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Diagnostics and supportive care for patients with non-Hodgkin lymphoma (NHL) in lower- and middle-income countries (LMICs) are lacking. We hypothesized that high-throughput transcription-based diagnostics could classify NHL specimens from Malawi amenable to targeted therapeutics. We established tissue microarrays and classified 328 cases diagnosed by hematoxylin and eosin as NHL at University of Malawi College of Medicine using immunohistochemistry (IHC) for conventional markers and therapeutic targets. A subset was analyzed using NanoString-based expression profiling with parsimonious transcriptional classifiers. Overall, 72% of lymphomas were high-grade B-cell tumors, subsets of which were enriched for expression of MYC, BCL2, and/or PD-L1. A 21-gene transcriptional classifier, previously validated in Western cohorts, divided 96% of diffuse large B-cell lymphomas (DLBCLs) with 100% of B-cell lymphomas, unclassifiable, into 1 cluster and 88% of Burkitt lymphomas into a separate cluster. Cell-of-origin categorization of 36 DLBCLs by NanoString lymphoma subtyping test (LST) revealed 69% concordance with IHC. All discordant cases were classified as germinal center B cell-like (GCB) by LST but non-GCB by IHC. In summary, utilization of advanced diagnostics facilitates objective assessment and segregation of biologically defined subsets of NHL from an LMIC without expert review, thereby establishing a basis for the implementation of effective and less toxic targeted agents.

// Thomas Melchardt 1, 2, 3, * , Clemens Hufnagl 1, 2, 3, * , David M. Weinstock 4 , Nadja Kopp 4 , Daniel Neureiter 5 , Wolfgang Trankenschuh 5 , Hubert Hackl 6 , Lukas Weiss 1, 2, 3 , Gabriel Rinnerthaler 1, 2, 3 , Tanja N. Hartmann 1, 2, 3 , Richard Greil 1, 2, 3 Oliver Weigert 7, 8 , Alexander Egle 1, 2, 3 1 Third Medical Department at The Paracelsus Medical University Salzburg, Salzburg, Austria 2 Salzburg Cancer Research Institute (SCRI), Salzburg, Austria 3 Cancer Cluster Salzburg (CCS), Salzburg, Austria 4 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA 5 Institute of Pathology, Paracelsus Medical University Salzburg, Salzburg, Austria 6 Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria 7 University Hospital of The Ludwig-Maximilians-University Munich, Medical Department III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Munich, Germany 8 German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany * These authors have contributed equally to this work Correspondence to: Alexander Egle, email: a.egle@salk.at Keywords: DLBCL, clonal evolution, TP53, tumor heterogeneity, subclonal selection Received: November 18, 2015 Accepted: May 22, 2016 Published: June 06, 2016 ABSTRACT Little information is available about the role of certain mutations for clonal evolution and the clinical outcome during relapse in diffuse large B-cell lymphoma (DLBCL). Therefore, we analyzed formalin-fixed-paraffin-embedded tumor samples from first diagnosis, relapsed or refractory disease from 28 patients using next-generation sequencing of the exons of 104 coding genes. Non-synonymous mutations were present in 74 of the 104 genes tested. Primary tumor samples showed a median of 8 non-synonymous mutations (range: 0-24) with the used gene set. Lower numbers of non-synonymous mutations in the primary tumor were associated with a better median OS compared with higher numbers (28 versus 15 months, p=0.031). We observed three patterns of clonal evolution during relapse of disease: large global change, subclonal selection and no or minimal change possibly suggesting preprogrammed resistance. We conclude that targeted re-sequencing is a feasible and informative approach to characterize the molecular pattern of relapse and it creates novel insights into the role of dynamics of individual genes.

Activating mutations in genes encoding G protein α (Gα) subunits occur in 4-5% of all human cancers, but oncogenic alterations in Gβ subunits have not been defined. Here we demonstrate that recurrent mutations in the Gβ proteins GNB1 and GNB2 confer cytokine-independent growth and activate canonical G protein signaling. Multiple mutations in GNB1 affect the protein interface that binds Gα subunits as well as downstream effectors and disrupt Gα interactions with the Gβγ dimer. Different mutations in Gβ proteins clustered partly on the basis of lineage; for example, all 11 GNB1 K57 mutations were in myeloid neoplasms, and seven of eight GNB1 I80 mutations were in B cell neoplasms. Expression of patient-derived GNB1 variants in Cdkn2a-deficient mouse bone marrow followed by transplantation resulted in either myeloid or B cell malignancies. In vivo treatment with the dual PI3K-mTOR inhibitor BEZ235 suppressed GNB1-induced signaling and markedly increased survival. In several human tumors, mutations in the gene encoding GNB1 co-occurred with oncogenic kinase alterations, including the BCR-ABL fusion protein, the V617F substitution in JAK2 and the V600K substitution in BRAF. Coexpression of patient-derived GNB1 variants with these mutant kinases resulted in inhibitor resistance in each context. Thus, GNB1 and GNB2 alterations confer transformed and resistance phenotypes across a range of human tumors and may be targetable with inhibitors of G protein signaling.

Low frequency clonal mutations recoverable by deep sequencing in patients with aplastic anemia

Over 90% of drugs with preclinical activity fail in human trials, largely due to insufficient efficacy. We hypothesized that adequately powered trials of patient-derived xenografts (PDX) in mice could efficiently define therapeutic activity across heterogeneous tumors. To address this hypothesis, we established a large, publically available repository of well-characterized leukemia and lymphoma PDXs that undergo orthotopic engraftment called the Public Repository of Xenografts (PRoXe; www.proxe.org). PRoXe includes all de-identified information relevant to the primary specimens and the PDXs derived from them. Using this repository, we demonstrate that large studies of acute leukemia PDXs that mimic human randomized clinical trials can characterize drug efficacy and generate transcriptional, functional and proteomic biomarkers in both treatment-naïve and relapsed/refractory disease.

The Bruton tyrosine kinase (BTK) inhibitor ibrutinib induces responses in 70% of patients with relapsed and refractory mantle cell lymphoma (MCL). Intrinsic resistance can occur through activation of the nonclassical NF-κB pathway and acquired resistance may involve the BTK C481S mutation. Outcomes after ibrutinib failure are dismal, indicating an unmet medical need. We reasoned that newer heat shock protein 90 (HSP90) inhibitors could overcome ibrutinib resistance by targeting multiple oncogenic pathways in MCL. HSP90 inhibition induced the complete degradation of both BTK and IκB kinase α in MCL lines and CD40-dependent B cells, with downstream loss of MAPK and nonclassical NF-κB signaling. A proteome-wide analysis in MCL lines and an MCL patient-derived xenograft identified a restricted set of targets from HSP90 inhibition that were enriched for factors involved in B-cell receptor and JAK/STAT signaling, the nonclassical NF-κB pathway, cell-cycle regulation, and DNA repair. Finally, multiple HSP90 inhibitors potently killed MCL lines in vitro, and the clinical agent AUY922 was active in vivo against both patient-derived and cell-line xenografts. Together, these findings define the HSP90-dependent proteome in MCL. Considering the disappointing clinical activity of HSP90 inhibitors in other contexts, trials in patients with MCL will be essential for defining the efficacy of and mechanisms of resistance after ibrutinib failure.

Follicular lymphoma is a clinically and genetically heterogeneous disease, but the prognostic value of somatic mutations has not been systematically assessed. We aimed to improve risk stratification of patients receiving first-line immunochemotherapy by integrating gene mutations into a prognostic model.We did DNA deep sequencing to retrospectively analyse the mutation status of 74 genes in 151 follicular lymphoma biopsy specimens that were obtained from patients within 1 year before beginning immunochemotherapy consisting of rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). These patients were recruited between May 4, 2000, and Oct 20, 2010, as part of a phase 3 trial (GLSG2000). Eligible patients had symptomatic, advanced stage follicular lymphoma and were previously untreated. The primary endpoints were failure-free survival (defined as less than a partial remission at the end of induction, relapse, progression, or death) and overall survival calculated from date of treatment initiation. Median follow-up was 7·7 years (IQR 5·5-9·3). Mutations and clinical factors were incorporated into a risk model for failure-free survival using multivariable L1-penalised Cox regression. We validated the risk model in an independent population-based cohort of 107 patients with symptomatic follicular lymphoma considered ineligible for curative irradiation. Pretreatment biopsies were taken between Feb 24, 2004, and Nov 24, 2009, within 1 year before beginning first-line immunochemotherapy consisting of rituximab, cyclophosphamide, vincristine, and prednisone (R-CVP). Median follow-up was 6·7 years (IQR 5·7-7·6).We established a clinicogenetic risk model (termed m7-FLIPI) that included the mutation status of seven genes (EZH2, ARID1A, MEF2B, EP300, FOXO1, CREBBP, and CARD11), the Follicular Lymphoma International Prognostic Index (FLIPI), and Eastern Cooperative Oncology Group (ECOG) performance status. In the training cohort, m7-FLIPI defined a high-risk group (28%, 43/151) with 5-year failure-free survival of 38·29% (95% CI 25·31-57·95) versus 77·21% (95% CI 69·21-86·14) for the low-risk group (hazard ratio [HR] 4·14, 95% CI 2·47-6·93; p0·0001; bootstrap-corrected HR 2·02), and outperformed a prognostic model of only gene mutations (HR 3·76, 95% CI 2·10-6·74; p0·0001; bootstrap-corrected HR 1·57). The positive predictive value and negative predictive value for 5-year failure-free survival were 64% and 78%, respectively, with a C-index of 0·80 (95% CI 0·71-0·89). In the validation cohort, m7-FLIPI again defined a high-risk group (22%, 24/107) with 5-year failure-free survival of 25·00% (95% CI 12·50-49·99) versus 68·24% (58·84-79·15) in the low-risk group (HR 3·58, 95% CI 2·00-6·42; p0.0001). The positive predictive value for 5-year failure-free survival was 72% and 68% for negative predictive value, with a C-index of 0·79 (95% CI 0·69-0·89). In the validation cohort, risk stratification by m7-FLIPI outperformed FLIPI alone (HR 2·18, 95% CI 1·21-3·92), and FLIPI combined with ECOG performance status (HR 2·03, 95% CI 1·12-3·67).Integration of the mutational status of seven genes with clinical risk factors improves prognostication for patients with follicular lymphoma receiving first-line immunochemotherapy and is a promising approach to identify the subset at highest risk of treatment failure.Deutsche Krebshilfe, Terry Fox Research Institute.

