P05.04.A Disconcordance between different molecular methods to assess homozygous deletion of theCDKN2A/B locus in IDH-mutant astrocytomas

Background

The fifth edition of the WHO Classification of Tumors of the Central Nervous System (WHO CNS 5), includes molecular parameters for both diagnosis and grading in addition to histological features. For IDH-mutant astrocytoma, homozygous deletion (HD) of CDKN2A/B now results in WHO grade 4, even in the absence of microvascular proliferation or necrosis. CDKN2A/B deletions can be determined by various techniques including shallow and targeted sequencing, and using genome wide DNA-methylation arrays. Various algorithms to call deletions also exist for each platform. Concordance between the various techniques and algorithms is however unknown. Because of the importance to properly call CDKN2A/B deletions, we compared two techniques to call HD in IDH-mutant astrocytoma patients.

Methods

Samples from 110 IDH-mutant astrocytoma patients enrolled in the GLASS-NL study, and therefore samples from at least two surgical resections per patient, were available. Overall survival (OS) was measured from date of first surgery.

Both DNA-methylation data and shallow whole-genome sequencing (sWGS) was collected from 219 samples from 101 patients. For DNA-methylation analysis, HD of CDKN2A/B was defined by <-0.6 log2 intensity combined with visual assessment on samples with log2 intensity between -0.6 and -0.2 (method 1), or by using a hard cutoff of <-0.415 log2 intensity, as determined by Shirahata et al. (method 2). Absolute copy number profiles were estimated by ACE from sWGS data, HD of CDKN2A/B was defined by a loss of at least 1.2 CDKN2A alleles (method 3). Agreement score and Cohen’s kappa (κ) as an index for interrater agreement was calculated.

Results

Method 1 and method 2 called an HD of CDKN2A/B in 39 and 33 cases, respectively; method 1 called an HD of CDKN2A/B in 9 cases in which method 2 did not detect an alteration. The agreement was strong with 95% agreement and κ = 0.842.

Method 3 called an HD of CDKN2A/B in 45 cases of which 12 and 19 were not detected by method 1 and method 2 respectively. Method 3 showed an almost perfect level of agreement with method 1, with 97% agreement and κ = 0.911, and a moderate agreement with method 2, with 89% agreement and κ = 0.671.

Survival analysis showed that there was no significant difference in survival when patients were stratified by CDKN2A/B status of the initial sample of all methods. However, when stratified by CDKN2A/B status of the first recurrence, all methods showed a stronger association with OS (method 1: p = 0.001, HR = 2.61[1.44-4.72]; method 2: p = 0.0024, HR = 2.34[1.33-4.11]; method 3: p = 0.0099, HR = 2.34[1.2-4.55]).

Conclusion

Different methods and different cutoffs to determine the presence of a HD in CDKN2A/B may result in different test outcomes. Quality of the DNA, tumor cell percentage of the sample and ploidy are likely to influence the call of homozygous CDKN2A/B deletion. Ring tests are recommended to improve reliability.

OS08.1.A Integrative molecular analysis of matched primary and recurrent IDH-mutant astrocytoma; an update from the GLASS-NL consortium

Background

The evolutionary processes that drive tumor progression in patients with IDH-mutant astrocytoma remain largely unclear. The GLASS-NL consortium was initiated to gain insight into the molecular mechanisms underlying glioma evolution and to identify markers of progression in IDH-mutant astrocytomas. Ultimately, such markers can assist clinical decision making. Here, we present the DNA methylation profiling, RNA-sequencing and shallow whole-genome sequencing (sWGS) of samples included in the GLASS-NL study.

Methods

Eligible were patients with an IDH-mutant, 1p19q non-codeleted, astrocytoma at first diagnosis who underwent surgical resection of the tumor at least twice separated by >6 months, and of whom paired tumor samples were available for analyses. Overall survival (OS) was measured from date of initial surgery.

DNA methylation profiling was performed with the 850kEPIC array, and transcriptome and sWGS by NGS. After quality control, DNA methylation data of 103, expression data of 91, and sWGS data of 92 patients was available for further analysis. Methylation classes were determined according to Capper et al. and copy number alterations (CNAs) were extracted from both sWGS and DNA-methylation data.

