| 1. |
- Waraky, Ahmed, et al.
(författare)
-
Aberrant MNX1 expression associated with t(7;12)(q36;p13) pediatric acute myeloid leukemia induces the disease through altering histone methylation.
- 2024
-
Ingår i: Haematologica. - 1592-8721. ; 109:3, s. 725-739
-
Tidskriftsartikel (refereegranskat)abstract
- Certain subtypes of acute myeloid leukemia (AML) in children have inferior outcome, such as AML with translocation t(7;12)(q36;p13) leading to a MNX1::ETV6 fusion along with high expression of MNX1. We have identified the transforming event in this AML and possible ways of treatment. Retroviral expression of MNX1 was able to induce AML in mice, with similar gene expression and pathway enrichment to t(7;12) AML patient data. Importantly, this leukemia was only induced in immune incompetent mice using fetal but not adult hematopoietic stem and progenitor cells. The restriction in transforming capacity to cells from fetal liver is in alignment with t(7;12)(q36;p13) AML being mostly seen in infants. Expression of MNX1 led to increased histone 3 lysine 4 mono-, di- and trimethylation, reduction in H3K27me3, accompanied with changes in genome-wide chromatin accessibility and genome expression, likely mediated through MNX1 interaction with the methionine cycle and methyltransferases. MNX1 expression increased DNA damage, depletion of the Lin- /Sca1+/c-Kit+ population and skewing toward the myeloid lineage. These effects, together with leukemia development, was prevented by pretreatment with the S-adenosylmethionine analog Sinefungin. In conclusion, we have shown the importance of MNX1 in development of AML with t(7;12), supporting a rationale for targeting MNX1 and downstream pathways.
|
|
| 2. |
- Kopparapu, Pradeep Kumar, et al.
(författare)
-
Gene-body hypermethylation controlled cryptic promoter and miR26A1-dependent EZH2 regulation of TET1 gene activity in chronic lymphocytic leukemia
- 2017
-
Ingår i: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 8:44, s. 77595-77608
-
Tidskriftsartikel (refereegranskat)abstract
- The Ten-eleven-translocation 1 (TET1) protein is a member of dioxygenase protein family that catalyzes the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine. TET1 is differentially expressed in many cancers, including leukemia. However, very little is known about mechanism behind TET1 deregulation. Previously, by characterizing global methylation patterns in CLL patients using MBD-seq, we found TET1 as one of the differentially methylated regions with gene-body hypermethylation. Herein, we characterize mechanisms that control TET1 gene activity at the transcriptional level. We show that treatment of CLL cell lines with 5-aza 2'-deoxycytidine (DAC) results in the activation of miR26A1, which causes decrease in both mRNA and protein levels of EZH2, which in turn results in the decreased occupancy of EZH2 over the TET1 promoter and consequently the loss of TET1 expression. In addition, DAC treatment also leads to the activation of antisense transcription overlapping the TET1 gene from a cryptic promoter, located in the hypermethylated intronic region. Increased expression of intronic transcripts correlates with decreased TET1 promoter activity through the loss of RNA Pol II occupancy. Thus, our data demonstrate that TET1 gene activation in CLL depends on miR26A1 regulated EZH2 binding at the TET1 promoter and silencing of novel cryptic promoter by gene-body hypermethylation.
|
|
| 3. |
- Kosalai, Subazini Thankaswamy, 1980, et al.
