Low Frequency of Molecular Alterations of H3.3-Atrx-Daxx Chromatin Remodeling Component Genes in Myelodysplastic Syndromes (MDS)

Abstract Abstract 3844 Novel sequencing technologies have allowed identification of a group of highly recurrent genetic mutations in myelodysplastic syndromes (MDS). Of importance, it has been noticed that a majority of these mutated genes in MDS encode important components of epigenetic regulation, including both DNA methylation and histone modifications. This phenomenon highlights the importance of epigenetic mechanisms in the pathogenesis of MDS. Recently, highly recurrent somatic mutations in the Histone H3.3-ATRX-DAXX chromatin remodeling pathway have been documented in pediatric glioblastoma (Schwartzentruber et al. Nature and Wu et al. Nature Genetics 2012), further supporting the importance of epigenetic regulation for tumorgenesis. We therefore examined potential genetic and epigenetic alterations of the same pathway in MDS. First, in a cohort containing 80 samples of MDS whole bone marrow mononuclear cell DNA (representative of both lower and higher risk disease), we performed Sanger sequencing covering genomic areas of reported mutations of H3F3A, H3F3B, ATRX, and DAXX in glioblastoma. Sequenced genomic areas included reported mutations in pediatric tumors: Lys27 and Gly34 of H3F3A and H3F3B; sequences upstream of and within the helices domain of ATRXX; and the whole coding sequence of DAXX. Overall, we only detected one mutation of H3F3A (K27N) in one MDS case (76 year old male with RA; INT-1; diploid). No other reported mutation of H3F3B, ATRX and DAXX genes was detected in any other patients of this MDS cohort. Because of the potential of epigenetic deregulation, we then examined status of DNA methylation for the promoters of ATRX and DAXX in MDS patients by bisulfite pyrosquencing. While no DNA hypermethylation of DAXX promoter was detected, 8 out of 40 (20%) patients had hypermethylation of the CpG island in the promoter region of ATRX. However, six of these eight patients were females. Based on reports of ATRX methylation in healthy females, it is likely that the 6 cases in female patients represent physiological × chromosome inactivation. Finally, we performed RT-PCR analysis using cDNA samples isolated from CD34+ hematopoietic stem cells of 40 MDS patients. Results indicated that expression of ATRX and DAXX were increased by 2 fold (p-value 0.07) and 5.2 fold (p-value 0.0003) respectively compared to control CD34+ cells. The implications of this phenomenon need to be studied further. Taken together, these results suggest that genetic mutations of the H3.3-ATRX-DAXX chromatin remodeling do not play a role in the pathogenesis of MDS. Disclosures: No relevant conflicts of interest to declare.

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Large Conserved Domains Of Low DNA Methylation Maintained By 5-Hydroxymethycytosine and Dnmt3a

Blood ◽

10.1182/blood.v122.21.2406.2406 ◽

2013 ◽

Vol 122 (21) ◽

pp. 2406-2406

Author(s):

