Supratentorial clear cell ependymomas with branching capillaries demonstrate characteristic clinicopathological features and pathological activation of nuclear factor-kappaB signaling

BACKGROUND

Clear cell ependymoma is one of the 4 main histological subtypes of ependymomas defined by the World Health Organization (WHO) classification of tumors of the CNS. DNA methylation profiling can distinguish 4 subgroups of intracranial ependymomas, including supratentorial (ST) ependymomas with Yes-associated protein 1 fusion (YAP1), ST ependymomas with fusion of v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA), posterior fossa ependymomas with balanced genome, and posterior fossa ependymomas with chromosomal instability. In addition, trisomy 19 is a genomic hallmark of ependymomas with rich branching capillaries. However, the relation of histological and molecular subtypes is unclear.

METHODS

Here, we report a series of 20 ependymomas histologically defined by clear cells and branching capillaries.

RESULTS

We observed a strong male predominance. Median age at surgery was 10.4 years (range, 0.8-68.4). All cases were ST, cortical, contrast enhancing, and most often frontal, cystic, and calcified. All tumors qualified as WHO grade III. Some of them exhibited neuronal differentiation. Trisomy 19 was recorded in 13 cases. All samples strongly accumulated p65RelA protein within nuclei, indicating pathological activation of the nuclear factor-kappaB pathway. We identified causative C11ORF95-RELA fusion in almost all cases. Median progression-free survival and overall survival were 11.4 years (95% CI: 5.1-17.8) and not reached, respectively.

CONCLUSION

ST clear cell ependymomas with branching capillaries display characteristic clinicopathological features and are associated with pathological activation of nuclear factor-kappaB signaling, which may indicate a potential novel target for therapy in these patients.

Papillary glioneuronal tumors: histological and molecular characteristics and diagnostic value of SLC44A1-PRKCA fusion

INTRODUCTION

Papillary Glioneuronal Tumor (PGNT) is a grade I tumor which was classified as a separate entity in the World Health Organization Classification of the Central Nervous System 2007 in the group of mixed glioneuronal tumors. This tumor is rare and subclassifying PGNT represents a challenge. Recently, a fusion between SLC44A1 and PRKCA which encodes a protein kinase C involved in MAPK signaling pathway has been described in two studies (five cases). The current study aimed at raising the cytogenetic, histological and molecular profiles of PGNT and to determine if SLC44A1-PRKCA fusion represented a specific diagnostic marker to distinguish it from other glioneuronal tumors.

RESULTS

We report on four pediatric cases of PGNT, along with clinico-radiologic and immunohistological features for which SLC44A1-PRKCA fusion assessment by fluorescence in situ hybridization, BRAF V600E and FGFR1 mutation by immunohistochemistry and direct DNA sequencing and KIAA1549-BRAF fusion by RT-PCR were performed. MAPK signaling pathway activation was investigated using phospho-ERK immunohistochemistry and western blot. We analyzed fifteen cases of tumors with challenging histological or clinical differential diagnoses showing respectively a papillary architecture or periventricular location (PGNT mimics). fluorescence in situ hybridization analysis revealed a constant SLC44A1-PRKCA fusion signal in all PGNTs. None of PGNT mimics showed the SLC44A1-PRKCA fusion signal pattern. All PGNTs were negative for BRAF V600E and FGFR1 mutation, and KIAA1549-BRAF fusion. Phospho-ERK analysis provides arguments for the activation of the MAPK signaling pathway in these tumors.

CONCLUSIONS

Here we confirmed and extended the molecular data on PGNT. These results suggest that PGNT belong to low grade glioma with MAPK signaling pathway deregulation. SLC44A1-PRKCA fusion seems to be a specific characteristic of PGNT with a high diagnostic value and detectable by FISH.

Preclinical evaluation of dasatinib alone and in combination with cabozantinib for the treatment of diffuse intrinsic pontine glioma

BACKGROUND

Platelet-derived growth factor receptor A is altered by amplification and/or mutation in diffuse intrinsic pontine glioma (DIPG). We explored in vitro on new DIPG models the efficacy of dasatinib, a multi-tyrosine kinase inhibitor targeting this receptor.

