Comparison of DNA Methylation and Expression Status Prior Azacytidine Treatment and their Relationship to Overall Survival and Clinical Response of MDS Patients

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3777-3777
Author(s):  
Monika Belickova ◽  
Anna T Jonasova ◽  
Jitka Vesela ◽  
Eliska Stara ◽  
Andrea Hrustincova ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Overall Survival ◽  
Clinical Response ◽  
Partial Remission ◽  
Methylation Status ◽  
Prognostic Impact ◽  
Aberrant Expression ◽  
Hematopoietic Stem ◽  
Cd34 Cells ◽  
Expression Status

Abstract Background Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic stem cells characterized by ineffective hematopoiesis. High-risk MDS patients are treated by hypomethylating agents, of which they benefit significantly. However, only half of the patients respond positively to the treatment. Aberrant DNA methylation and mRNA expression in MDS were documented in several studies, but their prognostic impact in response to hypomethylating therapy is still unclear. The aim of the project was to find a relationship between methylation and expression status prior to azacytidine (AZA) treatment and the overall survival and clinical response of MDS patients. Methods We performed methylation and expression profiling in CD34+ cells from 30 samples from MDS patients before AZA treatment and after 4-8 treatment cycles. HumanMethylation27 BeadChips and HumanHT-12 v4 Expression BeadChips (Illumina) were used to generate profiles. DNA and RNA were isolated from same CD34+ cells separated from bone marrow by magnetic beads. The β-values represent quantitative measurements of DNA methylation levels of specific CpGs, and range from 0 for completely unmethylated to 1 for completely methylated DNA. The nonparametric Mann-Whitney test was used for comparison of β-values and expression levels between responders and nonresponders. Results To determine whether DNA methylation and expression might predict a response to AZA treatment, we compared methylation and expression status at baseline with clinical responses in 30 MDS patients. Twelve patients of 30 (40%) achieved complete remission or partial remission, 10 had stable disease (33.3%), and 8 showed progression (26.7%). Median survival after initiation of AZA treatment in progression patient group was 8.7 months, stable group 21.2 months, and group with complete or partial remission 24.5 months. We found significant differences in methylation status in 20 genes (p<0.05) between groups of responders and nonresponders and the largest methylation differences showed CALCA (0.61 vs. 0.16, p<0.05), MAGEE2 (0.71 vs. 0.30, p<0.05), HMP19 (0.62 vs. 0.23, p<0.05), MEOX1 (0.36 vs. 0.84, p<0.05), and KCNQ1DN genes (0.33 vs. 0.84, p<0.05). The aberrant expression status did not correlate with the response to AZA. We also measured methylation changes caused by AZA treatment. In the group of patients with progression, we did not find any change in the methylation profile after treatment. On the contrary, we found significant methylation changes after AZA treatment in the group of patients responding to treatment (e.g. AMT, NOTCH, and WT1genes). Conclusions Our finding of different DNA methylation levels at baseline between groups of responders and nonresponders as well as detection of decreased methylation after AZA treatment in the group of patients with clinical response may represent useful prediction markers of treatment success. However, the data require detailed examination along with confirmative cohort of patients. Supported by grant (NT/13899, NT/14377, NT/14539, NT/13847) and the project for conceptual development of research organization (00023736) from the Ministry of Health of the Czech Republic. Disclosures: No relevant conflicts of interest to declare.

Prognostic Impact of the Number of Methylated Genes in Myelodysplastic Syndromes and Acute Myeloid Leukemias Treated with 5-Azacytidine

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1717-1717
Author(s):  
María Abáigar ◽  
Fernando Ramos ◽  
Rocío Benito ◽  
María Díez-Campelo ◽  
Javier Sánchez-del-Real ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Overall Survival ◽  
Tumor Suppressor ◽  
Myelodysplastic Syndromes ◽  
Tumor Suppressor Genes ◽  
Methylation Status ◽  
Prognostic Impact ◽  
Suppressor Genes ◽  
Myeloid Leukemias ◽  
Acute Myeloid