Mira Jeong ◽

Deqiang Sun ◽

Min Luo ◽

Yun Huang ◽

Myunggon Ko ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Hox Genes ◽

Conflicts Of Interest ◽

P Value ◽

Genomic Feature ◽

Conserved Domains ◽

Hematopoietic Stem ◽

Genome Wide ◽

The Impact

Abstract Identification of recurrent leukemia-associated mutations in genes encoding regulators of DNA methylation such as DNMT3A and TET2 have underscored the critical importance of DNA methylation in maintenance of normal physiology. To gain insight into how DNA methylation exerts the central role, we sought to determine the genome-wide pattern of DNA methylation in the normal precursors of leukemia cells: the hematopoietic stem cell (HSC), and investigate the factors that affect alterations in DNA methylation and gene expression. We performed whole genome bisulfite sequencing (WGBS) on purified murine HSCs achieving a total of 1,121M reads, resulting in a combined average of 40X coverage. Using Hidden Markov Model we identified 32,325 under-methylated regions (UMRs) with average proportion of methylation ≤ 10% and by inspecting the UMR size distribution, we discovered exceptionally large “methylation Canyons” which span highly conserved domains frequently containing transcription factors and are quite distinct from CpG islands and shores. Methylation Canyons are a distinct genomic feature that is stable, albeit with subtle differences, across cell-types and species. Canyon-associated genes showed a striking pattern of enrichment for genes involved in transcriptional regulation (318 genes, P=6.2 x 10-123), as well as genes containing a homeobox domain (111 genes, P=3.9 x 10-85). We compared Canyons with TF binding sites as identified from more than 150 ChIP-seq data sets across a variety of blood lineages (>10)19 and found that TF binding peaks for 10 HSC pluripotency TFs are significantly enriched in entirety of Canyons compared with their surrounding regions. Low DNA methylation is usually associated with active gene expression. However, half of Canyon genes associated with H3K27me3 showed low or no expression regardless of their H3K4me3 association while H3K4me3-only Canyon genes were highly expressed. Because DNMT3A is mutated in a high frequency of human leukemias24, we examined the impact of loss of Dnmt3a on Canyon size. Upon knockout of Dnmt3a, the edges of the Canyons are hotspots of differential methylation while regions inside of Canyon are relatively resistant. The methylation loss in Dnmt3a KO HSCs led Canyon edge erosion, Canyon size expansion and addition of 861 new Canyons for a total of 1787 Canyons. Canyons marked with H3K4me3 only were most likely to expand after Dnmt3a KO and the canyons marked only with H3K27me3 or with both marks were more likely to contract. This suggests Dnmt3a specifically is acting to restrain Canyon size where active histone marks (and active transcription) are already present. WGBS cannot distinguish between 5mC and 5hmC, so we determined the genome-wide distribution of 5hmC in WT and Dnmt3a KO HSCs using the cytosine-5-methylenesulphonate (CMS)-Seq method in which sodium bisulfate treatment convert 5hmC to CMS; CMS-containing DNA fragments are then immunoprecipitated using a CMS specific antiserum. Strikingly, 5hmC peaks were enriched specifically at the borders of Canyons. In particular, expanding Canyons, typically associated with highest H3K4me3 marking, were highly enriched at the edges for the 5hmC signal suggesting a model in which Tet proteins and Dnmt3a act concomitantly on Canyon borders opposing each other in alternately effacing and restoring methylation at the edges, particularly at sites of active chromatin marks. Using Oncomine data, we tested whether Canyon-associated genes were likely to be associated with hematologic malignancy development and found Canyon genes were highly enriched in seven signatures of genes over-expressed in Leukemia patients compared to normal bone marrow; in contrast, four sets of control genes were not similarly enriched. Further using TCGA data, we found that expressed canyon genes are significantly enriched for differentially expressed genes between patients with and without DNMT3A mutation (p value<0.05) Overall, 76 expressed canyon genes, including multiple HOX genes, are significantly changed in patients with DNMT3A mutation (p=0.0031). Methylation Canyons, the novel epigenetic landscape we describe may provide a mechanism for the regulation of hematopoiesis and may contribute to leukemia development. Disclosures: No relevant conflicts of interest to declare.

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Functional Characterization of Epigenetic Modifiers of Demethylating Therapy in AML

Blood ◽

10.1182/blood-2018-99-116818 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 1465-1465

Author(s):

Desiree Melanie Redhaber ◽

Laurent Phely ◽

Sophia Ehrenfeld ◽

Pia Veratti ◽

Silvia Schäfer ◽

...

Keyword(s):