(författare)
-
EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia
- 2019
-
Ingår i: Epigenetics. - : Informa UK Limited. - 1559-2294 .- 1559-2308. ; 14:11, s. 1125-1140
-
Tidskriftsartikel (refereegranskat)abstract
- EZH2 is overexpressed in poor-prognostic chronic lymphocytic leukaemia (CLL) cases, acting as an oncogene; however, thus far, the EZH2 target genes in CLL have not been disclosed. In this study, using ChIP-sequencing, we identified EZH2 and H3K27me3 target genes in two prognostic subgroups of CLL with distinct prognosis and outcome, i.e., cases with unmutated (U-CLL, n = 6) or mutated IGHV genes (M-CLL, n = 6). While the majority of oncogenic pathways were equally enriched for EZH2 target genes in both prognostic subgroups, PI3K pathway genes were differentially bound by EZH2 in U-CLL versus M-CLL. The occupancy of EZH2 for selected PI3K pathway target genes was validated in additional CLL samples (n = 16) and CLL cell lines using siRNA-mediated EZH2 downregulation and ChIP assays. Intriguingly, we found that EZH2 directly binds to the IGF1R promoter along with MYC and upregulates IGF1R expression in U-CLL, leading to downstream PI3K activation. By investigating an independent CLL cohort (n = 96), a positive correlation was observed between EZH2 and IGF1R expression with higher levels in U-CLL compared to M-CLL. Accordingly, siRNA-mediated downregulation of either EZH2, MYC or IGF1R and treatment with EZH2 and MYC pharmacological inhibitors in the HG3 CLL cell line induced a significant reduction in PI3K pathway activation. In conclusion, we characterize for the first time EZH2 target genes in CLL revealing a hitherto unknown implication of EZH2 in modulating the PI3K pathway in a non-canonical, PRC2-independent way, with potential therapeutic implications considering that PI3K inhibitors are effective therapeutic agents for CLL.
|
|
| 4. |
- Morsy, Mohammad Hamdy Abdelrazak, 1986
(författare)
-
Genome-wide epigenetic profiling of B cell leukemia and lymphoma
- 2019
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Epigenetic modifications, at the level of DNA methylation and post-translational modifications of histone tails cooperatively function in the organization of the genome, and thereby establish the gene expression profiles, phenotypes, and cellular fates. In this work, we investigated the aberrant epigenome in chronic lymphocytic leukemia (CLL) which is one of the most frequent lymphoid malignancies in the west including the Nordic countries. The overall aim of this work is to address the impact of altered epigenetic patterns in CLL on the disease progression with respect to gene expression profile and gain mechanistic insights on the interplay between the different epigenetic mechanisms, such as DNA methylation and histone modifications, in regulating the expression of CLL signature genes. The first study in this thesis aims to investigate the impact of gene body hypermethylation on transcriptional activation which was not completely understood then. Based on our previous MBD seq data (Methyl-CpG-Binding Domain based next generation Sequencing) datasets on CLL samples, of the top differentially methylated genes in CLL compared to normal B cells, we nominated Ten-eleven translocation (TET1) which was shown to harbor hypermethylation at CpG islands within gene body. We found that gene body of TET1 harbors an overlapping cryptic promoter, the transcript of which attenuates the corresponding gene transcription when unmethylated and its hypermethylation in CLL was found to be associated with the overexpression of TET1. The second study aimed at globally mapping the genomic targets of enhancer of zeste homolg 2 (EZH2) the catalytic subunit of Polycomb repressive complex 2 (PRC2) in CLL by chromatin immunoprecipitation followed by sequencing (ChIP-seq) along with its prototypical repressive chromatin feature (H3K27me3). The findings of this study unraveled a non-canonical implication of EZH2 in transcriptional activation apart from PRC2. We show a mechanism by which EZH2 transactivates IGF1R gene in the more adverse CLL subgroups with IGHV mutations (mutated CLL) and how it contributes to activating PI3K/AKT pathway through IGF1R signaling. The third project is somehow pertinent to the aforementioned first study and aims at drawing a more detailed mechanistic link between CpG methylation and transcriptional regulation in terms of the residence of PRC2, as it preferentially locates GC-rich elements. Integration of our previous global methylome datasets in CLL patients and transcriptome analysis by RNA-seq after induction of global demethylation in CLL cell lines has revealed a set of genes that are supposedly prone to hypermethylation within their intragenic regions in CLL, and such hypermethyation is found to be positively correlated with their overexpression in CLL. Out of the top significant genes, MNX1 was selected to probe the mutual exclusivity of PRC2 and intragenic CpG islands and the possible implication of gene body hypermethylation in upregulating MNX1 in CLL through impeding the PRC2-mediated repression. Altogether, the findings of our work underscore that aberrant epigenome is more likely to be the niche within which the cancer type-relevant aggressive traits are acquired and might pave the way for further detailed investigations that look forward to improve the therapy options and accordingly the clinical outcomes in CLL.
|
|
