Two-Track Epigenetic Remodeling and Backtracking to Embryonic Stem Cell Bivalency in B-Cell Acute Lymphoblastic Leukemias

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3557-3557
Author(s):  
Seung-Tae Lee ◽  
Marcus O. Muench ◽  
Marina Fomin ◽  
Jianqiao Xiao ◽  
Mi Zhou ◽  
...  
Keyword(s):  
Dna Methylation ◽  
B Cells ◽  
B Cell ◽  
De Novo ◽  
Embryonic Stem ◽  
Cell Leukemia ◽  
Childhood All ◽  
B Cell Leukemia ◽  
Functional Consequences ◽  
De Novo Methylation

Abstract Purpose: We sought to define the drivers and functional consequences of DNA methylation changes in childhood pre-B cell leukemia. A comprehensive analysis of such DNA methylation changes will reveal aspects of the etiology and pathogenesis of leukemias, and suggest potential therapeutic modalities. Background: The epigenome is extensively altered in carcinogenesis, but the proximate causes, functional consequences, and overall patterning of DNA methylation changes in the pediatric leukemias is not well defined. Methods: We bisulfite sequenced at single base pair resolution two common pre-B cell leukemia case DNAs and a pre-B cell control (CD19+/CD34+ pre-B cells from normal marrow), and analyzed DNA methylation by high definition microarray in another 227 subjects. RNA expression was available for 82 samples, including the sequenced pre-B cells and leukemias. Results: Epigenetic alteration of B-ALLs occurred in two tracks: de novo methylation of small functional compartments and demethylation of large inter-compartmental backbones. The de novo methylation occurred preferentially at polycomb targets and binding sites for the transcriptional co-repressor CtBP2. DNA methylation of ETV6-AML1 leukemia was overall equivalent to the control, with high hyperdiploid methylation levels being 4.4% lower. Hierarchical clustering revealed four groups, with ETV6-AML1 and hyperdiploid leukemias enriched within two separate groups. DNA methylation deviations were exaggerated in lamina-associated domains, with differences corresponding to these methylation clusters and/or cytogenetic groups. DNA methylation changes were correlated with gene expression changes, and a key polycomb expression signature was reversed when DNA methylation marks were pharmacologically removed in leukemia cell lines. Discussion: While leukemia cells retain the majority of their developmentally determined DNA methylation patterns, key modifications with leukemogenesis revealed both broad patterns and functional targets with some dependence on known characteristics of pre-B cell leukemias. Our data suggested a pivotal role of polycomb and CTBP2 in de novo methylation, which may be traced back to bivalency status of embryonic stem cells. Driven by these potent epigenetic modulations, suppression of polycomb target genes was observed along with disruption of developmental fate and cell cycle and mismatch repair pathways and altered activities of key upstream regulators. An appreciation and validation of the observed changes will lead to new insights into etiology, pathogenesis, and treatments of childhood ALL. Disclosures No relevant conflicts of interest to declare.

scholarly journals B-cell leukemia transdifferentiation to macrophage involves reconfiguration of DNA methylation for long-range regulation

Leukemia ◽  
2019 ◽  
Vol 34 (4) ◽  
pp. 1158-1162 ◽  
Author(s):  
Alberto Bueno-Costa ◽  
David Piñeyro ◽  
Marta Soler ◽  
Biola M. Javierre ◽  
Helena Raurell-Vila ◽  
...  
Keyword(s):  
Dna Methylation ◽  
B Cell ◽  
Long Range ◽  
Cell Leukemia ◽  
B Cell Leukemia

Expression of CD13/aminopeptidase N in precursor B-cell leukemia: role in growth regulation of B cells

2009 ◽  
Vol 59 (1) ◽  
pp. 125-135 ◽  
Author(s):  
Ankit Saxena ◽  
Ambak Rai ◽  
Vinod Raina ◽  
Tulika Seth ◽  
Dipendra Kumar Mitra
Keyword(s):  
B Cells ◽  
B Cell ◽  
Growth Regulation ◽  
Aminopeptidase N ◽  
Cell Leukemia ◽  
B Cell Leukemia

scholarly journals De novo acute B cell leukemia/lymphoma with t(14;18)

