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

Cancers ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1663 ◽  
Author(s):  
Arne Velthaus ◽  
Kerstin Cornils ◽  
Jan K. Hennigs ◽  
Saskia Grüb ◽  
Hauke Stamm ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Binding Protein ◽  
Actin Binding ◽  
Bone Marrow Niche ◽  
Actin Binding Protein ◽  
Acute Myeloid

Leukemia-initiating cells reside within the bone marrow in specialized niches where they undergo complex interactions with their surrounding stromal cells. We have identified the actin-binding protein Plastin-3 (PLS3) as potential player within the leukemic bone marrow niche and investigated its functional role in acute myeloid leukemia. High expression of PLS3 was associated with a poor overall and event-free survival for AML patients. These findings were supported by functional in vitro and in vivo experiments. AML cells with a PLS3 knockdown showed significantly reduced colony numbers in vitro while the PLS3 overexpression variants resulted in significantly enhanced colony numbers compared to their respective controls. Furthermore, the survival of NSG mice transplanted with the PLS3 knockdown cells showed a significantly prolonged survival in comparison to mice transplanted with the control AML cells. Further studies should focus on the underlying leukemia-promoting mechanisms and investigate PLS3 as therapeutic target.

The actin binding protein plastin-3 is involved in the pathogenesis of acute myeloid leukemia

2017 ◽  
Vol 53 ◽  
pp. S58
Author(s):  
Jasmin Wellbrock ◽  
Arne Velthaus ◽  
Kerstin Cornils ◽  
Saskia Grüb ◽  
Hauke Stamm ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Binding Protein ◽  
Actin Binding ◽  
Actin Binding Protein ◽  
Acute Myeloid

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.

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.

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 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.

Characterization of NPM1-Mutated/FLT3 ITD-Negative Acute Myeloid Leukemia with Normal Karyotype by Gene Expression Profiling.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 155-155 ◽  
Author(s):  
Lars Bullinger ◽  
Konstanze Dohner ◽  
Raphael Kranz ◽  
Frank G. Rucker ◽  
Stefan Frohling ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Expression Pattern ◽  
Myeloid Leukemia ◽  
Gene Expression Pattern ◽  
Normal Karyotype ◽  
Molecular Profile ◽  
Data Set ◽  
Mutational Status ◽  
Acute Myeloid

Abstract Acute myeloid leukemia (AML) with normal karyotype comprises a large number of molecularly distinct variants. For example the presence of internal tandem duplications (ITDs) of the FLT3 (fms-related tyrosine kinase 3) gene is associated with poor outcome, whereas mutations of the NPM1 (nucleophosmin) gene are prognostically favorable. However, this effect is mainly attributed to the NPM1-mutated/FLT3 ITD-negative AML cases. While NPM1-mutated cases are characterized by a distinct gene expression pattern, it remains unclear whether NPM1-mutated/FLT3 ITD-negative cases also display a characteristic signature, which might provide additional insights into the molecular basis for the good clinical outcome. Thus, we sought to identify a molecular profile for AML cases with NPM1-mutated/FLT3 ITD-negative normal karyotype disease. Towards this goal, we profiled gene expression of 138 samples of adult AML patients with normal karyotype using DNA microarray technology. All samples analyzed were derived from AML patients entered within the randomized multicenter treatment trial HD-98A of the German-Austrian AML Study Group (AMLSG). Based on supervised data analyses we were able to identify a 116-genes comprising expression pattern correlated with NPM1-mutated and FLT3 ITD-negative AML cases. In accordance with previous findings in NPM1-mutated cases (Alcalay et al. 2005, Verhaak et al. 2005), the NPM1-mutated/FLT3 ITD-negative pattern was also in part characterized by a prominent HOX gene cluster, which clearly separated the NPM1-wildtype from the NPM1-mutated cases. Similarly, the expression levels of BAALC and MN1 were correlated with the NPM1 mutational status, with NPM1-unmutated cases displaying higher BAALC and MN1 expression in our data set. However, as expected the newly defined signature also defined a NPM1-mutated group that did not contain many FLT3 ITD-positive samples. This group was characterized by several interesting genes including for example TLE1, which encodes a Groucho/TLE family protein. Groucho/TLE family proteins are transcriptional co-repressors, which mediate repression essential in embryonic development and are involved in regulation of Wnt signaling in adult tissue. Moreover, we identified several other genes of potential pathogenic relevance which also have been previously shown to be predictive in normal karyotype AML. Our findings support a distinct molecular mechanism associated with the favorable outcome of NPM1-mutated/FLT3 ITD-negative AML cases. Furthermore, the reported signature might contribute to improved risk stratification and clinical management of AML patients with normal karyotype disease.

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.

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