The genetics of angioimmunoblastic T-cell lymphoma (AITL) are very poorly understood. We defined the mutational landscape of AITL across 219 genes in 85 cases from the United States and Europe. We identified ≥2 mutations in 34 genes, nearly all of which were not previously implicated in AITL. These included loss-of-function mutations in TP53 (n = 4), ETV6 (n = 3), CCND3 (n = 2), and EP300 (n = 5), as well as gain-of-function mutations in JAK2 (n = 2) and STAT3 (n = 4). TET2 was mutated in 65 (76%) AITLs, including 43 that harbored 2 or 3 TET2 mutations. DNMT3A mutations occurred in 28 (33%) AITLs; 100% of these also harbored TET2 mutations (P < .0001). Seventeen AITLs harbored IDH2 R172 substitutions, including 15 with TET2 mutations. In summary, AITL is characterized by high frequencies of overlapping mutations in epigenetic modifiers and targetable mutations in a subset of cases. © 2014 by The American Society of Hematology.

There is a pressing need for methods to define the functional relevance of genetic alterations identified by next-generation sequencing of cancer specimens. We developed new approaches to efficiently construct full-length cDNA libraries from small amounts of total RNA, screen for transforming and resistance phenotypes, and deconvolute by next-generation sequencing. Using this platform, we screened a panel of cDNA libraries from primary specimens and cell lines in cytokine-dependent murine Ba/F3 cells. We demonstrate that cDNA library-based screening can efficiently identify DNA and RNA alterations that confer either cytokine-independent proliferation or resistance to targeted inhibitors, including RNA alterations and intergenic fusions. Using barcoded next-generation sequencing, we simultaneously deconvoluted cytokine-independent clones recovered after transduction of 21 cDNA libraries. This approach identified multiple gain-of-function alleles, including KRAS G12D, NRAS Q61K and an activating splice variant of ERBB2. This approach has broad applicability for identifying transcripts that confer proliferation, resistance and other phenotypes in vitro and potentially in vivo.

The majority of drugs tested in clinical trials for hematologic malignancies ultimately fail to confer benefit. In many cases, this results from the inability to accurately identify patients most likely to benefit and mechanisms that mediate resistance. At the same time, clinical trials commonly fail to capture essential specimens at early and late timepoints that could be used to identify predictors of response, pharmacodynamic markers of on-target activity and targetable resistance pathways. To overcome these challenges, we have developed a repository of >200 patient-derived xenografts (PDXs) of leukemias and lymphomas now available through the DFCI Public Repository of Xenografts (PRoXe; http://www.proxe.org). Because PDX models can be developed and propagated from a large number of patients, randomized in vivo studies using adequate numbers of PDXs offer the first opportunity to capture the diversity of disease biology in pre-clinical drug testing. We tested the novel MDM2 inhibitor CGM097, which is currently undergoing clinical testing in solid tumors, in 24 B-cell acute lymphoblastic leukemia (B-ALL) PDXs (including hypodiploid, near haploid, MLL- rearranged, CRLF2-rearranged, and BCR-ABL models) in a randomized, phase II-like trial. Only a small subset of B-ALLs harbor de novo TP53 mutations, suggesting that MDM2 antagonists may have broad activity in this disease. Each PDX was injected into 4 NOD.SCID.IL2Rɣ-/- (NSG) mice. Upon engraftment (>2% hCD45+/hCD19+ cells in the peripheral blood), mice were randomized to vehicle or CGM097 treatment arms. One animal from each treatment arm was sacrificed 26 hours after beginning treatment to examine pharmacodynamic endpoints. The remaining two mice continued on daily therapy until moribund. CGM097 markedly improved overall survival (median 73 vs 28 days for vehicle; p=0.0008). All 19 models with survival benefit from CGM were TP53 wild-type. Among 6 models (all TP53 wild-type) derived from patients with relapsed disease, the median survival improvement compared to vehicle was 53 days (p=0.0059), consistent with robust single-agent activity in relapsed disease. Specimens at the 26 hour timepoint and upon progression to moribund were captured from the majority of mice in the trial, allowing for comprehensive characterization of the trial population. Dynamic BH3 profiling (Montero et al. Cell 2015), in which CGM097 or vehicle is added to leukemia cells harvested from mice and the effect of CGM097 on "priming" for apoptosis was performed on 10 models and demonstrated 100% accuracy in predicting response to CGM097. To characterize the effects of MDM2 inhibition on p53-dependent gene expression, we measured expression of 120 p53-related genes using a custom Nanostring gene expression panel. Differential expression analysis identified 11 genes that were significantly upregulated (p≤0.05) by CGM097 treatment at the 26 hour timepoint, including the canonical p53 targets BBC3, CDKN1A and MDM2. All mice treated with CGM097 ultimately became moribund from progressive leukemia. Targeted deep sequencing identified acquired TP53 mutations in only 2 leukemias after progression on CGM097. This indicates that p53 mutation is not the primary genetic driver of resistance to MDM2 inhibition in B-ALL PDXs. Despite this, CGM097-dependent transcriptional changes were largely abolished in the majority of leukemias collected from mice upon progression on CGM097. In summary, we established a paradigm for "Phase II-like" trials in panels of human leukemia PDX models. With this approach, we defined CGM097 as a highly active agent across the diverse spectrum of TP53-wildtype B-ALL, and established 19 independent models of acquired resistance that are the ideal reagents for defining mechanisms and then testing combinations in vivo that overcome those mechanisms. The same paradigm could be applied as a new standard for pre-clinical testing of drugs to minimize the empiric nature of current drug development strategies. Disclosures Barzaghi-Rinaudo: Novartis Institutes for Biomedical Research: Employment. Letai:AbbVie: Consultancy, Research Funding; Tetralogic: Consultancy, Research Funding; AstraZeneca: Consultancy, Research Funding. Jeay:Novartis: Employment, Equity Ownership. Wuerthner:Novartis: Employment, Equity Ownership. Halilovic:Novartis: Employment, Equity Ownership.

Lymphomas represent nearly 70 distinct diseases with unique clinical presentations, therapeutic responses and underlying biology. There is a pressing shortage of publically available cell line and in vivo models of nearly all of these diseases, which has severely hampered efforts to understand and target their biology. To address this issue, we have established a repository of patient-derived xenografts (PDX) of lymphomas by engrafting human tumors into immunodeficient NOD/SCID/IL2rgnull (NSG) mice. These lymphomas, along with a spectrum of other PDXs of hematologic malignancies, are available to collaborators through the online portal PRoXe (Public Repository of Xenografts) at http://PRoXe.org. Blood and bone marrow specimens involved with tumor are injected by tail vein (IV) injection. Lymph node and extranodal biopsy specimens are implanted under the renal capsule as a 1x1x2mm tumor seed (renal), which maintains the in situ microarchitecture. A full description of xenografted lymphomas is included in the Table. Table 1.DiseaseType of implant# in 1st passage# in 2nd passage or higherT-cell prolymphocytic leukemiaIV1Angioimmunoblastic T-cell lymphomaIV11Mantle cell lymphomaIV12Double-hit DLBCLIV2Sézary SyndromeIV1Adult T-cell Leukemia/LymphomaIV1Diffuse large B cell lymphomaIV2Diffuse large B cell lymphomarenal2Marginal zone lymphomarenal11NK/T-cell lymphomarenal1Peripheral T-cell lymphoma-NOSrenal1Breast implant-associated anaplastic large cell lymphomarenal1 Engrafted PDXs have been extensively characterized by immunohistochemistry, flow cytometry, transcriptome sequencing and targeted DNA sequencing. Flow cytometric analysis of patient tumors and their respective xenografts consistently revealed highly concordant immunophenotypes compared to the original tumors. Similarly, immunohistochemistry of involved tissues confirmed retention of tumor immunophenotypes, architecture, and even tissue tropism in the PDXs. Examples include a Sézary syndrome PDX that was injected by tail vein and trafficked to spleen, bone marrow, blood and skin, a diffuse large B-cell lymphoma (DLBCL) PDX that infiltrated the CNS, and a second DLBCL PDX that was implanted into the renal capsule of the left kidney and progressed within 8 weeks to bilateral renal involvement. Other notable models include a breast implant-associated, ALK-negative anaplastic large cell lymphoma implanted under the renal capsule that metastasized to the liver and spleen while uniformly retaining CD30 positivity. Two double-hit lymphoma (DHL) PDXs maintained their CD20-negative phenotype through serial passage to P1. A peripheral T-cell lymphoma-NOS (PTCL) specimen implanted under the renal capsule engrafted in the spleen, with a notable admixture of nonmalignant T cells and scattered EBV-positive B cells. T-cell receptor gene rearrangement PCR performed on this PTCL demonstrated an identical rearrangement pattern in the primary tumor and the PDX. Luciferized mantle cell lymphoma and DHL PDXs clearly home to bone marrow, lymph nodes, spleen, and liver as early as two weeks after injection. These findings support the utility of these PDX lines as in vivo models that more accurately recapitulate the human disease than commonly used subcutaneous cell line models. In addition to generating PDXs that remain faithful to their source tumors, we have witnessed interesting examples of in vivo histologic transformation, opening the door to studies of disease progression. One primary follicular lymphoma specimen injected into a cohort of mice transformed to DLBCL in one mouse and a lymphoblastic lymphoma-like disease in another mouse, as confirmed by IHC and flow cytometry. Further xenografting of primary tumors is underway with the goal of establishing a large repository of lymphoma PDXs useful for biologic interrogation and preclinical trials. Disclosures Davids: Genentech: Other: ad board; Pharmacyclics: Consultancy; Janssen: Consultancy. Shipp:Gilead: Consultancy; Sanofi: Research Funding; BMS: Membership on an entity's Board of Directors or advisory committees, Research Funding; Bayer: Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Membership on an entity's Board of Directors or advisory committees.

