1,903 research outputs found
Transcriptional silencing of the Dickkopfs-3 (Dkk-3) gene by CpG hypermethylation in acute lymphoblastic leukaemia
Dkk-3 is a newly characterised mortalisation-related gene and an antagonist of the Wnt oncogenic signalling pathway whose
expression is decreased in a variety of cancer cell lines, suggesting that the Dkk-3 gene, located at chromosome 11p15.1, functions as
a tumour suppressor gene. Although 11p15 is a âhot spotâ for methylation in acute lymphoblastic leukaemia (ALL), the role of Dkk-3
abnormalities has never been evaluated in this disease. We analysed CpG island methylation of the Dkk-3 promoter in six ALL cell
lines and 183 ALL patients. We observed Dkk-3 hypermethylation in all cell lines and in cells from 33% (60/183) of ALL patients.
Moreover, Dkk-3 methylation was associated with decreased Dkk-3 mRNA expression and this expression was restored after
exposure to the demethylating agent 5-AzaC. Clinical features did not differ between hypermethylated and unmethylated patients.
Estimated disease-free survival (DFS) and overall survival at 10 and 11 years, respectively, were 49.8 and 45.6% for normal patients
and 10.5 and 15.1% for hypermethylated patients (PŒ0.001 and 0.09). Multivariate analysis demonstrated that Dkk-3 methylation
was an independent prognostic factor predicting DFS (PŒ0.0009). Our data suggest that Dkk-3 methylation occurs at an early stage
in ALL pathogenesis and probably influences the clinical behaviour of the disease
Reversion of epigenetically mediated BIM silencing overcomes chemoresistance in Burkitt lymphoma
In Burkitt lymphoma/leukemia (BL), achievement of complete remission with first-line chemotherapy remains a challenging issue, as most patients who respond remain disease-free, whereas those refractory have few options of being rescued with salvage therapies. The mechanisms underlying BL chemoresistance and how it can be circumvented remain undetermined. We previously reported the frequent inactivation of the proapoptotic BIM gene in B-cell lymphomas. Here we show that BIM epigenetic silencing by concurrent promoter hypermethylation and deacetylation occurs frequently in primary BL samples and BL-derived cell lines. Remarkably, patients with BL with hypermethylated BIM presented lower complete remission rate (24% vs 79%; P = .002) and shorter overall survival (P = .007) than those with BIM-expressing lymphomas, indicating that BIM transcriptional repression may mediate tumor chemoresistance. Accordingly, by combining in vitro and in vivo studies of human BL-xenografts grown in immunodeficient RAG2(-/-)Îłc(-/-) mice and of murine B220(+)IgM(+) B-cell lymphomas generated in EÎŒ-MYC and EÎŒ-MYC-BIM(+/-) transgenes, we demonstrate that lymphoma chemoresistance is dictated by BIM gene dosage and is reversible on BIM reactivation by genetic manipulation or after treatment with histone-deacetylase inhibitors. We suggest that the combination of histone-deacetylase inhibitors and high-dose chemotherapy may overcome chemoresistance, achieve durable remission, and improve survival of patients with BL
Epigenetic Signatures Associated with Different Levels of Differentiation Potential in Human Stem Cells
The therapeutic use of multipotent stem cells depends on their differentiation potential, which has been
shown to be variable for different populations. These differences are likely to be the result of key changes in their epigenetic
profiles
Identification of importin (IPO-8) as the most accurate reference gene for the clinicopathological analysis of lung specimens
Abstract
Background: The accurate normalization of differentially expressed genes in lung cancer is
essential for the identification of novel therapeutic targets and biomarkers by real time RT-PCR
and microarrays. Although classical "housekeeping" genes, such as GAPDH, HPRT1, and beta-actin
have been widely used in the past, their accuracy as reference genes for lung tissues has not been
proven.
Results: We have conducted a thorough analysis of a panel of 16 candidate reference genes for
lung specimens and lung cell lines. Gene expression was measured by quantitative real time RTPCR
and expression stability was analyzed with the softwares GeNorm and NormFinder, mean of
|ÎCt| (= |Ct Normal-Ct tumor|) ± SEM, and correlation coefficients among genes. Systematic
comparison between candidates led us to the identification of a subset of suitable reference genes
for clinical samples: IPO8, ACTB, POLR2A, 18S, and PPIA. Further analysis showed that IPO8 had
a very low mean of |ÎCt| (0.70 ± 0.09), with no statistically significant differences between normal
and malignant samples and with excellent expression stability.