Leukemia ◽  
2000 ◽  
Vol 14 (11) ◽  
pp. 1960-1966 ◽  
Author(s):  
A Stamatoullas ◽  
G Buchonnet ◽  
S Lepretre ◽  
P Lenain ◽  
B Lenormand ◽  
...  
Keyword(s):  
B Cell ◽  
De Novo ◽  
Cell Leukemia ◽  
B Cell Leukemia

scholarly journals Establishment and Maintenance of Genomic Methylation Patterns in Mouse Embryonic Stem Cells by Dnmt3a and Dnmt3b

2003 ◽  
Vol 23 (16) ◽  
pp. 5594-5605 ◽  
Author(s):  
Taiping Chen ◽  
Yoshihide Ueda ◽  
Jonathan E. Dodge ◽  
Zhenjuan Wang ◽  
En Li
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Es Cells ◽  
Embryonic Stem ◽  
Single Copy ◽  
Dna Methyltransferases ◽  
Methylation Patterns ◽  
Genomic Methylation ◽  
De Novo Methylation

ABSTRACT We have previously shown that the DNA methyltransferases Dnmt3a and Dnmt3b carry out de novo methylation of the mouse genome during early postimplantation development and of maternally imprinted genes in the oocyte. In the present study, we demonstrate that Dnmt3a and Dnmt3b are also essential for the stable inheritance, or “maintenance,” of DNA methylation patterns. Inactivation of both Dnmt3a and Dnmt3b in embryonic stem (ES) cells results in progressive loss of methylation in various repeats and single-copy genes. Interestingly, introduction of the Dnmt3a, Dnmt3a2, and Dnmt3b1 isoforms back into highly demethylated mutant ES cells restores genomic methylation patterns; these isoforms appear to have both common and distinct DNA targets, but they all fail to restore the maternal methylation imprints. In contrast, overexpression of Dnmt1 and Dnmt3b3 failed to restore DNA methylation patterns due to their inability to catalyze de novo methylation in vivo. We also show that hypermethylation of genomic DNA by Dnmt3a and Dnmt3b is necessary for ES cells to form teratomas in nude mice. These results indicate that genomic methylation patterns are determined partly through differential expression of different Dnmt3a and Dnmt3b isoforms.

scholarly journals The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

2020 ◽  
Author(s):  
Martí Duran-Ferrer ◽  
Guillem Clot ◽  
Ferran Nadeu ◽  
Renée Beekman ◽  
Tycho Baumann ◽  
...  
Keyword(s):  
Dna Methylation ◽  
B Cells ◽  
B Cell ◽  
De Novo ◽  
Genetic Alterations ◽  
Cell Tumor ◽  
Patient Specific ◽  
Maturation Stage ◽  
Cell Of Origin ◽  
Dna Methylome

AbstractWe report a systematic analysis of the biological and clinical implications of DNA methylation variability in five categories of B-cell tumors derived from B cells spanning the entire maturation spectrum. We used 2056 primary samples including training and validation series and show that 88% of the human DNA methylome is dynamically modulated under normal and neoplastic conditions. B-cell tumors display both epigenetic imprints of their cellular origin and de novo, disease-specific epigenetic alterations that in part are related to differential transcription factor binding. These differential methylation patterns were used by a machine-learning approach to create a diagnostic algorithm that accurately classifies 14 B-cell tumor entities and subtypes with different clinical management. Beyond this, we identified extensive patient-specific epigenetic variability targeting constitutively silenced chromatin regions, a phenomenon we could relate to the proliferative history of normal and neoplastic B cells. We observed that, depending on the maturation stage of the tumor cell of origin, mitotic activity leaves different imprints into the DNA methylome. Subsequently, we constructed a novel DNA methylation-based mitotic clock called epiCMIT (epigenetically-determined Cumulative MIToses), whose lapse magnitude represents a strong independent prognostic variable within specific B-cell tumor subtypes and is associated with particular driver genetic alterations. Our findings reveal DNA methylation as a holistic tracker of B-cell tumor developmental history, with implications in the differential diagnosis and prediction of the outcome of the patients.