Results

110 patients were identified from various medical centers in the Netherlands. The median time between surgical resections was 41.9 months (IQR:26.5-65.9) and after initial surgery, 63% and 22% of the patients were treated with radiotherapy or chemotherapy respectively. The proportion of samples assigned to the high grade methylation class increased ~three-fold at recurrence. 83% of patients that progressed from low to high grade, received treatment prior to recurrent surgery, as compared to 53% of the patients that remained low grade.

Genome wide DNA methylation levels of recurrent samples were lower than that of initial samples. This difference is explained by the increased number of high grades at recurrence, since near identical DNA methylation levels were observed in samples that remained low grade.

Analysis of CNAs revealed chromosomal arms that were more frequently altered in high grade samples. Univariate analysis showed that losses in 3p, 9p, 10q, 13q and 14q were associated with poor OS.

More than 800 differentially expressed genes between initial and recurrent tumor samples were found. Chromosomal enrichment analysis revealed a locus on chromosome 6 enriched with histone genes, to be significantly up-regulated over time.

Conclusion

Longitudinal methylation profiling of IDH-mutant astrocytoma reveals a shift towards a higher grade at tumor recurrence coinciding with reduced DNA methylation levels, and increased frequency of CNAs. Longitudinal expression analysis showed changes in expression of >800 genes, including an up-regulated locus enriched with histone genes. Further integrative analyses are ongoing and will be reported at the meeting.

Human cytomegalovirus and primary intracranial tumours: frequency of tumour infection and lack of correlation with systemic immune anti-viral responses

AIMS

Human cytomegalovirus (HCMV) is a ubiquitous beta human herpesvirus able to influence infected cell survival and proliferation and to modulate the host immune response. As there is accumulating evidence that HCMV is detected in primary intracranial astrocytic tumours, in this study we looked for the presence of HCMV in intracranial tumours and tried to correlate this eventual presence with the anti-HCMV systemic immunoreactivity and with the detection of HCMV in peripheral blood.

METHODS

In this study, we analysed 43 glioblastomas (GBM), 14 oligodendrogliomas (OL) and 20 meningiomas (MG) by immunofluorescence (IF) targeting HCMV immediate early antigen (IE1) and by nested PCR (nPCR) amplifying HCMV glycoprotein B (gB).

RESULTS

Detection of IE1 by IF showed the presence of HCMV in 70% of GBM, 57% of OL and 85% of MG, in contrast to gB nPCR, which detected HCMV in only 50% of GBM, 38% of OL and 46% of MG. Unexpectedly, HCMV DNA and antigens were detected within GBM, OL and MG of patients that exhibit negative viral serology. More surprisingly, PCR on the peripheral blood did not detect HCMV in patients with a HCMV-positive tumour.

CONCLUSIONS

Our results are in agreement with previous observations demonstrating HCMV in glial tumours and highlight the presence of HCMV in meningiomas. We also showed that anti-HCMV specific systemic immunoreactivity and detection of HCMV in peripheral blood are not predictive of HCMV presence in primary intracranial tumours.

PI3 kinase mutations and mutational load as poor prognostic markers in diffuse glioma patients

Introduction

Recent advances in molecular diagnostics allow diffuse gliomas to be classified based on their genetic changes into distinct prognostic subtypes. However, a systematic analysis of all molecular markers has thus far not been performed; most classification schemes use a predefined and select set of genes/molecular markers. Here, we have analysed the TCGA dataset (combined glioblastoma (GBM) and lower grade glioma (LGG) datasets) to identify all prognostic genetic markers in diffuse gliomas in order to generate a comprehensive classification scheme.