Abstract Abstract 1717 Background: Aberrant DNA methylation of tumor suppressor genes is a common event in myelodysplastic syndromes (MDS) and acute myeloid leukemias (AML). Therefore hypomethylating agents like azacytidine (AZA) and decitabine seem to be a good therapeutic approach for the treatment of these diseases. Clinical experience and recent published data have demonstrated that AZA is effective for the treatment of MDS and AML patients. However, the prognostic impact of the aberrant hypermethylation on response and outcome to AZA treatment remains to be determined. For this reason the influence of the methylation status of a selected set of tumor suppressor genes on the overall survival and clinical response in MDS and AML patients, prior to treatment with AZA was studied. Patients and Methods: A total of 78 patients with MDS or AML who had been treated with AZA were evaluated. Among these, 25 were excluded because they had received less than 4 cycles, AZA was used after allogeneic stem cell transplantation, response was not assessable, or there was not enough quality DNA available. So finally, the study was focused in 53 patients: 36 MDS and 17 AML. Most of the AML included in the study had low blast count (20–30%). Responses were assessed according to the IWG MDS criteria in accordance to Fenaux et.al, and IWG AML criteria following European LeukemiaNet recommendations. DNA methylation status was analyzed using the Methylation Specific Multiplex Ligation Probe Amplification (MS-MLPA), with a panel of 24 different tumor suppressor genes related to cell cycle control, apoptosis regulation, DNA repair, cell adhesion and cell growth. Results: In the study cohort 47% of patients had cytogenetic alterations prior to AZA treatment, 4 with isolated -5/del(5q), 7 with isolated −7/del(7q), 4 with trisomy 8, 4 with not isolated -5/del(5q), 1 with trisomy 14, and 5 with complex cytogenetics. Methylation analysis showed that most patients (74%) had at least one methylated gene, but only 10% of patients displayed more than 3 methylated genes. The most frequently methylated genes were IGSF4 (28.3%), CDKN2B (24.5%), ESR1 (22.6%), CDH13 (17%) and CDKN1B (11.3%). The presence of a high number (≥2) of methylated genes (p=0.02), an adverse cytogenetics (p=0.03) or anemia (p=0.04) were independent prognostic factors associated with shorter overall survival. Moreover, the analysis of those patients displaying “no methylation”, patients with 1 methylated gene, patients with 2 methylated genes and those with more than 3 methylated genes, showed that as the number of methylated genes increases, the survival was shorter. The patients displaying the highest level of methylation (more than 3 genes), had a very short survival (median OS of 9.3 months, p<0.001). Forty-nine per cent of all patients responded to azacytidine. The statistical analysis revealed that the number of methylated genes did not correlate in general with the clinical response to AZA, although four of the five patients with more than 3 genes methylated did not respond. By contrast, cytogenetics was the only factor that independently influenced the response to AZA. Thus 64.7% of patients with favorable cytogenetics responded to AZA, while only 28.6% of those with adverse cytogenetics responded (p=0.03). Interestingly, our study included 3 MDS patients with isolated chromosome 7 alterations, and all of them responded. Conclusion: In summary, these results suggest that the analysis of the methylation status before AZA treatment by a feasible methodology such as MS-MLPA could be used in a clinical setting in order to identify a group of patients with poor survival, in which other alternative therapeutic approaches might be considered. Disclosures: Ramos: Celgene, Novartis, Amgen, Pfizer, and Merck Sharp & Dohme: Honoraria. Hernández:Celgene: Research Funding.

scholarly journals SETBP1 overexpression is a novel leukemogenic mechanism that predicts adverse outcome in elderly patients with acute myeloid leukemia

Blood ◽  
2010 ◽  
Vol 115 (3) ◽  
pp. 615-625 ◽  
Author(s):  
Ion Cristóbal ◽  
Francisco J. Blanco ◽  
Laura Garcia-Orti ◽  
Nerea Marcotegui ◽  
Carmen Vicente ◽  
...  
Keyword(s):  
Overall Survival ◽  
Elderly Patients ◽  
Genetic Alterations ◽  
Leukemic Cells ◽  
Prognostic Impact ◽  
Hematopoietic Stem ◽  
Monosomy 7 ◽  
Protease Cleavage ◽  
Prognostic Group ◽  
Acute Myeloid

