scholarly journals Methscore As a New Prognostic Tool for Complex DNA Methylation Changes Assessment in Patients with Acute Myeloid Leukemia

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 32-33
Author(s):  
Sarka Sestakova ◽  
Cyril Šálek ◽  
Dávid Kundrát ◽  
Ivana Ježíšková ◽  
Jiří Mayer ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukemia ◽  
Methylation Level ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Cox Regression ◽  
Validation Cohort ◽  
Prognostic Impact ◽  
Logrank Test ◽  
Acute Myeloid

Changes in DNA methylation are characteristic for patients with acute myeloid leukemia (AML) and many studies have reported the prognostic significance of these epigenetic aberrations. We aimed for a complex evaluation of DNA methylation changes in AML patients at diagnosis. Therefore, we designed a sequencing panel targeting 239 regions annotated to 186 genes previously described in literature as having a prognostic impact or being commonly associated with AML pathogenesis (e.g. WT1, HOX genes). We used diagnostic whole-blood DNA samples of adult AML patients who were treated with curative intent starting with 3+7 induction regimen. In the testing cohort, we sequenced 128 AML patients and 11 samples from healthy donors. We analyzed another 50 AML patients from partner institution University Hospital Brno as an independent validation cohort. The libraries were prepared using SeqCap Epi Enrichments System (Roche) and sequenced on MiSeq instrument (Illumina). Data were processed in Linux opensource software and further analyzed in R. For each sample, we measured the methylation level of nearly 50 000 CpGs. In the testing cohort, we used the Cox regression to evaluate the effect of each CpG's methylation level on overall survival (OS). As a result, we found 1961 CpGs significantly effecting the OS (p<0.05) annotated to 141 genes. In gene ontology analysis, these loci were mainly connected to transcription and RNA regulation, DNA binding, and embryonic development. In 1097 CpGs, higher methylation indicated better outcome and, on the contrary, a poorer prognosis in the remaining 864 CpGs. Next, we used linear combination of the methylation levels and Cox's beta regression coefficients for each CpG to count a summarizing value that we called MethScore. Patients with lower MethScore (n=64) had markedly longer OS and event-free survival (EFS) than patients with higher MethScore (n=64, Logrank test for OS: p<2e-16, for EFS: p<2e-12). To further specify the prognostically most influential CpGs out of the selected 1961 loci, we subjected them individually to Cox multivariate regression analysis together with age, leukocytes count, cytogenetics, FLT3-ITD mutation, and transplantation in the 1st complete remission. Only 625 CpGs remained significant (p<0.05) and from these, we calculated MethScore-MVA via the same procedure as MethScore. MethScore-MVA was also very well predictive of patients' survival (Logrank test comparing patients with higher and lower MethScore-MVA for OS: p<7e-14, for EFS: p<2e-10). MethScore and MethScore-MVA proved to be the most significant variables in multivariate Cox regression for both OS (p=2e-12 and p=2e-13) and EFS (p=2e-12 and p=3e-12, respectively). To validate these results, we counted MethScore and MethScore-MVA for 50 patients from the validation cohort and performed the same Cox multivariate analysis. MethScore remained highly significant for both OS and EFS (p=0.002 and p=0.004, respectively). MethScore-MVA was significant for OS (p=0.02) but not for EFS (p=0.09). Here, we present the MethScore as a novel complex characterization of predictive DNA methylation changes in patients with AML. MethScore might be used as a new surrogate marker that could enrich the currently used cytogenetic and genetic markers to refine the prognostication of newly diagnosed AML patients. This study was supported by the Ministry of Health of the Czech Republic, project for conceptual development of research organizations (00023736, IHBT). Disclosures Šálek: Amgen: Consultancy, Honoraria, Research Funding. Mayer:Celgene: Research Funding.

scholarly journals Loss of H3K27 Methylation Identifies Poor Outcome in Adult-Onset Acute Myeloid Leukemia

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 24-24
Author(s):  
Anneke D. van Dijk ◽  
Fieke W Hoff ◽  
Yihua Qiu ◽  
Eveline S. de Bont ◽  
Sophia W.M. Bruggeman ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Overall Survival ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Molecular Genetic ◽  
Functional Enrichment ◽  
Prognostic Impact ◽  
Cox Regression Analysis ◽  
H3k27 Methylation ◽  
Acute Myeloid

