Discovery and Characterization of Super-Enhancer-Associated Dependencies in Acute Myeloid Leukemia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3539-3539 ◽  
Author(s):  
Michael Ryan Corces-Zimmerman ◽  
Matthew Eaton ◽  
Jeremy Lopez ◽  
Nan Ke ◽  
Christian Fritz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Specific Gene ◽  
Employment Equity ◽  
Super Enhancer ◽  
Equity Ownership ◽  
Key Drivers ◽  
Acute Myeloid

Abstract Misregulation of genes that play an important role in transcription and chromatin biology is a salient feature of many hematological cancers, including acute myeloid leukemia (AML). Numerous genome-wide analyses in AML have provided evidence linking recurring genetic mutations to epigenomic alterations and disease-specific gene expression programs but the prognostic value and clinical utility of these findings remain unclear. Recently, a novel class of densely clustered cis-regulatory elements termed super-enhancers have emerged as key effectors initiating and maintaining cell type-specific gene expression in a variety of physiological and disease settings, including cancer. Tumor-specific super-enhancers regulate key oncogenes and other cancer-essential genes, providing a novel target discovery strategy for detecting both known and unrecognized cancer dependencies of high diagnostic and therapeutic value. Here we describe the discovery and characterization of super-enhancer domains across a cohort of nearly 50 AML patients and relevant normal hematopoietic stem and progenitor cell controls. We identified unique, clone-specific cancer targets encoding protein kinases, chromatin regulators, and lineage-specific transcription factors, including key drivers of AML such as FLT3, CDK6, and MYB. In addition, we have identified clusters of AML cases with shared super-enhancer domains suggesting convergence on common key drivers of AML. We provide the biological and disease relevance of super-enhancer-associated genes in the context of tumor cell state and drug-target discovery and establish a molecular rationale for developing therapies based on these new insights. Disclosures Eaton: Syros Pharmaceuticals: Employment, Equity Ownership. Lopez:Syros Pharmaceuticals: Employment, Equity Ownership. Ke:Syros Pharmaceuticals: Employment, Equity Ownership. Fritz:Syros Pharmaceuticals: Employment, Equity Ownership. Olson:Syros Pharmaceuticals: Employment, Equity Ownership. Loven:Syros Pharmaceuticals: Employment, Equity Ownership.

scholarly journals Integrated Transcriptomic and Genomic Sequencing Identifies Prognostic Constellations of Driver Mutations in Acute Myeloid Leukemia and Myelodysplastic Syndromes

Blood ◽  
2019 ◽  
Vol 134 (Supplement_2) ◽  
pp. LBA-4-LBA-4 ◽  
Author(s):  
Ilaria Iacobucci ◽  
Manja Meggendorfer ◽  
Niroshan Nadarajah ◽  
Stanley Pounds ◽  
Lei Shi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Transcriptome Sequencing ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Genomic Sequencing ◽  
Expression Data ◽  
Employment Equity ◽  
Equity Ownership ◽  
Acute Myeloid

CG Mullighan and T Haferlach: are co-senior authors Introduction: Recent genomic sequencing studies have advanced our understanding of the pathogenesis of myeloid malignancies, including acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), and improved classification of specific subgroups. Unfortunately, these studies have mostly analyzed specific subtypes and/or used targeted DNA-sequencing, thus limiting discovery of novel mutational patterns and gene expression clusters. Here, we performed an integrated genome-wide mutational/transcriptomic analysis of a large cohort of adult AML and MDS samples to accurately define subtypes of diagnostic, prognostic and therapeutic relevance. Methods: We performed unbiased whole genome (WGS) and transcriptome sequencing (RNA-seq) of 1,304 adult individuals (598 AML and 706 MDS; Fig. 1A), incorporating analysis of somatic and presumed germline sequence mutations, chimeric fusions and structural complex variations. Transcriptomic gene expression data were processed by a rigorous bootstrap procedure to define gene expression subgroups in an unsupervised manner. Associations between genetic variants, gene expression groups and outcome were examined. Results: Genomic/transcriptome sequencing confirmed diagnosis according to WHO 2016 of AML with recurrent genetic abnormalities in 10.9% of cases. These cases had a distinct gene expression profile (Fig. 1A), good prognosis (Fig. 1B) and a combination of mutations in the following genes: KIT, ZBTB7A, ASXL2, RAD21, CSF3R and DNM2 in RUNX1-RUNXT1 leukemia; FLT3, DDX54, WT1 and CALR in PML-RARA promyelocytic leukemia; KIT and BCORL1 in CBFB-rearranged leukemia. In addition, 9% of cases showed rearrangements of KMT2A, with known (e.g. MLLT3) and non-canonical partners (e.g. ACACA, and NCBP1) and poor outcome. Although common targets of mutations have been previously described for myeloid malignancies, the heterogeneity and complexity of mutational patterns, their expression signature and outcome here described are novel. Gene expression analysis identified groups of AML and/or MDS lacking recurrent cytogenetic abnormalities (87%). The spectrum of the most frequently mutated genes (>10 cases) and associated gene expression subtypes is summarized in Figure 1A. TET2 (more frequent in MDS than AML, p=0.0011) and DNMT3A (more frequent in AML than MDS, p<0.0001) were the most frequently mutated genes. Interestingly, mutations in these genes promoting clonal hematopoiesis were significantly enriched in the subgroup with NPM1 mutations. Overall, NPM1 mutations occurred in 27.4% of AML and 1% of MDS and were characterized by four expression signatures with different combination of cooperating mutations in cohesin and signaling genes and outcome (Fig. 1C, gene expression, GE, groups 2, 3, 7 and 8). Co-occurring NPM1 and FLT3 mutations conferred poorer outcome compared to only NPM1, in contrast co-occurring mutations with cohesin genes had better outcome (Fig. 1D). Additional mutations that significantly co-occurred with NPM1 were in PTPN11, IDH1/2, RAD21 and SMC1A. Three gene expression clusters accounted for additional 9% of cases with mutual exclusive mutations in RUNX1,TP53 and CEBPA and co-occurring with a combination of mutations in DNA methylation, splicing and signaling genes (Fig. 1E, GE groups 4, 5 and 6). Interestingly, RUNX1 mutations were significantly associated with SRSF2 mutations but not with SF3B1, showed high expression of MN1 and poor outcome (Fig. 1F). In contrast to the distinct, mutation-associated patterns of gene expression in AML samples, the gene expression profile of MDS was less variable despite diversity in patterns of mutation. MDS was enriched in mutations of SF3B1 (27.2%), mutually exclusive with SFRS2 (14.4%) and U2AF1 (5.5%); TP53 (13.7%) and RUNX1 (10.5%) and a combination of mutations in epigenetic regulators with outcome dependent on mutational pattern (Fig. 1A, G-H). Moreover, structural variations and/or missense mutations of MECOM accounted for 2% of cases. Conclusions: the integration of mutational and expression data from a large cohort of adult pan myeloid leukemia cases enabled the definition of subtypes and constellations of mutations and have prognostic significance that transcends prior gene panel-based classification schema. Disclosures Meggendorfer: MLL Munich Leukemia Laboratory: Employment. Nadarajah:MLL Munich Leukemia Laboratory: Employment. Baer:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Mullighan:Illumina: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: sponsored travel; Pfizer: Honoraria, Other: speaker, sponsored travel, Research Funding; AbbVie: Research Funding; Loxo Oncology: Research Funding; Amgen: Honoraria, Other: speaker, sponsored travel. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