Abstract Acute myeloid leukemias (AMLs) result from multiple genetic alterations in hematopoietic stem cells. We describe a novel t(12;18)(p13;q12) involving ETV6 in a patient with AML. The translocation resulted in overexpression of SETBP1 (18q12), located close to the breakpoint. Overexpression of SETBP1 through retroviral insertion has been reported to confer growth advantage in hematopoietic progenitor cells. We show that SETBP1 overexpression protects SET from protease cleavage, increasing the amount of full-length SET protein and leading to the formation of a SETBP1–SET-PP2A complex that results in PP2A inhibition, promoting proliferation of the leukemic cells. The prevalence of SETBP1 overexpression in AML at diagnosis (n = 192) was 27.6% and was associated with unfavorable cytogenetic prognostic group, monosomy 7, and EVI1 overexpression (P < .01). Patients with SETBP1 overexpression had a significantly shorter overall survival, and the prognosis impact was remarkably poor in patients older than 60 years in both overall survival (P = .015) and event-free survival (P = .015). In summary, our data show a novel leukemogenic mechanism through SETBP1 overexpression; moreover, multivariate analysis confirms the negative prognostic impact of SETBP1 overexpression in AML, especially in elderly patients, where it could be used as a predictive factor in any future clinical trials with PP2A activators.

scholarly journals Diagnostic and Prognostic Value of B4GALT1 Hypermethylation and Its Clinical Significance as a Novel Circulating Cell-Free DNA Biomarker in Colorectal Cancer

Cancers ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 1598 ◽  
Author(s):  
Francesco Picardo ◽  
Antonella Romanelli ◽  
Laura Muinelo-Romay ◽  
Tommaso Mazza ◽  
Caterina Fusilli ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Lung Metastases ◽  
Methylation Status ◽  
Therapy Response ◽  
Progression Free Survival ◽  
Prognostic Impact ◽  
Aberrant Expression ◽  
Predictive Values ◽  
Methylation Specific Pcr ◽  
Specific Pcr

Epigenetic modifications of glyco-genes have been documented in different types of cancer and are tightly linked to proliferation, invasiveness, metastasis, and drug resistance. This study aims to investigate the diagnostic, prognostic, and therapy-response predictive value of the glyco-gene B4GALT1 in colorectal cancer (CRC) patients. A Kaplan–Meier analysis was conducted in 1418 CRC patients (GEO and TCGA datasets) to assess the prognostic and therapy-response predictive values of the aberrant expression and methylation status of B4GALT1. Quantitative methylation-specific PCR (QMSP) and droplet digital quantitative methylation-specific PCR (dd-QMSP) were respectively used to detect hypermethylated B4GALT1 in metastasis and plasma in four cohorts of metastatic CRC cases (mCRC). Both the downregulated expression and promoter hypermethylation of B4GALT1 have a negative prognostic impact on CRC. Interestingly a low expression level of B4GALT1 was significantly associated with poor cetuximab response (progression-free survival (PFS) p = 0.01) particularly in wild-type (WT)-KRAS patients (p = 0.03). B4GALT1 promoter was aberrantly methylated in liver and lung metastases. The detection of hypermethylated B4GALT1 in plasma of mCRC patients showed a highly discriminative receiver operating characteristic (ROC) curve profile (area under curve (AUC) value 0.750; 95% CI: 0.592–0.908, p = 0.008), clearly distinguishing mCRC patients from healthy controls. Based on an optimal cut-off value defined by the ROC analysis, B4GALT1 yield a 100% specificity and a 50% sensitivity. These data support the potential value of B4GALT1 as an additional novel biomarker for the prediction of cetuximab response, and as a specific and sensitive diagnostic circulating biomarker that can be detected in CRC.

Adverse Prognostic Impact of GAS6 Expression in De Novo Cytogenetically Normal Acute Myeloid Leukemia (CN-AML) (CALGB 8461, 9665, 20202; Alliance)

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1293-1293
Author(s):  
Susan Whitman ◽  
Jessica Kohlschmidt ◽  
Kati Maharry ◽  
Deedra Nicolet ◽  
Sebastian Schwind ◽  
...  
Keyword(s):  
De Novo ◽  
Conflicts Of Interest ◽  
Expression Profiles ◽  
White Blood Count ◽  
Categorical Variables ◽  
Prognostic Impact ◽  
Age Group ◽  
Wild Type ◽  
Aberrant Expression ◽  
Expression Status

