scholarly journals In Silico Modeling of Oncogenic Drivers in Waldenstrom Macroglobulinemia to Assess Additional Therapeutic Targets within the BCR Signaling Pathway Identifies MEK1/2 As a Target: Potential Therapeutic Role of Binimetinib

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1279-1279
Author(s):  
Aneel Paulus ◽  
Sharoon Akhtar ◽  
Shireen Vali ◽  
Ansu Kumar ◽  
Neeraj Kumar Singh ◽  
...  
Keyword(s):  
In Silico ◽  
Copy Number ◽  
Disease Stage ◽  
Advanced Stage ◽  
Employment Equity ◽  
Waldenström Macroglobulinemia ◽  
Waldenstrom Macroglobulinemia ◽  
Bcr Signaling ◽  
Equity Ownership

Abstract Background: The observation that B-cell receptor (BCR) signaling play a critical role in the survival of malignant Waldenstrom macroglobulinemia (WM) cells is highlighted by clinical efficacy of the BTK-inhibitor, ibrutinib in WM patients. BCR signaling leads to downstream activation of several intermediary components whose activity results in increased cell proliferation. Although disruption of this axis at the proximal end (BCR) has proved successful in WM, the exact role and impact of targeting the distal intermediaries remains unknown, particularly in aggressive forms of the disease. This is important as induction of resistance to ibrutinib is clearly documented which can either be mediated through mutational changes in BTK or other members within the BCR signalosome. Using a novel simulation-based approach, we reverse-engineered the WM cell molecular architecture to uncover the role of oncogenic intermediaries distal to the BCR complex in advanced-stage WM and conducted a virtual drug-screen targeting these pathways with in vitro validation. Methods: The human WM cell line, RPCI-WM1, was used in simulation and validation experiments. RPCI-WM1 was established from a highly drug-refractory advanced disease stage patient refractory to both rituximab and bortezomib. Publically available as well as proprietary genomic and cytogenetic data was utilized for the creation of the RPCI-WM1 patient avatar, which through simulation identified the salient and prominently dysregulated cellular pathways. Importantly, illustrating these pathways highlights common convergence points on increased proliferation and viability. These convergence points were then directly and indirectly targeted by simulated testing of a library of FDA approved drugs and those impacting these dysregulated pathways were shortlisted. A standardized library of equations models all the biological reactions such as enzymatic reactions, allosteric binding and protein modulation by phosphorylation, de-phosphorylation, ubiquitination, acetylation, prenylation and others. A library of FDA approved drug agents (n~150) and those in clinical study has been developed and was simulated individually and in combination on the RPCI-WM1 (advanced stage WM patient) avatar. Results: MYD88L265P mutation, absence of CXCR4 mutations and additional chromosomal aberrations (derivatives, translocations, deletions and amplifications of chromosomes 3, 6, 9, 13, 18 and 19), which are notable features of RPCI-WM1 cells were configured and modeled in silico. The RPCI-WM1 patient avatar was predicted to have increased IRAK1/4 engagement due to MYD88 mutation and high copy number (CN) of IL18. Downregulation of DUSP1 through MYD88-mediated signaling was noted to result in high ERK activity. Increase gene copy number of both FOS and ETS1, which are downstream of ERK, were noted. Notably, FOS is a key regulator of the AP1 complex, whose activity is regulated upstream by ERK. The transcription factor, ETS1 was also predicted as over expressed and ERK-mediated phosphorylation of ETS1 regulates the activity of ETS1. The RPCI-WM1 patient avatar model also indicated high AKT due to indirect convergence of multiple aberrations. Drug screening revealed sensitivity to the MEK inhibitor, binimetinib. Although no copy number variation in MEK-ERK pathway genes were detected, per simulation, MYD88 mutation through inactivation of DUSP1 activated ERK and downstream associated survival pathways. The simulation predictions were experimentally validated. As predicted, binimetinib significantly inhibited proliferation and viability of RPCI-WM1 cells (IC50 <100nM). Conclusions: Our study demonstrates the functional role and impact of MEK1/2 - an oncogenic component distal to the BCR, and whose activity can be targeted with binimetinib to elicit a lethal effect in advanced-stage WM cells. We also show the utility of a novel technology, which is capable of integrating genome-wide molecular data points to emulate the salient genomic drivers of a given tumor cell and test its sensitivity to numerous drugs in a high-throughput manner for truly personalized therapy. Disclosures Vali: Cellworks Group, Inc.: Employment, Equity Ownership. Kumar:Cellworks Group, Inc.: Employment. Singh:Cellworks Group, Inc.: Employment. Usmani:3Cellworks Research India Limited: Employment. Grover:3Cellworks Research India Limited: Employment. Abbasi:Cellworks Group, Inc.: Employment, Equity Ownership.

Carfilzomib Exerts Anti-Neoplastic Activity in Waldenstrom Macroglobulinemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4916-4916
Author(s):  
Antonio Sacco ◽  
Aldo M. Roccaro ◽  
Monette Aujay ◽  
Hai Ngo ◽  
Feda Azab ◽  
...  
Keyword(s):  
Cell Lines ◽  
Low Grade ◽  
Dependent Manner ◽  
Caspase 9 ◽  
Employment Equity ◽  
Waldenström Macroglobulinemia ◽  
Waldenstrom Macroglobulinemia ◽  
Synergistic Cytotoxicity ◽  
Equity Ownership ◽  
Dose Dependent