Outcomes among persons with lymphoma in sub-Saharan African (SSA) remain poor, largely due to resource limitations in diagnostics, therapeutics and supportive care. We hypothesized that subclassification of lymphoma specimens from SSA could improve diagnostic accuracy, thereby altering treatment recommendations and identifying cases responsive to less toxic, targeted agents. The Queen Elizabeth Central Hospital (QECH) in Malawi serves as the teaching hospital for the University of Malawi College of Medicine (UOMCOM) in Blantyre, Malawi's largest city. Pathologic diagnosis of lymphoma at QECH/UOMCOM is based solely on HE 25% £ 16); 274 males, 189 females, 35 unknown. HIV status was available for 10% (36 reactive; 12 non-reactive). At Brigham and Women's Hospital, we performed immunohistochemistry (IHC) for 28 markers and classified each case per the 2008 WHO Classification. 170 cases (34%) could not be classified, largely due to poor tissue antigenicity or lack of lesional tissue on TMA. The remaining 328 cases (66%) are classified in the Table . 37% of the 133 DLBCL were germinal center B cell-like (GCB), 59% non-GCB, and 4% could not be characterized (Hans criteria). We also performed targeted expression profiling with a previously-published, NanoString-based diagnostic molecular classifier of aggressive B-cell lymphomas. This classifier distinguishes ~85% of pathological BL cases from DLBCL in Western cohorts (Carey CD, J Mol Diagn 2015). Evaluable RNA was available in 64/133 (48%) DLCBL, 38/73 (52%) BL, and 8/9 (89%) BCL-U cases. Unsupervised clustering of transcriptional profiles identified 2 groups (n = 54, 56). All 38 BL cases were classified into Group I (100%; exact binomial 95% CI: 91-100), along with 14 DLBCL (22%; 13-34%) and 4 BCL-U (50%; 16-84%). Group II combined 50 of 64 DLBCL cases (78%; 66-87%), 4 of 8 BCL-U cases (50%; 16-84%), and no BL (0%; 0-9%). Concordance between the classifier and pathologic diagnosis was 84%. Overall, incorporation of phenotypic and transcriptional data allowed reclassification of 83 cases into categories that may be responsive to ibrutinib or idelalisib (MCL; non-GCB DLBCL; CLL/SLL); 75 into categories that could benefit from CHOP (ALCL; DLBCL; PBL; PTCL-NOS); 8 into T-ALL; and 30 additional cases of BL by IHC alone. 18 cases of DLBCL or BCL-U were also found to have a similar transcriptional profile to BL, suggesting that they may benefit from BL-directed therapy. Thus, our findings demonstrate that ancillary phenotypic and transcriptional characterization can reclassify a large fraction of lymphomas in SSA and guide potentially beneficial therapies. Implementation of these tools and enhanced drug access and supportive care are desperately needed to improve patient outcomes across the developing world. | | | Original Pathologic Classification (Malawi) | | --------------------------------- | --------------- | ------------------------------------------- | ---------------------------------------------------- | | | | DLBCL/high grade NHL (n=118) | NHL/low grade NHL/lymphoma NOS/low grade BCL (n=101) | BL (n=70) | Suspicious for NHL (n=21) | CLL/SLL (n=7) | FL (n=3) | ALCL (n=2) | LBL (n=1) | MZL (n=3) | PBL (n=2) | | Refined Diagnosis Using IHC n (%) | DLBCL | 70 (59) | 46 (45) | 8 (12) | 7 (32) | | 1 (33) | 1 (50) | | | | | | BL | 12 (10) | 14 (14) | 43 (62) | 4 (19) | | | | | | | | | PBL | 11 (9) | 2 (2) | 5 (7) | 1 (5) | | | | 1 (100) | | | | | BCL-U | 4 (3) | | 3 (4) | | 1 (14) | | | | | 1 (50) | | | CD5-/CD10- BCL | 10 (9) | 13 (13) | 2 (3) | | 2 (29) | 2 (67) | | | | | | | CLL/SLL | | 2 (2) | | | 4 (57) | | | | | | | | MCL | | 2 (2) | | | | | | | | | | | FL | | 1 (1) | | | | | | | | | | | MZL | | | | 2 (10) | | | | | 2 (67) | | | | ALK+ ALCL | | 1 (1) | | 1 (5) | | | | | | | | | PTCL, NOS | | | 1 (1) | | | | | | | | | | T-ALL | 2 (2) | 3 (3) | 1 (1) | 2 (10) | | | | | | | | | Myeloid sarcoma | | 2 (2) | | | | | | | 1 (33) | | | | cHL | 1 (1) | 1 (1) | 1 (1) | | | | 1 (50) | | | | | | Plasmacytoma | | 1 (1) | | | | | | | | 1 (50) | | | Reactive | | 1 (1) | | | | | | | | | | | Carcinoma NOS | 2 (2) | 6 (6) | | | | | | | | | | | Neuroendocrine | 6 (5) | 6 (6) | 6 (9) | 4 (19) | | | | | | | * CLL/SLL,chronic lymphocytic leukemia/small lymphocytic lymphoma;FL,follicular lymphoma;ALCL,anaplastic large cell lymphoma;LBL,lymphoblastic lymphoma;MZL,marginal zone lymphoma;PBL,plasmablastic lymphoma;BCL-U,BCL,unclassifiable,with features intermediate between DLBCL & BL;MCL,mantle cell lymphoma;PTCL-NOS,peirpheral T-cell lymphoma,not otherwise specified;T-ALL,T-lymphoblastic lymphoma;cHL,classical Hodgkin lymphoma Table 1. Disclosures Rodig: Bristol Myers Squibb: Research Funding; Perkin Elmer: Membership on an entity's Board of Directors or advisory committees.

The relative timing of genetic alterations that contribute to follicular lymphoma remains unknown. We analyzed a donor–recipient pair who both developed grade 2/3A follicular lymphoma 7 years after allogeneic transplantation and donor lymphocyte infusions. Both patients harbored identical BCL2/IGH rearrangements also present in 1 in 2,000 cells in the donor lymphocyte infusion, and the same V(D)J rearrangement, which underwent somatic hypermutation both before and after clonal divergence. Exome sequencing of both follicular lymphomas identified 15 shared mutations, of which 14 (including alterations in EP300 and KLHL6) were recovered from the donor lymphocyte infusion by ultra-deep sequencing (average read coverage, 361,723), indicating acquisition at least 7 years before clinical presentation. Six additional mutations were present in only one follicular lymphoma and not the donor lymphocyte infusion, including an ARID1A premature stop, indicating later acquisition during clonal divergence. Thus, ultrasensitive sequencing can map clonal evolution within rare subpopulations during human lymphomagenesis in vivo. Significance: For the first time, we define the molecular ontogeny of follicular lymphoma during clonal evolution in vivo. By using ultrasensitive mutation detection, we mapped the time-course of somatic alterations after passage of a malignant ancestor by hematopoietic cell transplantation. Cancer Discovery; 2(1); 47–55. ©2011 AACR. This article is highlighted in the In This Issue feature, p. 1

The BM86 antigen, originally identified in Rhipicephalus (Boophilus) microplus, is the basis of the only commercialized anti-tick vaccine. The long-term goal of our study is to improve BM86 based vaccines by induction of high levels of tick gut binding antibodies that are also cross-reactive with a range of BM86 homologues expressed in other important tick species. Here we have used a BD86 derived synthetic peptide, BD86-3, to raise a series of mouse monoclonal antibodies. One of these mAbs, named 12.1, recognized BM86 homologues in immuno-histochemical analyses in four out of five tick species including R. (B.) microplus, Rhipicephalus (Boophilus) decoloratus, Hyalomma anatolicum anatolicum and Rhipicephalus appendiculatus. Our results indicate that broadly cross-reactive tick gut binding antibodies can be induced after immunization with a synthetic peptide derived from the protein BD86.