scholarly journals EZH2 Mutations and Impact on Clinical Outcome Analyzed in 1604 Patients with Acute Myeloid Leukemia

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1528-1528
Author(s):  
Sebastian Stasik ◽  
Jan Moritz Middeke ◽  
Michael Kramer ◽  
Christoph Rollig ◽  
Alwin Krämer ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Acute Myeloid Leukemia ◽  
Board Of Directors ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Employment Equity ◽  
Advisory Committees ◽  
Mutational Status ◽  
Equity Ownership ◽  
Acute Myeloid

Abstract Purpose: The enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase and key epigenetic regulator involved in transcriptional repression and embryonic development. Loss of EZH2 activity by inactivating mutations is associated with poor prognosis in myeloid malignancies such as MDS. More recently, EZH2 inactivation was shown to induce chemoresistance in acute myeloid leukemia (AML) (Göllner et al., 2017). Data on the frequency and prognostic role of EZH2-mutations in AML are rare and mostly confined to smaller cohorts. To investigate the prevalence and prognostic impact of this alteration in more detail, we analyzed a large cohort of AML patients (n = 1604) for EZH2 mutations. Patients and Methods: All patients analyzed had newly diagnosed AML, were registered in clinical protocols of the Study Alliance Leukemia (SAL) (AML96, AML2003 or AML60+, SORAML) and had available material at diagnosis. Screening for EZH2 mutations and associated alterations was done using Next-Generation Sequencing (NGS) (TruSight Myeloid Sequencing Panel, Illumina) on an Illumina MiSeq-system using bone marrow or peripheral blood. Detection was conducted with a defined cut-off of 5% variant allele frequency (VAF). All samples below the predefined threshold were classified as EZH2 wild type (wt). Patient clinical characteristics and co-mutations were analyzed according to the mutational status. Furthermore, multivariate analysis was used to identify the impact of EZH2 mutations on outcome. Results: EZH2-mutations were found in 63 of 1604 (4%) patients, with a median VAF of 44% (range 6-97%; median coverage 3077x). Mutations were detected within several exons (2-6; 8-12; 14-20) with highest frequencies in exons 17 and 18 (29%). The majority of detected mutations (71% missense and 29% nonsense/frameshift) were single nucleotide variants (SNVs) (87%), followed by small indel mutations. Descriptive statistics of clinical parameters and associated co-mutations revealed significant differences between EZH2-mut and -wt patients. At diagnosis, patients with EZH2 mutations were significantly older (median age 59 yrs) than EZH2-wt patients (median 56 yrs; p=0.044). In addition, significantly fewer EZH2-mut patients (71%) were diagnosed with de novo AML compared to EZH2-wt patients (84%; p=0.036). Accordingly, EZH2-mut patients had a higher rate of secondary acute myeloid leukemia (sAML) (21%), evolving from prior MDS or after prior chemotherapy (tAML) (8%; p=0.036). Also, bone marrow (and blood) blast counts differed between the two groups (EZH2-mut patients had significantly lower BM and PB blast counts; p=0.013). In contrast, no differences were observed for WBC counts, karyotype, ECOG performance status and ELN-2017 risk category compared to EZH2-wt patients. Based on cytogenetics according to the 2017 ELN criteria, 35% of EZH2-mut patients were categorized with favorable risk, 28% had intermediate and 37% adverse risk. No association was seen with -7/7q-. In the group of EZH2-mut AML patients, significantly higher rates of co-mutations were detected in RUNX1 (25%), ASXL1 (22%) and NRAS (25%) compared to EZH2-wt patients (with 10%; 8% and 15%, respectively). Vice versa, concomitant