scholarly journals DNA Methyltransferase Inhibitors Promote Homologous Recombination Deficiency through Induction of Immune Signaling, Sensitizing Acute Myeloid Leukemia Cells to PARP Inhibitors

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3763-3763
Author(s):  
Aksinija A Kogan ◽  
Lena J Mclaughlin ◽  
Maria R. Baer ◽  
Stephen Baylin ◽  
Michael Topper ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Homologous Recombination ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Dna Methyltransferase ◽  
Immune Signaling ◽  
Dna Methyltransferase Inhibitors ◽  
Acute Myeloid

Acute myeloid leukemia (AML) patients unfit for intensive chemotherapy are treated with DNA methyltransferase inhibitors (DNMTis). However, while many AML patients respond to DNMTis, responses are not durable. We previously reporteda novel treatment strategy for AML that combines DNMTis with poly (ADP-ribose) polymerase inhibitors (PARPis), drugs classically used to treat breast and ovarian cancer patients with BRCA mutations and homologous recombination defects (HRD) (Faraoni and Graziani, 2018). We found that combining low doses of the potent PARP-trapping PARPi talazoparib with DNMTis increases PARP trapping and cytotoxicityin vitroand increases therapeutic efficacy in vivo (Muvarak et al, 2016). We have nowidentified a novel mechanism through which DNMTis may sensitize BRCA-proficient AML cells to PARPis. This mechanism is tied to the capacity of these drugs to reprogram cancer signaling networks, including altering DNA repair pathways (Tsai et al, 2012). In studies in AML cell lines (N=6) and peripheral blood mononuclear cells (PBMCs) from AML patients (N=4), we now show that treatment with the DNMTi decitabine (DAC) at a low concentration (10nM) can directly induce HRD, by significantly (p<0.01) down-regulating key genes central to HR activity, including multiple genes in the Fanconi anemia (FA) pathway, as a mechanism for enhanced PARPi sensitivity. How do DNMTis downregulate HR gene expression? We show for the first time that immune signaling is linked to induction of HRD. We have previously shown that DNMTis activate innate immune pathways involving interferon (IFN) □ and tumor necrosis factor (TNF) □, a phenomenon known as viral mimicry (Chiappinelli et al, 2015).First, The Cancer Genome Atlas (TCGA) AML data sets show an inverse correlation between type 1 interferon (IFN)/pro-inflammatory response and HR-related genes. Second, we verified in BRCA-proficient AML cell lines (N=6) that immune signaling by exogenous TNF□□or IFN□□treatment decreases HR gene expression and activity by more than two-fold for the majority of genes tested (p<0.0001). Third, treatment of AML cells with IFN□and the signal transducer and activator of transcription (STAT) 1/3 inhibitor ruxolitinib can rescue DAC-induced HRD. Importantly, we identified a common immune signaling pathway induced by both DNMTis and PARPis. PARPis have also been shown to activate type 1 IFN pathways via induction of cytoplasmic double-stranded DNA sensing through signaling of the cyclic GMP-AMP Synthase - Stimulator of Interferon Genes(cGAS-STING) pathway. We now find that inhibition of STING with inhibitor H-151 (500nM) not only rescues immune signaling induced by PARPi, but also by DAC and PARPi combination treatment. Moreover, the STING inhibitor also rescues DAC- and/or PARPi-induced HRD. These data suggest that STING may be a central signaling hub linked to HRD and also suggest ways in which epigenetic therapy, inhibitors of DNA damage response proteins, and targeted immune therapy can synergize to treat AML. Disclosures Baer: Takeda: Research Funding; Incyte: Research Funding; Kite: Research Funding; Forma: Research Funding; AI Therapeutics: Research Funding; Abbvie: Research Funding; Astellas: Research Funding.

scholarly journals Prospective Identification of Acute Myeloid Leukemia Patients Who Benefit from Gene-Expression Based Risk Stratification

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1397-1397
Author(s):  
Diego Chacon ◽  
Ali Braytee ◽  
Yizhou Huang ◽  
Julie Thoms ◽  
Shruthi Subramanian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Risk Stratification ◽  
Genetic Risk ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Risk Groups ◽  
High Fidelity ◽  
Improve Outcome ◽  
Acute Myeloid