Dna Methylation ◽

Dna Damage ◽

Candidate Genes ◽

Epigenetic Regulation ◽

Molecular Mechanisms ◽

Conflicts Of Interest ◽

Leukemia Cell ◽

Nucleoside Analogs ◽

Human Leukemia ◽

Hematopoietic Stem

Abstract Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults, and remains a difficult to treat disease, especially in elderly patients. AML arises in hematopoietic stem and progenitor cells and frequently carries alterations in genes involved in epigenetic regulation. Furthermore, azacitidine (AZA) and decitabine (DAC), two nucleoside analogs inhibiting DNA methylation (DNMTi), have shown clinical efficacy in the therapy of myelodysplastic syndrome (MDS) and AML, highlighting the importance of epigenetic regulation in AML. Up to now, the mechanism of action of AZA and DAC in AML has not been fully elucidated, and reliable biomarkers of therapy response to these drugs do not yet exist. To identify epigenetic response modifiers towards AZA and DAC treatment, we conducted a pooled shRNA-based screen in three human leukemia cell lines using an inducible custom shRNA library targeting more than 660 different genes involved in epigenetic pathways. After selection of retrovirally infected cells, shRNA expression was induced and a fraction of cells were treated with either AZA, DAC or left untreated. 10 days after shRNA induction, genomic DNA was extracted and deep-sequenced to identify genes conferring a selective advantage/disadvantage under these conditions. By comparing shRNA representation changes between the differentially treated groups, we identified multiple candidate genes sensitizing or protecting leukemic cells to/from AZA and DAC treatment. Notably, the DNMT1 gene itself expectedly emerged as an important sensitizer to DNMTi, as did other CXXC domain-containing genes binding to (un-)methylated CpG domains. Another prominent set of genes in the pooled analysis belonged to the DNA damage pathway, including genes such as PARP1 and BRCA1. The identified candidate genes were validated and confirmed in more than 80% when tested in single shRNAs competition assays. Their impact on DNA methylation and gene expression is currently being assessed, with ongoing experiments focusing on the mechanistic role of some of the validated target, as well as the clinical potential for combinatorial therapies. Thus, using an unbiased functional genetic approach, we identified multiple genes including CpG binding proteins and members of the DNA damage pathway as important modulators of DNMTi response. Our results will increase our understanding of the molecular mechanisms driving DNMTi efficacy, and may help to identify new biomarkers and novel targets for combinational therapy in AML. Disclosures No relevant conflicts of interest to declare.

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Stage-differentiated modelling of DNA methylation landscapes uncovers salient biomarkers and prognostic signatures in colorectal cancer progression

10.21203/rs.3.rs-244816/v1 ◽

2021 ◽

Author(s):

Sangeetha Muthamilselvan ◽

Abirami Raghavendran ◽

Ashok Palaniappan

Keyword(s):

Colorectal Cancer ◽

Dna Methylation ◽

Cpg Island ◽

Early Stage ◽

P Value ◽

Consensus Analysis ◽

One Stage ◽

Differentially Methylated Genes ◽

Methylation Patterns ◽

The Impact

Abstract Background: Aberrant DNA methylation acts epigenetically to skew the gene transcription rate up or down, with causative roles in the etiology of cancers. However research on the role of DNA methylation in driving the progression of cancers is limited. In this study, we have developed a comprehensive computational framework for the stage-differentiated modelling of DNA methylation landscapes in colorectal cancer (CRC), and unravelled significant stagewise signposts of CRC progression. Methods: The methylation β - matrix was derived from the public-domain TCGA data, converted into M-value matrix, annotated with AJCC stages, and analysed for stage-salient genes using multiple approaches involving stage-differentiated linear modelling of methylation patterns and/or expression patterns. Differentially methylated genes (DMGs) were identified using a contrast against controls (adjusted p-value <0.001 and |log fold-change of M-value| >2). These results were filtered using a series of all possible pairwise stage contrasts (p-value <0.05) to obtain stage-salient DMGs. These were then subjected to a consensus analysis, followed by Kaplan–Meier survival analysis to evaluate the impact of methylation patterns of consensus stage-salient biomarkers on disease prognosis.Results: We found significant genome-wide changes in methylation patterns in cancer cases relative to controls agnostic of stage. Our stage-differentiated analysis yielded the following stage-salient genes: one stage-I gene (FBN1), one stage-II gene (FOXG1), one stage-III gene (HCN1) and four stage-IV genes (NELL1, ZNF135, FAM123A, LAMA1). All the biomarkers were hypermethylated, indicating down-regulation and signifying a CpG island Methylator Phenotype (CIMP) manifestation. A significant prognostic signature consisting of FBN1 and FOXG1 survived all the steps of our analysis pipeline, and represents a novel early-stage biomarker. Conclusions: We have designed a workflow for stage-differentiated consensus analysis, and identified stage-salient diagnostic biomarkers and an early-stage prognostic biomarker panel. Our studies further yield a novel CIMP-like signature of potential clinical import underlying CRC progression.

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UTX, a Histone Demethylase, Is Inactivated through Homozygous Deletion, Mutation, and DNA Methylation in Multiple Myeloma.

Blood ◽

10.1182/blood.v114.22.1798.1798 ◽

2009 ◽

Vol 114 (22) ◽

pp. 1798-1798

Author(s):

Brian A Walker ◽

Paola E. Leone ◽

Nicholas J Dickens ◽

Kevin D Boyd ◽

David Gonzalez ◽

...