mutations in NPM1 were (non-significantly) more common in EZH2-wt patients (33%) vs EZH2-mut patients (21%). For other frequently mutated genes in AML there was no major difference between EZH2-mut and -wt patients, e.g. FLT3ITD (13%), FLT3TKD (10%) and CEBPA (24%), as well as genes encoding epigenetic modifiers, namely, DNMT3A (21%), IDH1/2 (11/14%), and TET2 (21%). The correlation of EZH2 mutational status with clinical outcomes showed no effect of EZH2 mutations on the rate of complete remission (CR), relapse free survival (RFS) and overall survival (OS) (with a median OS of 18.4 and 17.1 months for EZH2-mut and -wt patients, respectively) in the univariate analyses. Likewise, the multivariate analysis with clinical variable such as age, cytogenetics and WBC using Cox proportional hazard regression, revealed that EZH2 mutations were not an independent risk factor for OS or RFS. Conclusion EZH mutations are recurrent alterations in patients with AML. The association with certain clinical factors and typical mutations such as RUNX1 and ASXL1 points to the fact that these mutations are associated with secondary AML. Our data do not indicate that EZH2 mutations represent an independent prognostic factor. Disclosures Middeke: Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Membership on an entity's Board of Directors or advisory committees; Roche: Membership on an entity's Board of Directors or advisory committees. Rollig:Bayer: Research Funding; Janssen: Research Funding. Scholl:Jazz Pharma: Membership on an entity's Board of Directors or advisory committees; Abbivie: Other: Travel support; Alexion: Other: Travel support; MDS: Other: Travel support; Novartis: Other: Travel support; Deutsche Krebshilfe: Research Funding; Carreras Foundation: Research Funding; Pfizer: Membership on an entity's Board of Directors or advisory committees. Hochhaus:Pfizer: Research Funding; Incyte: Research Funding; Novartis: Research Funding; Bristol-Myers Squibb: Research Funding; Takeda: Research Funding. Brümmendorf:Janssen: Consultancy; Takeda: Consultancy; Novartis: Consultancy, Research Funding; Merck: Consultancy; Pfizer: Consultancy, Research Funding. Burchert:AOP Orphan: Honoraria, Research Funding; Bayer: Research Funding; Pfizer: Honoraria; Bristol Myers Squibb: Honoraria, Research Funding; Novartis: Research Funding. Krause:Novartis: Research Funding. Hänel:Amgen: Honoraria; Roche: Honoraria; Takeda: Honoraria; Novartis: Honoraria. Platzbecker:Celgene: Research Funding. Mayer:Eisai: Research Funding; Novartis: Research Funding; Roche: Research Funding; Johnson & Johnson: Research Funding; Affimed: Research Funding. Serve:Bayer: Research Funding. Ehninger:Cellex Gesellschaft fuer Zellgewinnung mbH: Employment, Equity Ownership; Bayer: Research Funding; GEMoaB Monoclonals GmbH: Employment, Equity Ownership. Thiede:AgenDix: Other: Ownership; Novartis: Honoraria, Research Funding.

scholarly journals Cohesin-dependent regulation of gene expression during differentiation is lost in cohesin-mutated myeloid malignancies

Blood ◽  
2019 ◽  
Vol 134 (24) ◽  
pp. 2195-2208 ◽  
Author(s):  
Daniel Sasca ◽  
Haiyang Yun ◽  
George Giotopoulos ◽  
Jakub Szybinski ◽  
Theo Evan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Potential Role ◽  
Regulation Of Gene Expression ◽  
Specific Gene ◽  
Myeloid Malignancy ◽  
Erythroid Maturation ◽  
Acute Myeloid

Cohesin mutations are common in myeloid malignancy. Sasca et al elucidate the potential role of cohesin loss in myelodysplastic syndrome and acute myeloid leukemia (MDS/AML). They demonstrate that cohesin binding is critical for erythroid-specific gene expression and that reduction in cohesin impairs terminal erythroid maturation and promotes myeloid malignancy.