Background: Acute myeloid leukemia (AML) is an epigenetically heterogeneous disease. The intensity of treatment is currently guided by cytogenetic and molecular genetic risk classifications; however these incompletely predict outcomes, requiring additional information for more accurate predictions. We aimed to identify potential prognostic implications of epigenetic modification of histone proteins, with a focus of H3K27 methylation in relation to mutations in chromatin, splicing and transcriptional regulators. Material and methods: Histone methylation mark expressions were evaluated in a cohort of 241 AML bone marrow (BM) and peripheral blood (PB) samples from patients admitted at the MD Anderson Cancer Center relative to their expression in CD34+ BM derived samples from healthy donors. Simultaneous analysis of 230 proteins was performed using the reverse phase protein array - a high-throughput, quantitative proteomic platform that enables identification of aberrant expressed proteins and the pathways they act in. Additional mutational analysis was performed on 65 BM samples. Results:H3K27Me3 was significantly lower in both BM and PB leukemic-derived samples compared to their expression in normal BM (figure 1A). A greater loss of H3K27Me3 associated with increased proliferative potential and shorter overall survival (OS) in the whole patient population (n=241, HR=0.64, 95% CI=0.47-0.87, p<0.01), as well as in subsets, e.g. cytogenetically normal AML (n=110, HR=0.62, 95% CI=0.40-0.97, p=0.03). To study the prognostic impact of H3K27Me3 in the context of cytogenetic aberrations and mutations, multivariate cox regression analysis was performed which identified H3K27Me3 level as an independent favorable prognostic factor in all (HR=0.74, 95%CI=0.57-0.95, p=0.02) as well as in P53 mutated AML (n=54, HR=0.48, 95%CI=0.26-0.87, p=0.02). A total of 78 AML patients had molecular data available for the major methylation affecting genes, i.e. IDH1, IDH2, DNMT3A and TET2. The level of H3K27Me3 was not prognostic in patients without any DNA methylation affecting mutation present, but patients with at least one mutation in any of these had better outcome when H3K27Me3 levels were high (highest tertile, figure 1A) compared to those with lower levels (median OS 7.1 vs. 24.1 months, HR=0.42, 95% CI=0.21-0.83, p=0.01, figure 1B). Mutations in U2AF1 and SRSF2 affect the spliceosome and are frequently found in antecedent hematological disorders (AHD), as well as are mutations in chromatin regulating genes ASXL1 and BCOR. We observed significant decreased H3K27Me3 in patients with these mutations corresponding with observed lower levels of H3K27Me3 in patients with AHD than those without (p=0.035). BCOR, SRSF2, U2AF1 and ASXL1 mutations confer poor prognosis in myeloid malignancies, however, in our cohort of 65 sequenced AML patients; not individual or a combination of these mutations were independent prognostic factors, but the degree of H3K27Me3 in these patients (HR= 0.49, 95% CI=0.25-0.95, p=0.03). To recognize dysregulated pathways in AML patients with the identified loss of H3K27Me3, we examined correlations of H3K27Me3 with the other 229 proteins on the array. H3K27Me3 is catalyzed by the polycomb group protein EZH2 and is linked to transcriptional repression via the formation of heterochromatin regions. To identify upregulated proteins and pathways upon the loss of H3K27Me3, we focused on significant negatively correlated proteins with H3K27Me3 leading us to the identification of 20 total and 6 phospho-proteins that showed increased expression upon decreased H3K27Me3. Functional enrichment analysis of this protein set revealed an upregulated anti-apoptotic phenotype. Conclusion:This study shows that proteomic profiling of epigenetic modifications on the histone level have clinical implications in AML and support the idea that epigenetic patterns contribute to a more accurate picture of the leukemic state complementing cytogenetic and molecular genetic subgrouping. Figure 1. A) Lower H3K27Me3 in BM and PB derived AML samples compared to normal CD34+. **** represents p<0.0001, ns = not significant. B) Overall survival probability in AML patients with any DNA methylation affecting mutation (i.e. IDH1/2, DNMT3A, TET2, n=53) according to H3K27Me3 low (blue) and high (orange) status. Figure 1 Disclosures No relevant conflicts of interest to declare.

scholarly journals High Blood BAALC Copy Numbers Determined By Digital Droplet PCR at Timepoint of Allogeneic Transplantation in Complete Remission Predicts Relapse in Patients with Acute Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 517-517
Author(s):  
Madlen Jentzsch ◽  
Marius Bill ◽  
Julia Schulz ◽  
Juliane Grimm ◽  
Stefanie Beinicke ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Copy Number ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Residual Disease ◽  
Absolute Quantification ◽  
Prognostic Impact ◽  
Healthy Controls ◽  
Copy Numbers ◽  
Acute Myeloid