Abstract Abstract 4916 Introduction Proteasome inhibition represents a valid therapeutical approach in several tumors and its use has been validated in Waldenstrom's macroglobulinemia (WM), where single-agent Bortezomib has been successfully tested in phase 2 clinical trials. Nevertheless, a significant fraction of patients relapse, or develop significant toxicity due to high toxicity in non-transformed cells. Therefore preclinical evaluation of new proteasome inhibitor with a more selective inhibition of neoplastic cells is needed in order to increase efficacy and improve patient outcome. We tested Carfilzomib, a tetrapeptide epoxyketone selective inhibitor of the chymotrypsin-like activity of the immunoproteasome and constitutive proteasome in WM. Methods WM and IgM secreting low-grade lymphoma cell lines (BCWM.1, MEC1, RL) were used. Expression of imunoproteasome and constitutive proteasome subunits (beta1, beta2, beta5; LMP2, MECL1, LMP7) were detected primary WM cells and cell lines by an ELISA-based assay. Cytotoxicity and DNA synthesis were measured by thymidine uptake and MTT, respectively. Cell signaling and apoptotic pathways were determined by Western Blot. Determination of the additive or synergistic effect of drugs combination was calculated using the CalcuSyn software based on the Chou-Talalay method. Results Primary CD19 bone-marrow derived WM cells express higher level of the immunopreoteasome as compared to the constitutive proteasome. Carfilzomib inhibited the chymotrypsin-like activity of both the immunoproteasome (LMP7) and the constitutive proteasome (beta5) and in WM cells, in a dose-dependent manner; leading to inhibition of proliferation (IC50: 5nM; 48h) and induction of cytotoxicity (IC50: 7.5nM; 48h) in WM cells. Carfilzomib mediated apoptosis in WM by increasing PARP-, caspase-9- and -3-cleavage; as well as by inducing activation of c-jun-N-terminal kinase and ER-stress in a dose-dependent manner. Moreover, combination of Carfilzomib and bortezomib induced synergistic cytotoxicity in WM cells, as shown by enhanced PARP-, caspase-9- and -3-cleavage; and synergy in inhibiting the chymotrypsin-like activity of the immunoproteasome and constitutive proteasome. Conclusion Taken together, these findings provide the pre-clinical rational for testing Carfilzomib in Waldenstrom Macroglobulinemia. Disclosures Aujay: Proteolix: Employment, Equity Ownership. Demo:Proteolix: Employment, Equity Ownership. Ghobrial:Millennium: Honoraria, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Speakers Bureau; Novartis: Honoraria, Speakers Bureau.

Two Novel Distinct Subtypes of Myeloid Neoplasms Molecularly Associated with Histone H3K36 Methylations

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2841-2841 ◽  
Author(s):  
Yosaku Watatani ◽  
Yasunobu Nagata ◽  
Vera Grossmann ◽  
Yusuke Okuno ◽  
Tetsuichi Yoshizato ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Copy Number Variations ◽  
Healthy Controls ◽  
Employment Equity ◽  
Gene Deletions ◽  
Myeloid Neoplasms ◽  
Frequent Mutations ◽  
Equity Ownership

Abstract Myelodysplastic syndromes (MDS) and related disorders are a heterogeneous group of chronic myeloid neoplasms with a high propensity to acute myeloid leukemia. A cardinal feature of MDS, as revealed by the recent genetic studies, is a high frequency of mutations and copy number variations (CNVs) affecting epigenetic regulators, such as TET2, IDH1/2, DNMT3A, ASXL1, EZH2, and other genes, underscoring a major role of deregulated epigenetic regulation in MDS pathogenesis. Meanwhile, these mutations/deletions have different impacts on the phenotype and the clinical outcome of MDS, suggesting that it should be important to understand the underlying mechanism for abnormal epigenetic regulation for better classification and management of MDS. SETD2 and ASH1L are structurally related proteins that belong to the histone methyltransferase family of proteins commonly engaged in methylation of histone H3K36. Both genes have been reported to undergo frequent somatic mutations and copy number alterations, and also show abnormal gene expression in a variety of non-hematological cancers. Moreover, germline mutation of SETD2 has been implicated in overgrowth syndromes susceptible to various cancers. However, the role of alterations in these genes has not been examined in hematological malignancies including myelodysplasia. In this study, we interrogated somatic mutations and copy number variations, among a total of 1116 cases with MDS and myelodysplastic/myeloproliferative neoplasms (MDS/MPN), who had been analyzed by target deep sequencing (n=944), and single nucleotide polymorphism-array karyotyping (SNP-A) (n=222). Gene expression was analyzed in MDS cases and healthy controls, using publically available gene expression datasets. SETD2 mutations were found in 6 cases, including 2 with nonsense and 4 with missense mutations, and an additional 10 cases had gene deletions spanning 1.8-176 Mb regions commonly affecting the SETD2 locus in chromosome 3p21.31, where SETD2 represented the most frequently deleted gene within the commonly deleted region. SETD2 deletion significantly correlated with reduced SETD2 expression. Moreover, MDS cases showed a significantly higher SETD2 expression than healthy controls. In total, 16 cases had either mutations or deletions of the SETD2 gene, of which 70% (7 out of 10 cases with detailed diagnostic information) were RAEB-1/2 cases. SETD2 -mutated/deleted cases had frequent mutations in TP53 (n=4), SRSF2 (n=3), and ASXL1 (n=3) and showed a significantly poor prognosis compared to those without mutations/deletions (HR=3.82, 95%CI; 1.42-10.32, P=0.004). ASH1L, on the other hand, was mutated and amplified in 7 and 13 cases, respectively, of which a single case carried both mutation and amplification with the mutated allele being selectively amplified. All the mutations were missense variants, of which 3 were clustered between S1201 and S1209. MDS cases showed significantly higher expression of ASH1L compared to healthy controls, suggesting the role of ASH1L overexpression in MDS development. Frequent mutations in TET2 (n=8) and SF3B1 (n=6) were noted among the 19 cases with ASH1L lesions. RAEB-1/2 cases were less frequent (n=11) compared to SETD2-mutated/deleted cases. ASH1L mutations did not significantly affect overall survival compared to ASH1L-intact cases. Gene Set Expression Analysis (Broad Institute) on suppressed SETD2 and accelerated ASH1L demonstrated 2 distinct expression signatures most likely due to the differentially methylated H3K36. We described recurrent mutations and CNVs affecting two histone methyltransferase genes, which are thought to represent novel driver genes in MDS involved in epigenetic regulations. Given that SETD2 overexpression and reduced ASH1L expression are found in as many as 89% of MDS cases, deregulation of both genes might play a more role than expected from the incidence of mutations and CNVs alone. Although commonly involved in histone H3K36 methylation, both methyltransferases have distinct impacts on the pathogenesis and clinical outcome of MDS in terms of the mode of genetic alterations and their functional consequences: SETD2 was frequently affected by truncating mutations and gene deletions, whereas ASH1L underwent gene amplification without no truncating mutations, suggesting different gene targets for both methyltransferases, which should be further clarified through functional studies. Disclosures Alpermann: MLL Munich Leukemia Laboratory: Employment. Nadarajah:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Shih:Novartis: Research Funding.