METHODS

Gene expression profiles were generated from 41 DIPGs biopsied at diagnosis and compared with the signature associated with sensitivity/resistance to dasatinib. A panel of 12 new DIPG cell lines were established from biopsy at diagnosis, serially passaged, and characterized by gene expression analyses. Effects of dasatinib (1-10 μM) on proliferation, invasion, and cytotoxicity were determined on 4 of these cell lines using live-cell imaging and flow cytometry assays. Downstream signaling and receptor tyrosine kinases (RTKs) were assessed by western blot and phospho-RTK array. The effect of the combination with the c-Met inhibitor cabozantinib was studied on cellular growth and invasion analyzed by the Chou-Talaly method.

RESULTS

DIPG primary tumors and cell lines exhibited the gene expression signature of sensitivity to dasatinib. Dasatinib reduced proliferation (half-maximal inhibitory concentration = 10-100 nM) and invasion (30%-60% reduction) at 100 nM in 4/4 cultures and induced apoptosis in 1 of 4 DIPG cell lines. Activity of downstream effectors of dasatinib targets including activin receptor 1 was strongly reduced. Since multiple RTKs were activated simultaneously in DIPG cell lines, including c-Met, which can be also amplified in DIPG, the benefit of the combination of dasatinib with cabozantinib was explored for its synergistic effects on proliferation and migration/invasion in these cell lines.

CONCLUSION

Dasatinib exhibits antitumor effects in vitro that could be increased by the combination with another RTK inhibitor targeting c-Met.

Current and evolving knowledge of prognostic factors for pediatric ependymomas

Ependymomas are one of the most common pediatric malignant brain tumors. Prognosis, especially in young children, remains poor due to their inherent chemo- and radio-resistance and effective treatment remains one of the more difficult tasks in pediatric oncology: up to half of the patients may die from the disease. The only reproducible prognostic factor is the extent of surgery; neither histological grading nor other biomarkers can be used to reliably make treatment decisions in clinical practice. None of the studies identifying new biomarkers have been conducted prospectively, only few have been undertaken within the context of a clinical trial and most have been conducted with limited samples (often including adults and childhood samples). International collaboration is needed to improve ependymoma prognostication.

Neuropathological and neuroradiological spectrum of pediatric malignant gliomas: correlation with outcome

BACKGROUND

The diagnostic accuracy and reproducibility for glioma histological diagnosis are suboptimal.

OBJECTIVE

To characterize radiological and histological features in pediatric malignant gliomas and to determine whether they had an impact on survival.

METHODS

We retrospectively reviewed a series of 96 pediatric malignant gliomas. All histological samples were blindly and independently reviewed and classified according to World Health Organization 2007 and Sainte-Anne classifications. Radiological features were reviewed independently. Statistical analyses were performed to investigate the relationship between clinical, radiological, and histological features and survival.

RESULTS

Cohort median age was 7.8 years; median follow-up was 4.8 years. Tumors involved cerebral hemispheres or basal ganglia in 82% of cases and brainstem in the remaining 18%. After histopathological review, low-grade gliomas and nonglial tumors were excluded (n = 27). The World Health Organization classification was not able to demonstrate differences between groups and patients survival. The Sainte-Anne classification identified a 3-year survival rate difference between the histological subgroups (oligodendroglioma A, oligodendroglioma B, malignant glioneuronal tumors, and glioblastomas; P = .02). The malignant glioneuronal tumor was the only glioma subtype with specific radiological features. Tumor location was significantly associated with 3-year survival rate (P = .005). Meningeal attachment was the only radiological criteria associated with longer survival (P = .02).

CONCLUSION

The Sainte-Anne classification was better able to distinguish pediatric malignant gliomas in terms of survival compared with the World Health Organization classification. In this series, neither of these 2 histological classifications provided a prognostic stratification of the patients.

