scholarly journals Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting

Blood ◽  
2010 ◽  
Vol 115 (23) ◽  
pp. 4798-4809 ◽  
Author(s):  
Eric Schafer ◽  
Rafael Irizarry ◽  
Sandeep Negi ◽  
Emily McIntyre ◽  
Donald Small ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Dna Methyltransferase ◽  
Cpg Island ◽  
Lymphoblastic Leukemia ◽  
Promoter Hypermethylation ◽  
Therapeutic Targeting ◽  
Specific Pcr ◽  
Genome Wide ◽  
Methylation Patterns ◽  
Infant Acute Lymphoblastic Leukemia

Abstract Cooperating leukemogenic events in MLL-rearranged (MLL-r) infant acute lymphoblastic leukemia (ALL) are largely unknown. We explored the role of promoter CpG island hypermethylation in the biology and therapeutic targeting of MLL-r infant ALL. The HELP (HpaII tiny fragment enrichment by ligation-mediated polymerase chain reaction [PCR]) assay was used to examine genome-wide methylation of a cohort of MLL-r infant leukemia samples (n = 5), other common childhood ALLs (n = 5), and normals (n = 5). Unsupervised analysis showed tight clustering of samples into their known biologic groups, indicating large differences in methylation patterns. Global hypermethylation was seen in the MLL-r cohort compared with both the normals and the others, with ratios of significantly (P < .001) hypermethylated to hypomethylated CpGs of 1.7 and 2.9, respectively. A subset of 7 differentially hypermethylated genes was assayed by quantitative reverse-transcription (qRT)–PCR, confirming relative silencing in 5 of 7. In cell line treatment assays with the DNA methyltransferase inhibitor (DNMTi) decitabine, MLL-r (but not MLL wild-type cell lines) showed dose- and time-dependent cytotoxicity and re-expression of 4 of the 5 silenced genes. Methylation-specific PCR (MSP) confirmed promoter hypermethylation at baseline, and a relative decrease in methylation after treatment. DNMTi may represent a novel molecularly targeted therapy for MLL-r infant ALL.

Specific promoter methylation identifies different subgroups of MLL-rearranged infant acute lymphoblastic leukemia, influences clinical outcome, and provides therapeutic options

Blood ◽  
2009 ◽  
Vol 114 (27) ◽  
pp. 5490-5498 ◽  
Author(s):  
Dominique J. P. M. Stumpel ◽  
Pauline Schneider ◽  
Eddy H. J. van Roon ◽  
Judith M. Boer ◽  
Paola de Lorenzo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Clinical Outcome ◽  
Cpg Island ◽  
Lymphoblastic Leukemia ◽  
Promoter Hypermethylation ◽  
Aberrant Dna Methylation ◽  
Methylation Patterns ◽  
Infant Acute Lymphoblastic Leukemia

Abstract MLL-rearranged infant acute lymphoblastic leukemia (ALL) remains the most aggressive type of childhood leukemia, displaying a unique gene expression profile. Here we hypothesized that this characteristic gene expression signature may have been established by potentially reversible epigenetic modifications. To test this hypothesis, we used differential methylation hybridization to explore the DNA methylation patterns underlying MLL-rearranged ALL in infants. The obtained results were correlated with gene expression data to confirm gene silencing as a result of promoter hypermethylation. Distinct promoter CpG island methylation patterns separated different genetic subtypes of MLL-rearranged ALL in infants. MLL translocations t(4;11) and t(11;19) characterized extensively hypermethylated leukemias, whereas t(9;11)-positive infant ALL and infant ALL carrying wild-type MLL genes epigenetically resembled normal bone marrow. Furthermore, the degree of promoter hypermethylation among infant ALL patients carrying t(4;11) or t(11;19) appeared to influence relapse-free survival, with patients displaying accentuated methylation being at high relapse risk. Finally, we show that the demethylating agent zebularine reverses aberrant DNA methylation and effectively induces apoptosis in MLL-rearranged ALL cells. Collectively these data suggest that aberrant DNA methylation occurs in the majority of MLL-rearranged infant ALL cases and guides clinical outcome. Therefore, inhibition of aberrant DNA methylation may be an important novel therapeutic strategy for MLL-rearranged ALL in infants.