Selective Inhibition of the Chymotrypsin-Like Activity of the Immunoproteasome and Constitutive Proteasome Represents a Valid Anti-Tumor Strategy in Waldenstrom Macroglobulinemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4911-4911
Author(s):  
Aldo M. Roccaro ◽  
Antonio Sacco ◽  
Monette Aujay ◽  
Hai Ngo ◽  
Feda Azab ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Dna Synthesis ◽  
Cell Lines ◽  
Parp Cleavage ◽  
Low Grade ◽  
Employment Equity ◽  
Waldenström Macroglobulinemia ◽  
Waldenstrom Macroglobulinemia ◽  
Synergistic Cytotoxicity ◽  
Equity Ownership

Abstract Abstract 4911 Introduction Proteasome inhibition represents a valid therapeutical approach in several tumors and its use has been validated in Waldenstrom macroglobulinemia (WM), where single-agent Bortezomib has been tested in phase 2 clinical trials, achieving 40% to 80% responses. Nevertheless, a significant fraction of patients relapse, or develop significant neuropathy. Therefore preclinical evaluation of new proteasome inhibitor is needed in order to improve patient outcome. We tested PR-047, a new orally bioavailable analog of carfilzomib which selectively inhibits the chymotrypsin-like activity of the immunoproteasome and constitutive proteasome, in WM. Methods WM and IgM secreting low-grade lymphoma cell lines (BCWM.1, MEC1, RL) were used. Bone marrow primary CD19+ cells and bone marrow stromal cells (BMSC) were obtained from patients with WM after informed consent. Expression of imunoproteasome and constitutive proteasome subunits (beta1, beta2, beta5; LMP2, MECL1, LMP7) were detected primary WM cells and cell lines by an ELISA-based assay. Cytotoxicity, DNA synthesis, cell cycle and apoptosis were measured by thymidine uptake, MTT, PI staining/flow cytometry analysis and DNA fragmentation, respectively. NF-kB activity has been evaluated on nuclear proteins using a DNA-binding ELISA-based assay. Cell signaling and apoptotic pathways were determined by Western Blot. Determination of the additive or synergistic effect of drugs combination was calculated using the CalcuSyn software based on the Chou-Talalay method. Results Primary bone-marrow derived WM cells are characterized by higher expression of the immunopreoteasome as compared to the constitutive proteasome. PR-047 inhibited the chymotrypsin-like activity of both the immunoproteasome (LMP7) and the constitutive proteasome (beta5) and in WM cells, leading to induction of cytotoxicity in primary WM cells; as well as to programmed cell death in a caspase-dependent and -independent manner, as shown by activation of c-jun-N-terminal kinase; inhibition of NF-kB; and initiation of the unfolded protein response. PR-047 induced cytotoxicity and inhibited DNA synthesis in primary WM cells (IC50: 50-80nM), as well as in IgM secreting low grade lymphoma cells (IC50: 30-50nM). Importantly, PR-047 exerted cytotoxicity in WM cells, even in the context of bone marrow milieu, by inhibiting IL-6- and IGF1-BMSC secretion and BMSCs-induced phosphorylation of Akt and ERK in WM cells. Moreover, combination of PR-047 and bortezomib induced synergistic cytotoxicity in WM cells, as shown by enhanced caspases-, PARP-cleavage; NF-kB inhibition; and synergy in inhibiting the chymotrypsin- and caspase-like activities of the immunoproteasome and constitutive proteasome. Conclusion These preclinical findings demonstrate that PR-047 targets WM cells, due to its anti-CT-L activity of both immunoproteasome and constitutive proteasome, providing the framework for testing PR-047 in this disease. Disclosures Aujay: Proteolix: Employment, Equity Ownership. Demo:Proteolix: Employment, Equity Ownership. Ghobrial:Millennium: Honoraria, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Speakers Bureau; Novartis: Honoraria, Speakers Bureau.