Keyword(s):

Dna Methylation ◽

Cell Lines ◽

Copy Number ◽

Conflicts Of Interest ◽

Cpg Island ◽

Chromatin Condensation ◽

Methylation Status ◽

Significant Proportion ◽

Histone Demethylase ◽

Homozygous Deletions

Abstract Abstract 1798 Poster Board I-824 Histone modifications are known to mediate transcriptional regulation through changes in chromatin condensation and as such can lead to aberrant transcriptional patterns resulting in malignant transformation. Modulation of chromatin structure via histone modification is becoming recognised as an important pathogenic mechanism in myeloma and has been suggested by the over-expression of MMSET, a histone methyltransferase, by the t(4;14) chromosomal rearrangement. More recently inactivation of UTX, a histone demethylase, has also been suggested to have a role in myeloma pathogenesis and both UTX and MMSET are mediators of transcriptional repression. UTX is inactivated in a number of different cancer cell lines but importantly, mutations and deletions have been detected in myeloma cell lines and we wished to follow up on this observation in uniformly treated clinical cases. UTX is a large gene found on the X chromosome covering 240 kb of genomic DNA and consists of 29 exons encoding a protein with both JmjC-domains and tricopeptide repeats responsible for histone demethylation and polycomb protein interactions. Inactivation of UTX occurs through deletions of individual exons through to large whole gene deletions as well as by mutations scattered throughout the 29 exons. A further mechanism of UTX inactivation which has not been looked for to date is via DNA methylation of the CpG island upstream of the transcriptional start site. We set out to determine the status of UTX in our dataset which includes expression, mapping, and methylation array data from presenting myeloma samples entered into the MRC Myeloma IX clinical trial. The gene expression of UTX was measured on 272 samples using Affymetrix U133 Plus 2.0 arrays and showed that 80% of samples do not express UTX transcripts but using expression quartile analysis we could not detect an effect on overall survival. The mechanism underlying the abrogation of expression was investigated further using the Affymetrix 500K SNP mapping array on a subset of 114 samples to detect copy number alterations. UTX was hemizygously deleted in 21 (42%) female samples and was completely deleted in 1 male sample, at the resolution of the arrays. In order to determine if individual exons were deleted, at a resolution below that detectable by mapping arrays, we performed quantitative PCR coupled with high resolution melting (HRM) analysis using the Rotor-gene Q real-time cycler (Qiagen). Exons were amplified, over 40 cycles, to obtain products of ∼200 bp using LC Green Plus mastermix (Idaho Technologies) in a 10 μl reaction on the Rotor-gene Q with a final HRM step from 72-95 °C with increments of 0.1 °C. Amplification plots combined with the HRM step allows us to identify both homozygous deletions and mutations within the exons. We screened all 114 samples for micro-deletions and mutations and found homozygous deletions in ∼7% of samples and identified a significant proportion of mutations using the HRM method which accounted for a total of ∼10% of gene inactivation. In order to determine if methylation could be responsible for inactivation of the remaining allele we used the Illumina Infinium humanmethylation27 array to study the methylation status at the UTX locus. This array interrogates 27,578 highly informative CpG sites per sample at the single-nucleotide resolution using bisulfite converted DNA. The results of this analysis are presented as an average beta-score where 1.0 is fully methylated and 0 is fully unmethylated. Samples were analyzed using Illumina GenomeStudio and the custom differential methylation algorithm. In samples with a diploid copy number of UTX the methylation signals covered 2 ranges: hemi-methylated (0.35-0.55, n=7) and hyper-methylated (0.73-0.89, n=14). In samples with 1 copy of UTX, which includes all males, there were 3 ranges: hypomethylated (0.08-0.21, n=5), hemi-methylated (0.35-0.51, n=3), and hypermethylated (0.66-0.88, n=48). All of the hypomethylated samples with a single copy of UTX were male, and at least 1 of these samples contained an inactivating exonic deletion resulting in complete loss of function. These data indicate that methylation of the residual allele contributes significantly to the inactivation of UTX along with interstitial deletions and mutations. We will go on to present data on the interaction of UTX with variation at the UTY locus and how this modulates behaviour of the myeloma clone. Disclosures No relevant conflicts of interest to declare.

