Comprehensive Analysis of MGMT Promoter Methylation: Correlation with MGMT Expression and Clinical Response in GBM

O6-methylguanine DNA-methyltransferase (MGMT) promoter methylation has been identified as a potential prognostic marker for glioblastoma patients. The relationship between the exact site of promoter methylation and its effect on gene silencing, and the patient's subsequent response to therapy, is still being defined. The aim of this study was to comprehensively characterize cytosine-guanine (CpG) dinucleotide methylation across the entire MGMT promoter and to correlate individual CpG site methylation patterns to mRNA expression, protein expression, and progression-free survival. To best identify the specific MGMT promoter region most predictive of gene silencing and response to therapy, we determined the methylation status of all 97 CpG sites in the MGMT promoter in tumor samples from 70 GBM patients using quantitative bisulfite sequencing. We next identified the CpG site specific and regional methylation patterns most predictive of gene silencing and improved progression-free survival. Using this data, we propose a new classification scheme utilizing methylation data from across the entire promoter and show that an analysis based on this approach, which we call 3R classification, is predictive of progression-free survival (HR  = 5.23, 95% CI [2.089–13.097], p<0.0001). To adapt this approach to the clinical setting, we used a methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) test based on the 3R classification and show that this test is both feasible in the clinical setting and predictive of progression free survival (HR  = 3.076, 95% CI [1.301–7.27], p = 0.007). We discuss the potential advantages of a test based on this promoter-wide analysis and compare it to the commonly used methylation-specific PCR test. Further prospective validation of these two methods in a large independent patient cohort will be needed to confirm the added value of promoter wide analysis of MGMT methylation in the clinical setting

Euclid preparation XVIII. The NISP photometric system

Euclid will be the first space mission to survey most of the extragalactic sky in the 0.95–2.02 µm range, to a 5 σ point-source median depth of 24.4 AB mag. This unique photometric dataset will find wide use beyond Euclid’s core science. In this paper, we present accurate computations of the Euclid YE, JE, and HE passbands used by the Near-Infrared Spectrometer and Photometer (NISP), and the associated photometric system. We pay particular attention to passband variations in the field of view, accounting for, among other factors, spatially variable filter transmission and variations in the angle of incidence on the filter substrate using optical ray tracing. The response curves’ cut-on and cut-off wavelengths – and their variation in the field of view – are determined with ∼0.8 nm accuracy, essential for the photometric redshift accuracy required by Euclid. After computing the photometric zero points in the AB mag system, we present linear transformations from and to common ground-based near-infrared photometric systems, for normal stars, red and brown dwarfs, and galaxies separately. A Python tool to compute accurate magnitudes for arbitrary passbands and spectral energy distributions is provided. We discuss various factors, from space weathering to material outgassing, that may slowly alter Euclid’s spectral response. At the absolute flux scale, the Euclid in-flight calibration program connects the NISP photometric system to Hubble Space Telescope spectrophotometric white dwarf standards; at the relative flux scale, the chromatic evolution of the response is tracked at the milli-mag level. In this way, we establish an accurate photometric system that is fully controlled throughout Euclid’s lifetime

Euclid preparation. XVIII. The NISP photometric system

Euclid will be the first space mission to survey most of the extragalactic sky in the 0.95-2.02 $\mu$m range, to a 5$\sigma$ point-source median depth of 24.4 AB mag. This unique photometric data set will find wide use beyond Euclid's core science. In this paper, we present accurate computations of the Euclid Y_E, J_E and H_E passbands used by the Near-Infrared Spectrometer and Photometer (NISP), and the associated photometric system. We pay particular attention to passband variations in the field of view, accounting among others for spatially variable filter transmission, and variations of the angle of incidence on the filter substrate using optical ray tracing. The response curves' cut-on and cut-off wavelengths - and their variation in the field of view - are determined with 0.8 nm accuracy, essential for the photometric redshift accuracy required by Euclid. After computing the photometric zeropoints in the AB mag system, we present linear transformations from and to common ground-based near-infrared photometric systems, for normal stars, red and brown dwarfs, and galaxies separately. A Python tool to compute accurate magnitudes for arbitrary passbands and spectral energy distributions is provided. We discuss various factors from space weathering to material outgassing that may slowly alter Euclid's spectral response. At the absolute flux scale, the Euclid in-flight calibration program connects the NISP photometric system to Hubble Space Telescope spectrophotometric white dwarf standards; at the relative flux scale, the chromatic evolution of the response is tracked at the milli-mag level. In this way, we establish an accurate photometric system that is fully controlled throughout Euclid's lifetime.Comment: 33 pages, 25 figures, accepted for publication in A&

Euclid preparation: XVIII. The NISP photometric system

Galaxie

Prognostic relevance of miRNA-155 methylation in anaplastic glioma

The outcome of patients with anaplastic gliomas varies considerably depending on single molecular markers, such as mutations of the isocitrate dehydrogenase (IDH) genes, as well as molecular classifications based on epigenetic or genetic profiles. Remarkably, 98% of the RNA within a cell is not translated into proteins. Of those, especially microRNAs (miRNAs) have been shown not only to have a major influence on physiologic processes but also to be deregulated and prognostic in malignancies. To find novel survival markers and treatment options we performed unbiased DNA methylation screens that revealed 12 putative miRNA promoter regions with differential DNA methylation in anaplastic gliomas. Methylation of these candidate regions was validated in different independent patient cohorts revealing a set of miRNA promoter regions with prognostic relevance across data sets. Of those, miR-155 promoter methylation and miR-155 expression were negatively correlated and especially the methylation showed superior correlation with patient survival compared to established biomarkers. Functional examinations in malignant glioma cells further cemented the relevance of miR-155 for tumor cell viability with transient and stable modifications indicating an onco-miRNA activity. MiR-155 also conferred resistance towards alkylating temozolomide and radiotherapy as consequence of nuclear factor (NF)kappa B activation. Preconditioning glioma cells with an NF kappa B inhibitor reduced therapy resistance of miR-155 overexpressing cells. These cells resembled tumors with a low methylation of the miR-155 promoter and thus mir-155 or NF kappa B inhibition may provide treatment options with a special focus on patients with IDH wild type tumors

Pathway inhibition: emerging molecular targets for treating glioblastoma

Insights into the molecular pathogenesis of glioblastoma have not yet resulted in relevant clinical improvement. With standard therapy, which consists of surgical resection with concomitant temozolomide in addition to radiotherapy followed by adjuvant temozolomide, the median duration of survival is 12–14 months. Therefore, the identification of novel molecular targets and inhibitory agents has become a focus of research for glioblastoma treatment. Recent results of bevacizumab may represent a proof of principle that treatment with targeted agents can result in clinical benefits for patients with glioblastoma. This review discusses limitations in the existing therapy for glioblastoma and provides an overview of current efforts to identify molecular targets using large-scale screening of glioblastoma cell lines and tumor samples. We discuss preclinical and clinical data for several novel molecular targets, including growth factor receptors, phosphatidylinositol-3 kinase, SRC-family kinases, integrins, and CD95 ligand and agents that inhibit these targets, including erlotinib, enzastaurin, dasatinib, sorafenib, cilengitide, AMG102, and APG101. By combining advances in tumor screening with novel targeted therapies, it is hoped that new treatment options will emerge for this challenging tumor type