Aurora Kinase Is a Therapeutic Target in Ibrutinib-Resistant Waldenstrom Macroglobulinemia: In-Silico Target Identification and in-Vitro Validation

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2754-2754
Author(s):  
Aneel Paulus ◽  
Kasyapa S. Chitta ◽  
Sharoon Akhtar ◽  
Hassan Yousaf ◽  
Davitte Cogen ◽  
...  
Keyword(s):  
In Silico ◽  
Copy Number ◽  
Aurora Kinase ◽  
Gene Copy ◽  
Molecular Architecture ◽  
Employment Equity ◽  
In Silico Modeling ◽  
Equity Ownership ◽  
The Impact

Abstract Background: Current tumor profiling analytics provide some insight into the various molecular abnormalities and their individual consequences on oncogenic signaling. However, these analyses are limited by their lack of integration where the combined effect of individual mutations, gene copy number variations and chromosomal aberrations are not consolidated to create the global molecular architecture that supports neoplastic growth, particularly in the context of drug resistance. Consequentially, identities of the preferential oncogenic pathway(s) tumor cells employ to oppose the effects of targeted therapies remain cryptic and unactionable. Here we present a simulation-based method, which not only replicates the molecular architecture of ibrutinib-resistant Waldenstroms Macroglobulinemia (WM, for which ibrutinib is the only FDA-approved agent) in silico, but also predicts cell sensitivity towards existing drugs, which we validated experimentally for potential clinical translation. Materials: We used the newly established human WM cell line, RPCI-WM1/IR, as a surrogate model of ibrutinib-refractory WM. Genomic data including whole exome sequencing (WES) and copy number analysis (CNA) was utilized for the creation of an avatar of RPCI-WM1/IR, which through simulation identified the salient and prominently dysregulated cellular pathways. Importantly, illustrating these pathways highlights common convergence points on increased proliferation and viability. These convergence points were then directly and indirectly targeted by simulated testing of a library of FDA approved drugs and those impacting these dysregulated pathways were nominated. Importantly, this simulation avatar approach not only looks for agents acting on the specific gene mutation, but also predicts the convergence points to be attacked. The personalized simulation avatar technology is a comprehensive functional proteomics representation of the WM physiology network. A standardized library of equations models all the biological reactions such as enzymatic reactions, allosteric binding and protein modulation by phosphorylation, de-phosphorylation, ubiquitination, acetylation, prenylation and others. Results: Several genomic aberrations were used to create the RPCI-WM1/IR simulation avatar. Functional activity (based on mutation or copy number alteration) of several ibrutinib targets or transcription factors associated with BTK activity such as FYN, SP1, BMX and FRK were predicted to be lost. Increased expression of CAV1, which also inhibits BTK mediated signaling, was increased. An increase in CSNK2B, which activates PU.1- a transcriptional target of BTK, was also observed. Of note, no CXCR4 mutations, which have been shown to impact ibrutinib response, were observed. Next, the cytotoxic potential of over 150 FDA approved drug (and some in experimental stages) were simulated individually and in combination on the RPCI-WM1/IR avatar. In silico modeling predicted aberrant activity of aurora kinase A (AURKA) and its associated signaling partners, which could be disrupted with the (AURKA) inhibitor, tozasertib. AURKA activation was predicted as upregulated due to alterations in several genes: RASA1 loss and SOS1 increase --> increased ERK --> increased ETS1 --> increased AURKA. High beta-catenin signaling (high CTNNB1 and FZD1/4 and low AXIN1 and GSK3B) was also shown to increase AURKA. The simulation predictions were experimentally validated in vitro where AURKA inhibition with tozasertib significantly inhibited proliferation of RPCI-WM1/IR cells (IC50~14nM) as well as inducing apoptosis (48hr, 20nM treatment) and cell-cycle arrest. Conclusions: Our data demonstrates the potential of in silico modeling in predicting novel drug targets, allowing guidance in 1.) Delineating operational oncogenic circuits in an ibrutinib-resistant state by reanimation of the molecular architecture in silico, 2.) Calculating the impact of individual genomic abnormalities and their collective influence on maintaining tumor survival and 3.) Performing a rapid in-silico drug-sensitivity screen directed by the pathway analyses, which can be validated experimentally using standard assays. This novel approach holds tremendous potential in creating highly personalized therapies for ibrutinib-refractory WM patients based on unique genetic signatures. Disclosures Vali: Cellworks Group, Inc.: Employment, Equity Ownership. Kumar:Cellworks Group, Inc.: Employment. Singh:Cellworks Group, Inc.: Employment. Abbasi:Cellworks Group, Inc.: Employment, Equity Ownership.

scholarly journals Role of Remission Status and Prior Transplant in Optimizing Survival Outcomes Following Allogeneic Hematopoietic Stem Transplantation (HSCT) in Patients Who Received Inotuzumab Ozogamicin (INO) for Relapsed / Refractory (R/R) Acute Lymphoblastic Leukemia (ALL)

Blood ◽  
2017 ◽  
Vol 130 (Suppl_1) ◽  
pp. 886-886
Author(s):  
Partow Kebriaei ◽  
Matthias Stelljes ◽  
Daniel J. DeAngelo ◽  
Nicola Goekbuget ◽  
Hagop M. Kantarjian ◽  
...  
Keyword(s):  
Board Of Directors ◽  
Survival Probability ◽  
Research Funding ◽  
Employment Equity ◽  
Inotuzumab Ozogamicin ◽  
Advisory Committees ◽  
Allogeneic Hsct ◽  
Post Transplant ◽  
Equity Ownership