Background: Acute myeloid leukemia (AML) is a highly heterogeneous malignancy and risk stratification based on genetic and clinical variables is standard practice. However, current models incorporating these factors accurately predict clinical outcomes for only 64-80% of patients and fail to provide clear treatment guidelines for patients with intermediate genetic risk. A plethora of prognostic gene expression signatures (PGES) have been proposed to improve outcome predictions but none of these have entered routine clinical practice and their role remains uncertain. Methods: To clarify clinical utility, we performed a systematic evaluation of eight highly-cited PGES i.e. Marcucci-7, Ng-17, Li-24, Herold-29, Eppert-LSCR-48, Metzeler-86, Eppert-HSCR-105, and Bullinger-133. We investigated their constituent genes, methodological frameworks and prognostic performance in four cohorts of non-FAB M3 AML patients (n= 1175). All patients received intensive anthracycline and cytarabine based chemotherapy and were part of studies conducted in the United States of America (TCGA), the Netherlands (HOVON) and Germany (AMLCG). Results: There was a minimal overlap of individual genes and component pathways between different PGES and their performance was inconsistent when applied across different patient cohorts. Concerningly, different PGES often assigned the same patient into opposing adverse- or favorable- risk groups (Figure 1A: Rand index analysis; RI=1 if all patients were assigned to equal risk groups and RI =0 if all patients were assigned to different risk groups). Differences in the underlying methodological framework of different PGES and the molecular heterogeneity between AMLs contributed to these low-fidelity risk assignments. However, all PGES consistently assigned a significant subset of patients into the same adverse- or favorable-risk groups (40%-70%; Figure 1B: Principal component analysis of the gene components from the eight tested PGES). These patients shared intrinsic and measurable transcriptome characteristics (Figure 1C: Hierarchical cluster analysis of the differentially expressed genes) and could be prospectively identified using a high-fidelity prediction algorithm (FPA). In the training set (i.e. from the HOVON), the FPA achieved an accuracy of ~80% (10-fold cross-validation) and an AUC of 0.79 (receiver-operating characteristics). High-fidelity patients were dichotomized into adverse- or favorable- risk groups with significant differences in overall survival (OS) by all eight PGES (Figure 1D) and low-fidelity patients by two of the eight PGES (Figure 1E). In the three independent test sets (i.e. form the TCGA and AMLCG), patients with predicted high-fidelity were consistently dichotomized into the same adverse- or favorable- risk groups with significant differences in OS by all eight PGES. However, in-line with our previous analysis, patients with predicted low-fidelity were dichotomized into opposing adverse- or favorable- risk groups by the eight tested PGES. Conclusion: With appropriate patient selection, existing PGES improve outcome predictions and could guide treatment recommendations for patients without accurate genetic risk predictions (~18-25%) and for those with intermediate genetic risk (~32-35%). Figure 1 Disclosures Hiddemann: Celgene: Consultancy, Honoraria; Roche: Consultancy, Honoraria, Research Funding; Bayer: Research Funding; Vector Therapeutics: Consultancy, Honoraria; Gilead: Consultancy, Honoraria; Janssen: Consultancy, Honoraria, Research Funding. Metzeler:Celgene: Honoraria, Research Funding; Otsuka: Honoraria; Daiichi Sankyo: Honoraria. Pimanda:Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Beck:Gilead: Research Funding.

A Precision Medicine Approach Incorporating Both Molecular and In Vitro Functional Data to Treat Patients with Relapsed/Refractory Acute Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4043-4043
Author(s):  
Pamela S. Becker ◽  
Sylvia Chien ◽  
Timothy J Martins ◽  
Andrew Herstein ◽  
Cody Hammer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Precision Medicine ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Expression Data ◽  
Allogeneic Transplant ◽  
Choice Of Treatment ◽  
Acute Myeloid

