Pitfalls in the assessment of MGMT expression and in its correlation with survival in diffuse astrocytomas: proposal of a feasible immunohistochemical approach

Immunohistochemical studies showed that O6-methylguanine-DNA methyltransferase (MGMT) protein expression is negatively associated with survival in glioblastomas treated with alkylating agents in accordance with previous results of methylation-specific PCR. Implementation of this data in routine clinical diagnostics is limited due to often inappropriate study designs, e.g. pooling of tumor entities, WHO grades or primary and secondary glioblastomas, disregard concerning the infiltration zone or various epidemiological factors. The aim of our study was to evaluate MGMT expression and its prognostic value taking into consideration the aforementioned deficiencies. For this, 162 astrocytic tumors WHO II-IV (36 diffuse astrocytomas WHO II, 51 anaplastic astrocytomas, 75 primary glioblastomas) as well as 25 glioblastoma infiltration zones and 19 glioblastoma relapses were analyzed for immunohistochemical MGMT protein expression using tissue microarray technique. Expression of MGMT significantly decreased from WHO grade II (25.6%) to glioblastoma (16.8%, p=0.01) with lowest levels in grade III tumors (10.2%, II/III p<0.0001). Significant negative associations of MGMT and survival were detected for WHO grade II and IV (p=0.003 and 0.013). The optimal cut-off value of MGMT positive nuclei in primary glioblastomas discriminating patients with significantly different survival rates was at 15% (Log-Rank p=0.0002). Individual relapse tumors showed changes of MGMT expression to a varying degree. The infiltration zone demonstrated a significant increase of MGMT (p<0.0001). We conclude that immunohistochemical MGMT assessment has potential as a powerful diagnostic tool but analysis should only be performed in a grade dependent manner, before radio-/chemotherapy and with special attention to the infiltration zone of diffuse astrocytoma

Genetic alterations in gliosarcoma and giant cell glioblastoma

The majority of glioblastomas develop rapidly with a short clinical history (primary glioblastoma IDH wild-type), whereas secondary glioblastomas progress from diffuse astrocytoma or anaplastic astrocytoma. IDH mutations are the genetic hallmark of secondary glioblastomas. Gliosarcomas and giant cell glioblastomas are rare histological glioblastoma variants, which usually develop rapidly. We determined the genetic patterns of 36 gliosarcomas and 19 giant cell glioblastomas. IDH1 and IDH2 mutations were absent in all 36 gliosarcomas and in 18 of 19 giant cell glioblastomas analyzed, indicating that they are histological variants of primary glioblastoma. Furthermore, LOH 10q (88%) and TERT promoter mutations (83%) were frequent in gliosarcomas. Copy number profiling using the 450k methylome array in 5 gliosarcomas revealed CDKN2A homozygous deletion (3 cases), trisomy chromosome 7 (2 cases), and monosomy chromosome 10 (2 cases). Giant cell glioblastomas had LOH 10q in 50% and LOH 19q in 42% of cases. ATRX loss was detected immunohistochemically in 19% of giant cell glioblastomas, but absent in 17 gliosarcomas. These and previous results suggest that gliosarcomas are a variant of, and genetically similar to, primary glioblastomas, except for a lack of EGFR amplification, while giant cell glioblastoma occupies a hybrid position between primary and secondary glioblastomas. This article is protected by copyright. All rights reserved

Biomarker and Histopathology Evaluation of Patients with Recurrent Glioblastoma Treated with Galunisertib, Lomustine, or the Combination of Galunisertib and Lomustine

Galunisertib, a Transforming growth factor-βRI (TGF-βRI) kinase inhibitor, blocks TGF-β-mediated tumor growth in glioblastoma. In a three-arm study of galunisertib (300 mg/day) monotherapy (intermittent dosing; each cycle =14 days on/14 days off), lomustine monotherapy, and galunisertib plus lomustine therapy, baseline tumor tissue was evaluated to identify markers associated with tumor stage (e.g., histopathology, Ki67, glial fibrillary acidic protein) and TGF-β-related signaling (e.g., pSMAD2). Other pharmacodynamic assessments included chemokine, cytokine, and T cell subsets alterations. 158 patients were randomized to galunisertib plus lomustine (n = 79), galunisertib (n = 39) and placebo+lomustine (n = 40). In 127 of these patients, tissue was adequate for central pathology review and biomarker work. Isocitrate dehydrogenase (IDH1) negative glioblastoma patients with baseline pSMAD2+ in cytoplasm had median overall survival (OS) 9.5 months vs. 6.9 months for patients with no tumor pSMAD2 expression (p = 0.4574). Eight patients were IDH1 R132H+ and had a median OS of 10.4 months compared to 6.9 months for patients with negative IDH1 R132H (p = 0.5452). IDH1 status was associated with numerically higher plasma macrophage-derived chemokine (MDC/CCL22), higher whole blood FOXP3, and reduced tumor CD3+ T cell counts. Compared to the baseline, treatment with galunisertib monotherapy preserved CD4+ T cell counts, eosinophils, lymphocytes, and the CD4/CD8 ratio. The T-regulatory cell compartment was associated with better OS with MDC/CCL22 as a prominent prognostic marker. View Full-Tex