Approximately 10% of B-ALLs harbor CRLF2 rearrangements and have a poor prognosis. Although these leukemias are addicted to JAK2 signaling, ATP-competitive type I JAK2 inhibitors have limited activity (Weigert et al. J Exp Med 2012). This may result from heterodimerization of JAK2 with other JAK family members (Koppikar et al. Nature 2012). Type II inhibitors bind JAK2 in the inactive conformation and may have non-cross resistance with type I inhibitors. In Ba/F3 cells dependent on CRLF2 and the gain-of-function allele JAK2 R683G, the type II JAK2 inhibitor NVP-CHZ868 was more potent (IC50 21nM) than the type I inhibitors NVP-BSK805 (IC50 443nM) and NVP-BVB808 (IC50 111nM). Unlike type I inhibitors, CHZ868 completely abrogated JAK2 and STAT5 phosphorylation. In addition, the JAK2 Y931C allele that confers 4-6-fold resistance to BSK805 and BVB808 did not affect the IC50 of CHZ868. We assessed in vivo efficacy of CHZ868 in mice transplanted with transgenic (CRLF2/JAK2 R683G/Cdkn2a-/- or CRLF2/JAK2 R683G/Pax5+/-/Ts1Rhr) or primary human CRLF2-rearranged B-ALLs. Mice treated for 5-6 days with CHZ868 (30mg/kg/day PO) had significant reductions in spleen size compared to control mice and complete loss of phospho-STAT5 in residual leukemia cells. In both murine leukemias and human xenografts, CHZ868 prolonged survival compared to controls (p30) clones sequenced harbored the same JAK2 L884P mutation. Ba/F3 cells expressing CRLF2 with JAK2 R683G/L884P had 14-fold resistance to CHZ868 (R683G IC50 16nM; R683G/L884P IC50 231nM). JAK2 L884P is homologous to an EGFR L747P activating mutation (He et al. Clin Cancer Res 2012), which destabilizes the P-loop and C-helix portion of the kinase domain. Next-generation sequencing of JAK2 from splenocytes of mice that progressed on CHZ868 treatment did not identify L884P or other missense mutations at >1% frequency, suggesting in vivo treatment failure was not due to JAK2 mutation. To improve CHZ868 efficacy, we tested for synergy with multiple chemotherapy agents in MHH-CALL4 cells, which harbor a CRLF2/IGH rearrangement and JAK2 I682F mutation. Among the tested agents, dexamethasone was highly synergistic with CHZ868. In mice transplanted with CRLF2/JAK2 R683G/Pax5+/-/Ts1Rhr murine B-ALL, a 14-day course of CHZ868 prolonged survival compared to vehicle (p Citation Format: Loretta S. Li, Nadja Kopp, Shuo-Chieh Wu, Jordy Van Der Zwet, Jacob V. Layer, Oliver Weigert, Amanda L. Christie, Alexandra N. Christodoulou, Huiyun Liu, Akinori Yoda, Thomas Radimerski, David M. Weinstock. Type II JAK2 inhibitor NVP-CHZ868 has potent activity in JAK2-dependent B-cell acute lymphoblastic leukemias (B-ALLs) in vivo. [abstract]. In: Proceedings of the AACR Special Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(17 Suppl):Abstract nr A23.

Background: Despite modern chemoimmunotherapy more than a third of patients with diffuse large B cell lymphoma (DLBCL) will experience relapse or refractory disease. Multiple mutations associated with the biology of DLBCL have recently been identified by next-generation sequencing in primary tumor samples, but little is known about their prognostic role. Furthermore, histological comparison of the primary tumor and relapsed disease is often not available in clinical practice due to the lack of centralized assessment and complicated by the difficulties to perform exome-wide sequencing in formalin fixed tissues. Therefore, the role of certain mutations and their mechanisms in clonal evolution during relapse is unknown and the rising of chemo-resistant DLBCL subclones has not been described in the literature so far. Methods: We identified all patients with available histologically confirmed relapsed or refractory DLBCL in our single center cohort of 346 patients with aggressive lymphoma treated at our tertiary cancer center in Salzburg, Austria. Primary formalin fixed paraffin embedded tumor sample, sample of refractory or relapsed disease and matched germ line were available for targeted next generation sequencing in 27 patients. A targeted exon capture and next-generation sequencing of all coding exons of 104 selected genes known to be frequently mutated in lymphoma were performed on a HiSeq 2500. Results: Sequencing was successful in 96.8% of all samples resulting in 25 patients with sequencing of the primary tumor and 24 patients with available pairs of primary lymphoma and histologically confirmed relapse. In these 24 patients two relapse samples were available in 10 patients and three relapse samples in one patient. Non-synonymous mutations were present in 74 of the 104 genes tested. Individual tumor samples showed between 0 and 29 non-synonymous mutations (median: 10). Less than six non-synonymous mutations in the primary tumor were associated with a better median OS than more mutations (28 versus 15 months p=0.031). We also compared the frequency of mutated genes in our cohort consisting of high risk patients defined by actual relapse with the literature containing patients with extensive sequencing but only little clinical data and clinical follow-up. Common mutated genes such as CARD11, CD58, CD79B, CREBBP, EZH2, BTG1 or B2M showed no difference in frequency to our patient cohort indicating no or only small driver function in resistant or refractory disease. Nevertheless, mutations previously reported to be at low frequency in DLBCL were significantly more often observed in our primary samples (NOTCH1, MYC, RB1, FAT2, ATM, SMARCA4, BCL7A) and relapsed samples (TP53, MCL1, ATM, FAT2, MYC, RB1, SMARCA4) of high risk patients when compared to the literature. We also observed the gain and the loss of several mutations between first diagnosis and histologically confirmed relapse. Overall, we observed an increase of the amount of non-synonymous mutations at first relapse in 12, no change in 6 and a decrease in 6 paired cases. A completely stable pattern of non-synonymous mutations was detected in 4 cases, but in the majority of cases relevant dynamic was observed: e.g.: gain of non-synonymous mutations in the p53 gene was seen in 3 patients (5 mutations), in the TNFRSF-14 gene in 2 patients (3 mutations), in the RB1 gene in 1 patient (1 mutation), in the NOTCH2 gene in 3 patients (4 mutations) and in the MYD88 gene in 1 patient (1 mutation) or loss of non-synonymous mutations in the CREBBP gene in 3 patients (3 mutations) or in the CRAD11 gene in 2 patients (2 mutations). Monitoring of subclones during disease was also possible using the allelic fraction over time e.g.: showing an increase of the NOTCH1 mutation burden in 2 biopsies after first diagnosis. Discussion: To the best of our knowledge clonal evolution detected by next generation sequencing has not been reported in DLBCL so far. We demonstrate the feasibility of such an approach from fixed tissue samples and using a curated set of target genes. In analogy to other lymphoid malignancies we can show the increase of allelic burden of certain mutations over time and the loss or gain of several others. While this approach is limited by the bias introduced by the selection of genes in the gene set, we feel that deep sequencing of selected mutations will provide further insights into subclone dynamics, which may be responsible for clonal evolution. Disclosures No relevant conflicts of interest to declare.

GNB1 encodes a beta subunit (Gβ) of heterotrimeric G proteins, which mediate signals downstream of G protein coupled receptors (GPCRs). We isolated a somatic mutant of GNB1 (K89E) by functional screening of a cDNA library derived from a blastic plasmacytoid dendritic cell neoplasm (BPDCN). A search of cancer genome databases identified recurrent mutations in GNB1 and the highly related protein GNB2. GNB1/2 K89E/T were found in B cell acute lymphoblastic leukemia (B-ALL) (1 case), follicular lymphoma (1) and myelodysplastic syndrome (MDS) (1) as well as BPDCN (1). Interestingly GNB1 K57E/T mutations were found only in myeloid diseases: [acute myeloid leukemia (2), atypical CML (2), polycythemia vera (1) and MDS (6)], while GNB1 I80N/T were found predominantly in B cell diseases [CLL (2), FL (2), DLBCL (1) and MDS (1)]. These mutated codons are all located on the GNB1 protein surface that is critical for interactions between Gβ and alpha subunits (Gα) or downstream effectors. Immunoprecipitation followed by mass spectrometry demonstrated that GNB1 K57E, I80T and K89E mutants failed to bind Gα, including GNAI2/3, GNA11/Q and GNA13 that are normally bound by wild-type (WT) GNB1. All mutations affecting these codons promoted cytokine-independent growth of human TF1 myeloid cells or mouse BaF3 lymphoid cells with activation of MEK/ERK and mTOR/PI3K pathways. Pertussis toxin treatment did not affect GNB1-dependent ERK activation or cell growth, implying a Gα-independent pathway. To investigate the function of GNB1 mutations in vivo, we performed a mouse bone marrow transplantation (BMT) experiment using wild-type and Cdkn2a-deficient donors. Loss of the cell cycle regulator CDKN2A is common in BPDCN, B-ALL, and several other hematologic malignancies. Bone marrow cells were isolated from 5-FU treated donor mice and infected with retrovirus expressing GNB1 WT, K57E, I80T or K89E. Transplantation of GNB1 mutant-expressing Cdkn2a-deficient bone marrow resulted in myeloid dendritic cell neoplasms that were CD11b+, CD11c+, CD19-, B220-, and CD3-. GNB1 mutants did not induce tumors in WT bone marrow after 12 months of observation suggesting that GNB1 requires additional cooperating mutations such as Cdkn2a loss. We performed the same BMT experiment using Cdkn2a-deficient bone morrow cells without 5-FU pretreatment. We found thatGNB1 I80T and K89E mutants induced a progenitor B cell ALL (CD11b-, CD11c-, CD19+, CD3-, TdT+). These data suggest that GNB1 mutations can promote tumorigenesis in more than one cell lineage, as observed in patients. In vivo treatment of the myeloid neoplasm with the dual PI3K/mTOR inhibitor BEZ235 suppressed GNB1-induced signaling and markedly increased survival. In several human tumors, we noted that GNB1 mutations co-occurred with oncogenic kinase alterations, including BCR/ABL, JAK2 V617F and BRAF V600K. Co-expression of patient-derived GNB1 alleles with the mutant kinases resulted in relative resistance to treatment with the corresponding kinase inhibitor in each context. Thus, GNB1 and GNB2 mutations confer transformation and targeted therapy resistance across a range of human tumors and may be targetable with inhibitors of PI3K/mTOR signaling. Disclosures Gotlib: Novartis Pharmaceuticals Corporation: Membership on an entity's Board of Directors or advisory committees, Research Funding, Travel Support Other. Deininger:BMS, Novartis, Celgene, Genzyme, Gilead: Research Funding; BMS, ARIAD, Novartis, Incyte, Pfizer: Advisory Board, Advisory Board Other; BMS, ARIAD, Novartis, Incyte, Pfizer: Consultancy. Tyner:Constellation Pharmaceuticals: Research Funding.