Abstract Introduction: Acute myeloid leukemia (AML) is a heterogeneous disorder such that each patient exhibits a unique pattern of mutations. Nevertheless, standard treatment approaches are largely used for all patients with the exception of those with the PML-RARA translocation or FLT3 mutations. We are conducting a feasibility study, "Individualized Treatment for Relapsed/Refractory Acute Leukemia Based on Chemosensitivity and Genomics/Gene Expression Data" (NCT02551718). This abstract summarizes the results in the AML patients. . Methods: The primary objective of this trial is to test the feasibility of rapidly assessing patient cells using a high throughput assay for in vitro drug sensitivity with individual drugs and drug combinations and mutation profiling by next generation sequencing (NGS) of 194 genes (MyAML) to enable prompt initiation of optimal therapy. The secondary objective is to evaluate the response to the chosen therapy. The eligibility criteria include diagnosis of acute leukemia, age ≥ 3, relapsed after or refractory to 2 prior lines of therapy, ECOG ≤ 3, and adequate organ function. The high throughput screen (HTS) is performed at a core facility under CLIA. The custom Oncopanel1 contains 160 drugs and drug combinations, including FDA approved and investigational agents, targeted agents including kinase, mTOR, proteasome, HDAC and other inhibitors, and chemotherapy drugs including alkylators, purine analogs, topoisomerase inhibitors and others. Patient blood or marrow samples enriched for leukemia cells are analyzed for survival after a 72-hour exposure to 8 customized drug concentrations spanning 4 logs in duplicate in 384 well plates adherent to matrix protein. DNA and RNA are isolated from the same enriched cell fractions for NGS (MyAML) and RNAseq. MyAML analyzes genes at high depth, including breakpoint hotspot loci with optimized detection of large insertion and deletions and other structural variants found in AML. Results: Fourteen patients signed consent, and 11 AML patients were enrolled in the study to date. Seven patients had unfavorable and 4 intermediate cytogenetic risk. Four were primary refractory, 5 had antecedent hematologic disorder. The average number of prior regimens was 4 (range 2 to 6). Six patients had relapsed within ≤3 months after allogeneic transplant, prior to enrollment on this study. HTS results were obtained within an average of 5.5 days; mutation testing was obtained within an average of 13 days (range 9-17), return time after receipt at MyAML was on average 8 (range 7-12) days. Drug regimens were chosen within 1-2 weeks from testing. For 2 patients, treatment start was delayed by about one month to allow recovery from toxicity from prior therapy. For the other patients, treatment was initiated on average 7.8, median 8 (range 4-11) days from start of testing. Of 7 patients treated so far, the median overall survival was 171 days, range 70 to >289 days. Regimens chosen based on HTS results, mutation analysis, and ability to obtain FDA approved drugs off label included: bortezomib (B)/daunorubicin/cytarabine, romidepsin, B/azacitidine (Aza), B/idarubicin (2 patients),cladribine, omacetaxine (HHT) then HHT/cytarabine, B/Aza/sorafenib, gemcitabine, bortezomib, sorafenib. Mutation analysis revealed previously unknown potential targets in those patients, including ABL kinase, FLT3 ITD in 2 patients, and FLT3 TKD mutations that led to choice of treatment with imatinib, sorafenib, and investigational Flt3 inhibitor for 4 patients, respectively. Other potentially targetable mutations identified included IDH1/2, NRAS, KRAS, KIT, TP53, WT1, and others (Table). None of these very heavily pre-treated patients obtained a complete remission, but 3 remain alive > 1 yr post early relapse after allogeneic transplant. One patient's marrow exhibited decline in blasts from 82% to 24%, and all patients exhibited a decline in circulating blasts with the chosen treatments. Conclusion: This trial has proven that application of rapid molecular and functional screening to choice of treatment for patients with advanced acute myeloid leukemia is feasible. Direct comparison of this precision medicine approach to results obtained with standard trials is planned. These data and the responses and correlation with gene expression data will contribute to a future algorithm to optimize precision medicine approaches to leukemia therapy. Table Table. Disclosures Becker: JW Pharmaceutical: Research Funding; Millennium: Research Funding; Glycomimetics: Research Funding; Pfizer: Other: Scientific Steering Committee for a post marketing study; Amgen: Research Funding; CVS Caremark: Other: Accordant Health Services Medical Advisory Board; Abbvie: Research Funding; Invivoscribe: Honoraria. Patay:Invivoscribe, Inc: Consultancy. Carson:Invivoscribe, Inc: Employment. Radich:Novartis: Consultancy, Other: laboratory contract; Bristol-MyersSquibb: Consultancy; TwinStrand: Consultancy; ARIAD: Consultancy; Pfizer: Consultancy.

