24 research outputs found
O-methylguanine-DNA methyltransferase (MGMT) mRNA expression predicts outcome in malignant glioma independent of MGMT promoter methylation
No full textBackground: We analyzed prospectively whether MGMT (O(6)-methylguanine-DNA methyltransferase) mRNA expression gains prognostic/predictive impact independent of MGMT promoter methylation in malignant glioma patients undergoing radiotherapy with concomitant and adjuvant temozolomide or temozolomide alone. As DNA-methyltransferases (DNMTs) are the enzymes responsible for setting up and maintaining DNA methylation patterns in eukaryotic cells, we analyzed further, whether MGMT promoter methylation is associated with upregulation of DNMT expression.
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Abstract
Background
We analyzed prospectively whether MGMT (O6-methylguanine-DNA methyltransferase) mRNA expression gains prognostic/predictive impact independent of MGMT promoter methylation in malignant glioma patients undergoing radiotherapy with concomitant and adjuvant temozolomide or temozolomide alone. As DNA-methyltransferases (DNMTs) are the enzymes responsible for setting up and maintaining DNA methylation patterns in eukaryotic cells, we analyzed further, whether MGMT promoter methylation is associated with upregulation of DNMT expression.
Methodology/Principal Findings:
Adult patients with a histologically proven malignant astrocytoma (glioblastoma: N = 53, anaplastic astrocytoma: N = 10) were included. MGMT promoter methylation was determined by methylation-specific PCR (MSP) and sequencing analysis. Expression of MGMT and DNMTs mRNA were analysed by real-time qPCR. Prognostic factors were obtained from proportional hazards models. Correlation between MGMT mRNA expression and MGMT methylation status was validated using data from the Cancer Genome Atlas (TCGA) database (N = 229 glioblastomas). Low MGMT mRNA expression was strongly predictive for prolonged time to progression, treatment response, and length of survival in univariate and multivariate models (p<0.0001); the degree of MGMT mRNA expression was highly correlated with the MGMT promoter methylation status (p<0.0001); however, discordant findings were seen in 12 glioblastoma patients: Patients with methylated tumors with high MGMT mRNA expression (N = 6) did significantly worse than those with low transcriptional activity (p<0.01). Conversely, unmethylated tumors with low MGMT mRNA expression (N = 6) did better than their counterparts. A nearly identical frequency of concordant and discordant findings was obtained by analyzing the TCGA database (p<0.0001). Expression of DNMT1 and DNMT3b was strongly upregulated in tumor tissue, but not correlated with MGMT promoter methylation and MGMT mRNA expression.
Conclusions/Significance:
MGMT mRNA expression plays a direct role for mediating tumor sensitivity to alkylating agents. Discordant findings indicate methylation-independent pathways of MGMT expression regulation. DNMT1 and DNMT3b are likely to be involved in CGI methylation. However, their exact role yet has to be defined
Thongs I've Seen (or Portrait of a Single-Subject Credential)
No full textThis is what happens when a 21st century teachers' college shares a neighborhood with a high school and a shopping mall. The fabric of the three become so intertwined that the teacher credential is just another brand. About the Author Helen M. Kress is an Assistant Professor of Education at D'Youville College in Buffalo, New York, USA. Her research interests include critical theories of education, youth cultures, multicultural curriculum, and qualitative research methods. She teaches philosophy and sociology of education to student teachers. Helen Kress can be contacted at: [email protected]
Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm
No full textIn mammalian cells, AU-rich elements (AREs) are well known regulatory sequences located in the 3' untranslated region (UTR) of many short-lived mRNAs. AREs cause mRNAs to be degraded rapidly and thereby suppress gene expression at the posttranscriptional level. Based on the number of AUUUA pentamers, their proximity, and surrounding AU-rich regions, we generated an algorithm termed AREScore that identifies AREs and provides a numerical assessment of their strength. By analyzing the AREScore distribution in the transcriptomes of 14 metazoan species, we provide evidence that AREs were selected for in several vertebrates and Drosophila melanogaster. We then measured mRNA expression levels genome-wide to address the importance of AREs in SL2 cells derived from D. melanogaster hemocytes. Tis11, a zinc finger RNA-binding protein homologous to mammalian tristetraprolin, was found to target ARE-containing reporter mRNAs for rapid degradation in SL2 cells. Drosophila mRNAs whose expression is elevated upon knock down of Tis11 were found to have higher AREScores. Moreover high AREScores correlate with reduced mRNA expression levels on a genome-wide scale. The precise measurement of degradation rates for 26 Drosophila mRNAs revealed that the AREScore is a very good predictor of short-lived mRNAs. Taken together, this study introduces AREScore as a simple tool to identify ARE-containing mRNAs and provides compelling evidence that AREs are widespread regulatory elements in Drosophila
Aircraft noise determination of novel wing configurations
No full textDuring different investigations the aircraft slats were identified as one of the major sources for airframe noise. This suggests that design modifications of the wing especially the slats could reduce aircraft noise. For this purpose different wing model configurations from a standard to a slatless wing were designed.