Abstract Introduction: Attaining complete remission (CR) prior to HSCT is associated with better outcomes post-HSCT. Inotuzumab ozogamicin (INO), an anti-CD22 antibody conjugated to calicheamicin, has shown significantly higher remission rates (CR/CRi and MRD negativity) compared with standard chemotherapy (SC) in patients (pts) with R/R ALL (Kantarjian et al. N Engl J Med. 2016). Pts treated with INO were more likely to proceed to HSCT than SC, which allowed for a higher 2-yr probability of overall survival (OS) than patients receiving SC (39% vs 29%). We investigated the role of prior transplant and proceeding directly to HSCT after attaining remission from INO administration as potential factors in determining post-HSCT survival to inform when best to use INO in R/R ALL patients. Methods: The analysis population consisted of R/R ALL pts who were enrolled and treated with INO and proceeded to allogeneic HSCT as part of two clinical trials: Study 1010 is a Phase 1/2 trial (NCT01363297), while Study 1022 is the pivotal randomized Phase 3 (NCT01564784) trial. Full details of methods for both studies have been previously published (DeAngelo et al. Blood Adv. 2017). All reference to OS pertains to post-HSCT survival defined as time from HSCT to death from any cause. Results: As of March 2016, out of 236 pts administered INO in the two studies (Study 1010, n=72; Study 1022, n=164), 101 (43%) proceeded to allogeneic HSCT and were included in this analysis. Median age was 37 y (range 20-71) with 55% males. The majority of pts received INO as first salvage treatment (62%) and 85% had no prior SCT. Most pts received matched HSCTs (related = 25%; unrelated = 45%) with peripheral blood as the predominant cell source (62%). The conditioning regimens were mainly myeloablative regimens (60%) and predominantly TBI-based (62%). Dual alkylators were used in 13% of pts, while thiotepa was used in 8%. The Figure shows post-transplant survival in the different INO populations: The median OS post-HSCT for all pts (n=101) who received INO and proceeded to HSCT was 9.2 mos with a 2-yr survival probability of 41% (95% confidence interval [CI] 31-51%). In patients with first HSCT (n=86) the median OS post-HSCT was 11.8 mos with a 2-yr survival probability of 46% (95% CI 35-56%). Of note, some patients lost CR while waiting for HSCT and had to receive additional treatments before proceeding to HSCT (n=28). Those pts who went directly to first HSCT after attaining remission with no intervening additional treatment (n=73) fared best, with median OS post-HSCT not reached with a 2-yr survival probability of 51% (95% CI 39-62%). In the latter group, 59/73 (80%) attained MRD negativity, and 49/73 (67%) were in first salvage therapy. Of note, the post-HSCT 100-day survival probability was similar among the 3 groups, as shown in the Table. Multivariate analyses using Cox regression modelling confirmed that MRD negativity during INO treatment and no prior HSCT were associated with lower risk of mortality post-HSCT. Other prognostic factors associated with worse OS included older age, higher baseline LDH, higher last bilirubin measurement prior to HSCT, and use of thiotepa. Veno-occlusive disease post-transplant was noted in 19 of the 101 pts who received INO. Conclusion: Administration of INO in R/R ALL pts followed with allogeneic HSCT provided the best long-term survival benefit among those who went directly to HSCT after attaining remission and had no prior HSCT. Disclosures DeAngelo: Glycomimetics: Research Funding; Incyte: Consultancy, Honoraria; Blueprint Medicines: Honoraria, Research Funding; Takeda Pharmaceuticals U.S.A., Inc.: Honoraria; Shire: Honoraria; Pfizer Inc.: Consultancy, Honoraria, Research Funding; Novartis Pharmaceuticals Corporation: Consultancy, Honoraria, Research Funding; BMS: Consultancy; ARIAD: Consultancy, Research Funding; Immunogen: Honoraria, Research Funding; Celgene: Research Funding; Amgen: Consultancy, Research Funding. Kantarjian: Novartis: Research Funding; Amgen: Research Funding; Delta-Fly Pharma: Research Funding; Bristol-Meyers Squibb: Research Funding; Pfizer: Research Funding; ARIAD: Research Funding. Advani: Takeda/ Millenium: Research Funding; Pfizer: Consultancy. Merchant: Pfizer: Consultancy, Research Funding. Stock: Amgen: Consultancy; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Seattle Genetics: Consultancy, Membership on an entity's Board of Directors or advisory committees. Wang: Pfizer: Employment, Equity Ownership. Zhang: Pfizer: Employment, Equity Ownership. Loberiza: Pfizer: Employment, Equity Ownership. Vandendries: Pfizer: Employment, Equity Ownership. Marks: Pfizer: Consultancy, Honoraria, Speakers Bureau; Amgen: Consultancy, Honoraria, Speakers Bureau.

Single Cell Profiling of B Cell Receptor Signaling and Apoptosis Networks in Chronic Lymphocytic Leukemia: Association with in Vitro Sensitivity to Fludarabine Monophosphate (F-ara-A).

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1263-1263
Author(s):  
Erik Evensen ◽  
Adam Palazzo ◽  
Ying-Wen Huang ◽  
Alessandra Cesano ◽  
Laura Z. Rassenti ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
B Cell ◽  
Single Cell ◽  
Phosphatase Activity ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Employment Equity ◽  
Bcr Signaling ◽  
Equity Ownership