scholarly journals Variants ofDNMT3Acause transcript-specific DNA methylation patterns and affect hematopoiesis

2018 ◽  
Vol 1 (6) ◽  
pp. e201800153 ◽  
Author(s):  
Tanja Božić ◽  
Joana Frobel ◽  
Annamarija Raic ◽  
Fabio Ticconi ◽  
Chao-Chung Kuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Hematopoietic Differentiation ◽  
Hematopoietic Stem ◽  
Acute Myeloid

De novo DNA methyltransferase 3A (DNMT3A) plays pivotal roles in hematopoietic differentiation. In this study, we followed the hypothesis that alternative splicing ofDNMT3Ahas characteristic epigenetic and functional sequels. SpecificDNMT3Atranscripts were either down-regulated or overexpressed in human hematopoietic stem and progenitor cells, and this resulted in complementary and transcript-specific DNA methylation and gene expression changes. Functional analysis indicated that, particularly, transcript 2 (coding for DNMT3A2) activates proliferation and induces loss of a primitive immunophenotype, whereas transcript 4 interferes with colony formation of the erythroid lineage. Notably, in acute myeloid leukemia expression of transcript 2 correlates with its in vitro DNA methylation and gene expression signatures and is associated with overall survival, indicating thatDNMT3Avariants also affect malignancies. Our results demonstrate that specificDNMT3Avariants have a distinct epigenetic and functional impact. Particularly, DNMT3A2 triggers hematopoietic differentiation and the corresponding signatures are reflected in acute myeloid leukemia.

The Actin Binding Protein Plastin-3 Is Involved in the Pathogenesis of Acute Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1662-1662
Author(s):  
Arne Velthaus ◽  
Kerstin Cornils ◽  
Saskia Grüb ◽  
Hauke Stamm ◽  
Daniel Wicklein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Stromal Cells ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Binding Protein ◽  
Actin Binding ◽  
Actin Binding Protein ◽  
Mutational Status ◽  
Acute Myeloid

Abstract Leukemia-initiating cells reside within the bone marrow (BM) in specialized niches where they undergo complex interactions with their surrounding stromal cells. In order to identify genes being implicated in the interaction of acute myeloid leukemia (AML) cells and stromal cells, we performed co-cultures of primary AML cells with primary endothelial cells and osteoblasts. The gene expression of co-cultured AML blasts was compared to AML cells grown without adherent cells using microarray analysis. Amongst those genes being dysregulated upon co-culture was the actin binding protein plastin-3 (PLS3). Further RT-qPCR analysis revealed an endogenous PLS3 expression in about 50% of BM samples from AML patients (n=25). In contrast, expression of PLS3 was only detected in 2 of 12 analyzed AML cell lines with Kasumi-1 showing strong and THP-1 showing only weak expression. Therefore, functional analysis of PLS3 in AML was studied using shRNA knockdown and overexpression of PLS3 in Kasumi-1 cells. We could show that PLS3 has an impact on the colony formation capacity of AML cells in vitro as the knockdown resulted in significantly reduced colony numbers while increased colony growth was observed in the Kasumi-1 cells overexpressing PLS3 (p<0.001 and p<0.001, respectively). To investigate the role of PLS3 in vivo, NSG mice were transplanted with the PLS3 knockdown Kasumi-1 cells. Compared to mice transplanted with Kasumi-1 cells transduced with a vector carrying a scrambled shRNA, the PLS3 knockdown mice survived significantly longer (median survival time 64 vs. 110 days, respectively; p<0.001; n=9 mice per group). Finally, we investigated whether the expression of PLS3 was associated with AML patients' outcome using published microarray-based gene expression data (Verhaak et al, Haematologica 2009;94). Clinical data of 290 AML patients were available. Based on the mean gene expression value, the patient cohort was divided into high vs low PLS3 expressors. The overall survival was analyzed in a multivariate Cox proportional hazards model including PLS3 gene expression and the baseline parameters age, karyotype and FLT3 mutational status. After a stepwise removal of insignificant terms, the patient's age and a high PLS3 expression remained as independent prognostic survival markers (for PLS3: HR 1.58 (CI 1.05 - 2.37) and for age: HR 1.01 (CI 1.00 - 1.03)). In conclusion, our results identify the actin binding protein PLS3 as potential novel therapeutic target in AML. Disclosures Stamm: Astellas: Other: Travel, Accommodation, Expenses. Heuser:BerGenBio: Research Funding; Tetralogic: Research Funding; Novartis: Consultancy, Research Funding; Celgene: Honoraria; Bayer Pharma AG: Research Funding; Pfizer: Research Funding; Karyopharm Therapeutics Inc: Research Funding. Fiedler:Kolltan: Research Funding; Ariad/Incyte: Consultancy; Novartis: Consultancy; Gilead: Other: Travel; Teva: Other: Travel; GSO: Other: Travel; Pfizer: Research Funding; Amgen: Consultancy, Other: Travel, Patents & Royalties, Research Funding. Wellbrock:Astellas: Other: Travel, Accommodation, Expenses.

