| 1. |
- Deneberg, Stefan, et al.
(författare)
-
microRNA-34b/c on chromosome 11q23 is aberrantly methylated in chronic lymphocytic leukemia
- 2014
-
Ingår i: Epigenetics. - : Informa UK Limited. - 1559-2294 .- 1559-2308. ; 9:6, s. 910-917
-
Tidskriftsartikel (refereegranskat)abstract
- A commonly deleted region in chronic lymphocytic leukemia (CLL) is the 11q22-23 region, which encompasses the ATM gene. Evidence suggests that tumor suppressor genes other than ATM are likely to be involved in CLL with del(11q). A microRNA (miR) cluster including the miR-34b and miR-34c genes is located, among other genes, within the commonly deleted region (CDR) at 11q. Interestingly, these miRs are part of the TP53 network and have been shown to be epigenetically regulated. In this study, we investigated the expression and methylation status of these miRs in a well-characterized cohort of CLL, including cases with/without 11q-deletion. We show that the miR-34b/c promoter was aberrantly hypermethylated in a large proportion of CLL cases (48%, 25/52 cases). miR-34b/c expression correlated inversely to DNA methylation (P = 0.003), and presence of high H3K37me3 further suppressed expression regardless of methylation status. Furthermore, increased miR-34b/c methylation inversely correlated with the presence of 11q-deletion, indicating that methylation and del(11q) independently silence these miRs. Finally, 5-azacytidine and trichostatin A exposure synergistically increased the expression of miR-34b/c in CLL cells, and transfection of miR-34b or miR-34c into HG3 CLL cells significantly increased apoptosis. Altogether, our novel data suggest that miR-34b/c is a candidate tumor suppressor that is epigenetically silenced in CLL.
|
|
| 2. |
- Deneberg, Stefan
(författare)
-
Prognostic and biological implications of epigenetic changes in leukemia
- 2011
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The field of epigenetic research in hematology and oncology is rapidly expanding. Even so, reliable data linking epigenetic changes to clinical outcomes are scarce. We conducted two retrospective studies in AML. The first (paper I) was performed in 107 AML patients without a previous history of MDS where we approximated the global DNA 5-methylcytosine content with a methylation sensitive restriction enzyme assay, the promoter DNA methylation status of three known tumor suppressor genes, CDKN2B (p15), HIC1 and CDH1, and in a subset of 20 patients genome-wide promoter methylation by the Illumina HumanMethylation27 array. Promoter methylation of CDKN2B was common (66%), and associated with better overall and disease free survival in uni- and multivariate analysis. Average genome wide promoter methylation levels were also associated with overall and disease free survival and correlated inversely with global 5-methylcytosine content, which in turn associated with response to induction therapy. The second study (paper II) was restricted to cytogenetically normal de-novo AML cases. In a test group of 58 samples we investigated genome wide promoter methylation by the Illumina HumanMethylation27 array and correlated the methylation patterns with the mutational status of NPM1, FLT3, CEBPA, IDH1, IDH2, DNMT3A and clinical parameters. We found increased promoter methylation in NPM1 and IDH mutated samples with specific methylation patterns for these two mutations. Compared with a control group of normal myeloid progenitor cells from 9 donors the most differentially methylated genes in AML were those that in previous studies were targeted by Polycomb group proteins in embryonic tissue. Furthermore, we found that the methylation levels of the Polycomb targeted genes were associated with overall and progression free survival. The prognostic association was confirmed in a validation cohort of 60 patients and retained significance in multivariate analysis. The third study of this thesis (paper III) was designed to search for the second tumor suppressor gene commonly thought to reside on chromosome 11q21-23 in CLL, based on the finding of two microdeletions in a previous study. Through DNA methylation screening we found a 48% prevalence of aberrant promoter methylation of the shared two-directional promoter of BTG4 / microRNA-34b/c. Functional studies with stress incubation of primary CLL samples as well as the HG3 cell line showed an selective up-regulation of miR-34b/c transcripts in unmethylated cells, but no induction of BTG4 regardless of methylation status. Chromatin immunoprecipitation experiments showed the presence of repressive chromatin marks in both CLL and normal lymphocytes, which may explain our observation that the basal expression levels of miR-34b/c were low both in normal lymphocytes and CLL cells regardless of methylation status, compatible with a “epigenetic switch” from conditional to permanent silencing in methylated samples. We conclude that DNA methylation patterns are associated with mutational status and clinical outcomes in AML. Furthermore we believe that miR-34b/c may function as a tumor suppressor gene in CLL, incapacitated by an epigenetic switch mechanism in approximately 50% of CLL samples.
|
|
| 3. |
- Deneberg, Stefan, et al.