Abstract Abstract 1263 Poster Board I-285 Background In conjunction with antigen-driven responses, ligand-independent signaling (termed tonic signaling) through both the pre-B cell receptor and B-cell receptor has an important role in B cell development, maturation and survival. In addition to the recognized role of CD79 alpha and CD79 beta BCR signaling, tyrosine phosphatases can impact tonic BCR signaling (Wienands et al. PNAS, 93 p.7865 (1996), Monroe Nat. Rev. Immunol. 6 p.283 (2006)). We previously subjected chronic lymphocytic leukemia (CLL) cells with modulators of BCR signaling and monitored their responses using flow cytometry-based Single Cell Network Profiling (SCNP). Of the many signaling modulators studied, hydrogen peroxide treatment (a general inhibitor of tyrosine phosphatase activity) augmented BCR signaling in a subset of CLL patient samples evaluated. In the remaining samples there was an apparent lack of response to hydrogen peroxide. These data suggested that differential phosphatase activity proximal to BCR signaling was driving the biology of these two patient groups. Objectives Studies were designed to evaluate whether there were any associations between tonic and/or ligand-dependent BCR signaling and in vitro sensitivity to fludarabine, as well as whether such response profiles showed a relationship to the hydrogen peroxide-dependent signaling we observed previously. Methods 23 CLL samples and 7 healthy PBMCs were treated with anti-m alone, hydrogen peroxide alone or the combination for 10 minutes. Separate aliquots of the same sample were exposed to F-ara-A for 48 hours. SCNP was carried out on gated B cells with quantitation of single cell measures of intracellular phosphorylated kinases and adaptor proteins downstream of the BCR. Additionally, the relative activation status of several protein markers of the apoptotic cascade (cytoplasmic cytochrome C, cleaved caspase 3, and cleaved PARP) was measured. Results As previously observed, CLL samples could be segregated into one of two groups exhibiting either responsive or refractory signaling after exposure to hydrogen peroxide alone. Moreover, responsive signaling in CLL cells was correlated in that all the measured components of the canonical B cell receptor network (p-Lyn, p-Syk, p-BLNK, p-PLC-gamma-2, p-Erk and p-Akt) showed the same phosphorylation response: either augmented in unison, or not activated at all. In vitro F-ara-A treatment (48 hours in the presence of 1mM F-ara-A) of parallel samples from these same CLL patients identified distinct populations of apoptosis responsive and refractory cells. Surprisingly, the capacity of patient samples to show augmented BCR signaling in response to hydrogen peroxide was associated prominently with the ability of cells in these patients to exhibit apoptotic proficiency to F-ara-A in vitro. This implies a link between mechanisms governing apoptosis in these CLL cells, survival pathways, and cell states that govern the role of phosphatase activity and BCR signaling potential. Conclusions This study reveals a link between tonic BCR signaling and regulation of apoptosis pathways. This suggests that the subgroup of CLL patients with active phosphatase activity (which suppresses BCR responses) have cell populations that are responsive to F-ara-A, a standard drug in CLL therapy. Conversely, the presence of CLL cells in a patient sample that remain unresponsive to hydrogen peroxide repression of phosphatase activity appear to identify patient samples which cannot undergo apoptosis in response to in vitro F-Ara-A exposure. The clinical implications of this work will be the focus of future translational studies. Disclosures Evensen: Nodality Inc.: Employment, Equity Ownership. Palazzo:Nodality Inc.: Employment, Equity Ownership. Huang:Nodality Inc.: Employment, Equity Ownership. Cesano:Nodality Inc.: Employment, Equity Ownership. Fantl:Nodality, Inc.: Employment, Equity Ownership.

Targeted Next-Generation Sequencing and Genome-Wide High-Resolution Copy Number DNA Arrays Allow the Identification of Five Novel RUNX1 Fusions In Hematological Malignancies.

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 1193-1193
Author(s):  
Vera Grossmann ◽  
Alexander Kohlmann ◽  
Hans-Ulrich Klein ◽  
Sonja Schindela ◽  
Susanne Schnittger ◽  
...  
Keyword(s):  
Copy Number ◽  
Partial Trisomy ◽  
Employment Equity ◽  
Reciprocal Translocations ◽  
Targeted Next Generation Sequencing ◽  
Genome Wide ◽  
Runx1 Gene ◽  
Equity Ownership ◽  
Genomic Regions ◽  
Generation Sequencing

Abstract Abstract 1193 RUNX1 is a crucial transcription factor involved in cell lineage differentiation during hematopoiesis. It contains a “Runt homology domain” (RHD; exons 3–5, amino acids 50–177) and a transactivation domain (TAD; exon 8, amino acids 291–371). RUNX1 can act as an activator or repressor of target gene expression and thus far two different mechanisms of somatically acquired alterations have been recognized: intragenic mutations and translocations. Most of the translocations involving RUNX1 lead to the formation of a fusion gene consisting of the 5` part of RUNX1 fused to sequences on partner chromosomes. We here present data on 5 cases, 4 acute myeloid leukemias (AML) and 1 chronic myelomonocytic leukemia (CMML) patient, respectively, where previous cytogenetic and FISH analyses revealed reciprocal translocations involving RUNX1. However, even sophisticated molecular diagnostic work-up failed to identify the corresponding RUNX1 fusion partners. Therefore, we used a combination of 454 shotgun pyrosequencing and long-oligonucleotide sequence capture microarrays to reveal these unknown RUNX1 partner genes in four cases. In detail, we performed DNA sequence enrichment using microarrays containing capture probes that were covering a contiguous region on chr. 21 (36,160,098 – 36,421,641), thereby allowing a specific enrichment by hybridization for genomic DNA where the RUNX1 gene is located (Roche NimbleGen 385K chip, Penzberg, Germany). This targeted next-generation sequencing (NGS) assay enabled to capture and sequence single reads mapping to both RUNX1 and other genomic regions (Burrows-Wheeler Aligner's Smith-Waterman algorithm). In median, 324 bp per patient (170,000 reads) with an 18-fold coverage were sequenced and in all cases chimeric reads were detectable, thereby confirming the presence of RUNX1 translocations and, moreover, identifying and characterizing 4 novel fusions on a molecular level. In one AML case, KCNMA1 was fused to RUNX1. KCNMA1, a potassium large conductance calcium-activated channel family member on chromosome 10q22.3, had recently been described to play a role in breast cancer invasion and metastasis to brain. In our case, as confirmed by RT-PCR and Sanger sequencing, the chimeric RUNX1-KCNMA1 fusion led to the disruption of the RHD of RUNX1. In the three additional cases, RUNX1 was fused to genomic regions on chromosomes 10q22, 17q21, and 5q13.3, respectively. The RUNX1-10q22 and the reciprocal 10q22-RUNX1 fusion were confirmed by PCR from genomic DNA and subsequent Sanger sequencing. According to its genomic structure the translocation RUNX1-chr.10q22 will result into the translation of a truncated RUNX1 protein with an intact RHD, but without TAD. Notably, in the remaining two cases, chr.17q21-RUNX1 and chr.5q13.3-RUNX1, only the reciprocal fusion events were detectable by PCR. In case chr.17q21-RUNX1 the translocation would disrupt RUNX1 after the RHD. In chr.5q13.3-RUNX1 the predicted fusion would not impact the RHD and TAD domains because the breakpoint is located before exon 1. In the fifth patient, we performed an analysis using a high-resolution genome-wide cytogenetic copy number DNA microarray to resolve a novel t(X;21)(p11;q22). In this case, the derivative chromosome × was duplicated, leading to a partial trisomy 21q and a partial trisomy X. On chr. 21 the breakpoint was mapped to be located in intron 6–7 within the RUNX1 gene. The breakpoint on the X-chromosome mapped to Xp11.23, thus leading to a truncated RUNX1 protein without the TAD domain. In summary, RUNX1 rearrangements either led to RUNX1 with an intact RHD and TAD (n=1), RUNX1 with an intact RHD but without TAD (n=3, dominant negative effect; similar to RUNX1-RUNX1T1), or to RUNX1 with a disrupted RHD and without TAD domains, leading to haploinsufficiency (n=1). In conclusion, the RUNX1 recombinome is an interesting target to understand pathogenetic heterogeneity in hematological malignancies. Here, we demonstrated that NGS and copy number DNA microarrays allow the identification of novel RUNX1 fusion partners not detectable by standard molecular techniques and reveals that cytogenetic reciprocal translocations lead to different types of RUNX1 alterations. Disclosures: Grossmann: MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Schindela:MLL Munich Leukemia Laboratory: Employment. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership, Research Funding.