Whole-Exome Sequencing Identifies Recurrent Mutations of BCOR in Acute Myeloid Leukemia with Normal Karyotype

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 71-71 ◽  
Author(s):  
Brunangelo Falini ◽  
Vera Grossmann ◽  
Enrico Tiacci ◽  
Antony Holmes ◽  
Alexander Kohlmann ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Exome Sequencing ◽  
Myeloid Leukemia ◽  
Normal Karyotype ◽  
Employment Equity ◽  
Normal Cells ◽  
Genetic Syndrome ◽  
Whole Exome ◽  
Equity Ownership ◽  
Acute Myeloid

Abstract Abstract 71 Acute myeloid leukemia (AML) with normal cytogenetics (CN-AML) represents about half of all adult AML. NPM1 and CEBPA mutations define WHO provisional entities accounting for ∼60% of CN-AML, but the remaining cases (∼40%) remain poorly characterized. To address this issue, we carried out whole-exome-sequencing (WES) of leukemic and normal cells from one patient with CN-AML that lacked mutations in NPM1, CEBPA, FLT3-ITD, and MLL-PTD. Using this approach, we identified a clonal somatic mutation of BCOR, a gene located on chromosome Xp11.4, that was present in the leukemic but not normal cells of the index AML case. The BCOR (BCL6 co-repressor) gene encodes for an ubiquitously expressed nuclear protein that is involved in repressing the activity of BCL6 and other transcriptional factors. BCOR is a key transcriptional regulator of early embryonic development, mesenchymal stem cell function and hemopoiesis. Germline mutations of BCOR are responsible for the oculo-facio-cardio-dental (OFCD) genetic syndrome that is inherited in an X-linked pattern and comprises microphtalmia, dysmorphic appearance, dental abnormalities (radiculomegaly), hammer-toe deformity and cardiac defects. WES findings in the index case were subsequently validated and further studied in a total cohort of 514 AML patients. We first performed deep-sequencing analyses of all exons of the BCOR gene in an initial set of 82 AML cases that were selected because they showed the same genetic characteristics of our index patient (i.e. normal karyotype without NPM1, CEBPA, FLT3-ITD and MLL-PTD mutations). Disruptive BCOR mutations (i.e., nonsense mutations, out-of-frame small indels, and consensus splice-site mutations) were detected in 14/82 (17.1%) of these cases. We next assessed the frequency of BCOR mutations in a series of unselected CN-AML patients (n=262) and found that they occurred in 4.2% of cases, mostly showing the typical features of BCOR-mutated cases (absence of NPM1, CEBPA, FLT3-ITD and MLL-PTD mutations). Almost mutual exclusion of BCOR and NPM1 mutations was further confirmed in a separate series of 71 NPM1-mutated only AML patients. No BCOR mutations were observed in the 89 AML cases with recurrent cytogenetic abnormalities investigated, including t(8;21)(q22;q22) (n= 29), inv(16)(p13q22) (n=40), t(15;17)(q22;q12) (n=10), and t(11q23)/MLL (n=10), and in the 10 patients with double CEBPA-mutated AML studied. BCOR mutations were: i) scattered across the whole length of the coding sequence with no hotspots identified; ii) somatic in origin and disruptive molecular events similar to germline BCOR mutations causing the OFCD genetic syndrome; iii) associated with markedly decreased BCOR mRNA levels, absence of full-length BCOR and absent or low expression of a truncated BCOR protein; iv) almost mutually exclusive with NPM1 (only 1.5% of the 197 NPM1-mutated AML investigated carried BCOR mutations); v) rarely associated with FLT3-ITD; and vi) frequently associated with DNMT3A and RUNX1 mutations, suggesting cooperation with the respective mutated pathways. Clinically, BCOR mutations correlated with poor outcome among the cohort of 160 CN-AML patients evaluated (28.0% versus 66.3% overall survival at 2 years, P=0.024). We also searched for BCOR mutations in the human AML cell lines OCI-AML2, OCI-AML3, KG1a, U937, HL-60, HL-60R, HB4, AML193, and MVP-11. Only HL-60 and HL-60R (a ATRA-resistant derivative of HL-60) carried a BCOR mutation that consisted of a hemizygous G to T transition at position 4616 in exon 10, leading to the Glu1442X nonsense mutation. Western blot analysis of HL-60 cells resulted in the absence of the full-length BCOR protein (predicted MW: 192 kDa) and presence of a low intensity 156 kDa band likely corresponding to a truncated BCOR protein. In conclusion, our results implicate for the first time BCOR in the pathogenesis of CN-AML and suggest it may act as tumor suppressor gene. Disclosures: Grossmann: MLL Munich Leukemia Laboratory: Employment. Kohlmann: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. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

scholarly journals High BAALC expression associates with other molecular prognostic markers, poor outcome, and a distinct gene-expression signature in cytogenetically normal patients younger than 60 years with acute myeloid leukemia: a Cancer and Leukemia Group B (CALGB) study

Blood ◽  
2008 ◽  
Vol 111 (11) ◽  
pp. 5371-5379 ◽  
Author(s):  
Christian Langer ◽  
Michael D. Radmacher ◽  
Amy S. Ruppert ◽  
Susan P. Whitman ◽  
Peter Paschka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Prognostic Factor ◽  
Myeloid Leukemia ◽  
Gene Expression Signature ◽  
Specific Gene ◽  
Stem Cell Markers ◽  
Inverse Association ◽  
Expression Signature ◽  
Acute Myeloid