Results

Of the molecular markers investigated (all genes mutated at a population frequency >1.7 % and frequent chromosomal imbalances) in the entire glioma dataset, 57 were significantly associated with overall survival. Of these, IDH1 or IDH2 mutations are associated with lowest hazard ratio, which confirms IDH as the most important prognostic marker in diffuse gliomas. Subsequent subgroup analysis largely confirms many of the currently used molecular classification schemes for diffuse gliomas (ATRX or TP53 mutations, 1p19q codeletion). Our analysis also identified PI3-kinase mutations as markers of poor prognosis in IDH-mutated + ATRX/TP53 mutated diffuse gliomas, median survival 3.7 v. 6.3 years (P = 0.02, Hazard rate (HR) 2.93, 95 % confidence interval (CI) 1.16 – 7.38). PI3-kinase mutations were also prognostic in two independent datasets. In our analysis, no additional molecular markers were identified that further refine the molecular classification of diffuse gliomas. Interestingly, these molecular classifiers do not fully explain the variability in survival observed for diffuse glioma patients. We demonstrate that tumor grade remains an important prognostic factor for overall survival in diffuse gliomas, even within molecular glioma subtypes. Tumor grade was correlated with the mutational load (the number of non-silent mutations) of the tumor: grade II diffuse gliomas harbour fewer genetic changes than grade III or IV, even within defined molecular subtypes (e.g. ATRX mutated diffuse gliomas).

Conclusion

We have identified PI3K mutations as novel prognostic markers in gliomas. We also demonstrate that the mutational load is associated with tumor grade. The increase in mutational load may partially explain the increased aggressiveness of higher grade diffuse gliomas when a subset of the affected genes actively contributes to gliomagenesis and/or progression.

Electronic supplementary material

The online version of this article (doi:10.1186/s40478-015-0265-4) contains supplementary material, which is available to authorized users.

[Traumatic brain injury and subarachnoid hemorrhage as a cause of hypopituitarism: a review]

Brain injuries namely traumatic brain injuries (TBI) and subarachnoid haemorrhage (SAH) are relevant causes of acquired adult hypopituitarism, perhaps more prevalent than ever believed. TBI represent a major health problem with an annual incidence of 300 cases per 100.000. SAH affects six new cases per 1.000.000 habitants in USA. In Belgium we estimate nearly 30.000 new TBI cases and 600 SAH cases per year. In the English literature, TBI secondary hypopituitarism has been well documented in 14 retrospective and prospective series accounting for 1.077 cases. In all these series the main pituitary deficits were: GH (14%), ACTH (14%), gonadotrope (18%), TSH (7%) and diabetes insipidus (4%). SAH was documented as a cause of hypopituitarism in three retrospective series accounting for 110 cases and in one prospective series. In all these series main pituitary deficits were GH (25%), ACTH (15%), gonadotrope (8.5%), TSH (6%) and diabetes insipidus (4%). In this review, we analyze recent data and discuss diagnostic and treatment features of secondary hypopituitarism due TBI and SAH.

[Glioblastoma, an example of translational research?]

Among patients which develop glioblastoma multiform (GBM), recurrence is the rule despite continuous progress in surgery, radiotherapy and chemotherapy. In the adult, GBM is the most frequent and most aggressive tumour of the Central Nervous System. A better understanding of the mechanisms by which these tumours relapse could promote the use of preventive therapy and could increase patients' survival. GBM stem cells have been recently described and it was demonstrated that they are specifically implied in the experimental tumorigenesis. It is thus very attractive to speculate on a possible relationship between these GBM stem cells and the neural stem cells which are persisting in the neurogenic zones of the adult brain. In this review, we formulate and discuss the hypothesis by which, in a patient with GBM, malignant stem cells might be present in the neurogenic zones, away from the tumour mass. This hypothesis could explain the tumour relapse observed after the first treatments.

[Recent advances in the treatment of brain tumours]

Neuronavigation is a tool for image guidance surgery. Based on the principle of the GPS, it is notably used for the ablation of brain tumors. Because of their millimetre precision, neuronavigation devices bring more safety and effectiveness due to the ever increasing performances of medical imaging. However, neuronavigation presents a major pitfall as it uses a static support (the images acquired preoperatively) to perform a dynamic process (the surgical ablation). To preserve the performance of neuronavigation, it is mandatory to update the images during surgery. This is now achievable by interventional MRI, intra-operative ultrasound and the incorporation of fluorescent tracers by the tumor cells. These major tools, now available at Sart Tilman University Hospital of combined with state-of-the-art chemotherapy, radiotherapy and experimental protocols (including gene therapy) will undoubtedly improve the prognosis of brain tumors.