Immunohistochemical detection of cytoplasmic LC3 puncta in human cancer specimens

Autophagy is an evolutionarily conserved catabolic process that involves the entrapment of cytoplasmic components within characteristic vesicles for their delivery to and degradation within lysosomes. Alterations in autophagic signaling are found in several human diseases including cancer. Here, we describe a validated immunohistochemical protocol for the detection of LC3 puncta in human formalin-fixed, paraffin-embedded cancer specimens that can also be applied to mouse tissues. In response to systemic chemotherapy, autophagy-competent mouse tumors exhibited LC3 puncta, which did not appear in mouse cancers that had been rendered autophagy-deficient by the knockdown of Atg5 or Atg7. As compared with normal tissues, LC3 staining was moderately to highly elevated in the large majority of human cancers studied, albeit tumors of the same histological type tended to be highly heterogeneous in the number and intensity of LC3 puncta per cell. Moreover, tumor-infiltrating immune cells often were highly positive for LC3. Altogether, this protocol for LC3 staining appears suitable for the specific detection of LC3 puncta in human specimens, including tissue microarrays. We surmise that this technique can be employed for retrospective or prospective studies involving large series of human tumor samples.

Critical oncogenic mutations in newly diagnosed pediatric diffuse intrinsic pontine glioma

Diffuse intrinsic pontine gliomas (DIPG) can not be cured with current treatment modalities. Targeted therapy in this disease would benefit from advanced technologies detecting relevant drugable mutations. Twenty patients with classic newly diagnosed DIPG underwent stereotactic biopsies and were analyzed for the presence of 983 different mutations in 115 oncogenes and tumor-suppressor genes using OncoMap, a mass spectrometric method of allele detection. Our results identified oncogenic mutations in TP53 (40%), PI3KCA (15%), and ATM/MPL (5%) while none were identified in a large number of other genes commonly mutated in malignant gliomas. The identification of oncogenic mutations in the PI3K pathway offers the potential of a therapeutic target at initial diagnosis in this devastating disease.

Mesenchymal transition and PDGFRA amplification/mutation are key distinct oncogenic events in pediatric diffuse intrinsic pontine gliomas

Diffuse intrinsic pontine glioma (DIPG) is one of the most frequent malignant pediatric brain tumor and its prognosis is universaly fatal. No significant improvement has been made in last thirty years over the standard treatment with radiotherapy. To address the paucity of understanding of DIPGs, we have carried out integrated molecular profiling of a large series of samples obtained with stereotactic biopsy at diagnosis. While chromosomal imbalances did not distinguish DIPG and supratentorial tumors on CGHarrays, gene expression profiling revealed clear differences between them, with brainstem gliomas resembling midline/thalamic tumours, indicating a closely-related origin. Two distinct subgroups of DIPG were identified. The first subgroup displayed mesenchymal and pro-angiogenic characteristics, with stem cell markers enrichment consistent with the possibility to grow tumor stem cells from these biopsies. The other subgroup displayed oligodendroglial features, and appeared largely driven by PDGFRA, in particular through amplification and/or novel missense mutations in the extracellular domain. Patients in this later group had a significantly worse outcome with an hazard ratio for early deaths, ie before 10 months, 8 fold greater that the ones in the other subgroup (p = 0.041, Cox regression model). The worse outcome of patients with the oligodendroglial type of tumors was confirmed on a series of 55 paraffin-embedded biopsy samples at diagnosis (median OS of 7.73 versus 12.37 months, p = 0.045, log-rank test). Two distinct transcriptional subclasses of DIPG with specific genomic alterations can be defined at diagnosis by oligodendroglial differentiation or mesenchymal transition, respectively. Classifying these tumors by signal transduction pathway activation and by mutation in pathway member genes may be particularily valuable for the development of targeted therapies.

Copy number gain of 1q25 predicts poor progression-free survival for pediatric intracranial ependymomas and enables patient risk stratification: a prospective European clinical trial cohort analysis on behalf of the Children's Cancer Leukaemia Group (CCLG), Societe Francaise d'Oncologie Pediatrique (SFOP), and International Society for Pediatric Oncology (SIOP)

PURPOSE

The high incidence of recurrence and unpredictable clinical outcome for pediatric ependymoma reflect the imprecision of current therapeutic staging and need for novel risk stratification markers. We therefore evaluated 1q25 gain across three age- and treatment-defined European clinical trial cohorts of pediatric intracranial ependymoma.