Abstract Allogeneic hematopoietic cell transplantation (HSCT) is a powerful consolidation option for acute myeloid leukemia (AML) patients (pts) in hematologic complete remission (CR). Disease recurrence after HSCT remains a major clinical problem & early identification of AML pts at risk of relapse is crucial to improve outcomes. High expression of the AML associated gene BAALC (Brain and acute leukemia, cytoplasmic) at diagnosis adversely impacts on outcomes in AML pts. Little is known about its prognostic capacity during disease course & as a marker of residual disease. Here we adopted digital droplet polymerase chain reaction (ddPCR) for absolute quantification of BAALC copy numbers in peripheral blood (PB) prior to HSCT in AML pts in hematologic CR. We identified 82 AML pts with PB in first (60%) or second CR (23%) or CRi (17%) up to 28 days prior to HSCT available. Median age at HSCT was 63.9 (range 50.8-76.2) years (y). All pts received non-myeloablative (NMA) conditioning (fludarabine 3x30 mg & 2 Gy total body irradiation). At diagnosis, mutation status (mut) of the NPM1, CEBPA, IDH1, IDH2,& DNMT3A gene & presence of FLT3-ITD or FLT3-TKD were assessed. In pre-HSCT PB, absolute quantification of BAALC copy numbers was performed by ddPCR & results were normalized to ABL1 copy numbers.Additionally, absolute BAALC copy numbers wereassessedin PB of healthy controls (n=7) with a median age of 62.7 (range 39.6-82.0) y. Pts were grouped according to the European LeukemiaNet (ELN) classification in 21% favorable, 23% intermediate-I, 24% intermediate-II, 23% adverse & 9% unknown. Pts & healthy control were evenly matched in age (P=1) & sex (P=1). BAALC/ABL1 copy numbers did not differ between AML pts at HSCT (median 0.03 [range 0.01-2.48]) & the healthy controls (median 0.04 [range 0.03-0.10], P=.34, Figure 1). A cut-off point of 0.14absolute BAALC/ABL1 copies was determined using the R package 'OptimalCutpoints' & used to define pts with high (26%) & low (74%) pre-HSCT BAALC/ABL1 copy numbers. The copy number at this cut-off point was higher than the two-fold standard deviation over the median of the healthy controls (0.10 BAALC/ABL1). Pts with high & low pre-HSCT BAALC/ABL1 copy numbers did not differ significantly in pre-treatment characteristics (i.e. hemoglobin, white blood count, platelets, blasts in bone marrow or PB, ELN genetic group, FLT3-ITD, FLT3-TKD, NPM1, CEBPA, DNMT3A, IDH1 or IDH2 mut) or remission status at HSCT (CR1 vs. CR2 vs. CRi). However, pts with high pre-HSCT BAALC/ABL1 copy numbers had a significantly higher cumulative incidence of relapse (CIR, P=.02, Figure 2a) & shorter overall survival (OS, P=.02, Figure 2b). High pre-HSCT BAALC/ABL1 copy numbers especially impacted on CIR when we restricted our analysis to pts with normal cytogenetics (P=.003). In multivariate analysis for the entire cohort, high pre-HSCT BAALC/ABL1 copy numbers retained the prognostic impact on CIR (Hazard Ratio [HR] 3.6, Confidence Interval [CI] 1.6-8.2, P=.002) after adjustment for disease status at HSCT (P=.006) & the prognostic impact on OS (HR 2.2, CI 1.1-4.3, P=.02). In conclusion, ddPCR is a feasible method for absolute quantification of BAALC copy numbers in PB, which may indicate residual disease burden in AML pts. High PB BAALC/ABL1 copy numbers (>0.14) in AML pts in hematologic CR at HSCT associated with higher CIR & shorter OS in univariate & multivariate models. AML pts with high PB BAALC/ABL1 copy numbers at HSCT should be closely monitored for relapse in the post-transplant period. In the future prospective studies will be required to validate the absolute PB BAALC/ABL1 copy number cut-off point & to evaluate whether AML pts with high BAALC/ABL1 copy numbersmight benefit from additional treatment before HSCT. Figure 1 Figure 1. Figure 2 Figure 2. Disclosures Poenisch: Mundipharma: Research Funding. Niederwieser:Amgen: Speakers Bureau; Novartis Oncology Europe: Research Funding, Speakers Bureau.

scholarly journals The Clinical Association and Prognostic Impact of IL1RAP Expression in Patients with De Novo Acute Myeloid Leukemia

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 2705-2705
Author(s):  
Chao-Hung Wei ◽  
Cheng-Hong Tsai ◽  
Jih-Luh Tang ◽  
Yuan-Yeh Kuo ◽  
Feng-Ming Tien ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Transcription Factors ◽  
Prognostic Factor ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
De Novo ◽  
Underlying Mechanism ◽  
Prognostic Impact ◽  
Low Expression ◽  
Acute Myeloid