Rat gap junction connexin-30 inhibits proliferation of glioma cell lines

Connexins, the structural components of gap junctions, control cell growth and differentiation and are believed to belong to a family of tumour suppressor genes. Studies on connexin localization in brain showed that several of these proteins were expressed in distinct compartments of the brain in a cell-type specific manner, indicating that different gap junctions play specific roles in the physiology of the mammalian brain. In this report, we first cloned rat connexin-30 cDNA from brain and showed that it was expressed in long-term primary culture of rat astrocytes. In order to examine the potential role of connexin-30 in tumour cell proliferation, we transfected the connexin-30 cDNA into two rat glioma cell lines (9L and C6) which have lost its expression. Transfected clones adequately expressed membrane-bound connexin-30 protein. Connexin-30-expressing clones showed slower growth, lower DNA synthesis and reduced proliferation in soft agar as compared with the parental and control cells. We concluded that connexin-30 may also probably be considered as a tumour suppressor in rat gliomas.

Nuclear factor-kappa B, cancer, and apoptosis

The role of nuclear factor (NF)-kappa B in the regulation of apoptosis in normal and cancer cells has been extensively studied in recent years. Constitutive NF-kappa B activity in B lymphocytes as well as in Hodgkin's disease and breast cancer cells protects these cells against apoptosis. It has also been reported that NF-kappa B activation by tumor necrosis factor (TNF)-alpha, chemotherapeutic drugs, or ionizing radiations can protect several cell types against apoptosis, suggesting that NF-kappa B could participate in resistance to cancer treatment. These observations were explained by the regulation of antiapoptotic gene expression by NF-kappa B. However, in our experience, inhibition of NF-kappa B activity in several cancer cell lines has a very variable effect on cell mortality, depending on the cell type, the stimulus, and the level of NF-kappa B inhibition. Moreover, in some experimental systems, NF-kappa B activation is required for the onset of apoptosis. Therefore, it is likely that the NF-kappa B antiapoptotic role in response to chemotherapy is cell type- and signal-dependent and that the level of NF-kappa B inhibition is important. These issues will have to be carefully investigated before considering NF-kappa B as a target for genetic or pharmacological anticancer therapies.

A cell type-specific and gap junction-independent mechanism for the herpes simplex virus-1 thymidine kinase gene/ganciclovir-mediated bystander effect

Tumor cells expressing the herpes simplex virus type 1 thymidine kinase (HSV-tk) gene are killed by nucleoside analogues such as ganciclovir (GCV). GCV affects not only the cells expressing HSV-tk but also neighboring cells that do not express the gene; this phenomenon commonly is called "bystander effect." GCV metabolites transfer via gap junctional intercellular communication (GJIC) accounts for the bystander effect in different cell lines, but other mechanisms have also been described. In this study, we analyzed the mechanisms of the bystander effect in two cell lines exhibiting different capacities of communication (DHD/K12 and 9L). The 9L cells exhibited a very good bystander effect, which was completely blocked by a long-term inhibitor of GJIC, 18 alpha-glycyrrhetinic acid. DHD/K12 cells exhibited a moderate bystander effect that was not abolished by 18 alpha-glycyrrhetinic acid or 1-octanol, another strong inhibitor of GJIC. Interestingly, we also observed a bystander effect in cultures where HSV-tk-expressing DHD/K12 cells were physically separated from their untransfected counterparts but grown in the same medium. Moreover, the transfer of filtered conditioned medium from GCV-treated HSV-tk-expressing DHD/K12 cells to DHD/K12 parental cells induced a decrease of survival in a concentration-dependent manner, suggesting that the bystander effect in this cell line was mediated by a soluble factor.

Posterior epidural migration of sequestered lumbar disc fragments. Report of two cases

The posterior epidural migration of sequestered lumbar disc fragments is an uncommon event. The authors report two such cases in which patients presented with either intense radicular pain or cauda equina syndrome. The radiological characteristics were the posterior epidural location and the ring enhancement of the mass after injection of contrast material. The major diagnostic pitfalls are discussed.