EXPERIMENTAL DESIGN

Frequency of 1q gain was assessed across 48 ependymomas (42 primary, 6 recurrent) using Affymetrix 500K single-nucleotide polymorphism arrays. Gain of 1q25 was then evaluated by interphase FISH across 189 tumors treated on the Children's Cancer Leukaemia Group/International Society for Pediatric Oncology (SIOP) CNS9204 (n = 60) and BBSFOP (n = 65) adjuvant chemotherapy trials, or with primary postoperative radiotherapy (SIOP CNS9904/RT, n = 64). Results were correlated with clinical, histologic, and survival data.

RESULTS

Gain of 1q was the most frequent imbalance in primary (7/42, 17%) and recurrent ependymomas (2/6, 33%). Gain of 1q25 was an independent predictor of tumor progression across the pooled trial cohort [HR = 2.55; 95% confidence interval (CI): 1.56-4.16; P = 0.0002] and both CNS9204 (HR = 4.03; 95% CI: 1.88-8.63) and BBSFOP (HR = 3.10; 95% CI: 1.22-7.86) groups. The only clinical variable associated with adverse outcome was incomplete tumor resection. Integrating tumor resectability with 1q25 status enabled stratification of cases into disease progression risk groups for all three trial cohorts.

CONCLUSIONS

This is the first study to validate a prognostic genomic marker for childhood ependymoma across independent trial groups. 1q25 gain predicts disease progression and can contribute to patient risk stratification. We advocate the prospective evaluation of 1q25 gain as an adverse marker in future international clinical trials.

Innovative Therapies for Children with Cancer pediatric phase I study of erlotinib in brainstem glioma and relapsing/refractory brain tumors

This multicenter phase I study aimed to establish the recommended dose (RD) of the epidermal growth factor receptor (EGFR) inhibitor erlotinib, given as monotherapy or with radiotherapy to children with malignant brain tumors. Group 1 included patients with refractory or relapsing brain tumors receiving erlotinib alone, and group 2 included newly diagnosed patients with brainstem gliomas receiving radiotherapy and erlotinib. A conventional 3 + 3 dose escalation and a continual reassessment method, respectively, were utilized in 4 dose levels: 75, 100, 125, and 150 mg/m² per day. Fifty-one children were enrolled (30 and 21, respectively); 50 received treatment. The RD of erlotinib was 125 mg/m² per day as monotherapy or in combination with radiotherapy. Overall, 230 adverse events in 44 patients were possibly treatment related (216, grades 1 and 2; 9, grade 3; 1, grade 4; 4, grade 5). Dermatologic and neurologic symptoms were common; intratumoral hemorrhage was confirmed in 3 patients. In group 1, 8 of 29 patients (28%) had stable disease with tumor regression approaching 50% in a malignant glioma and an anaplastic oligoastrocytoma. In group 2, overall survival was 12.0 months. EGFR overexpression by immunohistochemistry was found in 17 of 38 (45%) tumor samples analyzed, with a partial gain of 7p11.2 in 1 glioblastoma; phosphate and tensin homolog loss was frequent in brainstem glioma (15 of 19). Mean (95% CI) apparent clearance and volume of distribution for erlotinib were 4.0 L/h (3.4-4.5 L/h) and 98.6 L (69.8-127.0 L), respectively, and were independent of the dose level; mean half-life was 16.6 hours. Thus, erlotinib 125 mg/m² per day has an acceptable tolerability profile in pediatric patients with brain tumors and can be combined with radiotherapy.

Portrait of ependymoma recurrence in children: biomarkers of tumor progression identified by dual-color microarray-based gene expression analysis

Background

Children with ependymoma may experience a relapse in up to 50% of cases depending on the extent of resection. Key biological events associated with recurrence are unknown.