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Profiling of Aberrant DNA Methylation In AML Reveals Subclasses of CpG Islands with Epigenetic or Genetic Association

Blood ◽

10.1182/blood.v116.21.2498.2498 ◽

2010 ◽

Vol 116 (21) ◽

pp. 2498-2498

Author(s):

Claudia Gebhard ◽

Mohammed Sadeh ◽

Dagmar Glatz ◽

Lucia Schwarzfischer ◽

Rainer Spang ◽

...

Keyword(s):

Dna Methylation ◽

De Novo ◽

Conflicts Of Interest ◽

Cpg Island ◽

Cpg Islands ◽

Sequencing Data ◽

Cpg Island Methylator Phenotype ◽

Chip Sequencing ◽

Aberrant Dna Methylation ◽

Methylation Patterns

Abstract Abstract 2498 CpG islands show frequent and often disease-specific epigenetic alterations during malignant transformation, however, the underlying mechanisms are poorly understood. We used methyl-CpG immunoprecipitation (MCIp) to generate comparative DNA methylation profiles of 30 patients with acute myeloid leukemia for human CpG islands across the genome. DNA methylation profiles across 23.000 CpG islands revealed highly heterogeneous methylation patterns in AML with over 6000 CpG islands showing aberrant de novo methylation in AML. Based on these profiles we selected a subset of 380 CpG islands (covering 15.000 individual CpGs) for detailed fine-mapping analyses of aberrant DNA methylation in 185 patients with AML (50% normal karyotype). We found that a proportion of patients (5/185) displayed a concerted hypermethylation at almost all studied loci, representing the rare CpG island methylator phenotype (CIMP) in AML. Meta analysis of methylation profiling and published ChIP sequencing data separated CpG islands in two groups. A highly correlated subgroup of CpG island regions was strongly associated with histone H3 lysine 27 trimethylation in human hematopoietic progenitor cells, suggesting that disease-related de novo DNA methylation at these CpG islands is linked with polycomb group protein (PcG)-mediated repression. The group of mainly non-PcG target CpG islands showed heterogeneous methylation patterns across patients and unsupervised hierarchical clustering revealed a correlation of methylation profiles with genetic disease markers, including oncofusion proteins as well as CEBPA- and NPM1-mutations. Our study suggests that both epigenetic as well as genetic aberrations may underlay AML-related changes in CpG island DNA methylation states. Disclosures: No relevant conflicts of interest to declare.

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Promoter Methylation and Decreased Expression of Mir-124 In Myelodysplastic Syndromes

Blood ◽

10.1182/blood.v116.21.4014.4014 ◽

2010 ◽

Vol 116 (21) ◽

pp. 4014-4014

Author(s):

Yuesheng Meng ◽

Qiao Xia ◽

Jun Hu

Keyword(s):

Myelodysplastic Syndromes ◽

Promoter Methylation ◽

Molecular Mechanisms ◽

Conflicts Of Interest ◽

Quantitative Polymerase Chain Reaction ◽

Methylation Status ◽

Polymerase Chain Reaction Analysis ◽

Promoter Regions ◽

Hematopoietic Stem

Abstract Abstract 4014 The myelodysplastic syndromes (MDS) are a heterogeneous group of clonal disorders of hematopoietic stem/progenitor cells. Although demethylating agents such azacytidine and decitabine have been widely used to treat MDS, the underlying molecular mechanisms remain obscure. Abnormalities of microRNAs (miRNA) have been recently associated with hematological malignancies including MDS. The miR-124 was initially demonstrated to modulate neurogenesis. It was recently shown that EVI1-induced methylation and silencing of miR-124 were present in murine MDS cells. In the retrospective study we evaluated methylation status and expression levels of miR-124 in fifteen MDS patients (subtypes included RCUD, RCMD, RAEB-1, RAEB-2 and CMML). Genomic DNA samples were modified with bisulfite and methylation at three promoter regions of miR-124 was examined with methylation-specific real time quantitative polymerase chain reaction analysis (MQPCR). In general, we observed an increased methylation levels of miR-124 in MDS patients than that in normal bone marrow (NBM, P<0.01). In accordance with this, marked depression of miR-124 was seen in six patients when compared with NBM (more than 2 times lower), as determined with quantitative reverse-transcriptive PCR assay. Moreover, there were higher degrees of promoter methylation in cases with depressed miR-124 than that in remaining cases. A negative correlation between the expression and methylation levels was statistically significant (R= -0.498, P<0.01). The change of miR-124 was not directly related to short-term clinical response or prognosis, possibly due to limited size of the sample. However, the miR-124 amount returned to basal levels in two cases (RCMD and CMML subtypes respectively) after low-dose decitabine therapy and DNA methylation of all three loci disappeared. Continued work is underway to accumulate more cases and make long-term clinical follow-up. In conclusion, this primary work suggested a possible role of the methylation-mediated silencing of miR-124 in the pathogenesis or disease progression of MDS. Disclosures: No relevant conflicts of interest to declare.