Abstract Abstract 1293 Receptor tyrosine kinases (RTKs) constitutively activated by gene mutation, overexpression and/or autocrine activation via ligand expression have been shown to negatively impact on outcomes of AML patients (pts). AXL, a member of the TAM (TYRO3, AXL, MERTK) RTK gene family was reported to be overexpressed and associated with poor survival in AML (Rochlitz, et al, Leukemia, 1999: 13:1352–8). No AXL mutations have been described, suggesting its activation may occur via aberrant expression in leukemic blasts of a TAM RTK ligand, GAS6. GAS6 was shown to be overexpressed in AML (Dirks, et al Leuk. Res. 23:643–51); yet its prognostic relevance is unknown. We report clinical and molecular associations and prognostic impact of aberrant GAS6 expression, in the context of TAM RTKs and known prognostic markers in de novo CN-AML pts (n=270; aged 18–83 y) treated with cytarabine/anthracycline-based therapies. Sixty-nine (26%) pts expressed GAS6 (>background signal; derived from microarray gene expression profiles of AML samples). TYRO3 expression status [positive (+) vs negative (–)] was similar in GAS6+ and GAS6– pts (P=.74), while AXL+ (P<.001) and low expression MERTK (P=.02) were more frequent in GAS6+ pts. Compared to GAS6– pts, GAS6+ pts were older (P=.02), had more platelets (P=.03), lower % blood blasts (P=.01) and increased frequency of hepatomegaly (P=.006); were more often NPM1 (P<.001) and CEBPA (P=.02) wild-type, and RUNX1 (P<.001) and ASXL1 (P=.002) mutated and expressed higher MN1 levels (P=.05). In univariable analyses, none of the TAM RTKs associated with complete remission (CR) and only TYRO3+ associated with reduced disease-free (DFS; P=.005), overall (OS; P=.005) and event-free survival (EFS; P=.008). GAS6+ vs GAS6– pts had lower CR rates (P<.001), shorter DFS (P=.03), OS (P=.004) and EFS (P<.001). While no TAM RTK entered the CR multivariable (MVA) model, GAS6+ expression status remained an independent marker for lower CR rate after adjusting for NPM1 status, white blood count (WBC) and age group (Table). In the DFS, OS and EFS models (Table), there was an interaction between GAS6 and the combined dual receptor (TYRO3/AXL) variable. GAS6 independently associated with shorter survival in TYRO3–/AXL– pts but not TYRO3+/AXL+ pts after adjusting for other variables. We show for the 1st time that GAS6 expression is an independent prognostic marker in CN-AML; negatively impacting on CR attainment, independent of TAM RTKs and on survival endpoints in pts lacking TYRO3 and AXL expression, regardless of MERTK expression. Our results suggest that GAS6 expressed by AML blasts plays a role in chemotherapy resistance. As GAS6 is expressed but not its RTKs in a subgroup of pts with poor outcome, this may lead to the hypothesis that the prognostic impact of GAS6 in those patients is mediated by the encoded ligand acting on cells other than AML blasts including, for example, natural killer cells, where activation of AXL RTK is reported to suppress innate immunity. Table. MVA models Variable CR DFS OS EFS P OR (95% CI) P HR (95% CI) P HR (95% CI) P HR (95% CI) GAS6 expression, + v – .02 0.46 (0.24, 0.88) .03* 1.78 (1.07, 2.96) .05* 1.59 (1.00, 2.52) .03* 1.59 (1.06, 2.41) NPM1, mut v wt .001 2.97 (1.53, 5.77) – – – – .006 0.64 (0.46, 0.88) FLT3-ITD, present v absent – – .003 1.66 (1.19, 2.33) – – .005 1.55 (1.14, 2.11) WT1, mut v wt – – – – <.001 3.42 (1.97, 5.96) .03 1.84 (1.06, 3.18) RUNX1, mut v wt – – – – .002 2.00 (1.29, 3.10) – – ASXL1, mut v wt – – – – – – .003 1.66 (1.05, 2.60) DNMT3A
 R882 mut v wt
 Non-R882 v wt .006 .21 1.65 (1.15, 2.36) 1.33 (0.85, 2.08) WBC, continuous, 50 unit increase <.001 0.56 (0.41, 0.76) – – – – <.001 1.25 (1.12, 1.39) Age group, ≥ 60 y v < 60 y .01 0.40 (0.19, 0.83) <.001 2.09 (1.44, 3.03) <.001 2.64 (1.80, 3.87) <.001 2.16 (1.54, 3.02) OR, odds ratio; HR, hazard ratio; CI, confidence interval; mutated, mut; wild-type, wt. ORs > (<) 1.0 mean higher (lower) CR rate, and HRs > (<) 1.0 mean higher (lower) risk for relapse or death (DFS, EFS), respectively, for the higher values of the continuous variables and the first category listed for the categorical variables. Variables significant at α =.20 in univariable models were considered, although all considered variables are not shown. *There are interactions between GAS6 and TYRO3/AXL dual receptor status for DFS (P=.16), OS (P=.06) and EFS (P=.12). The P-values, HRs and CIs are for comparisons of GAS6+ v GAS6– pts within the TYRO3–/AXL– subset. Disclosures: No relevant conflicts of interest to declare.