Establishing the posh scaffold as a novel therapeutic target for treatment of B cell leukemia

2020 ◽  
Author(s):  
◽  
Leah Nicole Cardwell
Keyword(s):  
B Cells ◽  
B Cell ◽  
Cell Survival ◽  
Therapeutic Target ◽  
Mitogen Activated Protein Kinase ◽  
Rapid Progression ◽  
Cell Leukemia ◽  
Jnk Signaling ◽  
B Cell Leukemia ◽  
Novel Therapeutic

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI-COLUMBIA AT REQUEST OF AUTHOR.] More than 60,000 new cases of leukemia will be diagnosed in the U.S. this year. B cells comprise 10 [percent] of acute lymphoblastic leukemias (B-ALL) and almost all chronic lymphocytic leukemias (B-CLL). B-ALL are typified by rapid progression (weeks) and are predominant in children. B-CLL is characterized by slow progression (months) and are predominant in adults. Despite advances in current treatment therapies, over 23,000 people will die from leukemia this year. Thus, the focus of this research was to establish a novel therapeutic target for treatment of B cell leukemia. In B cells, intracellular c-Jun N-terminal kinase (JNK) signaling, a member of the mitogen-activated protein kinase (MAPK) family, regulates cell survival and death in response to cellular stimuli. Cell stressors predominantly induce sustained JNK activity and apoptosis, with chemotherapeutic drugs initiating JNK-mediated apoptosis in leukemic B cells. However, stimuli specific modulations in JNK activity also results in cell survival, proliferation, and differentiation, with several B-ALL/B-CLL exhibiting overactive JNK signaling for survival. JNK signaling is activated via a three-tiered cascade composed of MAP3K-MAP2K-MAPK (JNK) proteins. Scaffold-mediated formation of unique multi-protein-containing complexes regulate cell-type and stimuli-specific signaling cascades. Plenty of SH3 domains (POSH) is a scaffold protein that acts as a platform for concentrated assembly of unique MAPK-containing complexes to efficiently mediate pro- or anti-apoptotic JNK signaling outcomes. We are the first to characterize the function of the POSH scaffold in both healthy and leukemic B cells. Herein, we report that disruption of POSH scaffold function induces JNK-mediated apoptosis of several diverse acute and chronic B cell leukemias, healthy splenic B cells, but with limited survival functions in healthy bone marrow B cells, via use of our unique competitive inhibitor termed Tat-POSH-inhibitor. In addition to these findings, we also report experimental insights into POSH mechanistic functions, generation of POSH knockout mice, and the generation and characterization of novel cell-targeting aptamer- and micelle-based methods of Tat-POSH-inhibitor delivery. The work presented in this dissertation aims to establish POSH as a novel therapeutic target for treatment of acute and chronic B cell leukemias.

QSER1 protects DNA methylation valleys from de novo methylation

Science ◽  
2021 ◽  
Vol 372 (6538) ◽  
pp. eabd0875 ◽  
Author(s):  
Gary Dixon ◽  
Heng Pan ◽  
Dapeng Yang ◽  
Bess P. Rosen ◽  
Therande Jashari ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Embryonic Stem ◽  
Central Question ◽  
Mammalian Development ◽  
Uncharacterized Gene ◽  
Pathological Conditions ◽  
Genome Wide ◽  
A Genome ◽  
De Novo Methylation

DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to regulate the methylation landscape remains a central question. Using a knockin DNA methylation reporter, we performed a genome-wide CRISPR-Cas9 screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene, QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate genetic and biochemical interactions of QSER1 and TET1, supporting their cooperation to safeguard transcriptional and developmental programs from DNMT3-mediated de novo methylation.

Frequent Loss of the SLP-65 Adapter Protein in Childhood Acute B-Precursor Lymphoblastic Leukemia (ALL) with TEL/AML1 Rearrangement.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 741-741 ◽  
Author(s):  
Arndt Borkhardt ◽  
Christine Damm-Welk ◽  
Thomas Wossning ◽  
Bettina Storch ◽  
Uta Fuchs ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
B Cells ◽  
Tumor Suppressor ◽  
Protein Expression ◽  
B Cell ◽  
Cell Lines ◽  
Sh2 Domain ◽  
B Cell Differentiation ◽  
Cell Leukemia ◽  
B Cell Leukemia