Introduction One of the contributing factors to the relapse of acute myeloid leukemia (AML) is the presence of leukemia stem cells (LSCs). Interleukin 1 receptor accessory protein (IL1RAP) was reported to be one of the LSC markers. Most studies regarding clinical implications of IL1RAP expression in AML focused on small and selected patient groups. Besides, its correlation with other molecular alterations has not been reported yet in literature. In this study, we aimed to elucidate the relationship between bone marrow IL1RAP expression level and clinical and biological features in patients with de novo non-M3 AML. Furthermore, we would like to explore its prognostic impact and potential underlying mechanism. Method We enrolled 275 newly diagnosed de novo non-M3 AML patients. Among them, 187 (68%) patients received standard induction chemotherapy and 2-4 courses of high-dose cytarabine based post-remission therapy. Analyses of 54 gene mutations were performed by next generation sequencing. The global gene expressions were profiled with the Affymetrix GeneChip Human Transcriptome Array 2.0. Result We used the median as the cut-off value to define the higher and lower IL1RAP expression groups. The patients with higher IL1RAP expression had significantly higher white blood cell counts at diagnosis, higher peripheral blast counts, and higher lactate dehydrogenase levels. Higher IL1RAP expression was closely associated with t(8;21), favorable-risk cytogenetics based on the refined MRC classification, but inversely with unfavorable-risk cytogenetics. Compared with low-expression patients, the high-expression patients had significantly more FLT3/ITD and KIT mutations, but less mutations in U2AF1, TP53, or CEBPA. Among the 187 patients receiving standard intensive chemotherapy, those with lower IL1RAP expression had significantly longer overall survival (OS) than those with higher expression (P=0.047) after a median follow-up time of 91.1 months, but disease-free survival (DFS) was not significantly different between the two groups (P=0.311). Among the 77 patients who relapsed after first complete remission (CR), the second CR rate was similar between the two groups (P=0.649), but the second DFS was significantly longer in the low-expression patients than the high-expression patients (P=0.028) which was also reflected in a significantly longer survival after first relapse in the former group than the latter group (P=0.014). The prognostic impact of IL1RAP expression on OS could be externally validated in the TCGA cohort (P=0.038). Its prognostic implication remained significant in the subgroup of our cohort with intermediate-risk cytogenetics (P=0.006) and those with normal karyotype (P=0.025). In multivariate analysis incorporating age, transplantation status, 2017 ELN risk-stratification and IL1RAP expression as covariates, the higher IL1RAP expression was an independent poor prognostic factor for OS (HR=1.555, P=0.025). The Gene Set Enrichment Analysis revealed significant up-regulation of LSC related genes in the higher IL1RAP expressed patients (Figure 1 and 2). We further profiled genome-wide RNA expression with 70,523 probes to survey the potential molecular mechanisms underlying the IL1RAP expression signature. Totally, 313 differentially expressed genes were identified (>1.5-fold change and Student t-test P<0.0001, Figure 3). We used Ingenuity Pathway Analysis (Qiagen) to analyze the possible underlying mechanism and found that the top upstream regulators were transcription factors, such as GATA1/GATA2 (P=1.39*10-11 and 1.61*10-10, respectively), and ABCB6 (P=3.84*10-8), one of the ATP-Binding Cassette transporter superfamily. The hub genes in the regulation network included ELAVL1 and NFκB, in addition to GATA1 and GATA2. Conclusion Higher IL1RAP expression is associated with distinct clinical and genetic alterations. It is an independent prognostic factor for OS irrespective of the risk category based on the ELN classification. Transcription factors, such as GATA1 and GATA2, ABCB6, ELAVL1 and NFκB might be involved in the underlying mechanism. Further prospective large cohort is warrant to validate our findings. Disclosures Tien: Novartis: Other: Travel Grant. Hou:Celgene: Research Funding; Abbvie, Astellas, BMS, Celgene, Chugai, Daiichi Sankyo, IQVIA, Johnson & Johnson, Kirin, Merck Sharp & Dohme, Novartis, Pfizer, PharmaEssential, Roche, Takeda: Honoraria. Tien:Daiichi Sankyo: Honoraria; Roche: Honoraria; Abbvie: Honoraria; Alexion: Honoraria; Celgene: Honoraria; Johnson &Johnson: Honoraria; Novartis: Honoraria; Celgene: Research Funding; BMS: Honoraria; Pfizer: Honoraria; Roche: Research Funding.

scholarly journals Prognostic Impact of ABCA3 Expression in Pediatric Acute Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1694-1694
Author(s):  
Antony Ceraulo ◽  
Aminetou Mint-Mohamed ◽  
Delphine Maucort-Boulch ◽  
Helene Lapillone ◽  
Guy Leverger ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Validation Cohort ◽  
Multivariate Analyses ◽  
Prognostic Impact ◽  
Discovery Cohort ◽  
Pediatric Acute Myeloid Leukemia ◽  
Primer Sets ◽  
Pediatric Aml ◽  
Acute Myeloid

