D NUP214-ABL1 PHL3 PANSFD D ETV6-ABL1




23

FIGURE LEGENDS

Figure 1. In vivo efficacy of PI3K pathway inhibition in Ph-like ALL. Patient-derived

xenograft (PDX) models were treated with vehicle, PI3Kα inhibitor BYL719,

PI3Kδ inhibitor idelalisib, PI3K/mTOR inhibitor gedatolisib, or TORC1/TORC2 inhibitor

AZD2014 (n=5 mice/treatment arm) daily for 2-4 weeks depending on rapidity of

leukemia progression in vehicle-treated control animals. PI3K isoform or TORC1/TORC2

inhibition resulted in significant suppression of leukemia proliferation in peripheral blood

and end-of-study spleens of most PDX models of (A) CRLF2-rearranged, (B) JAK1-

mutant, (C) JAK2 fusion, and (D) ABL/PDGFR-mutant ALL versus vehicle controls.

Gedatolisib most effectively inhibited ALL proliferation with near-eradication of leukemia

in CRLF2/JAK-mutant models and marked suppression in ABL/PDGFR-mutant models.

Treatment groups were compared to the vehicle control for each PDX model via one-

way ANOVA with Dunnett’s post-test for multiple comparisons with α=0.05. *p<0.05,

**p<0.01, *** p<0.001, **** p<0.0001.

Figure 2. Constitutive activation of signaling phosphoproteins in Ph-like ALL PDX

models. (A) Schema of signaling nodes assessed and targets of kinase inhibitors. (B)

Gating strategy for phosphoflow cytometry analyses: live singlet CD10+ CD19+ (and

TSLPR+ if CRLF2-rearranged) human ALL cells in murine spleens were gated.

Fluorescence-minus-one (FMO) controls were used for each fluorophore-conjugated

phosphoprotein antibody to set negative (FMO-) and positive (FMO+) gates. The

percentage of cells in the FMO+ gate was calculated for all phosphoproteins for each

STI treatment and displayed graphically. All studied ALL samples were uniformly CD10+.

(C) Basal levels of each measured phosphoprotein in vehicle-treated mice from each

PDX model are displayed as percentages of human ALL cells in FMO+ gates. Data are




24

depicted for each PDX model (colored columns) as mean percentage of cells in FMO+

gate on the y-axis with standard error of the mean (black bars).

Figure 3. PI3K pathway inhibitors inhibit signaling phosphoproteins and induce

minimal compensatory signaling upregulation. Ph-like ALL PDX models were treated

with vehicle, BYL719, idelalisib, gedatolisib, or AZD2014 (n=3-4 mice/treatment) for 72

hours, then sacrificed at 1 hour after final dose for pharmacodynamic measurement of in

vivo target inhibition via phosphoflow cytometry. Heatmap data depict significant

changes in phosphoprotein levels in inhibitor- versus vehicle-treated controls using

%FMO+ cells (described in Figure 2) for each PDX model. Colorimetric scale depicts

normalization of each model to vehicle controls (white squares; left-most columns) with

statistically significant decreased phosphorylation (blue colors) or increased

phosphorylation (green colors) with inhibitor treatment as calculated by ANOVA with

Dunnett’s post-test for multiple comparisons. FMO+ data for all individual mice are

displayed in greater detail in Supplemental Figure 5.

Figure 4. Superior efficacy of combination STI treatment. Mice engrafted with (A)

CRLF2/JAK-mutant Ph-like ALL were treated with vehicle, ruxolitinib, gedatolisib, or both

ruxolitinib and gedatolisib for 3 or 4 weeks. Human ALL in murine spleens after

treatment completion was measured by quantitative flow cytometry as in Figure 1.

Significantly greater inhibition of ALL proliferation was observed with combined

ruxolitinib and gedatolisib treatment (orange asterisks), as measured by one-way

ANOVA with Tukey’s post-test for multiple comparisons with α=0.05. (B) ABL1-

rearranged Ph-like ALL PDX models were treated with vehicle, dasatinib, gedatolisib, or

both dasatinib and gedatolisib for 3 weeks. Enhanced anti-leukemia efficacy was also




25

observed in these models with combined dasatinib and gedatolisib treatment (orange

asterisks) versus dasatinib alone or gedatolisib alone. (C) Combination inhibitor

treatment markedly reduced splenomegaly in ALL-engrafted PDX mice treated as in (A)

or (B). (D) Immunoblotting of total and phosphorylated signal transduction proteins from

murine splenic lysates (obtained after 3 or 4 weeks of treatment) demonstrate greatest

inhibition of target phosphoproteins with combination inhibitor treatment of PDX models.

Total protein loss is observed with inhibitor treatment in some models. MUTZ5 (a

CRLF2/JAK2-mutant ALL cell line) and K562 (a BCR-ABL1-rearranged chronic myeloid

leukemia cell line) lysates were used as positive signaling controls, and β-actin

immunoblotting was used as a protein loading control. V=vehicle, R=ruxolitinib,

G=gedatolisib, RG= ruxolitinib + gedatolisib combination, D=dasatinib, DG=dasatinib +

gedatolisib combination. *p<0.05, **p<0.01, *** p<0.001, **** p<0.0001.