Distinct Methylation Patterns among Infants with MLL Rearranged Acute Lymphoblastic Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2794-2794
Author(s):  
Dominique J.P.M. Stumpel ◽  
Pauline Schneider ◽  
Eddy H.J. van Roon ◽  
Judith M. Boer ◽  
Renee X. Menezes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Acute Lymphoblastic Leukemia ◽  
Cpg Island ◽  
Lymphoblastic Leukemia ◽  
Methylation Pattern ◽  
Unique Type ◽  
Genome Wide ◽  
Pediatric All ◽  
Methylation Patterns

Abstract Acute Lymphoblastic Leukemia (ALL) in infants (i.e. children <1 year of age) is characterized by a high incidence of rearrangements of the MLL gene (∼80%) which is associated with a poor prognosis. The most frequent MLL rearrangements in infant ALL are translocations t(4;11), t(11;19) and t(9;11). Recently, gene expression profiling has established MLL rearranged leukemia as a unique type of leukemia (denoted MLL), that is clearly distinguishable from other ALL subtypes. Currently, these gene expression profiles are slowly revealing important genetic properties underlying this aggressive type of leukemia, however, any epigenetic data on MLL are still lacking. Therefore, the present study was designed to unravel the MLL-specific methylation patterns underlying infant MLL by applying differential methylation hybridization (DMH) using CpG island microarrays containing ∼9000 CpG island probes, in duplicate. Primary infant ALL samples carrying t(4;11) (n=21), t(11;19) (n=17) and t(9;11) (n=6) were compared to infant ALL (n=13) and non-infant pediatric ALL (n=15) samples without MLL rearrangements. In addition, healthy pediatric bone marrow samples (n=9) were included as a reference. Compared to healthy controls, 656 CpG island probes were identified as significantly hypermethylated in t(4;11) positive samples, and 131 CpG island probes in t(11;19) positive samples (p<0.01, false discovery rate <5%). Interestingly, t(11;19) positive ALL patients shared 95% of their methylated probes with t(4;11) patients, suggesting a common methylation pattern which is completely absent in both infant and non-infant ALL patients lacking MLL rearrangements. Remarkably, displaying only a single probe significantly methylated as compared to healthy bone marrow, this common methylation pattern is also absent in t(9;11) positive ALL patients, indicating that based on genome-wide methylation, these patients represent a distinct entity clearly distinguishable from other MLL subgroups. Moreover, the fact that t(4;11) patients exhibit 532 methylated CpG island probes that were not found to be methylated in t(11;19) patients, demonstrates that these patients also exhibit a t(4;11) specific set of methylated genes. Identification of the genes represented by these CpG island probes and subsequent validation of the results obtained in this study is currently being performed (using pyrosequencing and methylation specific PCR analyses). In conclusion, these data reveal that different types of MLL rearranged infant ALL show distinct genome-wide methylation patterns. Specifically, infant ALL patients carrying t(4;11) and t(11;19) are characterized by severe CpG island hypermethylation, as compared to both t(9;11) positive infant ALL patients, as well as pediatric ALL patients lacking MLL rearrangements. Therefore, t(4;11) and t(11;19) patients in particular may well be suitable candidates for DNA methylation inhibiting therapeutic intervention. Finally, these promising results for the first time provide epigenetic insights into the complex biology of infant MLL, and clearly warrant further investigation currently being performed at our laboratory.