Abstract Background. Despite progress in the molecular and genetic classification of pediatric acute myeloid leukemia (AML), the prognosis remains heterogeneous. The ATP-binding cassette transporter A3 (ABCA3) seems specifically involved in the resistance of pediatric AML to intensive chemotherapy. However, studies having investigated the prognostic impact of ABCA3 expression have yielded conflicting results with respect to patient outcomes while the small sample size of these studies precluded the use of multivariate analysis. Here we investigated the prognostic impact of ABCA3 expression in a representative series of homogeneously treated pediatric AML. Methods. Samples derived from 233 patients with available high-quality RNA and enrolled in the ELAM2 protocol (NCT00149162). qRTPCR amplification of 2 conserved ABCA3 mRNA sequences was performed with GUS and ABL as reference genes. Primer sets were complementary to exons 6-7 and exons 19-20 junctions. Patients were classified according to their standardized cytogenetic and molecular (NPM1 mutations, FLT3-ITD, CEBPA double mutations) risk subgroups (Rubnitz JE, Blood 2012;119:5980-5988, Creutzig U, Blood 2012;120:3187-3205). Treatment consisted of 1 induction course (AraC and mitoxantrone) and 3 consolidation courses (course 1 and 3 with high dose AraC); all children with either intermediate or high-risk disease were candidates for hematopoietic stem cell transplant (HSCT) in complete remission (CR) after 1 to 2 consolidation courses. Results. The discovery cohort included 120 patients. Median age, median WBC, CR rate, relapse rate, median follow-up, 5-years EFS, DFS, and OS were 9.4 years, 19.3 G/L, 95%, 29%, 60 months, 58±6%, 61±6%, and 71±5 months, respectively. The two primer sets yielded consistent results (R=0.9, p<10-4, Spearman Rank Correlation). Lower ABCA3 expression was positively associated with CBFB-MYH11 AML (p=0.002) and thereby with favorable cytogenetics (p=0.036) and low-risk AML (p=0.027). Higher ABCA3 expression was associated with higher relapse rate (p=0.006), shorter EFS (5-years, 34±9 vs 61±6 % p=0.0005), DFS (36±9 vs 62±6% p=0.0028), and OS (49±12 vs 79.5±5% p=0.0007). Multivariate analyses identified age, WBC, risk group, and ABCA3 expression as independent prognostic factors for EFS, DFS, and OS (Table 1). The validation cohort included 113 patients in whom the proportions of AML1-ETO- and MLL-positive AML were significantly higher than in the discovery cohort: 26,5% vs 6,7% (p<10-4) and 24.8 vs 14.2% (p=0.03). There was no significant difference in patients' outcome between the 2 cohorts. Using the same cutoff value in the validation cohort, higher ABCA3 expression remained significantly associated with shorter 5-years EFS: 63±7% vs 43±9% (p=0.025) with a trend for shorter DFS: 45±9 vs 53±11% (p=0.065). Multivariate analyses identified ABCA3 expression as an independent negative prognostic factor for EFS and DFS (Table 1). In the entire patients population, ABCA3 expression independently predicted EFS, DFS, and OS (not shown). In the low- (n=74) and adverse-risk (n=59) groups, higher ABCA3 expression remained associated with shorter 5-years EFS (low: 46±12 vs 75±7%, p=0.006; adverse: 12±10 vs 44±16%, p=0.018), DFS (low: 49±13 vs 75±7%; high: 12±11 vs 45±16%, p=0.016), and OS (low: 76±10 vs 94±4%; adverse: 32±14 vs 57±18%, p=0.046). Conclusion. ABCA3 expression represents an independent prognostic factor in pediatric AML. As they indicate that the level of ABCA3 expression is significantly associated with survival for currently accepted cytogenetic and molecular prognostic categories, our findings suggest that assessing ABCA3 expression will permit a better assessment of disease risk. Finally our results suggest that inhibiting ABCA3 expression, such as with indomethacin, could be beneficial in order to overcome drug resistance in pediatric AML. Disclosures No relevant conflicts of interest to declare.

scholarly journals Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks

Blood ◽  
2011 ◽  
Vol 118 (20) ◽  
pp. 5573-5582 ◽  
Author(s):  
Stefan Deneberg ◽  
Philippe Guardiola ◽  
Andreas Lennartsson ◽  
Ying Qu ◽  
Verena Gaidzik ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukemia ◽  
Odds Ratio ◽  
Myeloid Leukemia ◽  
Negative Impact ◽  
Prognostic Impact ◽  
Aberrant Methylation ◽  
Genome Wide ◽  
Methylation Patterns ◽  
Acute Myeloid

Abstract Cytogenetically normal acute myeloid leukemia (CN-AML) compose between 40% and 50% of all adult acute myeloid leukemia (AML) cases. In this clinically diverse group, molecular aberrations, such as FLT3-ITD, NPM1, and CEBPA mutations, recently have added to the prognostic accuracy. Aberrant DNA methylation is a hallmark of cancer, including AML. We investigated in total 118 CN-AML samples in a test and a validation cohort for genome-wide promoter DNA methylation with Illumina Methylation Bead arrays and compared them with normal myeloid precursors and global gene expression. IDH and NPM1 mutations were associated with different methylation patterns (P = .0004 and .04, respectively). Genome-wide methylation levels were elevated in IDH-mutated samples (P = .006). We observed a negative impact of DNA methylation on transcription. Genes targeted by Polycomb group (PcG) proteins and genes associated with bivalent histone marks in stem cells showed increased aberrant methylation in AML (P < .0001). Furthermore, high methylation levels of PcG target genes were independently associated with better progression-free survival (odds ratio = 0.47, P = .01) and overall survival (odds ratio = 0.36, P = .001). In summary, genome-wide methylation patterns show preferential methylation of PcG targets with prognostic impact in CN-AML.