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 Tipifarnib Modulates Interferon (IFN)-γ-Inducible Genes in Acute Myeloid Leukemia

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 2726-2726
Author(s):  
Jayakumar Vadakekolathu ◽  
Stephen Reeder ◽  
Clare Coveney ◽  
Sergio Rutella
Keyword(s):  
Gene Expression ◽  
Dna Damage ◽  
Acute Myeloid Leukemia ◽  
In Silico ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Gene Signature ◽  
Ifn Γ ◽  
Kg1 Cells ◽  
Acute Myeloid

Background Acute myeloid leukemia (AML) is a molecularly and clinically heterogeneous hematological malignancy. Chemotherapy resistance is common, and relapse is the major cause of treatment failure. Investigation of new molecularly-targeted and immunomodulating agents therefore remains a high priority. Interferon (IFN)-γ regulates inflammatory responses and tumor immunosurveillance. Prolonged IFN-γ signaling may promote immune-independent resistance to genotoxic anti-cancer therapies. Herein, we aimed to establish whether tipifarnib, a farnesyl-transferase and CXCL12/CXCR4 pathway inhibitor currently being tested in phase I/II clinical trials in individuals with myeloid malignancies, modulates IFN-γ signaling. Methods We previously defined an IFN-γ-responsiveness gene signature in AML cell lines (Vadakekolathu J, et al. Blood 2017; 130: 3945A). Herein, we employed targeted gene expression profiling for the high-dimensional analysis of canonical signaling pathways and their modulation by tipifarnib in Kasumi-1 AML cells [AML with t(8;21)] and KG1 AML cells (leukemia stem cell [LSC]-like AML). AML cells were either incubated with 100 nM or 500 nM tipifarnib for 6 hours, or left untreated, prior to in vitro challenge with 10 ng/mL IFN-γ for 24 hours. RNA (approximately 100 ng per sample) was incubated with a reporter and capture probe mix for hybridization (mRNA Pan-Cancer Pathways Panel; NanoString Technologies, Seattle, USA). Transcript counts were analyzed on the nCounter FLEX analysis system. The nSolver™ software package and nSolver Advanced Analysis module were used for quality controls. The captured transcript counts were normalized to the geometric mean of the housekeeping reference genes included in the assay and the code set's internal positive controls. Differentially expressed genes were assessed in silico for correlations with clinical-biological disease characteristics and potential prognostic value in The Cancer Genome Atlas (TCGA)-AML cases (162 sequenced AML samples with putative copy-number alterations, mutations and mRNA expression z-scores [threshold±2.0]). Results Unsupervised hierarchical clustering of mRNA expression identified a set of IFN-γ-stimulated genes (ISGs) that were up-regulated (>2.0 fold-change compared with baseline) in Kasumi-1 cells, but not in KG1 cells, in response to IFN-γ treatment. When assessed in silico for prognostic power in TCGA-AML patients treated with curative intent on a '7+3' chemotherapy backbone, ISGs in our experimentally-derived signature (SOCS1, FAS, ETV7, IL15, SOCS3, PIM1, TNFSF10, STAT1, PLAT, PRDM1, CASP7, BCL2A1) were either up-regulated, amplified, deleted or mutated in 59 (36%) of queried samples. Patients with abnormalities of ISGs experienced worse clinical outcomes, as indicated by shorter relapse-free-survival (RFS; median 12.1 versus 24.2 months in AML patients without ISG abnormalities, p=0.041) and shorter overall survival (OS; median 11.8 versus 24.8 months in AML patients without ISG abnormalities, p=0.036). Interestingly, abnormalities in ISGs significantly correlated with TP53 mutations (log ratio= 1.65; p=0.026), an established adverse prognosticator in AML. Pre-treatment with tipifarnib at either 100 nM or 500 nM concentration attenuated IFN-γ-induced changes in gene expression in Kasumi-1 AML cells (Fig. 1A), including the down-regulation of Wnt, Ras, Hedgehog and Notch signaling and the up-regulation of genes implicated in DNA damage response (Fig. 1B). In contrast, tipifarnib exerted no effects on cancer-associated canonical pathways in IFN-γ-unresponsive KG1 cells (Fig. 1A). Conclusions Our study shows that an experimentally-derived IFN-γ responsiveness gene signature correlates with poor clinical outcomes in AML and suggests that tipifarnib might attenuate IFN-γ signaling, potentially affecting AML susceptibility to DNA damage induced by chemotherapeutic agents. Grant support: Qatar National Research Fund (#NPRP8-2297-3-494) and Kura Oncology, San Diego, CA, USA. Figure 1 Disclosures Rutella: MacroGenics, Inc.: Research Funding; NanoString Technologies, Inc.: Research Funding; Kura Oncology: Research Funding.