The Bruton's Tyrosine Kinase Inhibitor, PCI-32765, Is Well Tolerated and Demonstrates Promising Clinical Activity In Chronic Lymphocytic Leukemia (CLL) and Small Lymphocytic Lymphoma (SLL): An Update on Ongoing Phase 1 Studies

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 57-57 ◽  
Author(s):  
Jan A. Burger ◽  
Susan O'Brien ◽  
Nathan Fowler ◽  
Ranjana Advani ◽  
Jeff Porte Sharman ◽  
...  
Keyword(s):  
B Cell ◽  
Phase 1 ◽  
Study Drug ◽  
Lymphocytic Leukemia ◽  
Clinical Activity ◽  
B Cell Malignancies ◽  
Employment Equity ◽  
Bcr Signaling ◽  
Equity Ownership ◽  
Grade 3

Abstract Abstract 57 Introduction: Bruton's tyrosine kinase (Btk) is a downstream mediator of B-cell receptor (BCR) signaling and is not expressed in T-cells or NK-cells. As such, Btk represents an ideal therapeutic target for B-cell malignancies dependent upon BCR signaling. Chronic lymphocytic leukemia (CLL)/small lymphocytic leukemia (SLL) has been reported to have constitutively active BCR signaling. PCI-32765 is a potent, selective, irreversible and orally bioavailable small molecule inhibitor of Btk that has pre-clinical activity in B-cell malignancies (Proc Natl Acad Sci 2010;107(29):13075-80). PCI-32765 was therefore moved forward to a Phase 1 study in B-cell malignancies including patients (pts) with CLL/SLL. A subsequent CLL/SLL-specific Phase 1b study was initiated to further explore safety, pharmacokinetics (PK), pharmacodynamics (PD), and efficacy of PCI-32765. This report includes a composite summary of the CLL/SLL experience in both of these studies. Pts and Methods: Pts with CLL/SLL who had relapsed or refractory disease after >1 prior treatment regimens were eligible for treatment in each of the studies whereas the second Phase 1b study also included a cohort of elderly pts (aged ≥ 65 years) with CLL/SLL who required treatment and were “treatment-naive”. Responses were assessed by the investigator using the International Working Group CLL criteria (Hallek et al, Blood 2008 for pts with CLL) and the International Workshop to Standardize Response Criteria for Non-Hodgkin's Lymphomas (Cheson et al, J Clin Oncol 2007 for pts with SLL). Results: To date, 30 CLL/SLL patients (including 4 treatment-naive) have been enrolled across the 2 studies. Eighty-four percent of subjects are men with an overall median age of 68 (range 44–82) years. Of the subjects with prior therapy for CLL/SLL the median number of prior therapies is 3 (range 1–4). Treatment has been well-tolerated; Grade ≥ 3 toxicities have been infrequent (10/30 pts; 33%). Two study-drug related serious adverse events have been reported: 1 case of viral adenitis (Grade 3) and 1 case of viral infection (Grade 2). Two adverse events have led to discontinuation of study drug: a small bowel obstruction (Grade 3) and exacerbation of chronic obstructive disease (Grade 3); both events were reported as unrelated to study drug. No study-drug related deaths have reported. There has been no change in either NK cell or T cell counts. Target inhibition as measured by a probe of Btk drug occupancy showed inhibition of Btk at PCI-32765 exposure levels of ≥ 245 ng•h/mL. Of the 14 patients currently evaluable for response using the pre-defined criteria, the overall response rate is 64% (1 complete remission [CR], 8 partial remissions [PR], and 4 SD). Both studies are ongoing and open to enrollment. An update on response rate, response duration, safety, and PD information will be presented on enrolled patients based on a November 2010 database cut-off. Conclusion: PCI-32765 is a novel oral and selective “first-in-human” inhibitor of Btk that induces objective partial and complete responses in a substantial proportion of pts with CLL/SLL and has a favorable safety profile. These data support further studies of both monotherapy and also combination treatment with PCI-32765 in CLL/SLL. Disclosures: O'Brien: Pharmacyclics, Inc: Honoraria, PI grant. Fowler:Pharmacyclics: Consultancy, Research Funding. Advani:Pharmacyclics, Inc: Honoraria, PI grant. Sharman:Pharmacyclics, Inc: Honoraria, PI grant. Furman:Pharmacyclics, Inc: PI grant. Izumi:Pharmacyclics, Inc: Employment. Buggy:Pharmacyclics, Inc: Employment, Equity Ownership. Loury:Pharmacyclics: Employment, Equity Ownership. Hamdy:Pharmacyclics, Inc: Employment, Equity Ownership.