scholarly journals Clinical Impact of KMT2C and SPRY4 Expression Levels in Intensively Treated Younger Adult Acute Myeloid Leukemia Patients

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1663-1663
Author(s):  
Sabine Kayser ◽  
Maximilian Feszler ◽  
Julia Krzykalla ◽  
Matthias Schick ◽  
Thomas Hielscher ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
De Novo ◽  
Prognostic Impact ◽  
Risk Class ◽  
Expression Levels ◽  
Blast Cells ◽  
Pharmaceutical Industries ◽  
Acute Myeloid

Abstract Background:Recent publications suggest important roles of lysine methyltransferase 2C (KMT2C, located on 7q) and sprouty 4 (SPRY4, located on 5q) as candidate genes in leukemogenesis of acute myeloid leukemia (AML). The prognostic impact of the gene expression levels (ELs) of both genes on outcome in AML patients (pts) is currently unclear. Aim:To evaluate the prognostic impact of KMT2C and SPRY4 expression in correlation to clinical characteristics and genetic abnormalities assessed at diagnosis in a cohort of intensively treated adult AML pts. Methods: We retrospectively studied 268 AML pts (median age, 48 years; range, 17-60 years) who had been enrolled on 2 AML SHG trials (0295 and 0199, n=148; only normal cytogenetics pts (CN)) and the SAL-AML2003 trial (n=120; only abnormal cytogenetics pts (CA)). Acute promyelocytic and core-binding factor leukemia pts were excluded. Type of AML was de novo in 235 (88%), secondary in 19 (7%) and therapy-related in 14 (5%) of the 268 pts. Regarding baseline characteristics, CN pts had significantly higher white blood counts (WBC; p=0.001) and blast cells in peripheral blood (p=0.02) as compared to CA pts; all other factors were comparable. Cytogenetic analyses could be performed in 263 (98%) of the 268 pts. Cytogenetic risk classification according to ELN guidelines was intermediate-II in 55 (47%) and adverse in 63 (53%) of the CA pts, respectively. Abnormalities (abn) of 5q were present in 21 (18%) and abn of 7q in 16 (14%) of the CA pts. NPM1 and FLT3-ITD were analyzed in 145 (98%) of the CN pts. Of those, 59 (41%) were only NPM1 positive (pos), 12 (8%) were only FLT3-ITD pos, 34 (23%) were double pos and 40 (28%) were double negative (neg). KMT2C and SPRY4 ELs, normalized to ABL1and log2-transformed for analysis, were measured in triplets on cDNA obtained at diagnosis by RT-qPCR. Based on cDNA availability, KMT2C ELs could be analyzed in 143 (97%) of the CN and in all of the 120 CA pts, respectively. SPRY4 ELs could be measured in 30 (21%) of the CN and 107 (89%) of the CA pts, respectively. Results: KMT2C ELs were significantly lower in CN pts with de novo as compared to secondary AML (p= 0.02), whereas there was no difference in CA pts. No significant association was found for SPRY4 and type of AML. KMT2C ELs were significantly lower in FLT3-ITD pos as compared to FLT3-ITD neg CN pts (p=0.046), whereas there was no difference for SPRY4 ELs between the two groups (p=0.57). In addition, there was a significantly lower KMT2C expression in CN pts with intermediate-I risk as compared to NPM1 pos / FLT3-ITD neg pts (p=0.01). Regarding CA pts, there was no difference of KMT2C or SPRY4 ELs in adverse as compared to intermediate-II risk pts (p=0.08; p=0.20, respectively). When focusing on specific subgroups, KMT2C ELs were significantly lower in abn7q CA pts as compared to those without abn7q (p=0.002), whereas there was no difference of SPRY4 ELs in CA pts with or without abn5q (p=0.27). In univariate analysis higher SPRY4 ELs showed a significant favorable impact on relapse-free (RFS, p=0.03) and a trend towards a beneficial impact on overall survival (OS, p=0.06) for CA patients. A similar effect for KMT2C was not observed (RFS, p=0.96; OS, p=0.92). In subgroup analyses of pts with adverse risk cytogenetics, there was no impact of KMT2C or SPRY4 ELs on RFS (p=0.73; p=0.39) or OS (p=0.49; p=0.46), respectively. The same was true for FLT3-ITD pos CN pts (RFS, p=0.73; p=0.37; OS, p=0.91; p=0.36, respectively). In multivariate analyses on RFS and OS in CA pts including age, gender, KMT2C and SPRY4 ELs, logarithm of WBC, blast cells in bone marrow and cytogenetic risk group as variables, only higher age (OS, Hazard ratio (HR),1.28 per 10 years; 95%-confidence interval (CI): 1.02-1.59; p=0.03) and complex karyotype as compared to intermediate-II risk cytogenetics (RFS, HR: 2.25; 95%-CI: 1.20-4.22; p=0.01; OS, HR: 2.97; 95%-CI: 1.65-5.35; p<0.001) had an adverse impact. An effect of KMT2C or SPRY4 on RFS (p=0.84; p=0.16) or OS (p=0.85; p=0.45) was not found in the multivariate setting. In addition, in a multivariate model on CN pts (risk class according to NPM1 and FLT3-ITD mutational status instead of cytogenetic risk class) neither KMT2C nor SPRY4 had an impact on RFS (p=0.13; p=0.39, respectively) or OS (p=0.36; p=0.56, respectively). Conclusions:Lower KMT2C and SPRY4 ELs are associated with distinct genetic risk groups. An impact on prognosis was evident in univariable analyses for SPRY4 but not for KMT2C ELs in CA pts. Disclosures Kayser: Novartis: Consultancy. Platzbecker:Amgen: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; TEVA Pharmaceutical Industries: Honoraria, Research Funding; Janssen-Cilag: Honoraria, Research Funding; Celgene Corporation: Honoraria, Research Funding. Heuser:Tetralogic: Research Funding; Novartis: Consultancy, Research Funding; Celgene: Honoraria; Bayer Pharma AG: Research Funding; Pfizer: Research Funding; Karyopharm Therapeutics Inc: Research Funding; BerGenBio: Research Funding. Thiede:AgenDix: Employment, Other: Ownership.