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Correlation of Morphological Dysplasia and Immunophenotypic Features in Myelodysplastic Syndromes

Blood ◽

10.1182/blood.v128.22.5548.5548 ◽

2016 ◽

Vol 128 (22) ◽

pp. 5548-5548

Author(s):

Elvira D Rodrigues Pereira Velloso ◽

Rosana M Cosentino ◽

Liliana Mitie Suganuma ◽

Rodrigo de Souza Barroso ◽

Nydia Strachman Bacal ◽

...

Keyword(s):

Clinical Data ◽

Myelodysplastic Syndromes ◽

Conflicts Of Interest ◽

Intraclass Correlation ◽

Myeloid Cell ◽

High Sensitivity ◽

World Health ◽

Hematopoietic Stem ◽

Morphological Criteria ◽

Increased Risk

Abstract The Myelodysplastic Syndromes (MDS) are a group of clonal hematopoietic stem cell diseases characterized by cytopenias, dysplasia in one or more myeloid cell lines, ineffective hematopoiesis and increased risk for development of acute myeloid leukemia (AML).The pathological hallmark of myelodysplastic syndromes (MDS) is marrow dysplasia, which represents the basis of the World Health Organization (WHO) classification of these disorders. However, morphological diagnosis of MDS may have difficulties, with poor inter-observer agreement.Recently, Della Porta and col.(on behalf of Rete Ematologica Lombarda (REL) Network), described a new morphological score system to define dysplasia, that showed high sensitivity and specificity (>90%) andbetter inter-operator agreement (Leukemia 2015;29:66-75). In addition, new toolsfor diagnostic and prognostic purposes were developed.Flow cytometry (FCM) was addedin standard European Leukemia Net guidelinesasrecommended tool for diagnosis and prognosis in MDS, and a simple MDS-FCM scoring system based on four parameters (mainly CD34 and granulocytic cells) by Ogata and col. showed a good specificity (Haematologica 2009;94:1066-1074). The aim of this study is to correlate morphological and immunophenotypic features in suspicion of MDS. The study comprised two steps: the first used for morphological validation, included 33 bone marrow (BM) smears from patients with suspected MDS with or without therapy, reviewed by four experts hematologists blinded to clinical data. Dysplasia was evaluated using WHO 2008 criteria and Della Porta's score: 100 erythroblasts, 100 granulocytic cells and 30 megakaryocytes for dysplasia and 500 nucleated cells for blast cells percentage. The second step included 69 BM samples from patients with suspected MDS (27 with final diagnosis of MDS) and was used to correlate cytology and immunophenotypic findings. The morphological aspects were reviewed by one of the expert hematologists, using the same previous criteria and blinded to clinical data. Inter-operator reproducibility of morphological analyses was assessed by Intraclass Correlation Coefficient (ICC). Acceptable reproducibility was defined as ICC > 0.4. The correlation of minimal morphological criteria with immunophenotypic criteria of Ogata and col. was assessed by Discordance rate and Spearman correlation. The results are shown in table. In conclusion our study shows good inter observer reproducitibility, in both used criteria. The use of new criteria of Della Porta to the erythroid series was slightly better, suggesting that can be useful in diagnosing myelodisplasias. Immunophenotypic data had a good agreement with morphologic data in confirmed cases of MDS. Table 1 Table 1. Disclosures No relevant conflicts of interest to declare.