AbstractBAALC expression is considered an independent prognostic factor in cytogenetically normal acute myeloid leukemia (CN-AML), but has yet to be investigated together with multiple other established prognostic molecular markers in CN-AML. We analyzed BAALC expression in 172 primary CN-AML patients younger than 60 years of age, treated similarly on CALGB protocols. High BAALC expression was associated with FLT3-ITD (P = .04), wild-type NPM1 (P < .001), mutated CEBPA (P = .003), MLL-PTD (P = .009), absent FLT3-TKD (P = .005), and high ERG expression (P = .05). In multivariable analysis, high BAALC expression independently predicted lower complete remission rates (P = .04) when adjusting for ERG expression and age, and shorter survival (P = .04) when adjusting for FLT3-ITD, NPM1, CEBPA, and white blood cell count. A gene-expression signature of 312 probe sets differentiating high from low BAALC expressers was identified. High BAALC expression was associated with overexpression of genes involved in drug resistance (MDR1) and stem cell markers (CD133, CD34, KIT). Global microRNA-expression analysis did not reveal significant differences between BAALC expression groups. However, an analysis of microRNAs that putatively target BAALC revealed a potentially interesting inverse association between expression of miR-148a and BAALC. We conclude that high BAALC expression is an independent adverse prognostic factor and is associated with a specific gene-expression profile.

scholarly journals Chimeric Antigen Receptor-Modified T Cells for the Treatment of Acute Myeloid Leukemia Expressing CD33

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4058-4058 ◽  
Author(s):  
Degang Song ◽  
Michael H. Swartz ◽  
Steve G. Biesecker ◽  
Fernando Borda ◽  
Rutul R. Shah ◽  
...  
Keyword(s):  
T Cells ◽  
Acute Myeloid Leukemia ◽  
Chimeric Antigen Receptor ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Employment Equity ◽  
Car T Cells ◽  
Car T ◽  
Equity Ownership ◽  
Acute Myeloid

Abstract Relapsed acute myeloid leukemia (AML) is an aggressive disease with very poor outcomes. Redirection of T-cell specificity via chimeric antigen receptor (CAR) has shown promising anti-tumor activity in clinical trials, particularly for B cell linage malignancies. CD33 is a transmembrane protein expressed on normal and malignant myeloid-derived cells as well (as on subsets of activated T cells and NK cells). Since this protein is commonly expressed on AML cells, we sought to evaluate the efficacy of targeting AML with CD33-specific CAR-T cells. We generated a lentiviral construct to co-express CD33-specific CAR and a kill switch based on a tag derived from the epidermal growth factor receptor. The latter allows for the conditional elimination of CAR-T cells in vivo. Following transduction of primary T cells, we confirmed CAR and kill switch co-expression by flow cytometry and western blot analyses. Elimination of genetically modified T cells was demonstrated using the clinically-available antibody, cetuximab. CD33 CAR-T cells demonstrated specific cytotoxicity to CD33+ target cell lines. CD33 CAR-T cells were also activated to produce IFNg, TNF, and IL-2 cytokines in response to CD33+ target cells. Furthermore, adoptive transfer of CD33 CAR-T in immunocompromised (NSG) mice bearing established CD33+(CD19neg) AML (MOLM-13) tumor resulted in reduction of tumor burden and improvement of overall survival, compared to control mice receiving CD19 CAR-T cells or no immunotherapy (Figure). Sampling of blood demonstrated the persistence of the CD33 CAR-T cells with no detection of AML (MOLM-13) tumor cells. These pre-clinical data demonstrate the effectiveness of CD33 CAR-T cells in targeting CD33+ AML tumor cells and provide a rationale for future clinical evaluation in AML patients with unmet medical need. Disclosures Song: Intrexon Corporation: Employment, Equity Ownership. Swartz:Intrexon Corporation: Employment, Equity Ownership. Biesecker:Intrexon Corporation: Employment, Equity Ownership. Borda:Intrexon Corporation: Employment. Shah:Intrexon Corporation: Employment, Equity Ownership. Wierda:Genentech: Research Funding; Gilead: Research Funding; Abbvie: Research Funding; Novartis: Research Funding; Acerta: Research Funding. Cooper:MD Anderson Cancer Center: Employment; Intrexon: Equity Ownership; Sangamo BioSciences: Patents & Royalties; Targazyme,Inc.,: Equity Ownership; City of Hope: Patents & Royalties; ZIOPHARM Oncology: Employment, Equity Ownership, Patents & Royalties; Miltenyi Biotec: Honoraria; Immatics: Equity Ownership. Chan:Intrexon Corporation: Employment, Equity Ownership.

scholarly journals A Phase 2 Randomized Study of Low Dose Ara-C with or without Glasdegib (PF-04449913) in Untreated Patients with Acute Myeloid Leukemia or High-Risk Myelodysplastic Syndrome

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 99-99 ◽  
Author(s):  
Jorge E. Cortes ◽  
Florian H. Heidel ◽  
Michael Heuser ◽  
Walter Fiedler ◽  
B. Douglas Smith ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
High Risk ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Low Dose ◽  
P Value ◽  
Employment Equity ◽  
Equity Ownership ◽  
Acute Myeloid