Approximately 10% of B-ALLs harbor CRLF2 rearrangements, which may portend a poor prognosis. Although these leukemias are addicted to JAK2 signaling, ATP-competitive type I JAK2 inhibitors have limited activity in vitro or in vivo (Weigert et al. J Exp Med 2012). This may result from heterodimerization of JAK2 with other JAK family members (Koppikar et al. Nature 2012). Type II inhibitors bind JAK2 in the inactive conformation, which may overcome this resistance. When assayed in MHH-CALL4 cells harboring a CRLF2/IGH rearrangement and JAK2 I682F mutation, the type II JAK2 inhibitors NVP-BBT594 and NVP-CHZ868 were 10-35-fold more potent than the type I JAK2 inhibitors NVP-BSK805 and NVP-BVB808. Similarly, in Ba/F3 cells dependent on CRLF2 and the gain-of-function allele JAK2 R683G, the IC50 for CHZ868 was 5-20-fold lower than the IC50s for BSK805 and BVB808. Unlike type I inhibitors, which induce paradoxical hyperphosphorylation of JAK2, CHZ868 completely blocks JAK2 and STAT5 phosphorylation. In addition, the JAK2 Y931C allele that confers 4-6-fold resistance to BSK805 and BVB808 did not alter sensitivity to CHZ868. CHZ868 abrogates STAT5 phosphorylation in Ba/F3 cells expressing CRLF2 with JAK2 R683G/Y931C while BVB808 does not. CHZ868 is the first type II JAK2 inhibitor amenable to in vivo use. We assessed its efficacy in mice transplanted with transgenic (CRLF2/JAK2 R683G/Cdkn2a-/- or CRLF2/JAK2 R683G/Pax5+/-/Ts1Rhr) or primary human CRLF2-rearranged B-ALLs. Splenocytes from patient-derived xenografts (PDXs) treated with CHZ868 in vivo for 3 days are more primed for apoptosis as demonstrated by a 2-6-fold EC50 reduction for PUMA permeabilizing activity compared to vehicle. Transcriptional profiling of splenocytes from CHZ868-treated PDXs revealed downregulation of critical survival pathways including E2F1, STAT3, and AKT-mediated signaling. Of note, 2 of the most downregulated genes are STAT targets, PIM1 and Myc. Mice treated for 5-6 days with CHZ868 had significant reductions in spleen size and complete loss of phospho-STAT5 in residual leukemia cells. In both murine leukemias and human xenografts, CHZ868 prolonged survival compared to controls (p30 clones sequenced harbored the same JAK2 L884P mutation. Ba/F3 cells expressing CRLF2 with JAK2 R683G/L884P displayed cross-resistance to CHZ868, while sensitivity to type I inhibitors was not affected. Structural modeling of the JAK2 JH1 domain suggested that L884P alters the binding pocket for type II inhibitors. JAK2 L884P is homologous to an EGFR L747P activating mutation, which destabilizes the P-loop and C-helix portion of the kinase domain (He et al. Clin Cancer Res 2012). The fact that L884P was reported in two B-ALL patients lacking additional JAK2 mutations (Torra et al. Blood (ASH Annual Meeting Abstracts) 2010) raised the possibility it was also an activating mutation. We confirmed L884P is an activating allele, as Ba/F3 cells expressing CRLF2, IL7R, and JAK2 L884P proliferated in the absence of TSLP ligand. To improve CHZ868 efficacy, we tested for synergy with multiple chemotherapy agents currently used in B-ALL treatment. Dexamethasone was the most highly synergistic with CHZ868 in MHH-CALL4 cells. To assess the combination in vivo, we treated mice transplanted with CRLF2/JAK2 R683G/Pax5+/-/Ts1Rhr murine B-ALL with vehicle, CHZ868, dexamethasone, or CHZ868 + dexamethasone for 14 days post engraftment. CHZ868 treatment prolonged survival compared to vehicle (p Disclosures Hofmann: Novartis Institutes for BioMedical Research: Employment. Baffert:Novartis: Employment. Vangrevelinghe:Novartis Institutes for BioMedical Research: Employment. Gaul:Novartis: Employment. Radimerski:Novartis: Employment. Weinstock:Novartis: Consultancy, Research Funding.

Mantle cell lymphoma (MCL) makes up approximately 6% of non-Hodgkin’s lymphoma cases and has an aggressive disease course with a particularly poor outcome. To date there is no standard treatment and despite good initial response to chemotherapy, most patients relapse with long-term survival achieved in less than 40%. In almost all cases, MCL is distinguished by overexpression of Cyclin D1 (CCND1) usually caused by a translocation between chromosomes 11 and 14. Both CCND1 and BTK are known clients of heat shock protein 90 (HSP90). In previous studies, we demonstrated potent cytotoxic activity of second- (NVP-AUY922, PU-H71) and third-generation (NVP-HSP990) HSP90 inhibitors against the MCL cell lines Granta519, JeKo1, MAVER1, Rec1, and Z-138 (IC50s for AUY922, 3-11nM; HSP990, 5-24nM; PU-H71, 40-287 nM). Immunobloting of MCL cell lines exposed to 50nM AUY922 demonstrated reduced expression of client proteins CCND1, CDK4 and AKT and induction of G0/G1 cell cycle arrest within 6-8h followed by apoptosis within 27h. We now demonstrate that combining Ibrutinib with AU922 results in synergistic or additive effects in all lines except for the highly Ibrutinib- sensitive JEKO-1. In fact, AUY922 overcame ibrutinib-resistance due to activation of non B-cell receptor (BCR)-driven alternative NFkB signaling in Granta519 and Z-138 cells. Due to the promising results of AUY922 we conducted two in vivo studies. Current mouse MCL models are generated by injecting MCL cell lines in matrigel subcutaneously. The MCL grows as a solid tumor and treatment is typically initiated when mean tumor volume is approximately 200 mm3. First, we xenografted luciferized MAVER1 (ibrutinib-sensitive) and Z-138 (ibrutinib-resistant) cells into SCID beige mice (10 million cells per mouse). Mice were randomized to receive either AUY922 (50 mg/kg by tail vein injection thrice weekly) or vehicle. Tumors analyzed from mice sacrificed after 5 days of treatment showed complete loss of cyclin D1 and Ki67 staining by immunohistochemistry in those receiving AUY922. Tumor growth was significantly slowed in AUY922 treated animals in both lines, which translated into a survival advantage (p Disclosures Weinstock: Novartis: Consultancy, Research Funding.

To identify new oncogene alleles directly from primary tumor specimens, we generate and screen cDNA libraries from patient samples for gain-of-function alterations that can substitute for cytokine signaling in cytokine-dependent cells. Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive leukemia of plasmacytoid dendritic cells with a dismal prognosis. No driver oncogenes have been identified in cases of BPDCN. Screening of a cDNA library generated from a BPDCN resulted in multiple cytokine-independent clones that expressed a full-length transcript of GNB1 with a K89E mutation. GNB1 encodes a beta subunit of the heterotrimeric G-protein, a binding complex that transduces signals from G-protein coupled receptors to multiple downstream pathways. Gain-of-function mutations have been reported in alpha subunits of the G-protein, including GNAQ/GNA11 in uveal melanoma and GNAS in pituitary tumors, however, the contributions of beta subunits to cancer remains undefined. To investigate downstream signaling from GNB1 K89E, we performed gene expression profiling and mass spectrometry (MS)-based phosphoproteomics and found significant activation of RAS/MAPK and PI3K/AKT pathways in GNB1 K89E-expressing cells compared to isogenic cells expressing wild-type GNB1. ERK and AKT activation by GNB1 K89E were confirmed by western blotting. To target GNB1 K89E signaling, we screened kinase inhibitors using a multiplex assay of small molecules and found selective sensitivity of GNB1 K89E cells to MEK and pan-PI3-kinase inhibitors. To assay the transforming effects of GNB1 K89E in vivo, we transduced GNB1 (wild-type or K89E) into bone marrow from Cdkn2a-deficient donors after 5-FU treatment and transplanted into wild-type recipients. We opted to utilize Cdkn2a-deficient donors as the loss of CDKN2A is common in cases of BPDCN. Within 4 months after transplantation, all mice (n=10) that received bone marrow transduced with GNB1 K89E developed a lethal malignancy characterized by pancytopenia and massive hepatosplenomegaly. Spleens were infiltrated by large, spindly cells with extensive dendritic projections, as well as extensive fibrosis that completely effaced the normal splenic architecture. The cells were negative for T-cell (CD2, CD3) and B-cell (CD19, B220) markers but positive for the dendritic cell/macrophage markers MAC-2 and MAC-3. Further characterization by flow cytometry demonstrated that the cells infiltrating the spleen were CD8, CD103, MHC class II, CD26, FLT3 and CD11c positive, consistent with neoplastic dendritic cells. Serial transplantation of splenic cells from five different GNB1 K89E-transplanted mice into secondary wild-type recipients resulted in 100% fatality within 50 days. We searched published datasets from exome, transcriptome and whole genome sequencing of hematologic malignancies for GNB1 mutations. We identified one case of K89E in B-cell acute lymphoblastic leukemia (ALL), four cases with I80T/N in chronic lymphocytic leukemia or B-cell lymphomas, six cases with K57E/T in myeloid neoplasms, and D76G in T-cell ALL. Expression of any of these alleles but not wild-type GNB1 was sufficient to promote cytokine-independent growth of human TF1 cells. The published structure of GNB1 (Ford et al. Science 1998) reported a small number of residues, including K57, I80 and K89 that mediate interactions with both G-alpha subunits and effector proteins. In fact, affinity purification followed by MS using tagged GNB1 (wild-type, I80T and K89E) demonstrated that, unlike wild-type GNB1, the GNB1 mutants fail to bind distinct Gα subunits. The repertoire of protein interactors, which includes potential G protein effectors, also differed between different GNB1 alleles. Thus, gain-of-function mutations in GNB1 occur across a broad range of hematologic malignancies, modify essential interaction G-protein subunit interactions, can drive in vivo transformation, and activate targetable downstream kinases. Disclosures: Tyner: Incyte Corporation: Research Funding.