Prognostic Impact of Bone Marrow B Lymphocyte Precursors (hematogones) Detection in 95 Acute Lymphoblastic Leukemia Cases

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4791-4791 ◽  
Author(s):  
Sylvain P Chantepie ◽  
Audrey Emmanuelle Dugué ◽  
Patrice Chevallier ◽  
Aline Schmidt-Tanguy ◽  
Véronique Salaün ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Overall Survival ◽  
Prognostic Factors ◽  
Acute Lymphoblastic Leukemia ◽  
Lymphoblastic Leukemia ◽  
Prognostic Impact ◽  
Hematopoietic Stem ◽  
Time Points ◽  
Number Of Patients

Abstract Abstract 4791 Acute lymphoblastic leukemia (ALL) multiparameter flow cytometry (MFC) study of bone marrow aspiration after chemotherapy is crucial for determining minimal residual disease (MRD). Hematogones (HGs) have to be distinguishing from leukemic cells in B-cell subtypes and could be quantify during follow-up. To date, the incidence of Hgs in ALL and their prognostic significance have not been investigated. The aim of this multicenter study was to quantify Hgs after chemotherapy in ALL adult patients and to define its prognostic value. We retrospectively analyzed the incidence of HGs in 95 ALL patients, 71 with B-ALL (75%), 24 (25%) with T-ALL in first line treatment. The median age was 37 years [8–71], 20% had t(9;22) cytogenetic abnormality, and 70% had abnormal karyotype. 4/5-color MFC analysis MRD and HGs were performed at different time point (TP) after diagnosis: TP1 (post-induction, day 45 [41–61], n=78), TP2 (post-consolidation, day 111 [94–144] 25, n=42), TP3 (post-intensification/before hematopoietic stem cell transplantation (HSCT), day 179 [125–268], n=58), TP4 (n=11), TP5 (n=17), TP6 (n=9) after a median of 33, 91 and 167 days after HSCT, respectively. A total of 39 patients (41%) relapsed with a median of 26 months [7.7–47.9]. Forty seven patients (50%) received an HSCT in a complete (98%) or partial remission (2%). At TP1, TP2, TP3, TP4, TP5, TP6, the median HGs [range] were as followed: 0.00 [0.00–6.90]%, 0.30 [0.00–11.2]%, 0.98 [0.00–33.00]%, 0.52 [0.00;23.00]%, 5.50 [0.00;25.00]%, 4.60 [0.00;34.00]%, 5.90 [0.32;11.80]%, respectively. Figure 1 showed the percentage of patients with negative MRD (Figure 1A) and detectable HGs (figure 1B) during the follow up of ALL patients. There is a progressive increase of the percentage of patients with detectable HGs during the time of treatment and follow-up. Interestingly, there was no correlation between age and HGs level while in physiological situation the HGs rate decreases with increasing age. There was a negative correlation between positive MRD and detectable HGs at TP1 (p=0.022) but not at TP3 (p=0.88). In univariate analysis positive MRD at P1 and P3, age (/10), the presence of t(9;22) and absence of HGs at TP3 (figure 2) were bad prognostic factors for relapse free-survival (RFS) and overall survival (OS). The presence of HGs at other different time of evaluation was not associated with a significant decrease of relapse or death. However, patients who had a negative MRD at TP1 and detectable HGs in the bone marrow at TP3 exhibited a better RFS and OS (p=0.018 and p=0.065 respectively). Patients who had negative MRD at TP3 and had detectable HGs at TP3 had also a better RFS and OS (p=0.007 and p=0.011, respectively) compared to patients with negative MRD at TP3 and without HGs (figure 3). In patients who had a positive MRD at TP1, detectable HGs at TP3 identified a subgroup of patient with favorable OS compared to patient with positive MRD at TP1 and without detectable HGs (p=0.072). These results should be taken with cautious because of the decreasing number of patients evaluated at different time points. However, HGs analysis could represent a new area of investigation in search of new prognostic factors in the context of adult ALL. Figure 1. Percentage of patients with (A) negative MRD and (B) detectable HGs at different time points after starting of treatment. Figure 1. Percentage of patients with (A) negative MRD and (B) detectable HGs at different time points after starting of treatment. Figure 2. Overall survival according to HGs status at TP3. Figure 2. Overall survival according to HGs status at TP3. Figure 3. Overall survival in patients with negative MRD at TP3 according to HGs status. Figure 3. Overall survival in patients with negative MRD at TP3 according to HGs status. Disclosures: No relevant conflicts of interest to declare.