Abstract Background: The Hedgehog signaling pathway (HhP) is aberrantly activated in leukemias and myelodysplastic syndrome (MDS), promoting cancer stem cell maintenance. HhP inhibition reduces leukemic stem cells. Glasdegib is a potent, selective, oral HhP inhibitor, with activity in pre-clinical and clinical studies. The addition of glasdegib to standard chemotherapy (CT) has an acceptable safety profile and appears to have clinical activity in MDS and acute myeloid leukemia (AML). Methods: In this study (NCT01546038), previously untreated AML or high-risk MDS patients (pts) ineligible for intensive CT were randomized 2:1 to receive low-dose cytarabine (LDAC) 20 mg subcutaneously twice a day x 10 days q28 days + oral glasdegib 100 mg daily or LDAC alone for as long as pts received clinical benefit. The primary endpoint was overall survival (OS). The final analysis was conducted after completion of recruitment (Oct 2015) and at least 92 OS events. Results: As of Apr 2016, 132 pts (116 AML, 16 MDS) were randomized to LDAC + glasdegib (n = 88) or LDAC alone (n = 44) (stratified as good/intermediate [int.] vs poor risk) (Table). Demographic and baseline characteristics were similar between arms in median age, baseline cytogenetic risk, and diagnosis. Eighty-four pts received LDAC + glasdegib and 41 pts LDAC alone (7 randomized/not treated pts were followed for survival). Median treatment duration was 83 days for LDAC + glasdegib and 47 days for LDAC alone; median follow up was 14.3 months and 12.4 months, respectively. In the glasdegib arm, 12 pts were continuing treatment and 25 were in follow up; in the LDAC arm, 1 pt was on treatment and 5 in follow up. Cytopenias and gastrointestinal toxicities were the adverse events (AEs) occurring more frequently in the LDAC + glasdegib arm. Hh-associated AEs in the glasdegib arm included dysgeusia (23.8%), muscle spasms (20.2%) and alopecia (10.7%). Serious AEs of febrile neutropenia were more frequent in the glasdegib arm, but sepsis rates were lower and pneumonia rates were similar. The most common cause of death was disease progression in both arms. Grade 2-4 QTcF prolongation was more frequent in the LDAC arm. Investigator-reported complete response (CR) rates were numerically higher for LDAC + glasdegib (n = 17, 15%) vs LDAC alone (n = 1, 2.3%), p-value 0.0142. Based on intent to treat analysis of 96 events, median OS (mOS) for LDAC + glasdegib was 8.3 (80% confidence interval [CI] 6.9, 9.9) vs 4.9 months (80% CI 3.5, 6.0) for LDAC alone (HR 0.511, 80% CI 0.386, 0.675; one-sided log rank p-value 0.0020 stratified by cytogenetic risk). For good/int. risk, mOS for LDAC + glasdegib was 12.2 vs 6.0 months for LDAC alone (HR 0.464, p-value 0.0035). For poor risk, mOS for LDAC + glasdegib was 4.4 vs 2.3 months (HR 0.575, p-value 0.0422). In AML pts, mOS for LDAC + glasdegib was 8.3 vs 4.3 months for LDAC alone (HR 0.462, p-value 0.0004). Conclusions: The addition of glasdegib to LDAC for AML and high-risk MDS pts improved OS compared with LDAC alone. The improvement was consistent among subgroups, particularly in good/int. risk pts. Treatment was associated with an acceptable safety profile. The addition of glasdegib to LDAC may be a treatment option for pts with AML or high-risk MDS. Disclosures Cortes: ARIAD: Consultancy, Research Funding; Bristol-Myers Squib: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Teva: Research Funding. Heuser:Tetralogic: Research Funding; Celgene: Honoraria; Bayer Pharma AG: Research Funding; Novartis: Consultancy, Research Funding; Pfizer: Research Funding; Karyopharm Therapeutics Inc: Research Funding; BerGenBio: Research Funding. Fiedler:Gilead: Other: Travel; Novartis: Consultancy; Ariad/Incyte: Consultancy; Teva: Other: Travel; Pfizer: Research Funding; Kolltan: Research Funding; Amgen: Consultancy, Other: Travel, Patents & Royalties, Research Funding; GSO: Other: Travel. Smith:Actinium Pharmaceuticals, Inc.: Research Funding. Robak:Pfizer: Research Funding. Montesinos Fernandez:Gamida Cell: Consultancy. Ma:Pfizer: Employment, Equity Ownership. Shaik:Pfizer: Employment, Equity Ownership. Zeremski:Pfizer: Employment, Equity Ownership. O'Connell:Pfizer: Employment, Equity Ownership. Chan:Pfizer: Employment, Equity Ownership.

Concomitantly Targeting BCL-2 with Venetoclax (ABT-199/GDC-0199) and MAPK Signaling with Cobimetinib (GDC-0973) in Acute Myeloid Leukemia Models

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2544-2544 ◽  
Author(s):  
Lina Han ◽  
Qi Zhang ◽  
Ce Shi ◽  
Joel Leverson ◽  
Monique Dail ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Cell Lines ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Genetic Alterations ◽  
Leukemia Cells ◽  
Intrinsic Resistance ◽  
Employment Equity ◽  
Equity Ownership ◽  
Acute Myeloid