Within the German Aerospace Center (DLR) project LEISA these wing configurations will be investigated. The wind tunnel measured lift and drag coefficients can be integrated in the fast time flight simulation tool (NAPSim) developed by DLR. With this tool it is possible to simulate noise abatement flight procedures flown by generic airplanes. The tool has an interface to the DLR noise calculation software SIMUL to compute and compare the different noise impact produced by these configurations. Furthermore the simulation can calculate economical aspects like time and fuel consumption, which are used to evaluate the different configurations, because one constraint is to achieve nearly the same performance that results from a standard wing design.
In this paper the calculation of flight paths and the flight mechanics of an airplane with different wings and thus resulting noise is described
Not1 mediates recruitment of the deadenylase Caf1 to mRNAs targeted for degradation by tristetraprolin
No full textInterphase chromosome positioning in in vitro porcine cells and ex vivo porcine tissues
No full textCopyright @ 2012 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and 85 reproduction in any medium, provided the original author and source are credited. The article was made available through the Brunel University Open Access Publishing Fund.BACKGROUND: In interphase nuclei of a wide range of species chromosomes are organised into their own specific locations termed territories. These chromosome territories are non-randomly positioned in nuclei which is believed to be related to a spatial aspect of regulatory control over gene expression. In this study we have adopted the pig as a model in which to study interphase chromosome positioning and follows on from other studies from our group of using pig cells and tissues to study interphase genome re-positioning during differentiation. The pig is an important model organism both economically and as a closely related species to study human disease models. This is why great efforts have been made to accomplish the full genome sequence in the last decade. RESULTS: This study has positioned most of the porcine chromosomes in in vitro cultured adult and embryonic fibroblasts, early passage stromal derived mesenchymal stem cells and lymphocytes. The study is further expanded to position four chromosomes in ex vivo tissue derived from pig kidney, lung and brain. CONCLUSIONS: It was concluded that porcine chromosomes are also non-randomly positioned within interphase nuclei with few major differences in chromosome position in interphase nuclei between different cell and tissue types. There were also no differences between preferred nuclear location of chromosomes in in vitro cultured cells as compared to cells in tissue sections. Using a number of analyses to ascertain by what criteria porcine chromosomes were positioned in interphase nuclei; we found a correlation with DNA content.This study is partly supported by Sygen International PLC
Serial stereotactic biopsy of brainstem lesions in adults improves diagnostic accuracy compared with MRI only.
No full textObjective: The aim of the current prospective study was
to analyse the validity of MRI based diagnosis of
brainstem gliomas which was verified by stereotactic
biopsy and follow-up evaluation as well as to assess
prognostic factors and risk profile.
Methods: Between 1998 and 2007, all consecutive adult
patients with radiologically suspected brainstem glioma
were included. The MRI based diagnosis of the lesions
was made independently by an experienced neuroradiologist.
Histopathological evaluation was performed in all
patients from paraffin embedded specimens obtained by
multimodal image guided stereotactic serial biopsy
technique. Histopathological results were compared with
prior radiological assessment. Length of survival was
estimated with the Kaplan–Meier method and prognostic
factors were calculated using the Cox model.
Results: 46 adult patients were included. Histological
evaluation revealed pilocytic astrocytoma (n=2), WHO
grade II glioma (n=14), malignant glioma (n=12),
metastasis (n=7), lymphoma (n=5), cavernoma
(n=1), inflammatory disease (n=2) or no tumour/
gliosis (n=3). Perioperative morbidity was 2.5% (n=1).