(författare)
-
Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks
- 2011
-
Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 118:20, s. 5573-5582
-
Tidskriftsartikel (refereegranskat)abstract
- Cytogenetically normal acute myeloid leukemia (CN-AML) comprise between forty and fifty percent of all adult acute myeloid leukemia (AML) cases. In this clinically diverse group molecular aberrations such as FLT3ITD, NPM1 and CEBPA mutations recently have added to the prognostic accuracy. Aberrant DNA methylation is a hallmark of cancer including AML. We investigated in total 118 CN-AML samples in a test and a validation cohort for genome-wide promoter DNA methylation with Illumina Methylation Bead arrays and compared them to normal myeloid precursors and global gene expression. IDH and NPM1 mutations were associated with different methylation patterns (p=0.0004 and 0.04, respectively). Genome-wide methylation levels were elevated in IDH mutated samples (p=0.006). We observed a negative impact of DNA methylation on transcription. Genes targeted by Polycomb group (PcG) proteins and genes associated with bivalent histone marks in stem cells showed increased aberrant methylation in AML (p<0.0001). Furthermore, high methylation levels of PcG target genes were independently associated with better progression free (OR 0.47, p=0.01) and overall survival (OR 0.36, p=0.001). In summary, genome wide methylation patterns show preferential methylation of PcG targets with prognostic impact in CN-AML.
|
|
| 4. |
|
|
| 5. |
|
|
| 6. |
|
|
| 7. |
- Dolinska, Monika, et al.
(författare)
-
Characterization of Bone Marrow Niche in Chronic Myeloid Leukemia Patients Identifies CXCL14 as a New Therapeutic Option
- 2023
-
Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 142:1, s. 73-89
-
Tidskriftsartikel (refereegranskat)abstract
- Although tyrosine kinase inhibitors (TKIs) are effective in treating chronic myeloid leukemia (CML), they often fail to eradicate the leukemia-initiating stem cells (LSCs), causing disease persistence and relapse. Evidence indicates that LSC persistence may be because of bone marrow (BM) niche protection; however, little is known about the underlying mechanisms. Herein, we molecularly and functionally characterize BM niches in patients with CML at diagnosis and reveal the altered niche composition and function in these patients. Long-term culture initiating cell assay showed that the mesenchymal stem cells from patients with CML displayed an enhanced supporting capacity for normal and CML BM CD34+CD38- cells. Molecularly, RNA sequencing detected dysregulated cytokine and growth factor expression in the BM cellular niches of patients with CML. Among them, CXCL14 was lost in the BM cellular niches in contrast to its expression in healthy BM. Restoring CXCL14 significantly inhibited CML LSC maintenance and enhanced their response to imatinib in vitro, and CML engraftment in vivo in NSG-SGM3 mice. Importantly, CXCL14 treatment dramatically inhibited CML engraftment in patient-derived xenografted NSG-SGM3 mice, even to a greater degree than imatinib, and this inhibition persisted in patients with suboptimal TKI response. Mechanistically, CXCL14 upregulated inflammatory cytokine signaling but downregulated mTOR signaling and oxidative phosphorylation in CML LSCs. Together, we have discovered a suppressive role of CXCL14 in CML LSC growth. CXCL14 might offer a treatment option targeting CML LSCs.
|
|
| 8. |
- Dolinska, Monika, et al.
(författare)
-
Characterization of the bone marrow niche in patients with chronic myeloid leukemia identifies CXCL14 as a new therapeutic option
- 2023
-
Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 142:1, s. 73-89
-
Tidskriftsartikel (refereegranskat)abstract
- Although tyrosine kinase inhibitors (TKIs) are effective in treating chronic myeloid leukemia (CML), they often fail to eradicate the leukemia-initiating stem cells (LSCs), causing disease persistence and relapse. Evidence indicates that LSC persistence may be because of bone marrow (BM) niche protection; however, little is known about the underlying mechanisms. Herein, we molecularly and functionally characterize BM niches in patients with CML at diagnosis and reveal the altered niche composition and function in these patients. Long -term culture initiating cell assay showed that the mesenchymal stem cells from patients with CML displayed an enhanced supporting capacity for normal and CML BM CD34+CD38- cells. Molecularly, RNA sequencing detected dysregulated cytokine and growth factor expression in the BM cellular niches of patients with CML. Among them, CXCL14 was lost in the BM cellular niches in contrast to its expression in healthy BM. Restoring CXCL14 significantly inhibited CML LSC maintenance and enhanced their response to imatinib in vitro, and CML engraftment in vivo in NSG-SGM3 mice. Importantly, CXCL14 treatment dramatically inhibited CML engraftment in patient-derived xenografted NSG-SGM3 mice, even to a greater degree than imatinib, and this inhibition persisted in patients with suboptimal TKI response. Mechanistically, CXCL14 upregulated inflammatory cytokine signaling but downregulated mTOR signaling and oxidative phosphorylation in CML LSCs. Together, we have discovered a suppressive role of CXCL14 in CML LSC growth. CXCL14 might offer a treatment option targeting CML LSCs.
|
|
| 9. |
|
|
| 10. |
|
|