The miR-139-5p regulates proliferation of supratentorial paediatric low-grade gliomas by targeting the PI3K/AKT/mTORC1 signalling

Paediatric low-grade gliomas (pLGGs) are a heterogeneous group of brain tumours associated with a high overall survival: however, they are prone to recur and supratentorial lesions are difficult to resect, being associated with high percentage of disease recurrence. Our aim was to shed light on the biology of pLGGs

Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons

Alternative splicing—the production of multiple messenger RNA isoforms from a single gene—is regulated in part by RNA binding proteins. While the RBPs transformer2 alpha (Tra2α) and Tra2β have both been implicated in the regulation of alternative splicing, their relative contributions to this process are not well understood. Here we find simultaneous—but not individual—depletion of Tra2α and Tra2β induces substantial shifts in splicing of endogenous Tra2β target exons, and that both constitutive and alternative target exons are under dual Tra2α–Tra2β control. Target exons are enriched in genes associated with chromosome biology including CHEK1, which encodes a key DNA damage response protein. Dual Tra2 protein depletion reduces expression of full-length CHK1 protein, results in the accumulation of the DNA damage marker γH2AX and decreased cell viability. We conclude Tra2 proteins jointly control constitutive and alternative splicing patterns via paralog compensation to control pathways essential to the maintenance of cell viability

TSIL: a program for the calculation of two-loop self-energy integrals

TSIL is a library of utilities for the numerical calculation of dimensionally regularized two-loop self-energy integrals. A convenient basis for these functions is given by the integrals obtained at the end of O.V. Tarasov's recurrence relation algorithm. The program computes the values of all of these basis functions, for arbitrary input masses and external momentum. When analytical expressions in terms of polylogarithms are available, they are used. Otherwise, the evaluation proceeds by a Runge-Kutta integration of the coupled first-order differential equations for the basis integrals, using the external momentum invariant as the independent variable. The starting point of the integration is provided by known analytic expressions at (or near) zero external momentum. The code is written in C, and may be linked from C, C++, or Fortran. A Fortran interface is provided. We describe the structure and usage of the program, and provide a simple example application. We also compute two new cases analytically, and compare all of our notations and conventions for the two-loop self-energy integrals to those used by several other groups.Comment: 31 pages. Updated to reflect new functionality through v1.4 May 2016 and new information about use with C++. Source code and documentation are available at http://www.niu.edu/spmartin/TSIL or http://faculty.otterbein.edu/DRobertson/tsil

Calculation of Graviton Scattering Amplitudes using String-Based Methods

Techniques based upon the string organisation of amplitudes may be used to simplify field theory calculations. We apply these techniques to perturbative gravity and calculate all one-loop amplitudes for four-graviton scattering with arbitrary internal particle content. Decomposing the amplitudes into contributions arising from supersymmetric multiplets greatly simplifies these calculations. We also discuss how unitarity may be used to constrain the amplitudes.Comment: 25 pages +5 figs. , SWAT-94-37 UCLA/TEP/94/30, Plain TeX. (Typos in eqns. fixed

Report on the Lille experiments upon the comparative efficiency of ropes and belts for the transmission of power

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Invited Review: DNA methylation‐based classification of paediatric brain tumours

DNA methylation-based machine learning algorithms represent powerful diagnostic tools that are currently emerging for several fields of tumour classification. For various reasons, paediatric brain tumours have been the main driving forces behind this rapid development and brain tumour classification tools are likely further advanced than in any other field of cancer diagnostics. In this review, we will discuss the main characteristics that were important for this rapid advance, namely the high clinical need for improvement of paediatric brain tumour diagnostics, the robustness of methylated DNA and the consequential possibility to generate high-quality molecular data from archival formalin-fixed paraffin-embedded pathology specimens, the implementation of a single array platform by most laboratories allowing data exchange and data pooling to an unprecedented extent, as well as the high suitability of the data format for machine learning. We will further discuss the four most central output qualities of DNA methylation profiling in a diagnostic setting (tumour classification, tumour sub-classification, copy number analysis and guidance for additional molecular testing) individually for the most frequent types of paediatric brain tumours. Lastly, we will discuss DNA methylation profiling as a tool for the detection of new paediatric brain tumour classes and will give an overview of the rapidly growing family of new tumours identified with the aid of this technique

One-Loop Corrections to Two-Quark Three-Gluon Amplitudes

We present the one-loop QCD amplitudes for two external massless quarks and three external gluons ($\bar{q}qggg$). This completes the set of one-loop amplitudes needed for the next-to-leading-order corrections to three-jet production at hadron colliders. We also discuss how to use group theory and supersymmetry to minimize the amount of calculation required for the more general case of one-loop two-quark $n$-gluon amplitudes. We use collinear limits to provide a stringent check on the amplitudes.Comment: plain Tex, 46 pages with 13 figures in a uuencoded file, corrected case j=1 of eq. (IV.7), and signs in eq. (4.9