Abstract The adaptor protein SLP-65 plays an essential role during B cell differentiation. A crucial consequence of SLP-65 deficiency in mice is a high incidence of pre-B-cell leukemia, suggesting a tumor suppressor role for SLP-65 in pre-B-cells. While the link between SLP-65 deficiency and leukemia development is established in mice, experiments mainly using microarrays for gene expression profiling suggested normal expression of SLP-65 in human precursor B-cell ALL. This analysis however does not discriminate between normal and aberrant SLP-65 transcripts with the latter being unable to generate functional protein. To examine the correlation between SLP-65 deficiency and childhood precursor B-cell ALL, we determined SLP-65 expression in 119 precursor B-cell ALL samples by both RNA and protein methods. The expression of SLP-65 was compared to clinical and laboratory findings, cytogenetics as well as to the outcome data within this uniformly treated cohort of patients. Loss of slp-65 protein was significantly associated with the occurrence of the TEL/AML1 rearrangement (p=0.026) but not with any other clinical or cytogenetic feature. We found a profound disconnection between slp-65 mRNA and protein expression in 38 out of the 119 leukemic samples pointing to a posttranscriptional regulation of slp-65 (Table). To confirm that SLP-65 transcript expression does not automatically correlate with its protein expression, we analyzed a panel of human cell lines derived from precursor B-cell ALL patients. The cell lines HPB-NULL and BV-173 showed a deficiency in SLP-65 protein expression, although SLP-65 transcripts can easily be detected in both lines. Together, the data suggest that SLP-65 expression might be regulated at the posttranscriptional level and that the presence of SLP-65 transcripts does not necessarily lead to SLP-65 protein and function. In one particular patient, we found a truncated slp-65 transcript and the predicted slp-65 protein lacks its SH2 domain. We tested whether this SLP-65 protein lacking the SH2 domain is functional in pre-B cells. To this end, we transfected murine SLP-65 −/− pre-B cells with retroviral constructs for either wild-type (wt SLP-65) or truncated SLP-65 (SLP-65delSH2) and analysed pre-BCR downregulation, Ca2+ release and pre-B cell differentiation. The results showed that, in contrast to wt SLP-65, SLP-65delSH2 failed to induce any effects in the performed experiments. Together with previous findings showing that SLP-65-deficient mice develop pre-B cell leukemia, the data suggest that SLP-65 acts as a tumor suppressor that limits pre-B cell proliferation by inducing differentiation. Disconnection between slp-65 transcripts and protein expression total slp-65 protein+ (51 patients) slp-65 protein weak (19 patients) slp-65 protein- (49 patients) PCR+ 108 51(9 TEL/AML+, 42 TEL/AML-) 19 (9 TEL/AML+, 10 TEL/AML-) 38 (15 TEL/AML+, 23 TEL/AML-) PCR- 11 0 0 11 (T-ALL)

scholarly journals Genome-wide promoter methylation of hairy cell leukemia

2019 ◽  
Vol 3 (3) ◽  
pp. 384-396 ◽  
Author(s):  
Alberto J. Arribas ◽  
Andrea Rinaldi ◽  
Giorgia Chiodin ◽  
Ivo Kwee ◽  
Afua Adjeiwaa Mensah ◽  
...  
Keyword(s):  
Dna Methylation ◽  
B Cells ◽  
B Cell ◽  
Hairy Cell Leukemia ◽  
Methylation Profile ◽  
Hairy Cell ◽  
Cell Leukemia ◽  
Dna Methylation Profiling ◽  
B Cell Subsets ◽  
Methylation Profiling

Abstract Classic hairy cell leukemia (HCL) is a tumor of mature clonal B cells with unique genetic, morphologic, and phenotypic features. DNA methylation profiling has provided a new tier of investigation to gain insight into the origin and behavior of B-cell malignancies; however, the methylation profile of HCL has not been specifically investigated. DNA methylation profiling was analyzed with the Infinium HumanMethylation27 array in 41 mature B-cell tumors, including 11 HCL, 7 splenic marginal zone lymphomas (SMZLs), and chronic lymphocytic leukemia with an unmutated (n = 7) or mutated (n = 6) immunoglobulin gene heavy chain variable (IGHV) region or using IGHV3-21 (n = 10). Methylation profiles of nontumor B-cell subsets and gene expression profiling data were obtained from public databases. HCL had a methylation signature distinct from each B-cell tumor entity, including the closest entity, SMZL. Comparison with normal B-cell subsets revealed the strongest similarity with postgerminal center (GC) B cells and a clear separation from pre-GC and GC cellular programs. Comparison of the integrated analysis with post-GC B cells revealed significant hypomethylation and overexpression of BCR–TLR–NF-κB and BRAF-MAPK signaling pathways and cell adhesion, as well as hypermethylation and underexpression of cell-differentiation markers and methylated genes in cancer, suggesting regulation of the transformed hairy cells through specific components of the B-cell receptor and the BRAF signaling pathways. Our data identify a specific methylation profile of HCL, which may help to distinguish it from other mature B-cell tumors.