Methodology/Principal Findings

To discover the biology behind the recurrence of ependymomas, we performed CGHarray and a dual-color gene expression microarray analysis of 17 tumors at diagnosis co-hybridized with the corresponding 27 first or subsequent relapses from the same patient. As treatment and location had only limited influence on specific gene expression changes at relapse, we established a common signature for relapse. Eighty-seven genes showed an absolute fold change ≥2 in at least 50% of relapses and were defined as the gene expression signature of ependymoma recurrence. The most frequently upregulated genes are involved in the kinetochore (ASPM, KIF11) or in neural development (CD133, Wnt and Notch pathways). Metallothionein (MT) genes were downregulated in up to 80% of the recurrences. Quantitative PCR for ASPM, KIF11 and MT3 plus immunohistochemistry for ASPM and MT3 confirmed the microarray results. Immunohistochemistry on an independent series of 24 tumor pairs at diagnosis and at relapse confirmed the decrease of MT3 expression at recurrence in 17/24 tumor pairs (p = 0.002). Conversely, ASPM expression was more frequently positive at relapse (87.5% vs 37.5%, p = 0.03). Loss or deletion of the MT genes cluster was never observed at relapse. Promoter sequencing after bisulfite treatment of DNA from primary tumors and recurrences as well as treatment of short-term ependymoma cells cultures with a demethylating agent showed that methylation was not involved in MT3 downregulation. However, in vitro treatment with a histone deacetylase inhibitor or zinc restored MT3 expression.

Conclusions/Significance

The most frequent molecular events associated with ependymoma recurrence were over-expression of kinetochore proteins and down-regulation of metallothioneins. Metallothionein-3 expression is epigenetically controlled and can be restored in vitro by histone deacetylase inhibitors.

Neuronal differentiation distinguishes supratentorial and infratentorial childhood ependymomas

Ependymomas are glial neoplasms occurring in any location throughout the central nervous system and supposedly are derived from radial glia cells. Recent data suggest that these tumors may have different biological and clinical behaviors according to their location. Pediatric supratentorial and infratentorial ependymoma (SE and IE) were compared with respect to clinical and radiological parameters and immunohistochemistry (IHC). Neuronal markers were specifically assessed by IHC and quantitative PCR (qPCR). No single morphological or radiological characteristic was associated with location or any neuronal marker. However, there was a significant overexpression of neuronal markers in SE compared with IE: neurofilament light polypeptide 70 (NEFL)-positive tumor cells were found in 23 of 34 SE and in only 4 of 32 IE (P < .001). Among SE, 10 of 34 exhibited high expression of NEFL, defined as more than 5% positive cells. qPCR confirmed the upregulation of neuronal markers (NEFL, LHX2, FOXG1, TLX1, and NPTXR) in SE compared with IE. In addition, strong NEFL expression in SE was correlated with better progression-free survival (P = .007). Our results support the distinction of SE and IE. SEs are characterized by neuronal differentiation, which seems to be associated with better prognosis.