Alpha-MSH stimulates neurite outgrowth of neonatal rat corticospinal neurons in vitro

Peptides related to melanocortin (alpha MSH) and corticotropin (ACTH), collectively termed melanocortins, exert trophic effects on the outgrowth of neurites from peripheral and central nervous system in vitro. Here we study the neurite outgrowth promoting effect of alpha-MSH on corticospinal (CS) neurons in vitro. Corticospinal neurons were identified in cell culture of neonatal rat cortex by immunostaining of cholera toxin subunit B (CTB), retrogradely transported from the cervical parts of the spinal cord. The CTB-immunoreactive neurons represent a small percentage (3-5%) of the total cell population after 72 h in vitro. The axons or dendrites of cortical and CTB-labelled layer V neurons were visualized using antibodies against axon- or dendrite-specific markers and measured using a semi-automatic quantification device. Here we report that alpha-MSH stimulates axonal as well as dendrite outgrowth from both total and CTB-labelled neurons with a bell-shape response curve. Axonal outgrowth of CTB-labelled neurons was dose-dependently stimulated with a maximal effect of 50% at 10(-10) M alpha-MSH. The maximal effect for stimulation of axon outgrowth for the total cortex population was observed at 10(-8) M alpha-MSH. In addition dendrite outgrowth of both total and CTB-labelled neurons is stimulated in a dose-dependent manner with maximal effects (varying between 46 and 48%) at 10(-8) M alpha-MSH. Explanations in the shift for the optimal alpha-MSH concentration for stimulation of axonal outgrowth of CTB-labelled layer V neurons as compared to total cortex neurons are discussed.

Effects of Schwann cell transplantation in a contusion model of rat spinal cord injury

Cultured Schwann cells were transplanted at various delays into a spinal cord contusion injury performed at low thoracic level in adult female rats. The Schwann cells were purified from the dorsal root ganglia of adult syngeneic animals. the transplants were well tolerated, and the transplanted Schwann cells invaded the injured spinal cord. As quantified using video image analysis, the survival and growth of the transplanted cells were poor when the grafting procedure was performed 3-4 days after injury and very good when performed immediately or 10 days after injury, in which cases post-traumatic micro- and macrocavitation were strongly reduced. In animals grafted immediately after injury but not in animals grafted after 10 days, post-traumatic astrogliosis was much reduced. The Schwann cells transplanted area was invaded by numerous regenerating axons, the vast majority of which were, based on the neurotransmitter (CGRP and SP) profile, originating from dorsal root ganglion. No regeneration of the corticospinal tract as assessed after anterograde tracing or of descending aminergic fibers could be demonstrated.

In vitro and in vivo modulation of 5-hydroxytryptamine-, thyrotropin-releasing hormone- and calcitonin-gene related peptide-like immunoreactivities in adult rat sensory neurons

In a previous work we have shown that culturing adult rat dorsal root ganglia neurons modifies their neurotransmitter phenotype in such a way that cultured neurons synthesize transmitters that are not found in situ, while several other transmitters are expressed in a much higher percentage of neurons in culture than in situ [Schoenen J. et al. (1989) J. Neurosci. Res. 22, 473-487]. The aim of the present study was to investigate the origin and the nature of the relevant environmental signals that allow this plasticity to be expressed, focusing on three neurotransmitters: 5-hydroxytryptamine, thyrotropin-releasing hormone and calcitonin-gene related peptide. The main results can be summarized as follows: (1) culturing cells in fetal calf serum or on feeder layers of astrocytes, Schwann cells or fibroblasts partially inhibits the serotoninergic phenotype of dorsal root ganglia neurons; (2) in vivo disconnection of dorsal root ganglia from their spinal targets but not from their peripheral or supraspinal targets induces a significant increase of the percentage of 5-hydroxytryptamine- and thyrotropin-releasing hormone-positive neurons in disconnected ganglia; (3) growth factors such as ciliary neuronotrophic factor or basic fibroblast growth factor but not nerve growth factor repress 5-hydroxytryptamine and calcitonin gene-related peptide immunoreactivity in cultured sensory neurons. In conclusion, neurotransmitter gene expression of adult dorsal root ganglia neurons is controlled by complex influences. Our data suggest that thyrotropin-releasing hormone and 5-hydroxytryptamine gene expression are tonically repressed in vivo by factors originating from the spinal segmental level and that growth factors such as ciliary neurotrophic factor or basic fibroblast growth factor could be potential vectors of this repressing effect.