Abstract Pro-survival molecules including BCL-2 play critical roles in leukemia transformation and chemoresistance. ABT-199/GDC-0199 (venetoclax) is an orally available BH3-mimetic that binds with high affinity to BCL-2, but lacks affinity for BCL-XL and MCL-1. We have recently demonstrated anti-leukemia potency of venetoclax in acute myeloid leukemia (AML) models (Pan et al. Cancer Discovery 2014). However, venetoclax poorly inhibits MCL-1, causing resistance in leukemia cells that rely on MCL-1 for survival. The RAF/MEK/ERK (MAPK) cascade is a major effector pathway in AML that is activated by upstream mutant proteins such as FLT3, KIT and RAS. Additionally, the MAPK pathway regulates BCL-2 family proteins by stabilizing anti-apoptotic MCL-1 and inactivating pro-apoptotic BIM. In this study, we evaluated the anti-tumor effects of concomitant BCL-2 and MAPK blockade by venetoclax in combination with MEK1/2 inhibitor GDC-0973 (cobimetinib).. We initially examined activity of these agents in a panel of myeloid leukemia cell lines with diverse genetic alterations (Fig. 1A). The IC50 values of cobimetinib ranged from < 0.01 µM to > 1 µM after 72 hours of drug treatment but did not correlate with the basal level of p-ERK1/2. In 7 out of 11 cell lines, combination of the agents elicited synergistic growth inhibition. Notably synergism of venetoclax with cobimetinib was observed in venetoclax-resistant cell lines (MOLM14, OCI-AML3, NB4 and THP1). Ongoing analysis of pharmacodynamic markers include transcriptome assessment by RNA sequencing, functional proteomics by reverse phase protein array (RPPA) and quantification of BCL-2:BIM and MCL-1:BIM complexes using the electrochemiluminescent ELISA assay (Meso Scale Discovery, MSD-ELISA). The preliminary MSD data revealed that BCL-2:BIM complex was disrupted in most cell lines and accumulated following cobimetinib treatment, which may be due to the disruption of MCL-1:BIM complex by inhibition of MEK (Fig. 1B). In a long-term culture of primary AML blasts in serum-free stem cell growth medium supplemented with cytokines and StemRegenin 1 (SR1) to main the immature state of leukemia cells, the combination of venetoclax and cobimetinib induced distinct apoptotic cell death, with AML #1 sensitive to venetoclax but resistant to cobimetinib. Alternatively, AML #2 and #3 samples were resistant to venetoclax but sensitive to cobimetinib and the combination of both drugs (Fig. 1C). We next investigated signaling patterns and BCL-2 family protein expression in AML stem/progenitor cells using a 34-antibody panel and time-of-flight mass cytometry (CyTOF). In AML#1, BCL-2 was expressed in leukemia blasts, with enrichment in a progenitor AML population phenotypically defined as CD45dim CD34+ CD38+ CD123+ CD33+ (Fig. 1D). The high expression level of BCL-2 and low expression of MCL-1 and BCL-XL may account for sensitivity to venetoclax in AML#1. Both basal and G-CSF- or SCF-stimulated p-ERK was efficiently down-regulated by cobimetinib; however, G-CSF-evoked p-STAT3/5 and SCF-induced p-AKT were only slightly reduced (Fig. 1E). Notably we observed increased phosphorylation of STAT5 pathway upon treatment with cobimetinib, suggesting that active MAPK signals inhibit phosphorylation of the JAK-STAT pathway, as previously reported (Krasilnikov et al. Oncogene, 2003 and Lee at al. Cancer Cell, 2014). To test the efficacy of both compounds in vivo, we injected NSG mice with genetically engineered OCI-AML3/Luc/GFP cells. Bioluminescent imaging (BLI) demonstrated significantly reduced leukemia burden in treated groups compared to controls, more prominently in the cobimetinib single agent and venetoclax plus cobimetinib co-treated mice (Fig. 1F). The efficacy study is ongoing and median survival for cobimetinib and venetoclax co-treated mice has yet to be determined (Fig. 1G). In summary, our data demonstrates that combinatorial blockade of MAPK and BCL-2 pathways is synergistic in the majority of AML cell lines tested and can overcome intrinsic resistance to venetoclax. Ongoing studies will evaluate efficacy of this combination therapy in primary human AML xenografts and elucidate mechanisms of synergy. Disclosures Leverson: AbbVie: Employment, Equity Ownership. Dail:Genentech: Employment, Equity Ownership. Phillips:AbbVie: Employment, Other: Shareholder, Patents & Royalties. Chen:Abbvie: Employment, Equity Ownership. Jin:Abbvie: Employment, Equity Ownership. Jabbour:Pfizer: Consultancy, Research Funding. Sampath:Genentech: Employment, Equity Ownership. Konopleva:Novartis: Research Funding; AbbVie: Research Funding; Stemline: Research Funding; Calithera: Research Funding; Threshold: Research Funding.

Molecular Characterization of Philadelphia Chromosome Positive Acute Myeloid Leukemia - New Provisional Entity?

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3846-3846
Author(s):  
Simone Weber ◽  
Manja Meggendorfer ◽  
Niroshan Nadarajah ◽  
Karolína Perglerová ◽  
Susanne Schnittger ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Who Classification ◽  
Array Cgh ◽  
Philadelphia Chromosome ◽  
Employment Equity ◽  
Equity Ownership ◽  
Tandem Duplications ◽  
Acute Myeloid ◽  
Philadelphia Chromosome Positive