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive malignancy previously known as blastic natural killer cell lymphoma, CD4+CD56+ hematodermic neoplasm, or agranular CD4+ NK cell leukemia. BPDCN has recently been classified as the malignant counterpart of plasmacytoid dendritic cells (pDCs), the most common dendritic cell subset in peripheral blood. Clinical outcomes in BPDCN are poor, with median survival of less than 12 months. The pathogenesis and genetic changes associated with pDC transformation are largely unknown, and the optimal treatment for this disease is unclear. Loss of the CDKN2A locus on 9p21 is the most common copy number alteration, and the sole targeted sequencing effort reported to date focused only on somatic mutations in TP53 and TET2 (Jardin et al. Br J Haem 2011). The goal of this study was to characterize the genetics of BPDCN by next-generation sequencing of all exons of 219 genes known to be recurrently mutated in hematologic malignancies. We sequenced a discovery cohort of seven adult patients with BPDCN, and confirmed the somatic status of single nucleotide variants (SNVs) and insertion-deletions (InDels) not present in dbSNP using paired germline tissue where available. All cases met World Health Organization criteria for pathological diagnosis of BPDCN. We confirmed the presence of TET2 (4 of 7 patients) and TP53 (1 of 7) mutations in BPDCN, and noted that the overall mutational spectrum was overlapping with previously sequenced hematologic neoplasms. Specifically, we observed mutations in ASXL1 (in 2 patients: K586* and an InDel causing a frameshift at S795), IDH2 (R140Q), KRAS (G13D), ABL1 (T315I), ARID1A (R1721*), GNA13 (E313*), U2AF1 (Q157L), and SRSF2 (P95L) that have been reported in myeloid and mature B cell neoplasms. Also of interest was an IRF8 R404W mutation; IRF8 is a transcription factor that drives pDC development and germline loss of IRF8 in humans is associated with dendritic cell deficiency. The most striking finding was the presence of premature stop, frame shift, and splice site mutations in the splicing factor ZRSR2 on chromosome Xp22.1 in 4 of 7 (57.1%) BPDCNs. ZRSR2 mutations were present in 71-84% of sequence reads at their respective locations, consistent with homo/hemizygous alterations in a dominant clone. Xenografting of one BPDCN that harbored a ZRSR2 premature stop mutation resulted in leukemia engraftment that retained the ZRSR2 mutation. From a validation cohort of 32 additional adult and pediatric BPDCNs, ZRSR2 mutations were present in 11 cases, for a total of 15 of 39 (38.5%) patients. Ten of 15 mutations were premature stop, frame shift, or splice site, while the remaining were missense variants. ZRSR2 is recurrently mutated in MDS and AML but at a much lower frequency (1-5%), and ZRSR2 mutations have not been described as characteristic of any other malignancy. Thus, ZRSR2 mutations are approximately 10-fold more prevalent among BPDCNs as compared to MDS or AML, indicating a unique association between BDPCN and ZRSR2 mutation. BPDCN is predominantly a disease of the male sex, both in previous studies and in our cohort (28 males among 36 patients, 77.8%). In a prior report (Yoshida et al. Nature 2012), 12 of 12 cases of MDS with ZRSR2 nonsense and frame shift mutations were male. All 10 cases of BPDCN with ZRSR2 nonsense, frame shift, and splice site mutations in our cohort were male (P=0.076 by two-sided Fisher’s exact test). Thus, we hypothesize that BPDCN may be more common in males because of a gene dosage effect related to the chr.X location of ZRSR2. There was also a trend toward an association between ZRSR2 loss-of-function mutation and age ≥65 (P=0.068). There was no statistically significant difference in overall survival between patients with and without mutations in ZRSR2, although we were limited by the small cohort size and the heterogeneity of therapies received. We conclude that loss of ZRSR2 function is specifically associated with pDC transformation and leukemogenesis, as well as male sex and older age. Further studies to confirm these findings in additional cohorts and define the mechanism linking ZRSR2 mutation with BPDCN are underway. Disclosures: DeAngelo: Ariad, Novartis, BMS: Consultancy. Neuberg:Synta Pharmaceuticals: Trust owns stock; I am a Trustee Other.

Although next-generation sequencing can delineate the genetic alterations within a primary tumor specimen, it can be difficult to distinguish the small number of driver mutations from the large number of passenger mutations. To overcome this issue, we developed a system for identifying oncogenic alterations directly from tumor cells. In this system, retroviral cDNA libraries built from cancer cell lines and directly from primary cancer samples are transduced into BaF3 cells, an IL3-dependent B cell line. Transformation by oncogenes promotes IL3-independent survival, allowing for the isolation of individual transformed clones and sequencing of the integrated cDNA. In the past, we identified CRLF2 as a novel oncogene in acute lymphoblastic leukemia (Yoda et al. PNAS 2010). We have improved the method and demonstrated 100% sensitivity for isolating well-characterized oncogenes, including EGFR, HER2, RAS and ALK (Shindoh et al. PLoS One 2012). Recently, we isolated a mutated GNB1 K89E allele from a cDNA library generated from a primary blastic plasmacytoid dendritic cell neoplasm (BPDCN). BPDCN is a rare and aggressive leukemia with a dismal prognosis. GNB1 encodes the beta subunit of the heterotrimeric G-protein, a binding complex that transduces signals from G-protein coupled receptors to multiple downstream pathways. Gain-of-function mutations have been reported in alpha subunits of the G-protein, however, the contributions of beta subunits to cancer remains undefined. To investigate downstream signaling from GNB1 K89E, we performed gene expression profiling and mass spectrometry (MS)-based phosphoproteomics and found significant activation of RAS/MAPK and PI3K/AKT pathways in GNB1 K89E-expressing cells compared to isogenic cells expressing wild-type GNB1. To target GNB1 K89E signaling, we screened kinase inhibitors using a multiplex panel of small molecules and found selective sensitivity of GNB1 K89E cells to MEK and pan-PI3-kinase inhibitors. Next, we transduced GNB1 alleles into bone marrow cells from Cdkn2a-deficient mice and transplanted into wild-type recipient mice. Within 4 months after transplantation, all mice (n=10) that received bone marrow transduced with GNB1 K89E developed a lethal dendritic cell malignancy, confirming the transforming effects of GNB1 K89E in vivo. A search of published cancer mutations identified four cases with GNB1 I80T/N in chronic lymphocytic leukemia or B-cell lymphomas, five cases with GNB1 K57E/T in myeloid malignancies, one case of GNB1 K89E in acute lymphoblastic leukemia, and two cases with GNB2 M101T/V in ovarian cancer. All of these alleles promoted GM-CSF-independent growth in human TF1 cells. Interestingly, the mutated codons are all located on the GNB1 molecular surface that is critical for interactions between GNB1 and both alpha subunits and downstream effectors. Immunoprecipitation followed by MS demonstrated that GNB1 K89E and I80T mutants failed to bind inhibitory G alpha subunits GNAI2 and GNAI3 as well as GNA11 that are bound by wild-type GNB1. Thus, gain-of-function mutations in G-protein beta subunits occur across a broad range of malignancies, can drive in vivo transformation, and activate targetable downstream kinases by modifying essential interactions with partner proteins. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):PR07. Citation Format: Akinori Yoda, Guillaume Adelmant, Nobuaki Shindoh, Bjoern Chapuy, Yuka Yoda, Oliver Weigert, Nadja Kopp, Shuo-Chieh Wu, Sunhee S. Kim, Huiyun Liu, Trevor Tivey, Jeffrey W. Tyner, Jason Gotlib, Michael W. Deininger, Shannon Turley, Jarrod A. Marto, Andrew A. Lane, David M. Weinstock. Novel oncogenic mutations in the beta subunit of heteromeric G-proteins identified by functional cDNA library screening. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr PR07.

Abstract 672 Long-term disease-free survival is achieved in over 80% of children with B-cell acute lymphoblastic leukemia (B-ALL) but only 40% of adults. Particular genomic alterations in B-ALL, including rearrangements of MLL and the cytokine receptor subunit CRLF2, confer a poor prognosis in both children and adults. In addition, current therapies for B-ALL are associated with significant short- and long-term toxicities, highlighting the critical need for new therapeutics. The novel compound JQ1 inhibits the BET class of human bromodomain proteins from mediating the assembly of macromolecular protein complexes that are required for transcriptional activation and polymerase elongation. In hematologic and epithelial tumors, JQ1 can downregulate the expression of c-MYC and thereby suppress malignant growth and survival. We investigated the therapeutic potential of JQ1 across multiple genetically-defined subsets of B-ALL. JQ1 potently induced apoptotic cell death (IC50∼30–300 nM) in all B-ALL cell lines (697, CEMO-1 NALM-6, MHH-CALL4, MUTZ-5, Reh, RS4;11, SEMK2) studied. Among the most sensitive lines (IC5030% bone marrow involvement by human CD45+/CRLF2+ B-ALL cells, mice were randomized to receive JQ1 (50mg/kg intraperitoneally daily) or vehicle (DMSO). After 5 days of treatment, sentinel mice were sacrificed for pharmacodynamic endpoints. Spleens from mice treated with JQ1 had markedly reduced c-Myc expression and STAT5 phosphorylation compared with spleens from vehicle-treated mice. In survival cohorts (n=9 per arm), treatment with JQ1 significantly prolonged overall survival (p=0.0002) compared with vehicle. These results demonstrate that BET bromodomain inhibition is a promising therapeutic strategy for patients with B-ALL, including subsets with high-risk cytogenetics. Moreover, the surprising finding that JQ1 also targets IL7R expression suggests that bromodomain inhibitors may be especially useful in malignant and nonmalignant disorders dependent on IL7R. Disclosures: Bradner: Tensha Therapeutics: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Acetylon Pharmaceuticals: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; SHAPE Pharmaceuticals: Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Weinstock:Novartis: Consultancy, Research Funding.