Molecular Predictors of Outcome in Patients with MDS and AML Following MDS after Allogeneic Hematopoietic Stem Cell Transplantation

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 912-912 ◽  
Author(s):  
Michael Heuser ◽  
Christian Koenecke ◽  
Razif Gabdoulline ◽  
Patrick Löffeld ◽  
Vera Dobbernack ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cell ◽  
High Risk ◽  
Complete Remission ◽  
Research Funding ◽  
Prognostic Impact ◽  
Complex Karyotype ◽  
Hematopoietic Stem ◽  
Signal Transducers ◽  
Active Disease

Introduction: The landscape of molecular aberrations in patients with myelodysplastic syndromes (MDS) has been well characterized and has identified ASXL1, BCOR, CUX1, IDH1, IDH2, SRSF2, RUNX1, U2AF1, TP53 and others as negative prognostic markers for overall survival (OS). We comprehensively investigated the prognostic impact of genetic aberrations in the context of allogeneic hematopoietic stem cell transplantation (alloHSCT) in a large cohort of patients with high risk MDS or secondary AML following MDS (sAML). Patients and Methods: 308 Patients with a diagnosis of MDS (47.4%) or sAML (52.6%) who received an alloHSCT at four German university medical centers and for whom genomic DNA was available at a time with active disease before transplantation were evaluated for the presence of mutations in 54 genes by Illumina high-throughput sequencing. Results: At least one mutation was identified in 82% of our patients with a median number of 2 mutations per patient. The most frequently mutated genes were ASXL1 (24.4%), DNMT3A, (23.1%), RUNX1 (16.9%), TET2 (16.9%), STAG2 (12%), TP53 (11.7%), and SRSF2 (11%) in agreement with previous reports. Mutation frequencies were similar between MDS and sAML patients for all mutated genes except SRSF2, TET2 and WT1, which were more frequently mutated in sAML. We grouped the mutated genes into functional classes and found that patients most frequently had mutations in modifiers of DNA methylation (42.2%), followed by chromatin modifiers (41.5%), splicing genes (31.1%), transcription factors (30.8%), signal transducers (28.8%) and tumor suppressors (14.6%). Mean variant allele frequencies were highest in modifiers of DNA methylation (33.2%), while signal transducers had the lowest allele frequency (20.4%). We next assessed the prognostic impact of gene classes and individual genes on outcome of patients after alloHSCT. Median follow up from transplantation was 4.15 years. Median patient age at time of HSCT was 58 years (range 19-75). 76 patients (25%) werein complete remission and 232 patients (75%) had active disease before transplantation. Low, intermediate, and high risk cytogenetics according to IPSS were found in 116 (38%), 59 (19%), and 115 (37%) patients, respectively. Matched and mismatched related donor HSCT was performed in 71 and 4 patients, respectively (23.1 and 1.3%), and matched and mismatched unrelated donor HSCT in 171 and 62 patients, respectively (55.5 and 20.1%). The six functional gene classes had no prognostic impact on survival, cumulative incidence of relapse and non-relapse mortality. We therefore evaluated the prognostic impact of individual gene mutations, of aberrations of chromosomes 3, 5, 7, 8, 17, 20 or a complex karyotype, and of transplant characteristics on OS. Parameters with significant impact on OS in univariate analysis were included in a multivariate cox proportional hazards model. Significant predictors of OS in multivariate analysis were mutations in PTPN11 (HR 3.1, present in 2.3% of pts.), IDH2 (HR 2.6, present in 4.2%), PHF6 (HR 2.2, present in 4.9%), NRAS (HR 1.8, present in 7.5%), presence of a complex karyotype (HR 1.8, present in 16.6%), transplantation from haploidentical donor (HR 5.5), RAEB/sAML not in complete remission before transplantation compared to untreated RA/RARS or RAEB/sAML and treated RAEB/sAML in remission (HR 2.0), GvHD prophylaxis other than calcineurin inhibitor with methotrexate or mycophenolate mofetil (HR 1.7) and female sex of the donor (HR 1.7). TP53 mutations lost their unfavorable prognostic impact when complex karyotype was added to the multivariate model. Competing risk analysis for cumulative incidence of relapse and non-relapse mortality showed that IDH2 and NRAS mutations and a complex karyotype were significantly associated with higher risk for relapse while PTPN11 and PHF6 mutations predicted for a higher incidence of non-relapse mortality. Importantly, a negative prognostic impact of ASXL1, BCOR, CUX1, IDH1, SRSF2, RUNX1 and U2AF1 seen previously in MDS patients not undergoing alloHSCT was not found in the transplant setting, suggesting that alloHSCT may overcome the unfavorable effect of these mutations. Conclusion: By extensive genetic characterisation of 308 MDS or sAML patients undergoing alloHSCT we identified mutations in IDH2, NRAS and complex karyotype as predictors of relapse and reduced OS and provide a matrix to refine risk prediction for allogeneic HSCT. Disclosures Heuser: Karyopharm: Research Funding. Platzbecker:Boehringer: Research Funding; Celgene: Honoraria, Research Funding; Novartis: Honoraria, Research Funding. Thiede:Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; AgenDix GmBH: Equity Ownership.