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Aberrant DNA methylation characterizes juvenile myelomonocytic leukemia with poor outcome

Blood ◽

10.1182/blood-2010-08-298968 ◽

2011 ◽

Vol 117 (18) ◽

pp. 4871-4880 ◽

Cited By ~ 60

Author(s):

Christiane Olk-Batz ◽

Anna R. Poetsch ◽

Peter Nöllke ◽

Rainer Claus ◽

Manuela Zucknick ◽

...

Keyword(s):

Dna Methylation ◽

Cox Regression ◽

Cpg Island ◽

Cpg Islands ◽

Prognostic Scores ◽

Juvenile Myelomonocytic Leukemia ◽

Hematopoietic Stem ◽

Prognostic Features ◽

Aberrant Dna Methylation ◽

Myelomonocytic Leukemia

Abstract Aberrant DNA methylation contributes to the malignant phenotype in virtually all types of cancer, including myeloid leukemia. We hypothesized that CpG island hypermethylation also occurs in juvenile myelomonocytic leukemia (JMML) and investigated whether it is associated with clinical, hematologic, or prognostic features. Based on quantitative measurements of DNA methylation in 127 JMML cases using mass spectrometry (MassARRAY), we identified 4 gene CpG islands with frequent hypermethylation: BMP4 (36% of patients), CALCA (54%), CDKN2B (22%), and RARB (13%). Hypermethylation was significantly associated with poor prognosis: when the methylation data were transformed into prognostic scores using a LASSO Cox regression model, the 5-year overall survival was 0.41 for patients in the top tertile of scores versus 0.72 in the lowest score tertile (P = .002). Among patients given allogeneic hematopoietic stem cell transplantation, the 5-year cumulative incidence of relapse was 0.52 in the highest versus 0.10 in the lowest score tertile (P = .007). In multivariate models, DNA methylation retained prognostic value independently of other clinical risk factors. Longitudinal analyses indicated that some cases acquired a more extensively methylated phenotype at relapse. In conclusion, our data suggest that a high-methylation phenotype characterizes an aggressive biologic variant of JMML and is an important molecular predictor of outcome.

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Impact of Non-CMV Specific Intravenous Immunoglobulin on Intravenous Ganciclovir Effectiveness

Blood ◽

10.1182/blood-2018-99-115022 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 5741-5741

Author(s):

Mikhail Yu. Drokov ◽

Dmitry S. Tikhomirov ◽

Larisa Kuzmina ◽

Tatiana A. Tupoleva ◽

Vera Vasilyeva ◽

...

Keyword(s):

Intravenous Immunoglobulin ◽

Conflicts Of Interest ◽

P Value ◽

Logrank Test ◽

Intravenous Ganciclovir ◽

Hematopoietic Stem ◽

Transplant Center ◽

Ganciclovir Treatment ◽

Cmv Disease ◽

Cmv Reactivation

Abstract Introduction Cytomegalovirus (CMV) reactivation is one of the main problems in allogenic hematopoietic stem cell transplantation (allo-HSCT). Standard of care for CMV-disease is still ganciclovir at 10 mg/kg b.i.d. Use of non-CMV specific intravenous immunoglobulin (IVIG) is still controversial and mostly determined by internal care protocols in every transplant center. Here we report data about impact of non-CMV specific IVIG during ganciclovir treatment in allo-HSCT CMV-patients. Patients and methods Thirty two patients with hematological malignancies transplanted in NRCH were included in this study. Detailed patients characteristics are listed in Table 1. All patients were CMV-positive by PCR (Amplisens EBV/ CMV /HHV6-screen-FL", InterLabService, Russia) and required to start therapy with ganciclovir 10 mg/kg when was included to this study. Patients in IVIG group also received non-CMV specific IVIG during ganciclovir treatment with a median total dose 20 g (7.5-90 g.). Kaplan-Meier estimator was used to determine probability of achievement of CMV-negativity from time of ganciclovir was started to CMV-negativity (by PCR) or last contact. The logrank test is used to compare differences between two groups. Fisher's exact test was used for 2×2 tables. P-value less than 0.05 was considered statistically significant Results Influence of IVIG in allo-HSCT patients on probability of achievement of CMV-negativity (by PCR) are shown in the Figure 1. As we can see there is no significant differences on the achievement of CMV-negativity (by PCR) in patients with/without IVIG during ganciclovir therapy. Conclusion The use of non-CMV specific immunoglobulins after allo-HSCT still lies in the plane of faith and the possibilities of the transplantation center than any evidence base. Using IVIG in patients after allo-HSCT is still not a routine in terms of CMV-reactivation/disease therapy and mostly based on an "experience" of every transplant center. According to our data there is no difference between IVIG/no-IVIG groups during ganciclovir treatment so use of IVIG, for our opinion, does not really make sense for CMV-disease treatment. Anyway a large randomized trial is required for determine indications for therapy with IVIG. Disclosures No relevant conflicts of interest to declare.