Abstract Introduction Philadelphia chromosome positive (Ph+) acute myeloid leukemia (Ph+AML) is discussed to be a new provisional entity for the upcoming WHO classification. Whether Ph+AML represents a distinct entity or rather embodies chronic myeloid leukemia in myeloid blast crisis (CML-BC) without preceding clinical manifestation is under debate mostly due to lack of robust criteria to reliably differentiate these two diseases. Further, while Ph+AML is clearly distinguishable from Ph+ acute lymphoblastic leukemia (Ph+ALL) based on immunophenotyping, recent studies demonstrated that Ph+AML retain typical characteristics of lymphoid disease. Aim Ph+AML, CML-BC and Ph+ALL were analyzed by a panel of 24 genes and array CGH to get more insights into these Ph+ leukemias and to potentially define delimiting genetic features. Patients and Methods We examined 24 pts with Ph+AML (11 females/13 males, median age: 58 (24-83)), 11 CML-BC (7 females/4 males, median age: 60 (32-79)) and 11 Ph+ALL (7 females/4 males, median age: 67 (44-77)). AML and ALL were diagnosed according to WHO classification by morphology, MPO and flow cytometry. CML-BC all were diagnosed as CML before and treated accordingly. All cases revealed the BCR-ABL1 fusion gene. Next generation sequencing was performed for ASXL1, BCOR, CBL, CSF3R, DNMT3A, ETV6, FLT3 tyrosine kinase domain(FLT3 -TKD), IDH1/2, JAK1/2/3, KRAS, NPM1, NRAS, PTPN11, RUNX1, TET2, TP53, WT1 and ZRSR2 using the MiSeq Instrument (Illumina, San Diego, CA). Partial tandem duplications in MLL (MLL- PTD), internal tandem duplications in FLT3 (FLT3- ITD)and deletions in IKZF1 were analyzed by quantitative real-time PCR or genescan analysis. 45 cases were investigated by array CGH (Agilent, Waldbronn, Germany). Results With respect to cytogenetic abnormalities besides Philadelphia chromosome, several unbalanced abnormalities were found in Ph+ALL (mean: 9, range: 2-31), while less aberrations were found in Ph+AML and CML-BC (mean: 4, range: 0-28 and mean: 4, range: 0-16, respectively; p=0.03). Of these the most prominent aberrations which were present in all three groups included loss of 7p encompassing IKZF1 (Ph+AML: 7/23, 30%; Ph+ALL: 8/11, 73%; CML-BC: 2/10, 20%), loss of 9p encoding CDKN2A/B (Ph+AML: 2/23, 9%; Ph+ALL: 6/11, 55%; CML-BC: 2/10, 20%) as well as gain of 8q (Ph+AML: 6/23, 26%; Ph+ALL: 3/11, 27%; CML-BC:4/11, 36%). Loss of 5q (5/23, 22%), gain of 13q (4/23, 17%) and loss of 21q (3/23, 9%) was exclusively present in Ph+AML. While in Ph+ALL loss of 10q (3/11, 27%), 2p (3/11, 18%), 11q (3/11, 18%) and gain of 4q (3/11, 18%) was exclusively found. Regarding recurrent balanced aberrations no rearrangements were found in Ph+AML and Ph+ALL, while 3/11 (27%) CML-BC pts harbored balanced 3q26-rearrangements. With respect to molecular genetics, alterations were found in 15/24 (63%) Ph+AML, 8/11 (73%) CML-BC and 8/11 (73%) Ph+ALL pts. Commonly shared molecular aberrations were deletions in IKZF1 (Ph+AML: 3/24, 13%; Ph+ALL: 8/11, 73%; CML-BC: 2/10, 20%) as well as mutations (mut) in RUNX1 (Ph+AML: 5/19, 26%; Ph+ALL: 1/7, 14%; CML-BC: 5/10, 50%). Further, mut found in Ph+AML and CML-BC affected ASXL1 (Ph+AML: 2/22, 9%; CML-BC: 2/11, 18%) and IDH1 (Ph+AML: 2/22, 9%; CML-BC: 1/11, 9%). Additionally, Ph+AML harbored alterations in TP53 (3/21, 14%), TET2 (2/21, 10%) and DNMT3A (1/20, 5%). For CML-BC, additional mut were found in WT1 (2/9, 22%), ETV6 (1/9, 11%) and KRAS (1/9, 11%). Regarding FLT3 -ITD, NPM1 and the remaining genes no alterations were found. Overall, Ph+ALL differed from the combined cohort of Ph+AML and CML-BC in that mut in ASXL1, DNMT3A, ETV6, IDH1, KRAS, TET2 and WT1 as well as MLL -PTD occurred not in the former but only in the latter (12/31 cases with at least one gene mutated, p=0.07). Intriguingly, the mean±SD number of mut in these genes did not significantly differ between Ph+AML and CML-BC cases (0.36±0.58 vs. 0.67±0.71, p=0.23). Conclusion Comparing cytogenetic alterations Ph+AML could be clearly distinguished from CML-BC or Ph+ALL by harboring loss of 5q and gain of 13q, which are typically found in myeloid diseases. Beside, Ph+AML and CML-BC showed a high frequency of molecular mutations which were hardly found in Ph+ALL. This data supports the concept discussed by the WHO that Ph+AML is a specific entity and can be distinguished from CML-BC and Ph+ALL. However, further studies are warranted to define the most appropriate parameters to distinguish Ph+AML from CML-BC. Disclosures Weber: MLL Munich Leukemia Laboratory: Employment. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Nadarajah:MLL Munich Leukemia Laboratory: Employment. Perglerová:MLL2 s.r.o.: Employment. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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