There was no permanent morbidity and no mortality. All
patients with ‘‘no tumour’’ or ‘‘inflammatory disease’’
survived. Patients with low grade glioma and malignant
glioma showed a 1 year survival rate of 75% and 25%,
respectively; the 1 year survival rate for patients with
lymphoma or metastasis was 30%. In the subgroup with a
verified brainstem glioma, negative predictors for length of
survival were higher tumour grade (p=0.002) and
Karnofsky performance score (70 (p=0.004).
Conclusion: Intra-axial brainstem lesions with a radiological
pattern of glioma represent a very heterogeneous
tumour group with completely different outcomes.
Radiological features alone are not reliable for diagnostic
classification. Stereotactic biopsy is a safe method to
obtain a valid tissue diagnosis, which is indispensible for
treatment decision
Identification of suitable controls for miRNA quantification in T-cells and whole blood cells in sepsis
No full textComplex immune dysregulation is a hallmark of sepsis. The occurring phases of immunosuppression and hyperinflammation require rapid detection and close monitoring. Reliable tools to monitor patient’s immune status are yet missing. Currently, microRNAs are being discussed as promising new biomarkers in sepsis. However, no suitable internal control for normalization of miRNA expression by qPCR has been validated so far, thus hampering their potential benefit. We here present the first evaluation of endogenous controls for miRNA analysis in human sepsis. Novel candidate reference miRNAs were identified via miRNA microArray. TaqMan qPCR assays were performed to evaluate these microRNAs in T-cells and whole blood cells of sepsis patients and healthy controls in two independent cohorts. In T-cells, U48 and miR-320 proved suitable as endogenous controls, while in whole blood cells, U44 and miR-942 provided best stability values for normalization of miRNA quantification. Commonly used snRNA U6 exhibited worst stability in all sample groups. The identified internal controls have been prospectively validated in independent cohorts. The critical importance of housekeeping gene selection is emphasized by exemplary quantification of imuno-miR-150 in sepsis patients. Use of appropriate internal controls could facilitate research on miRNA-based biomarker-use and might even improve treatment strategies in the future. © 2019, The Author(s)
Relative proximity of chromosome territories influences chromosome exchange partners in radiation-induced chromosome rearrangements in primary human bronchial epithelial cells
No full textCopyright © 2013 The Authors. This article is made available through the Brunel Open Access Publishing Fund. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-No Derivative Works License, which permits non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.Copyright © 2013 The Authors. It is well established that chromosomes exist in discrete territories (CTs) in interphase and are positioned in a cell-type specific probabilistic manner. The relative localisation of individual CTs within cell nuclei remains poorly understood, yet many cancers are associated with specific chromosome rearrangements and there is good evidence that relative territorial position influences their frequency of exchange. To examine this further, we characterised the complexity of radiation-induced chromosome exchanges in normal human bronchial epithelial (NHBE) cells by M-FISH analysis of PCC spreads and correlated the exchanges induced with their preferred interphase position, as determined by 1/2-colour 2D-FISH analysis, at the time of irradiation. We found that the frequency and complexity of aberrations induced were reduced in ellipsoid NHBE cells in comparison to previous observations in spherical cells, consistent with aberration complexity being dependent upon the number and proximity of damaged CTs, i.e. lesion proximity. To ask if particular chromosome neighbourhoods could be identified we analysed all radiation-induced pair-wise exchanges using SCHIP (statistics for chromosome interphase positioning) and found that exchanges between chromosomes (1;13), (9;17), (9;18), (12;18) and (16;21) all occurred more often than expected assuming randomness. All of these pairs were also found to be either sharing similar preferred positions in interphase and/or sharing neighbouring territory boundaries. We also analysed a human small cell lung cancer cell line, DMS53, by M-FISH observing the genome to be highly rearranged, yet possessing rearrangements also involving chromosomes (1;13) and (9;17). Our findings show evidence for the occurrence of non-random exchanges that may reflect the territorial organisation of chromosomes in interphase at time of damage and highlight the importance of cellular geometry for the induction of aberrations of varying complexity after exposure to both low and high-LET radiation.Department of Healt