Abstract 1651 Mantle cell lymphoma (MCL) is associated with particularly poor outcome, with long-term survival achieved in less than 40% of patients. In addition to the characteristic t(11;14) that results in overexpression of cyclin D1, a variety of other molecular pathways are dysregulated in MCL. Cyclin D1 is a known client of heat shock protein 90 (HSP90), suggesting that inhibitors of HSP90 may destabilize cyclin D1 and have activity in this disease. Yet, first-generation HSP90 inhibitors such as 17-AAG generally lack potency in MCL cell lines. We assessed the pre-clinical activity of second- (NVP-AUY922, PU-H71) and third-generation (NVP-HSP990) HSP90 inhibitors, which have greater potency and superior in vivo pharmacokinetics, in the MCL cell lines Granta519, JeKo1, MAVER1, Rec1, and Z-138. To define the genetics of these lines, we utilized an exon-capture followed by next-generation sequencing approach to identify single nucleotide variants and insertions/deletions across the entire coding sequence of 197 genes known to be recurrently altered in lymphoid malignancies. Sequencing to a median depth of coverage∼400 recovered alterations previously described in MCL (e.g. in ATM, RB1, TP53, NOTCH1) as well as variants in genes that have not previously been associated with MCL (e.g. in MLL2, KDM6A, FLT3, IKZF3, JAK3, RFXAP). Dose response curves of these cell lines treated with structurally diverse HSP90 inhibitors showed 10–100-fold greater potency for NVP-AUY922 (IC50, 3–11 nM), NVP-HSP990 (IC50, 5–24 nM) and PU-H71 (IC50, 40–287 nM), compared with 17-AAG (IC50, 29–1503 nM). In vitro exposure of all lines to 50 nM AUY922 resulted in G0/G1 cell cycle arrest within 6–8 hrs followed by apoptosis within 24–72 hours. Immunoblotting after exposure to AUY922 demonstrated rapid reductions in HSP90 client proteins, including cyclin D1, CDK4 and AKT, in all lines as well as accumulation of HSP70 in all lines except REC1, which harbors an HSP70 locus deletion. Cell killing by AUY922 (based on Annexin V/PI flow cytometry, caspase 3/7 activation and PARP cleavage) varied between cell lines, with Granta519 being the most sensitive (>50% cell death after 24 hr exposure) and Rec1 being the least sensitive ( Disclosures: Weinstock: Novartis: Consultancy, Research Funding.

Abstract 299 Angioimmunoblastic T-cell lymphoma (AITL) is a subtype of T-cell lymphoma that manifests with a broad array of neoplastic and paraneoplastic manifestations, including generalized lymphadenopathy, hepatosplenomegaly, systemic symptoms, rash and hypergammaglobulinemia. AITL accounts for approximately 20% of T-cell lymphomas and 1–2% of all non-Hodgkin lymphomas (NHL). Median survival among patients with AITL is less than 3 years, although the course of illness varies widely. Histologic examination of AITL characteristically demonstrates proliferation of high endothelial venules and a polymorphic infiltrate, malignant cells that resemble CD4+ follicular helper T-cells and occasional EBV-positive lymphoid cells. The genetics of AITL remain almost completely undefined, in part because of the low tumor cell fraction and the abundance of non-malignant bystander cells. We reasoned that targeted sequencing of selected genes of interest would increase coverage and thereby enable the detection of low frequency variants present with malignant AITL cells. To define a targeted mutational landscape of AITL, we performed exon capture and next-generation sequencing of all coding exons of 197 genes known to be recurrently altered in cases of NHL. Single nucleotide variants (SNVs) and insertions/deletions were confirmed by manual review of sequencing reads and a subset was validated by Sanger sequencing of tumor and germline tissue. Twenty-six cases collected from three sites in the USA had adequate tumor specimens available and resulted in high-quality reads (median depth of coverage∼300). Median age among the 26 cases was 66.5 years (range 30–89). Twelve (46%) patients were male. Among 21 cases with adequate clinical annotation, all 21 had advanced stage disease (11 stage 3, 10 stage 4), 13 (62%) had B-symptoms and 19 (90%) had an ECOG performance score of 0–2. Ten patients received CHOP-like regimens, 4 received non-anthracycline containing chemotherapy regimens, 5 received prednisone monotherapy, 2 received cyclosporine monotherapy, and one patient underwent allogeneic stem cell transplantation after cytoreduction with alemtuzumab. Among the 17 patients with staging after first-line treatment, 8 (47%) achieved a complete response, 3 (18%) achieved a partial response, 1 (6%) had stable disease and 5 (29%) had progression of disease. Median overall survival among the 26 patients was 420 days with a median follow-up of 426 days (range 21–3532). Recent studies have identified both TET2 and DNMT3A mutations in a small number of AITL samples as well as hematopoietic stem cells from the same patients. From the 26 cases, we identified 28 TET2 mutations (13 frameshift, 8 nonsense, 5 missense, 2 splice site) in 17 (65.4%) cases, including 5 cases with 2 TET2 mutations and 2 cases with 3 TET2 mutations. Among the latter, the fractions of mutant reads suggested that one mutation was present within all tumor cells and the other 2 mutations were present in subclones. Six of 17 cases with TET2 mutations also harbored mutations in DNMT3A, compared with 0 of 9 cases that lacked TET2 mutations (p=0.06). Median age for patients with wild-type TET2 was 56 years (range 30–83), 68 years for patients with one TET2 mutation (range 55–89), and 77 years for patients with 2 or 3 TET2 mutations (range 59–84; p Known gain-of-function mutations were identified at JAK3 V722I (n=2) and IDH2 R172K (n=1). Frame-shift mutations were recovered in ABCA7 (n=1), ARID1B (n=1), CREBBP (n=2), GNAS (n=1), IKZF2 (n=2), PRDM1 (n=2), SMARCA2 (n=1), and TNFRSF14 (n=1). Nonsense mutations were recovered in ALPK2 (n=1), CCND3 (n=2), and CHD8 (n=2). Only 2 cases harbored TP53 mutations (M133R, S261_splice). Additional missense variants were identified across a large number of genes, including several previously described in the COSMIC database. In conclusion, the genetics of AITL vary broadly across cases, with a small number of genes previously associated with NHL harboring recurrent mutations. Mutations of DNMT3A commonly occur in combination with one or more mutations in TET2. Mutation of either locus is associated with advanced age, supporting the hypothesis that the mutations are acquired over time within hematopoietic stem cells. Disclosures: Horwitz: Seattle Genetics: Consultancy, Research Funding; Allos: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy; Genzyme: Consultancy; Kyowa Hakko Kirin Pharma: Consultancy; Johnson & Johnson: Consultancy; Infinity Pharmaceuticals, Inc.: Research Funding. Weinstock:Novartis: Consultancy, Research Funding.

Abstract 3671 Follicular lymphoma (FL) is characterized by the translocation t(14;18), which results in overexpression of the anti-apoptotic protein BCL2 through juxtaposition to the immunoglobulin heavy chain (IGH) locus. Additional genetic aberrations are required and recurrent mutations have been identified in FL, however their timing during lymphomagenesis remains unknown. We performed ultra-sensitive mutation detection to define in vivo clonal diversification in paired follicular lymphomas from a donor-recipient sibling pair that presented more than 9 years after hematopoietic cell transplantation. Briefly, a 41-year old woman with chronic myeloid leukemia (CML) underwent myeloablative bone marrow transplantation from her HLA-matched sister in 2000. She received three donor leukocyte infusions (DLI) for molecular relapse, with the last in June 2002. In November 2009, the donor was diagnosed with grade 2/3A FL. Six months later, the recipient was diagnosed with grade 2/3A FL. The FLs shared identical BCL2/IGH rearrangements, which was also recovered from the DLI at a frequency of 1-in-2000 cells. Both FLs also shared the same V(D)J rearrangement, with the exception of single base-pair mismatches and insertions/deletions (InDels) consistent with ongoing somatic hypermutation (SHM) during clonal divergence. Alignment with germline VH3-66 sequence indicated that the common ancestor had initiated SHM. Whole exome sequencing of both FLs identified 12 single nucleotide variants (SNVs) and 2 InDels in both lymphomas, 3 SNVs unique to the donor's FL, and 4 unique to the recipient's FL. All candidate mutations were validated and confirmed to be somatic by Sanger sequencing. Among the identical mutations identified in both FLs were two SNVs in BCL2, an in-frame deletion in EP300, and an in-frame insertion in KLHL6, which were recently found to be recurrently mutated in lymphoma. Among the SNVs unique to the recipient's FL was an ARID1A (adenine-thymine (AT)-rich interactive domain-containing protein 1A) R1276 premature stop. Loss-of-function mutations in ARID1A have been reported in solid cancers, but not yet in hematologic malignancies. On immunohistochemical staining both lymphomas had decreased ARID1A/BAF250 protein expression, suggesting that loss of ARID1A occurred through separate mechanisms in each FL (i.e. convergent evolution). In fact, the donor's lymphoma was found to have a copy number loss at this locus (1p35.3) by qPCR. To determine whether the somatic mutations that we identified were present at a low frequency within the DLI, we PCR amplified regions flanking each mutation site from the DLI and subjected the products to ultra-sensitive deep sequencing (average read coverage at mutation site, 361,723; range, 16,684–1,169,555). To correct for background frequencies of non-germline calls, we PCR amplified and deep sequenced the same positions from the donor's buccal swab (average read coverage at the mutation site, 418,499; range, 20,711–1,070,734). Eleven of the 12 SNVs and the 2 InDels that were identified in both lymphomas were ‘enriched' in the DLI, i.e., recovered at frequencies significantly above background, indicating that those mutations were present more than 7 years prior to presentation of either lymphoma. All 4 SNVs unique to the recipient's FL and a RAFTLIN V254M mutation identified only in the donor's FL were not enriched in the DLI, consistent with subsequent acquisition during clonal diversification. Of the final two mutations, one was detected only in the donor's FL and was enriched in the DLI. The other was initially detected only in the donor's FL, but deep sequencing recovered the mutation in 4.7% of reads from the recipient's FL and demonstrated enrichment in the DLI. The presence of a mutation in the donor's FL and DLI but not within the majority of recipient's FL cells is consistent with at least two scenarios: (i) the recipient's FL is derived from a clonally diversified population of ancestor cells transferred from the donor or (ii) the mutant allele was lost in a subset or in all cells of the recipient's FL during clonal evolution. In conclusion, we utilized ultra-sensitive mutation detection to elucidate the molecular ontogeny of follicular lymphoma during clonal evolution in separate hosts. This approach has broad applicability for identifying genetic variants within tumor populations that confer phenotypes like therapeutic resistance or metastatic potential. Disclosures: No relevant conflicts of interest to declare.