scholarly journals Epigenetics Meets Genetics in Acute Myeloid Leukemia: Clinical Impact of a Novel Seven-Gene Score

2014 ◽  
Vol 32 (6) ◽  
pp. 548-556 ◽  
Author(s):  
Guido Marcucci ◽  
Pearlly Yan ◽  
Kati Maharry ◽  
David Frankhouser ◽  
Deedra Nicolet ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
High Expression ◽  
Prognostic Impact ◽  
Sequencing Analysis ◽  
Gene Score ◽  
Expression Levels ◽  
Acute Myeloid

PurposeMolecular risk stratification of acute myeloid leukemia (AML) is largely based on genetic markers. However, epigenetic changes, including DNA methylation, deregulate gene expression and may also have prognostic impact. We evaluated the clinical relevance of integrating DNA methylation and genetic information in AML.MethodsNext-generation sequencing analysis of methylated DNA identified differentially methylated regions (DMRs) associated with prognostic mutations in older (≥ 60 years) cytogenetically normal (CN) patients with AML (n = 134). Genes with promoter DMRs and expression levels significantly associated with outcome were used to compute a prognostic gene expression weighted summary score that was tested and validated in four independent patient sets (n = 355).ResultsIn the training set, we identified seven genes (CD34, RHOC, SCRN1, F2RL1, FAM92A1, MIR155HG, and VWA8) with promoter DMRs and expression associated with overall survival (OS; P ≤ .001). Each gene had high DMR methylation and lower expression, which were associated with better outcome. A weighted summary expression score of the seven gene expression levels was computed. A low score was associated with a higher complete remission (CR) rate and longer disease-free survival and OS (P < .001 for all end points). This was validated in multivariable models and in two younger (< 60 years) and two older independent sets of patients with CN-AML. Considering the seven genes individually, the fewer the genes with high expression, the better the outcome. Younger and older patients with no genes or one gene with high expression had the best outcomes (CR rate, 94% and 87%, respectively; 3-year OS, 80% and 42%, respectively).ConclusionA seven-gene score encompassing epigenetic and genetic prognostic information identifies novel AML subsets that are meaningful for treatment guidance.

Validation of a DNA Methylation Signature of Favorable Prognosis in Newly Diagnosed Acute Myeloid Leukemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1615-1615
Author(s):  
Rodolphe F Taby ◽  
Sarvari Venkata Yellapragada ◽  
Heike Kroeger ◽  
Rong He ◽  
Steven M. Kornblau ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukemia ◽  
Gene Silencing ◽  
Myeloid Leukemia ◽  
Conflicts Of Interest ◽  
Cpg Island ◽  
Young Patients ◽  
Prognostic Impact ◽  
Conventional Chemotherapy ◽  
Acute Myeloid