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&lt;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&lt;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 CENPE expression is associated with its DNA methylation status in esophageal adenocarcinoma and independently predicts unfavorable overall survival

PLoS ONE ◽  
2019 ◽  
Vol 14 (2) ◽  
pp. e0207341 ◽  
Author(s):  
Xueqiang Zhu ◽  
Xing Luo ◽  
Gang Feng ◽  
Hui Huang ◽  
Yangke He ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Overall Survival ◽  
Esophageal Adenocarcinoma ◽  
Methylation Status

Demethylation Profiling of CD34-Positive Hematopoietic Cells in Patients with Myelodysplastic Syndromes.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3440-3440
Author(s):  
Francesco D’Alo’ ◽  
Manuela Giachelia ◽  
Annalisa Di Ruscio ◽  
Daniela Gumiero ◽  
Emiliano Fabiani ◽  
...  
Keyword(s):  
Stem Cell ◽  
Myelodysplastic Syndromes ◽  
Methylation Status ◽  
Normal Karyotype ◽  
Refractory Anemia ◽  
Trisomy 8 ◽  
Hematopoietic Stem ◽  
Demethylating Agents ◽  
New Genes ◽  
Cd34 Cells

Abstract Myelodysplastic syndromes (MDS) are a genetic and epigenetic disease of the hematopoietic stem cell. Aberrant CpG islands methylation in the contex of the promoter of multiple genes plays a pivotal role in the pathogenesis of MDS and leads to silencing of tumor suppressor genes, including cell-cycle inhibitors, inducers of apoptosis, DNA repair genes, transcription factors, cell adhesion mediators, hormonal receptors and detoxifiers. Demethylating agents, such as decitabine and azacitidine, are able to revert epigenetic silencing induced by hypermethylation and are currently used to treat all subtypes of MDS. Some of the target genes of demethylating drugs have been well studied and correlated to clinical response of patients, such as p15INK4B, but most of them remain to be identified and characterized. We isolated CD34+ cells from two patients with previously untreated MDS, a 70 year old female, with a diagnosis of Refractory Anemia with Excess Blasts (RAEB) and a complex karyotype including deletion of 5q11–q34 and trisomy 8, and a 59 years old male, with a diagnosis of RAEB in transformation, according to FAB and a normal karyotype. CD34+ cells were isolated from bone marrow samples by immunomagnetic beads, with a yield of about 2 x 106 cells per patients. Purity of the CD34+ cell fraction, evaluated by flow cytometry, was 58% and 86%, respectively. Cells were cultured in 24-well plates in IMDM medium with L-Glutamine, antibiotics, 30% of inactivated Foetal Bovine Serum and 10 ng/ml each of IL-3, Stem Cell Factor (SCF), Thrombopoietin and FLT3-ligand. After 24 hours, decitabine was added to the culture medium to a final concentration of 1 m M. A corresponding amount of acetic acid was added to different wells for the mock treatment control. Each experiment was conducted in triplicate. Cells were collected after 72 hours of treatment and RNA was extracted by the Qiagen RNeasy Kit, processed by two-cycle cDNA synthesis kit (Invitrogen), in vitro transcripted to cRNA and hybridized on Affymetrix HG-U133A chips. Five chips were used for each patient: three for treated cells and two for mock -treated cells. Microarray data were normalized and analysed by GeneSpring software version 7.2 and the ANOVA Welch’s test was applied. We selected genes with a p value less than 0.01 and a fold change higher than 2. Using these conditions, 60 genes were upregulated by decitabine in both patients. Some of the most interesting genes were GATA binding protein 2 (GATA2), cyclin-dependent kinase inhibitor 1A (CDKN1A, p21), cyclin A1 (CCNA1), decay accelerating factor