scholarly journals SIRT6 Inhibition As a Novel Approach for Treating Acute Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5222-5222
Author(s):  
Michele Cea ◽  
Antonia Cagnetta ◽  
Debora Soncini ◽  
Paola Minetto ◽  
Davide Lovera ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Dna Damage ◽  
Dna Repair ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Allogeneic Bone ◽  
A Genome ◽  
Acute Myeloid

Abstract Currently available therapeutics against Acute Myeloid Leukemia (AML) have improved patient outcome. However, resistance develops even to novel therapies and patient overall survival remains low, especially for patients who are not eligible for allogeneic bone marrow transplantation. Therefore, there is an urgent need to overcome the biologic mechanisms underlying drug resistance in AML, to enhance the efficacy of existing treatments and to facilitate the design of novel approaches. Recently, our group has demonstrated that SIRT6, a NAD+-dependent histone deacetylase involved in genome maintenance, is frequently up-regulated in Multiple Myeloma and its targeting induces cancer cell killing (Cea M. et al, Blood 2016). Furthermore, gene expression analyses performed by our groups show that SIRT6 is also up-regulated in AML and confers poor prognosis in a series of 200 primary AML cases from our Hematology Clinic. Thus, these data suggested a role for SIRT6 in AML biology. High SIRT6 expression was typically observed in AML cell lines characterized by constitutive DNA damage and intense replicative stress. Likewise, primary AML cases exhibiting an intermediate-to-high chromosome instability (CIN) gene expression signature were also those with the highest SIRT6 expression, and worst prognosis. Subsequent studies demonstrated that SIRT6 silencing or its chemical inhibition, as observed in Multiple Myeloma exacerbates DNA damage in response to genotoxic agents, sensitizing AML cells to cytarabine (ARA-C) and idarubicin in vitro. Overall, enhancing genotoxic stress while concomitantly blocking DNA double-strand breaks (DSBs) repair response, may represent an innovative strategy to increase chemosensitivity of AML cells. Mechanistic studies revealed that SIRT6 acts as a genome guardian in AML cells by binding DNA damage sites and activating DNA-PKcs and CtIP by deacetylation, which in turn promotes DNA repair. Overall our data suggest that genomic instability is present in all hematologic malignancies including AML. Strategies aimed to shift the balance towards high DNA damage and reduced DNA repair by SIRT6 inhibition can decrease AML growth and may benefit patients with otherwise unfavorable outcomes. Disclosures Gobbi: Gilead: Honoraria; Takeda: Consultancy; Janssen: Consultancy, Honoraria; Roche: Honoraria; Celgene: Consultancy; Mundipharma: Consultancy, Research Funding; Novartis: Consultancy, Research Funding.