Abstract 62 Mutation within the kinase domain of tyrosine kinases is a common mechanisms of resistance to enzymatic inhibitors. Inhibitors of janus kinase 2 (JAK2) are under evaluation in patients with myeloproliferative neoplasms (MPNs), B-cell acute lymphoblastic leukemia (B-ALL) with rearrangements of the cytokine receptor subunit CRLF2, and other tumors with constitutive JAK2 signaling. To identify resistance mutations in JAK2, we randomly mutagenized human JAK2 R683G, which is observed in approximately half of CRLF2-rearranged B-ALL. We transduced the mutagenized JAK2 cDNA library into murine Ba/F3 cells that express CRLF2. Expression of CRLF2 and JAK2 R683G confers IL3 independent growth in Ba/F3 cells. The transduced population was selected in the JAK2-selective inhibitor NVP-BVB808 in the absence of IL3. Multiple BVB808-resistant clones were recovered that harbored either E864K, Y931C or G935R mutations in JAK2. Alignment of homologous regions of the JAK2 kinase domain (JH1) with ABL1 demonstrated that the three mutations are located in regions homologous to imatinib resistance hotspots in ABL1. Codons Y931 and G935 are within the hinge region of the kinase domain. Based on structural modeling, Y931C is likely to inhibit substrate binding. E864K is located in the middle of b3 following the P-loop in the N-lobe and may modify the structure and flexibility of the preceding P-loop, thus destabilizing the conformation required for inhibitor binding. We expressed JAK2 V617F alleles harboring Y931C, G935R or E864K in Ba/F3-EPOR cells and exposed the cells to the JAK2 enzymatic inhibitors JAK inhibitor-1, NVP-BSK805, TG101348, tofacitinib (formerly tasocitnib), ruxolitinib (formerly INCB18424) and BVB808. All three mutations conferred 2- to >10-fold resistance against BVB808, NVP-BSK805, TG101348, ruxolitinib and JAK inhibitor-1. Y931C and E864K but not G935R conferred resistance to tofactinib. Modeling of G935R indicated that a 935R side-chain would occlude the hydrophobic channel of the ATP-binding pocket. As a consequence, this mutation would decrease the binding affinity of compounds occupying the hydrophobic channel like JAK inhibitor-1 or BSK805, but not affect the potency of tofactinib, which does not bind in this region. Mutation of G935 to arginine, histidine or glutamine reduced the inhibitory effects of JAK inhibitor-1, but not tofacitinib, on JAK2 kinase domain activity. None of the codon 935 mutations had significant effects on Km or Vmaxin vitro. BVB808 treatment partially reduced activation state-specific phosphorylation of STAT5 in Ba/F3-EPOR/JAK2 V617F cells but not in Ba/F3-EPOR/JAK2 V617F/G935R or G935H cells. JAK2 is a known client of HSP90, and HSP90 inhibitors promote the degradation of both wild-type and mutant JAK2. We hypothesized that resistance mutations within the JAK2 kinase domain would not affect JAK2 degradation induced by HSP90 inhibitors. We assayed the cytotoxicity of the resorcinylic isoxazole amide NVP-AUY922 and the benzoquinone ansamycin 17-AAG in Ba/F3 cells that express the erythropoietin receptor (EPOR) and JAK2 V617F, which is observed in more than half of MPNs. Mutation of JAK2 V617F to include E864K, Y931C or G935R did not affect sensitivity to either AUY922 or 17-AAG. In fact, AUY922 was more active against cells harboring G935R (GI50, 3.87 nM) or E864K (GI50, 6.14 nM) compared to cells with no resistance mutation (GI50, 14.7 nM; p Disclosures: Gaul: Novartis: Employment. Vangrevelinghe:Novartis: Employment. De Pover:Novartis: Employment. Regnier:Novartis: Employment. Erdmann:Novartis: Employment. Hofmann:Novartis: Employment. Eck:Novartis: Consultancy, Research Funding. Kung:Novartis Pharmaceuticals: Consultancy, Research Funding. Radimerski:Novartis Pharma AG: Employment. Weinstock:Novartis: Consultancy, Research Funding.

Abstract 576 Enzymatic inhibitors of Janus kinase 2 (JAK2) are in clinical development for the treatment of B-cell acute lymphoblastic leukemia (B-ALL) with rearrangements of the cytokine receptor subunit CRLF2, myeloproliferative neoplasms, and other tumors with constitutive JAK2 signaling. In addition, JAK2 is a client of heat shock protein 90 (HSP90) and HSP90 inhibition results in JAK2 degradation. To explore the utility of blocking JAK2 in CRLF2-rearranged B-ALL, we exposed the MHH-CALL4 and MUTZ-5 cell lines, which both have CRLF2/IGH rearrangements and activating JAK2 mutations to a panel of JAK2 inhibitors (JAK inhibitor-1, INCB18424, tofacitinib, NVP-BSK805, NVP-BVB808, TG101348) and the HSP90 inhibitor NVP-AUY922. Both MUTZ-5 and MHH-CALL4 were highly sensitive to AUY922 (GI50, 25–26 nM), with 50- to >1,000-fold superior potency compared with the panel of JAK2 enzymatic inhibitors. AUY922 and the structurally divergent HSP90 inhibitors 17-AAG, PU-H71 and HSP990 were all potently active against a panel of Ba/F3 lines dependent on CRLF2 and JAK2 signaling (GI50, 1–11 nM). Treatment of MUTZ-5 and MHH-CALL4 cells with JAK inhibitor-1 reduced but did not eliminate phospho (P-) STAT5 and P-ERK1/2 in both lines but promoted increases in P-AKT in MUTZ-5 and P-JAK2 in MHH-CALL4. In contrast, AUY922 treatment more extensively reduced or eliminated phosphorylation of all the targets. The combination of AUY922+JAK inhibitor-1 had little or no additional effect on target phosphorylation compared with AUY922 alone and pairwise dose-response studies with isobologram analysis failed to identify synergistic effects. We performed transcriptional profiling on MUTZ-5 and MHH-CALL cells treated with either vehicle (DMSO), JAK inhibitor-1, AUY922 or JAK inhibitor-1+AUY922. Unsupervised hierarchical clustering distinguished samples treated with AUY922 (or combination) from those treated with JAK inhibitor-1 or vehicle. To formally assess whether AUY922 targets the same genes as JAK inhibitor-1, we defined a ‘JAK inhibitor signature' from the top/bottom 250 most differentially expressed genes following treatment with JAK inhibitor-1. Using gene set enrichment analysis (GSEA), the ‘JAK inhibitor signature' was highly enriched upon treatment with AUY922 (p=0.003). GSEA also demonstrated that STAT5A signatures were enriched upon treatment with JAK inhibitor-1, AUY922, or JAK inhibitor-1+AUY922. To identify additional targets of HSP90 inhibition beyond the inhibition of JAK2, we used the C3 database from the MsigDB compendium to perform a transcription factor binding site enrichment analysis on the most differentially expressed genes between JAK inhibitor-1 and AUY922. The top 5 hits were all heat-shock factors (HSF, FDR Disclosures: Romanet: Novartis Pharma AG: Employment. Murakami:Novartis Pharma AG: Employment. Sallan:Enzon Pharmaceuticals: Honoraria. Kung:Novartis Pharmaceuticals: Consultancy, Research Funding. Radimerski:Novartis Pharma AG: Employment. Weinstock:Novartis: Consultancy, Research Funding.

SummaryA variety of cancers depend on JAK2 signaling, including the high-risk subset of B cell acute lymphoblastic leukemias (B-ALLs) with CRLF2 rearrangements. Type I JAK2 inhibitors induce paradoxical JAK2 hyperphosphorylation in these leukemias and have limited activity. To improve the efficacy of JAK2 inhibition in B-ALL, we developed the type II inhibitor CHZ868, which stabilizes JAK2 in an inactive conformation. CHZ868 potently suppressed the growth of CRLF2-rearranged human B-ALL cells, abrogated JAK2 signaling, and improved survival in mice with human or murine B-ALL. CHZ868 and dexamethasone synergistically induced apoptosis in JAK2-dependent B-ALLs and further improved in vivo survival compared to CHZ868 alone. These data support the testing of type II JAK2 inhibition in patients with JAK2-dependent leukemias and other disorders.