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Polymorphisms in the CYP450 Genes Influences Regimen Related Toxicity and Outcome in Patients with Beta Thalassaemia Major Undergoing HSCT.

Blood ◽

10.1182/blood.v114.22.869.869 ◽

2009 ◽

Vol 114 (22) ◽

pp. 869-869

Author(s):

Poonkuzhali Balasubramanian ◽

Salamun Desire ◽

Vikram Mathews ◽

Kavitha M Lakshmi ◽

Shaji R Velayudhan ◽

...

Keyword(s):

Risk Factors ◽

Annual Meeting ◽

Conflicts Of Interest ◽

Univariate Analysis ◽

P Value ◽

Thalassaemia Major ◽

Hematopoietic Stem ◽

Beta Thalassaemia ◽

Variant Genotype ◽

The Impact

Abstract Abstract 869 Polymorphisms in drug metabolizing enzymes are known to contribute to inter-individual differences in the pharmacokinetics (PK) of the two most commonly used drugs for conditioning for hematopoietic stem cell transplantation (HSCT), busulfan (Bu) and cyclophosphamide (Cy) and their metabolites in plasma. We have previously reported the impact of CYP genes on the PK of Cy, [Blood (ASH Annual Meeting Abstracts), Nov 2004; 104: 99] and the influence of Cy PK on transplant outcome [Blood (ASH Annual Meeting Abstracts), Nov 2004; 104: 1820]. We have now extended this study to evaluate a total of 19 polymorphisms in 11 genes that are known to be involved in the metabolism of Bu and Cy. 180 of the 276 patients with thalassemia major who underwent HSCT between March 1991 and Dec 2008 and for who genomic DNA was available were included in the study. The following polymorphisms were screened using PCR followed by RFLP and/ or gel electrophoresis: GSTA1*B, GSTM1 and GSTT1 deletion, GSTP1*B, CYP2B6*2, *3, *4, *5 and *6, CYP2C9*2, *3 and *4, CYP2C19*2, *3, CYP3A4*1B, CYP3A5*3, *6 and ALDH1A1*2 and ALDH3A1*2. Polymorphism frequencies were associated with regimen related toxicities, other transplant related complications using Fischer's Exact test and Cox-proportional hazard's model.. Significant associations are shown in the Table. On univariate analysis, CYP2B6*4 variant genotype was associated with incidence of hemorrhagic cystitis (HC); CYP2C9*3 variant genotype was associated with the severity of HC; CYP2C19*3 and 2C9*2 genotypes were associated with overall and even-free survival (OS and EFS) and CYP2C9*2 and CYP2C9*3 genotype was associated with transplant related mortality (TRM). Multivariate analyses performed adjusting for known clinical risk factors still showed these genotypes to be significantly associated with outcome parameters. Variant genotypes of polymorphisms that result in decreased metabolism of Cy are protective against regimen related toxicities while these polymorphisms were risk factors for EFS and OS in the present study. This is the first report on the influence of common GST, CYP and ALDH polymorphisms on outcome of HSCT in patients with thalassaemia major. Screening for these polymorphisms in patients with beta thalassaemia undergoing HSCT can help identify patients at higher risk of complications.Table:EndpointGenotypeRelative risk (95% CI)P- value HCCYP2B6*4 variant0.3 (0.13-0.889)0.028 HC grade 1 vs. HC grade 2-4CYP2C9*3 variant0.2 (0.073-0.962)0.043 TRM2C9*2 variant2.7 (1.08-6.77)0.034 2C9*3 variant2.3 (1.0-5.7)0.049 OS and EFS2C19*3 variant3.3 (1.2-9.3)0.018 2C9*2 variant1.3 (0.93-2.03)0.070 Disclosures: No relevant conflicts of interest to declare.

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