ROR1 Expression Accelerates Leukemia Development in RORxTCL1 Transgenic Mice,

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3905-3905
Author(s):  
George F. Widhopf ◽  
Bing Cui ◽  
Esther Avery ◽  
George Chen ◽  
Masato Obara ◽  
...  
Keyword(s):  
B Cells ◽  
B Cell ◽  
Adoptive Transfer ◽  
Conflicts Of Interest ◽  
Leukemia Cell ◽  
Leukemia Cells ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Cell Turnover ◽  
Cell Leukemia ◽  
B Cell Leukemia

Abstract Abstract 3905 ROR1 is a receptor tyrosine kinase-like orphan receptor and an oncofetal protein that is expressed on chronic lymphocytic leukemia (CLL) B cells, but not on normal B cells or most other adult tissues. The leukemia-associated expression of ROR1 suggests that it potentially could contribute to the development and/or progression of CLL. To investigate its functional significance in the development and/or progression of CLL, we generated B6 mice transgenic (Tg) for human ROR1 (hROR1) under the control of the murine Ig promoter/enhancer, which drives B-cell-restricted expression of hROR1. These mice developed increased numbers of splenic B lymphocytes relative to that of control littermates lacking the hROR1 transgene; a few of these animals also developed hROR1+/CD5+/B220low B cell leukemia resembling human CLL at 15–18 months of age. We crossed hROR1-Tg mice with B6 Eμ-TCL1-Tg mice (TCL1), which at 7 months of age develop CD5+B220low leukemia B cells detectable in the blood and resembling human CLL cells except lacking expression of mouse ROR1. We found the F1 animals with both transgenes (ROR1XTCL1) developed hROR1+/CD5+/B220low B-cell CLL at a significantly younger median age than did littermate-control mice having either transgene alone. Comparison of the number of CD5+B220low leukemia B cells in ROR1xTCL1 or TCL1 Tg mice at five, six, and seven months of age demonstrated that ROR1xTCL1 Tg mice have significantly higher median percentages of circulating leukemic cells in the blood compared to that of age-matched TCL1 Tg mice (Welchs's t test based on the average of all 3 measurements, p=0.038). ROR1xTCL1 leukemia B cells also expressed higher levels of hROR1 than non-leukemia B cells of ROR1 Tg mice. To confirm that ROR1 enhances leukemia-cell expansion, we adoptively transferred CD5+B220low leukemia B cells from ROR1xTCL1 Tg mice into syngeneic ROR1-Tg mice. Adoptive transfer of equal numbers (1×105) of leukemia B cells from ROR1xTCL1 or TCL1 Tg mice resulted in transfer of leukemia in both cases without requiring prior conditioning of recipient animals. However, animals engrafted with ROR1xTCL1 leukemia cells developed more aggressive disease and more marked splenomegaly than did animals engrafted with TCL1 leukemia cells. Moreover, eight weeks after adoptive transfer, animals engrafted with ROR1xTCL1 leukemia cells had ≥4-fold greater median numbers of neoplastic B cells in the spleen (e.g. 4 × 108) than did animals engrafted with TCL1 leukemia cells. In vivo labeling studies with bromodeoxyuridine (BrdU), measurement of the relative proportions of Ki-67-positive leukemia cells from either type of adoptive host animals, and use of the terminal deoxynucleotidyl transferase (dUTP) nick end-labeling (TUNEL) assay to detect cells that had undergone apoptosis. These studies revealed that animals engrafted with hROR1+ leukemia cells had significantly lower-rates of leukemia-cell turnover due to higher rates of cell proliferation and lower rates of apoptosis than that animals engrafted with TCL1 leukemia cells. These studies indicate that hROR1 can accelerate development of de novo B-cell leukemia, lower the rate of leukemia-cell turnover, and enhance disease progression in this model system. Disclosures: No relevant conflicts of interest to declare.

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