Abstract Abstract 1615 Poster Board I-641 Epigenetic modifications are defined as heritable alterations in gene expression with no accompanying change in DNA sequence. Disruption of the epigenetic balance has major impact on chromatin structure and transcriptional activity. Hypermethylation of CpG islands within or near gene promoter regions is associated with gene silencing via transcriptional inactivation in human carcinogenesis. This gene silencing has the potential not only to affect disease progression, but also drug resistance and clinical outcome. We have previously reported that patients with Acute Myeloid Leukemia (AML) who are cured by conventional chemotherapy often display intense and simultaneous hypermethylation of multiple genes. To confirm these data, we evaluated the aberrant promoter methylation of these 9 genes in 68 patients with AML [excluding Acute Promyelocytic Leukemia, patients with inv-16 or t(8:21) and patients over the age of 65] enrolled on a clinical trial of conventional chemotherapy (idarubicin + cytarabine). Methylation at diagnosis was studied using bisulfite pyrosequencing. The patients had a median age of 52.5 years, median WBC count of 8,450/mm3, and the cytogenetic distribution was 3% favorable, 48% diploid and 49% poor-risk. Complete response rate was 71%. After a median follow-up of 24 months, median survival was 17 months, and median relapse-free survival 14 months. Dense methylation (>25% of CpG sites) was present in 7% of cases for HIN1; 12% for NOR1 and OLIG2; 15% for SLC26A4; 19% for NPM2 and P15INK4b; 24% for PGRA; 25% for CDH13 and 26% for PGRB genes. In univariate analyses, traditional factors like age, achievement of a complete remission, cytogenetics, history of myelodysplastic syndrome or myeloproliferative neoplasm, a sustained hematological response, and platelet count at diagnosis had their usual prognostic impact suggesting that this cohort is typical of the general AML population. Individually, dense methylation of each of NOR1, NPM2, HIN1, P15INK4b, SLC26A4, PGRA and PGRB genes was associated with a trend for improved overall survival, which was significant for PGRB (p=0.03) and near-significant for HIN1 (p=0.08) and NPM2 (p=0.1). A subgroup of 8 patients out of the 68 (11.8%) was strikingly distinct with 5 genes or more methylated in each case, and corresponded to a previously described CpG Island Methylator Phenotype (CIMP) in AML. These cases had similar age and cytogenetics as CIMP-negative cases. Median OS in CIMP-positive cases had not yet been reached at the time of analysis, compared to 15 months for CIMP-negative cases (p=0.03). The estimated 2-year survival rate was of 88% for CIMP-positive cases, compared to 40% for CIMP-negative cases (p=0.01). These results validate our previous findings of an association between increased DNA methylation and good prognosis in relatively young patients with AML who receive standard induction chemotherapy. The mechanism of this association between CIMP and survival is unknown, and we speculate that it relates to the inactivation of a gene that protects cells from the effects of chemotherapy. We conclude that epigenetic profiling using DNA methylation can help identify an AML patient subpopulation that may particularly benefit from conventional chemotherapy. Disclosures No relevant conflicts of interest to declare.

Quantitative DNA methylation predicts survival in adult acute myeloid leukemia

Blood ◽  
2010 ◽  
Vol 115 (3) ◽  
pp. 636-642 ◽  
Author(s):  
Lars Bullinger ◽  
Mathias Ehrich ◽  
Konstanze Döhner ◽  
Richard F. Schlenk ◽  
Hartmut Döhner ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Large Scale ◽  
Methylation Status ◽  
Multivariable Analysis ◽  
Molecular Heterogeneity ◽  
Prognostic Impact ◽  
Outcome Predictor ◽  
Acute Myeloid

Abstract Acute myeloid leukemia (AML) is characterized by molecular heterogeneity that is not fully reflected in the current classification system. Recent insights point toward a significant role of aberrant DNA methylation in leukemogenesis. Therefore, we investigated the prognostic impact of DNA methylation in AML. To screen for promoter methylation in AML we applied a combination of base-specific cleavage biochemistry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), a powerful methodology allowing for quantitatively investigating DNA methylation status in a large series of both promoter regions and leukemia samples. We analyzed 92 genomic regions in 182 patient samples, correlated findings with clinical and molecular data, and validated the results in an independent cohort of 74 AML samples. Using this approach, we were able to identify novel leukemia subgroups based on distinct DNA methylation patterns. Furthermore, we defined a methylation-based outcome predictor for patient survival (P < .01) that in multivariable analysis provided independent prognostic information (hazard ratio, 1.52; 95% CI, 1.06-2.16). Here, we report the first large-scale methylation-based outcome predictor in AML, and thereby our findings support the use of genomic methylation markers for improved molecular classification and prognostication in adult AML.

scholarly journals Evaluation of acute myeloid leukemia blast percentage on MethylC-Capture Sequencing results

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Erna Yang ◽  
Desheng Gong ◽  
Wei Guan ◽  
Jieying Li ◽  
Xuefeng Gao ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bone Marrow ◽  
Acute Myeloid Leukemia ◽  
Methylation Level ◽  
Myeloid Leukemia ◽  
Promoter Regions ◽  
Aberrant Dna Methylation ◽  
Next Generation Sequencing Ngs ◽  
Capture Sequencing ◽  
Acute Myeloid

AbstractAberrant DNA methylation is often related to the diagnosis, prognosis, and therapeutic response of acute myeloid leukemia (AML); however, relevant studies on the relationship between bone marrow myeloblast percentage and the DNA methylation level in AML have not been reported. We evaluated the effects of AML blast percentage on DNA methylation level using the MethylC-capture sequencing (MCC-Seq) approach based on next-generation sequencing (NGS) and found that the methylation level of both genome-wide and promoter regions significantly increased when the percentage of AML blasts reached ≥ 40%, indicating that an accurate DNA methylation level in cancer cells can be obtained when the bone marrow samples of AML patients have more than 40% myeloblasts.

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