Landmark Analyses of DNMT3A Mutations in Hematological Malignancies

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 407-407
Author(s):  
Vera Grossmann ◽  
Alexander Kohlmann ◽  
Claudia Haferlach ◽  
Tamara Alpermann ◽  
Melanie Wild ◽  
...  
Keyword(s):  
Overall Survival ◽  
Mutation Rate ◽  
Mutation Frequency ◽  
Cpg Methylation ◽  
Homozygous Mutation ◽  
Wild Type ◽  
Employment Equity ◽  
Acute Leukemias ◽  
Equity Ownership

Abstract Abstract 407 CpG methylation is an epigenetic modification that is important for cellular development. The DNMT3A gene, located on chromosome 2p23.3, encodes for a DNA methyltransferase and plays a central role in de novo CpG methylation. Recently, DNMT3A has been reported to be mutated in 22% of AML and 8% of MDS (Ley et al., N Engl J Med, 2010; Walter et al., Leukemia, 2011). Further, DNMT3A mutations were observed to be associated with a short overall survival in both diseases, respectively. In order to determine the role of DNMT3A mutations in leukemia we investigated two different entities by next-generation sequencing: 145 AML patients and 83 cases harboring a T-cell acute lymphoblastic leukemia (T-ALL). We applied an amplicon based deep-sequencing assay (454 Life Sciences, Branford, CT) in combination with the 48.48 Access Array technology (Fluidigm, South San Francisco, CA). The peripheral blood or bone marrow samples were obtained from untreated patients. The AML cohort was restricted to cases with normal karyotype (CN-AML). 87/145 (60%) cases were specifically selected to be wild-type for NPM1, FLT3-ITD, CEBPA, and MLL-PTD, whereas 58/145 (40%) samples were mutated in NPM1 (n=33) or double-mutated in NPM1 and FLT3-ITD (n=25). In our cohort of AML cases without mutations in NPM1, FLT3-ITD, CEBPA, and MLL-PTD, we observed a DNMT3A mutation frequency of 17.2% (15/87 cases). The DNMT3A mutation rate in the NPM1 mutated/FLT3 wild-type cases (16/33, 48.5%, P=0.001) and NPM1/FLT3-ITD mutated cases (19/25, 76%, P<0.001) was significantly higher, confirming the association of DNMT3A mutations with NPM1 and FLT3-ITD mutations that had been reported previously (Ley et al.). Interestingly, also in the cohort of T-ALL we detected patients that carried a DNMT3A mutation (16/83, 19.3%), which is very similar to the mutation frequency in AML, and has not been described yet. To further address the biology of DNMT3A mutations in acute leukemias we combined the AML and T-ALL cohorts and identified in total 31 distinct missense mutations in 65 patients (49 AML, 16 T-ALL). Most frequently, amino acid R882 located in exon 23 was mutated (n=29 cases). In addition, we identified 7 frame-shift alterations, 5 nonsense and 2 splice-site mutations. Moreover, 9 of the 65 mutated cases had two independent mutations. Focusing on AML, only three (6.1%) of the 49 DNMT3A-mutated cases were observed to harbor two different mutations concomitantly. In contrast, in the cohort of T-ALL we detected two different mutations in 6/16 (37.5%, P=0.003) cases. Further, in the cohort of AML, no homozygous mutation was detected, however, in the T-ALL group, two cases harbored a homozygous mutation. Therefore, only 3/49 AML (6.1%) cases, but 8/16 T-ALL (50%) cases showed biallelic mutation status (P<0.001). With respect to overall survival, no association was seen in the complete cohort of CN-AML cases (n=145). After limiting this cohort to the cases without mutations in NPM1, FLT3-ITD, CEBPA and MLL-PTD (n=87), an inferior survival was observed for DNMT3A-mutated patients as compared to DNMT3A wild-type patients (n=15 vs. n=72; alive at 2 years: 27.9% vs. 56.6%; P=0.048). Remarkably, also in the cohort of T-ALL a worse survival for patients with DNMT3A mutations was seen which has not been reported thus far (n=13 vs. n=64; alive at 1 years: 28.6% vs. 80.9%; P=0.001). Subsequently, we were interested whether gain-of-function mutations of the DNMT3A gene were associated with trisomy 2 and acquired uniparental disomy (aUPDs) of the short arm of chromosome 2 where DNMT3A is located. As such, we investigated 9 cases harboring a trisomy 2 (AML n=4, MDS n=4, and CMML n=1) and one MDS patient harboring an aUPD 2p, as confirmed by SNP microarray analyses (SNP Array 6.0, Affymetrix, Santa Clara, CA). Not all, but 3/9 cases with trisomy 2 harbored a DNMT3A mutation (one AML, MDS, and CMML case each), suggesting that duplication of DNMT3A mutations can enhance the effect of the mutation. Moreover, the single case with aUPD 2p also showed a mutation, further suggesting that LOH leading to loss of the wild-type DNMT3A may be another mechanism of disease leading to progression of leukemia. In conclusion, we here report on a high mutation rate of DNMT3A in both AML and T-ALL and independently confirmed an inferior overall survival in these two entities, respectively. This indicates a significant role of DNMT3A alterations in myeloid as well as in lymphoid neoplasms. Disclosures: Grossmann: MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Alpermann:MLL Munich Leukemia Laboratory: Employment. Wild:MLL Munich Leukemia Laboratory: Employment. Weissmann:MLL Munich Leukemia Laboratory: Employment. Eder:MLL Munich Leukemia Laboratory: Employment. Dicker:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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