for complement (CD55, DAF), immediate early response 3 (IER3), nuclear factor interleukin 3 regulated (NFIL3) and chemokine (C-X-C motif) receptor 4 (CXCR4). Interestingly, the patient with a normal karyotype showed a higher percentage of up-regulated genes after decitabine treatment compared to the patient with the 5q11-q34 deletion and a trisomy 8. This suggests that epigenetic changes in gene expression may have higher impact when the karyotype is normal. Functional significance of these data remains to be elucidated. Expression and methylation status of these genes will be investigated in a larger group of MDS patients. This approach aims to characterize new genes, as methylation targets in MDS and possible markers of disease, and to identify patients responding to demethylating agents.

MicroRNA Expression and Regulation of Hematopoiesis in CD34+ Cells: A Bioinformatic Circuit Diagram of the Hematopoietic Differentiation Control.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1334-1334
Author(s):  
Robert W. Georgantas ◽  
Richard Hildreth ◽  
Jonathan Alder ◽  
Carlo M. Croce ◽  
George A. Calin ◽  
...  
Keyword(s):  
Protein Expression ◽  
Expression Profiles ◽  
In Vivo Studies ◽  
Luciferase Reporter ◽  
Hematopoietic Differentiation ◽  
Aberrant Expression ◽  
Hematopoietic Stem ◽  
Cd34 Cells

Abstract MicroRNAs (miRs) are a recently realized class of epigenetic elements which block translation of mRNA to protein. MicroRNAs have been shown to control cellular metabolism, apoptosis, differentiation and development in numerous organisms including drosophila, rat, mouse, and humans. Recently, miRs have been implicated in the control of hematopoiesis. Importantly, both aberrant expression and deletion of miRs are have been associated with the development of various cancers. In a previous study, we determined the gene expression profiles of HSC-enriched, HPC-enriched, and total CD34+ cells from human PBSC, BM, and CB. One rather surprising finding from this study was that virtually all of “hematopoietic important” genes were expressed at virtually identical levels within all populations examined. One of our hypotheses to explain this phenomena was that miRs may control differentiation by controlling protein expression from these “hematopoietic” RNAs. To examine the possible role of miRs in normal hematopoiesis and their relation to the HSPC transcriptome, we used mir-miroarrays to determine the miR expression profile of primary normal human mobilized blood and bone marrow CD34+ hematopoietic stem-progenitor cells (HSPCs). We have combined this miR data with (1) our extensive mRNA expression data obtained previously for CD34+ HSPCs, CD34+/CD38−/Lin- stem cell-enriched, CD34+/CD38+/Lin+ progenitor-enriched populations, and total CD34+ HSPC (Georgantas, Cancer Research 64:4434) and (2) miR target predictions from various published algorithms. Combining these datasets into one integrated database allowed us to bioinformaticly examine the global interaction of HSPC mRNAs and miRs during hematopoiesis. The 3′UTR sequences from many of these “hematopoietic” mRNA were cloned behind a luciferase reporter. K562 cells were transfected with these luc-3′UTR constructs, confirmating that expression of many important hematopoietic proteins are controlled by miRs. Based on our bioinformatic and protein expression studies, we present a global in silico model by which microRNAs control and direct hematopoietic differentiation. Actual in vitro and in vivo studies addressing the action of specific miRs in hematopoietic differentiation are presented in separate abstracts.

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