Promoter methylation is associated with the age-dependent loss of N-cadherin in the rat kidney

2008 ◽  
Vol 294 (1) ◽  
pp. F170-F176 ◽  
Author(s):  
Adebayo D. Akintola ◽  
Zachary L. Crislip ◽  
Jeffrey M. Catania ◽  
Gang Chen ◽  
Warren E. Zimmer ◽  
...  
Keyword(s):  
Promoter Region ◽  
Dna Methyltransferase ◽  
Cpg Island ◽  
Rat Kidney ◽  
Promoter Hypermethylation ◽  
Pcr Analysis ◽  
Specific Pcr ◽  
Age Dependent ◽  
Proximal Tubular Epithelial Cells ◽  
Flanking Region

The cadherins are cell adhesion molecules required for cellular homeostasis, and N-cadherin is the predominant cadherin expressed in proximal tubular epithelial cells in humans and rats. Our laboratory previously reported an age-dependent decrease in renal N-cadherin expression; the levels of N-cadherin mRNA and protein expression decreased in parallel, implicating a transcriptional mechanism in the age-dependent loss of expression ( 19 ). In this study, we examined the hypothesis that promoter hypermethylation underlies the loss of N-cadherin expression in aging rat kidney. We cloned the 5′ flanking region of the rat N-cadherin gene and observed basic promoter activity in a 3,992-bp region localized immediately upstream of the ATG start site. Nucleotide analysis revealed 87% identity with the human N-cadherin minimal promoter region. Consistent with a role for regulation by DNA methylation, we found that a dense CpG island, which spans 1,104 bp (−1,158 to −55), flanks the rat N-cadherin gene; a similar CpG profile was found in the human N-cadherin 5′ flanking region. Methylation-specific PCR analysis demonstrated that the promoter region of N-cadherin is heavily methylated in aged, but not young, rat kidney. Interestingly, the promoter is not methylated in age-matched, calorically restricted animals. In contrast, the promoter region is not methylated in either young or aged rat liver; this corresponds to the finding that aging is not associated with decreased N-cadherin expression in the liver. In addition, N-cadherin expression is markedly induced in NRK-52E cells treated with the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine, further suggesting that methylation at CpG in the promoter region may underlie the age-dependent decrease in renal N-cadherin expression.

scholarly journals Potent obatoclax cytotoxicity and activation of triple death mode killing across infant acute lymphoblastic leukemia

Blood ◽  
2013 ◽  
Vol 121 (14) ◽  
pp. 2689-2703 ◽  
Author(s):  
Karen A. Urtishak ◽  
Alena Y. Z. Edwards ◽  
Li-San Wang ◽  
Amanda Hudome ◽  
Blaine W. Robinson ◽  
...  
Keyword(s):  
Cell Death ◽  
Acute Lymphoblastic Leukemia ◽  
Lymphoblastic Leukemia ◽  
Specific Form ◽  
Intrinsic Resistance ◽  
Therapeutic Targeting ◽  
Key Points ◽  
Disease Specific ◽  
Infant Acute Lymphoblastic Leukemia

Key Points Infant acute lymphoblastic leukemia is sensitive to therapeutic targeting by apoptosis, necoptosis, and autophagy activation whether MLL is rearranged or germline. The disease-specific form of triple death mode killing by obatoclax overcomes the intrinsic resistance of MLL-rearranged infant acute lymphoblastic to cell death.

Abstract 40: Disturbed Flow Alters Genomewide DNA Methylation Patterns, Regulating Endothelial Gene Expression and Atherosclerosis

2014 ◽  
Vol 34 (suppl_1) ◽  
Author(s):  
Jessilyn Dunn ◽  
Haiwei Qiu ◽  
Soyeon Kim ◽  
Daudi Jjingo ◽  
Ryan Hoffman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Methylation Status ◽  
Western Diet ◽  
Dependent Manner ◽  
Gene Promoters ◽  
Genome Wide ◽  
Methylation Patterns ◽  
Endothelial Gene Expression