scholarly journals A Novel Combination Regimen of BET and FLT3 Inhibition for FLT3-ITD Acute Myeloid Leukemia

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1373-1373
Author(s):  
Lauren Lee ◽  
Yoshiyuki Hizukuri ◽  
Paul Severson ◽  
Ben Powell ◽  
Chao Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Culture Medium ◽  
Tumor Regression ◽  
Bone Marrow Stroma ◽  
Marrow Stroma ◽  
Acute Myeloid

Background: Acute myeloid leukemia patients with FLT3-ITD mutations have a high risk of relapse and death. FLT3 tyrosine kinase inhibitors such as quizartinib and gilteritinib improve overall survival in relapsed patients, but their efficacy is limited and most such patients die of the disease. This is because even with potent FLT3 inhibition, the disease persists within the bone marrow microenvironment, mainly due to bone marrow stroma activating parallel signaling pathways that maintain pro-survival factors. BET inhibitors suppress pro-survival factors such as c-Myc and Bcl2, but these drugs thus far have shown only limited single-agent clinical potential. PLX51107 is a novel BET inhibitor designed to inhibit BET activity in intermittent daily fashion to allow for greater tolerability. We investigated whether the addition of PLX51107 to potent FLT3 inhibition with quizartinib could overcome the protective effect of the bone marrow stroma through inhibition of c-Myc expression. Methods: We developed a plasma inhibitory activity assay for c-Myc (c-Myc PIA) to assess in vivo efficacy of the PLX51107 in patients and to identify c-Myc-inhibitory doses of the drug. We tested PLX51107 alone and in combination with quizartinib in murine models of AML and against primary FLT3-ITD AML cells co-cultured with human bone marrow stroma. In addition, we analyzed gene expression patterns in the treatment models to explore the basis of any observed synergistic cytotoxic effect. Results: In a murine xenograft model of AML using MV4-11 cells, PLX51107 alone induced suppression of tumor growth in association with a 90% decrease in c-Myc gene expression. The combination of PLX51107 and quizartinib induced complete tumor regression in 5 out of 7 animals after 14 days of treatment (Figure 1). Animals treated with a 5-day course of quizartinib alone displayed tumor regression persisting until day 26 of treatment, while the addition of PLX51107 resulted in tumor regression until day 39. In patients treated with a dose of 120 mg/day of PLX51107, the c-Myc PIA demonstrated a robust suppression of c-Myc expression for roughly 6 hours, returning to baseline between 7 and 9 hours post-treatment (Figure 2). The mean plasma concentration to achieve this inhibition was 3.3 uM, which, accounting for the difference in protein drug binding between plasma and culture medium with 10% FBS, corresponded to a concentration of 250 nM PLX51107 in culture medium. With this same concentration and schedule (i.e., at concentrations and exposure times equivalent to what human patients would experience taking 120 mg daily of PLX51107 and 60 mg daily of quizartinib), the combination induced synergistic cytotoxicity in a series of 10 different FLT3-ITD AML patient blast samples co-cultured with bone marrow stroma (Figure 3). C-Myc RNA and protein were directly suppressed in these primary samples, and ingenuity pathway analysis of RNA expression confirmed that c-Myc associated genes displayed the highest level of down-regulation. Conclusions: These studies suggest that combination therapy with approximately 120 mg/day PLX51107 and 60 mg/day quizartinib will be a more effective therapy for relapsed FLT3-ITD AML than 60 mg/day of quizartinib alone. The combination of FLT3 inhibition and BET inhibition may represent an attractive therapeutic option for FLT3-ITD AML. Disclosures Hizukuri: Daiichi Sankyo Co, Ltd: Employment. Severson:Plexxikon Inc.: Employment. Powell:Plexxikon Inc.: Employment. Zhang:Plexxikon Inc.: Employment. Ma:Plexxikon Inc: Employment. Narahara:Daiichi Sankyo Co, Ltd: Employment. Sumi:Daiichi Sankyo, Inc.: Employment. Bollag:Plexxikon Inc.: Employment. Levis:FUJIFILM: Consultancy, Research Funding; Daiichi Sankyo Inc: Consultancy, Honoraria; Agios: Consultancy, Honoraria; Astellas: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Amgen: Consultancy, Honoraria; Menarini: Consultancy, Honoraria.

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