Abstract A193: From MT3 modulation to HDACi treatment in ependymomas

Ependymoma, the third most common brain tumor in the paediatric population, presents limited treatment options, especially in the case of local relapse. Aiming to understand tumor progression, we performed a microarray analysis over 27 relapses of ependymomas using their own samples at diagnosis as a control. Consistent down regulation of metallothionein 3 was found in 87% of relapses. MT3 is mostly expressed in the brain. This protein inhibits growth in a variety of cell types; a characteristic not shared by the others members of the MT family. To investigate the involvement of epigenetic factors in MT3 silencing, methylation of CpG islands were analyzed by DNA bisulfite treatment followed by MT3 promoter sequencing. There were no hypermethylated regions over the sequence and the methylation pattern observed could not be correlated with gene expression level. Treatment of primary culture ependymoma cells with 5-Aza-2′-Deoxycytidine, a demethylating agent, failed to induce MT3 transcriptional reactivation, confirming the CpG islands results. On the other hand, a treatment with 300 nMTrichostatin A (TSA), a deacethylation agent, increased MT3 expression by 100 times. Deregulation in epigenetic control by histone modification is known being important in the development of some neoplasias suggesting HDAC inhibitors a new class of promising chemotherapeutic agents, that are currently evaluated in early clinical trials. MTS tests were performed using the HDAC inhibitor SAHA (vorinostat) and 5-Aza-2′-Deoxycytidine. NEM65 ependymoma primary cell culture, ependymoma cell lines Res196, Res253 and Res254; SF188 glioma cell line and DAOY meduloblastoma cells were treated for 72 hours with different concentrations of these agents in three independent experiments. The cell viability of Res196, Res253, Res254, SF188 and DAOY was significantly decreased by 3µM SAHA (30%, 38%, 41%, 20% and 38%, respectively), but NEM65 seemed to be resistant, about 80% of cell viability at 6µM. In contrast, treatment of these cells with 5-Aza-2′-Deoxycytidine proved no effect, neither in cell viability decrease nor in MT3 expression. Trying to understand the differences between sensible cell lines and the resistant NEM65 we performed gene expression analysis by Q-PCR after SAHA treatment. We analysed MT3, Bcl2, Bax and Caspase3 genes. Interestingly, SAHA increased MT3 expression level at least 100 times in the sensible cells, but only 3 times in the resistant NEM65. For the genes involved in apoptosis, we could not establish a coherent correlation between their expression level and cell death, only two cell lines presented Bcl2 down regulation (Res253 and SF188) and two (Res196 and DAOY) showed Bax over expression, so the mechanism of cell death deserves further investigation. For NEM65 we observed that apoptosis pathway was not activated: there was over expression of Bcl2 and under expression of Bax. It seems that the sensibility of SAHA treatment is dependant on MT3 expression and this new class of drugs may represent a potential new treatment for ependymoma.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):A193.

Pharmacokinetic and biological study of erlotinib in children as monotherapy for refractory brain tumors or with radiation for newly diagnosed brain stem gliomas

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Background: This multicenter phase I study was designed to determine the recommended dose (RD) of erlotinib, a small-molecule EGFR TKI, in patients ≤ 21 years as monotherapy or in combination with radiation therapy (RT). Methods: Group 1 included patients with brain tumors refractory to or relapsing after conventional therapy; receiving erlotinib alone. Group 2 included newly diagnosed patients with brain stem gliomas, who received RT (54Gy) and erlotinib. Conventional 3+3 dose escalation was used for Group 1; a continual reassessment method for Group 2. Four dose levels were planned: 75, 100, 125 and 150 mg/m2/day. Results: A total of 51 patients were enrolled (30 in Group 1; 21 in Group 2); 50 received treatment. Median age was 10 and 6 years, respectively. The RD of erlotinib was 125 mg/m2/day as monotherapy or in combination with RT. 203 adverse events in 44 patients were possibly treatment-related; 188 were G1/2; 9 G3, 2 G4, and 4 G5. Dermatologic and neurologic symptoms were most common; intratumoral hemorrhage was noted in 4 patients. In Group 1, 8 patients (27.6%) had stable disease, 2 with 45% tumor regression. In Group 2, 3 patients (14%) had partial response and 8 (38%) were stabilized; median OS was 12 months. Pharmacokinetic data of 46 patients were analyzed; patients’ weight and erlotinib clearance (CL) were significantly correlated. Mean (± SD) apparent CL and volume of distribution for erlotinib were 143.7 mL/h/kg (± 66.3) and 3.5 L/kg (± 3.0), respectively, and were independent of dose level. Mean half-life for erlotinib was 20.4 hours. Biomarker analyses on archived tumor or biopsy tissue prior to study entry for newly diagnosed brain stem glioma found 18/37 tumors tested were EGFR IHC+; 16/37 and 23/36 were pAKT+ and pMAPK+, respectively. High EGFR expression was more common in supratentorial gliomas; PTEN loss was most common in brain stem glioma (15/19) and was not observed in ependymomas. Conclusions: Erlotinib 125 mg/m2/day has an acceptable tolerability profile in pediatric patients with brain tumors, and can be safely combined with RT. Further studies are required to define the efficacy of this treatment approach and to establish the impact of biomarkers on outcomes in pediatric glial tumors.

No significant financial relationships to disclose.