Atherosclerosis preferentially occurs in arterial regions of disturbed blood flow (d-flow), which alters gene expression, endothelial function, and atherosclerosis. Here, we show that d-flow regulates genome-wide DNA methylation patterns in a DNA methyltransferase (DNMT)-dependent manner. We found that d-flow induced expression of DNMT1, but not DNMT3a or DNMT3b, in mouse arterial endothelium in vivo and in cultured endothelial cells by oscillatory shear (OS) compared to unidirectional laminar shear in vitro. The DNMT inhibitor 5-Aza-2’deoxycytidine (5Aza) or DNMT1 siRNA significantly reduced OS-induced endothelial inflammation. Moreover, 5Aza reduced lesion formation in two atherosclerosis models using ApoE-/- mice (western diet for 3 months and the partial carotid ligation model with western diet for 3 weeks). To identify the 5Aza mechanisms, we conducted two genome-wide studies: reduced representation bisulfite sequencing (RRBS) and transcript microarray using endothelial-enriched gDNA and RNA, respectively, obtained from the partially-ligated left common carotid artery (LCA exposed to d-flow) and the right contralateral control (RCA exposed to s-flow) of mice treated with 5Aza or vehicle. D-flow induced DNA hypermethylation in 421 gene promoters, which was significantly prevented by 5Aza in 335 genes. Systems biological analyses using the RRBS and the transcriptome data revealed 11 mechanosensitive genes whose promoters were hypermethylated by d-flow but rescued by 5Aza treatment. Of those, five genes contain hypermethylated cAMP-response-elements in their promoters, including the transcription factors HoxA5 and Klf3. Their methylation status could serve as a mechanosensitive master switch in endothelial gene expression. Our results demonstrate that d-flow controls epigenomic DNA methylation patterns in a DNMT-dependent manner, which in turn alters endothelial gene expression and induces atherosclerosis.

scholarly journals Persistent epigenetic memory impedes rescue of the telomeric phenotype in human ICF iPSCs following DNMT3B correction

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Shir Toubiana ◽  
Miriam Gagliardi ◽  
Mariarosaria Papa ◽  
Roberta Manco ◽  
Maty Tzukerman ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Pharmacological Intervention ◽  
Icf Syndrome ◽  
Genome Wide ◽  
Mammalian Genomes ◽  
Induced Pluripotent ◽  
Methylation Patterns

DNA methyltransferase 3B (DNMT3B) is the major DNMT that methylates mammalian genomes during early development. Mutations in human DNMT3B disrupt genome-wide DNA methylation patterns and result in ICF syndrome type 1 (ICF1). To study whether normal DNA methylation patterns may be restored in ICF1 cells, we corrected DNMT3B mutations in induced pluripotent stem cells from ICF1 patients. Focusing on repetitive regions, we show that in contrast to pericentromeric repeats, which reacquire normal methylation, the majority of subtelomeres acquire only partial DNA methylation and, accordingly, the ICF1 telomeric phenotype persists. Subtelomeres resistant to de novo methylation were characterized by abnormally high H3K4 trimethylation (H3K4me3), and short-term reduction of H3K4me3 by pharmacological intervention partially restored subtelomeric DNA methylation. These findings demonstrate that the abnormal epigenetic landscape established in ICF1 cells restricts the recruitment of DNMT3B, and suggest that rescue of epigenetic diseases with genome-wide disruptions will demand further manipulation beyond mutation correction.

scholarly journals In vitro drug-resistance profile in infant acute lymphoblastic leukemia in relation to age, MLL rearrangements and immunophenotype

Leukemia ◽  
2004 ◽  
Vol 18 (3) ◽  
pp. 521-529 ◽  
Author(s):  
N L Ramakers-van Woerden ◽  
H B Beverloo ◽  
A J P Veerman ◽  
B M Camitta ◽  
A H Loonen ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Acute Lymphoblastic Leukemia ◽  
Lymphoblastic Leukemia ◽  
Resistance Profile ◽  
Drug Resistance Profile ◽  
Infant Acute Lymphoblastic Leukemia
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