Figure 5. Survival advantage with inhibitor monotherapy and combination

inhibitor treatment. Animals engrafted with (A) relapsed (ALL121) or de novo (JH331)

CRLF2/JAK-mutant Ph-like ALL were treated with vehicle, ruxolitinib chow, gedatolisib

10 mg/kg intraperitoneally daily, or both ruxolitinib and gedatolisib until moribund (n=5

mice/treatment cohort) for up to 120 days. Similarly, animals engrafted with (B) de novo

ABL1-mutant ALL (NH011, PHL3) were treated with vehicle, dasatinib 10 mg/kg twice

daily via oral gavage, gedatolisib, or both dasatinib and gedatolisib for up to 120 days. X-

axes depict duration of inhibitor treatment (week 0 = treatment initiation) in mice after

documentation of human leukemia engraftment (≥5% ALL in peripheral blood). Kaplan-

Meier survival curves for each xenograft model were compared statistically using the

log-rank test (p-values indicated on graphs for each model). Dotted lines delineate

median survival in each study with corresponding values for listed each treatment (black

numbers).




26

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A

vehicle

B

C

D

Figure 1

BYL719 idelalisib gedatolisib AZD2014




Figure 2

A

C

Basa

l pho

spho

prot

ein

activ

atio

n (%

FMO

+)B

NH3

62JH

331

JH61

2AL

L121

ALL4

364

JL49

1N

L482

AN

L432

NH0

11PH

L3

pAkt S473p4EBP1pS6 pERK pSTAT5

NH3

62JH

331

JH61

2AL

L121

ALL4

364

JL49

1N

L482

AN

L432

NH0

11PH

L3

NH3

62JH

331

JH61

2AL

L121

ALL4

364

JL49

1N

L482

AN

L432

NH0

11PH

L3

NH3

62JH

331

JH61

2AL

L121

ALL4

364

JL49

1N

L482

AN

L432

NH0

11PH

L3

NH3

62JH

331

JH61

2AL

L121

ALL4

364

JL49

1N

L482

AN

L432

NH0

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L3




Figure 3

pS6

vehi

cle

BYL7

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geda

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ibAZ

D201

4

p4EBP1

vehi

cle

BYL7

19id

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geda

tolis

ibAZ

D201

4

NH362JH331JH612

ALL121ALL4364

JL491NL482A

NL432NH011

PHL3

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vehi

cle

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pSTAT5

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isib

geda

tolis

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4

p <0.0001p <0.001p <0.01p <0.05no changep <0.05p <0.01p <0.001p <0.0001

Decreasedphosphorylation

Increasedphosphorylation




IGH@-CRLF2 JAK2 R683G (JH331)

800

400

200

0ALL

cells

x 1

0e6

in sp

leen

****

**** ****

BCR-JAK2 (NL482A)

800

600

400

200

0ALL

cells

x 1

0e6

in sp

leen

**** **** ****

IGH@-CRLF2 JAK2 R683G (ALL121)

ALL

cells

x 1

0e6

in sp

leen

********

****

1500

1000

500

0

P2RY8-CRLF2 JAK2 R683G (ALL4364)AL

L ce

lls x

10e

6 in

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en

500

250

0

****

****

****

NUP214-ABL1 (NH011)

Treatment group

ALL

cells

x 1

0e6

in sp

leen

1000

800

600

400

200

0

*******

****

ETV6-ABL1 (PHL3)

Treatment group

600

400

200

0ALL

cells

x 1

0e6

in sp

leen

****

***

****

vehicleruxolitinibgedatolisibruxolitinib + gedatolisib

vehicledasatinibgedatolisibdasatinib + gedatolisib

A C

B

D

pSTAT5STAT5

V R G RG V R G RG

ALL4364 ALL121

MU

TZ5

pS6S6

p4EBP14EBP1

β-actin

V RG G R V DG G D

ALL121 PHL3

V D G DG V D G DG

NH011 PHL3

K562

pSTAT5STAT5

pS6S6

p4EBP14EBP1

β-actin

pCrkLCrkL

Figure 4

***

**

**

**

****




Figure 5

Days of treatment

Perc

ent s

urvi

val

A

B

Days of treatment

Perc

ent s

urvi

val

IGH@-CRLF2 JAK2 R683G (JH331)IGH@-CRLF2 JAK2 R683G (ALL121)

NUP214-ABL1 (NH011) ETV6-ABL1 (PHL3)

Days of treatment Days of treatment

p<0.01

p<0.01

p<0.0001

22 38 48 78 38 78 87

42 57 67 50 69 77

NR

NR

p<0.05

NR




doi:10.1182/blood-2016-05-707653Prepublished online October 24, 2016;

Carroll and Stephan A. GruppTiffaney L. Vincent, Cheryl L. Willman, Alexander E. Perl, Stephen P. Hunger, Mignon L. Loh, Martin Sarah K. Tasian, David T. Teachey, Yong Li, Feng Shen, Richard C. Harvey, I-Ming Chen, Theresa Ryan, murine xenograft models of Ph-like acute lymphoblastic leukemiaPotent efficacy of combined PI3K/mTOR and JAK or ABL inhibition in

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