Conclusion: Our data show that IPO8 is the most accurate reference gene for clinical lung
specimens. In addition, we demonstrate that the commonly used genes GAPDH and HPRT1 are
inappropriate to normalize data derived from lung biopsies, although they are suitable as reference
genes for lung cell lines. We thus propose IPO8 as a novel reference gene for lung cancer samples
Promoter hypermethylation of cancer-related genes: a strong independent prognostic factor in acute lymphoblastic leukemia
Promoter hypermethylation plays an important
role in the inactivation of cancerrelated
genes. This abnormality occurs
early in leukemogenesis and seems to be
associated with poor prognosis in acute
lymphoblastic leukemia (ALL). To determine
the extent of hypermethylation in
ALL, we analyzed the methylation status
of the CDH1, p73, p16, p15, p57, NES-1,
DKK-3, CDH13, p14, TMS-1, APAF-1,
DAPK, PARKIN, LATS-1, and PTEN genes
in 251 consecutive ALL patients.Atotal of
77.3% of samples had at least 1 gene
methylated, whereas 35.9% of cases had
4 or more genes methylated. Clinical features
and complete remission rate did not
differ among patients without methylated
genes, patients with 1 to 3 methylated
genes (methylated group A), or patients
with more than 3 methylated genes (methylated
group B). Estimated disease-free
survival (DFS) and overall survival (OS) at
11 years were 75.5% and 66.1%, respectively,
for the nonmethylated group; 37.2%
and 45.5% for methylated group A; and
9.4% and 7.8% for methylated group B
(P < .0001 and P .0004, respectively).
Multivariate analysis demonstrated that
the methylation profile was an independent
prognostic factor in predicting DFS
(P < .0001) and OS (P .003). Our results
suggest that the methylation profile may
be a potential new biomarker of risk prediction
in AL
Promoter hypomethylation of the LINE-1 retrotransposable elements activates sense/antisense transcription and marks the progression of chronic myeloid leukemia
Aberrant genome-wide hypomethylation is thought to be
related to tumorigenesis by promoting genomic instability.
Since DNA methylation is considered an important mechanism
for the silencingof retroelements, hypomethylation
in human tumors may lead to their reactivation. However,
the role of DNA hypomethylation in chronic myeloid
leukemia (CML) remains to be elucidated. In this study,
the methylation status of the LINE-1 (L1) retrotransposon
promoter was analysed in CML samples from the chronicphase
(CP, nŒ140) and the blast crisis (BC, nŒ47). L1
hypomethylation was significantly more frequent in BC
(74.5%) than in CP (38%) (Po0.0001). Furthermore,
L1 hypomethylation led to activation of both ORF1 sense
transcription (Po0.0001) and c-MET gene antisense
transcription (Po0.0001), and was significantly associated
with high levels of BCRâABL (PÂŒ0.02) and
DNMT3b4 (PŒ0.001) transcripts. Interestingly, in
CP-CML, extensive L1 hypomethylation was associated
with poorer prognosis in terms of cytogenetic response
to interferon (PŒ0.004) or imatinib (PŒ0.034) and
progression-free survival (PŒ0.005). The above results
strongly suggest that activation of both sense and
antisense transcriptions by aberrant promoter hypomethylation
of the L1 elements plays a role in the progression
and clinical behavior of the CML
Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
Abstract
Background
Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events.
Results
The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer.
Conclusions
This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies
MicroRNA expression profiling in Imatinib-resistant Chronic Myeloid Leukemia patients without clinically significant ABL1-mutations
The development of Imatinib Mesylate (IM), the first specific inhibitor of BCR-ABL1, has had a major impact in patients with Chronic Myeloid Leukemia (CML), establishing IM as the standard therapy for CML. Despite the clinical success obtained with the use of IM, primary resistance to IM and molecular evidence of persistent disease has been observed in 20-25% of IM treated patients. The existence of second generation TK inhibitors, which are effective in patients with IM resistance, makes identification of predictors of resistance to IM an important goal in CML. In this study, we have identified a group of 19 miRNAs that may predict clinical resistance to IM in patients with newly diagnosed CML
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