Abstract B71: Molecular heterogeneity and novel oncogenic fusions in RELA- and YAP1-negative supratentorial ependymoma

Introduction: One of the DNA methylation-based molecular subgroups of supratentorial ependymoma (ST-EPN), designated ST-EPN-RELA, mostly harbors fusions of the uncharacterized gene C11orf95 and RELA (ST-EPN-RELA). Rarely, no C11orf95-RELA fusion is detected in tumors predicted to belong to the ST-EPN-RELA group. With this study we aimed to refine the molecular classification of ST-EPN and to identify alternative oncogenic mechanisms in the absence of a classic fusion type.

Methods and Materials: In an unbiased approach, t-Distributed Stochastic Neighbor Embedding was applied to 53,468 DNA methylation profiles from brain tumors, other cancer types, and control tissues. Only samples clustering with a reference set of ST-EPN-RELA were selected for further analyses (n=614), including RNA- and/or DNA-panel sequencing, histopathologic reevaluation, and immunohistochemistry for L1CAM. Fusions were validated using RT-PCR on total RNA and Sanger sequencing. Clinical data were analyzed retrospectively for 150 patients.

Results: We identified one large and four satellite clusters. The large cluster (n=479; designated ST-EPN-RELA 1) and one of the satellite clusters (n=12; ST-EPN-RELA 2) predominantly contained samples with a calibrated score ≥ 0.9 for ST-EPN-RELA based on the current version of the Heidelberg Brain Tumor Classifier. Samples of the three other satellite clusters (n=41, n=17, and n=25 samples) contained 65.9%, 88.2%, and 96.0% of samples with a calibrated score < 0.9 for any methylation class, and were thus predicted as unclassifiable. These clusters were provisionally designated ST-EPN-RELA-like A, B, and C, and initial histologic diagnoses showed a wide spectrum of rare morphologies beside EPN, e.g., sarcoma and teratoma. Within clusters ST-EPN-RELA-like A and C, sequencing revealed fusions of C11orf95 with different partner genes, including MAML2 (n=14), MAML3 (n=2), and NCOA2 (n=7), while ST-EPN-RELA-like B included classic C11orf95-RELA fusions (n=11) in samples with initial diagnoses other than EPN. Copy number variation analysis showed clear differences between the clusters. L1CAM-positivity was observed in all groups. Within the cluster ST-EPN-RELA 1, samples separated according to fusion types, 1 versus 2/3. Analysis of clinical data showed significant differences in overall survival between cases with confirmed C11orf95-RELA fusion type 1 (n=25, median OS=88 months) and type 2/3 (n=20, median OS=67 months). Clinical data collection for the satellite clusters is currently ongoing.

Conclusion: Molecular refinement of ST-EPN-RELA revealed novel subgroups harboring fusions of C11orf95 with numerous fusion partners different from RELA, which will be included in the next update of the Heidelberg Classifier. Preliminary analysis suggests differences in clinical outcome related to the fusion type. Findings of this study will improve diagnostic accuracy and clinical management and need to be considered when developing targeted treatment strategies against ST-EPN.

Citation Format: D.R. Ghasemi, K. Okonechnikov, A. Korshunov, M. Sill, T. Zheng, J.M. Huebner, K.K. Maass, J. Benzel, M. Snuderl, J. Gojo, U. Schüller, N.U. Gerber, I. Stoler, P. Hernáiz-Driever, T. Milde, D. Sturm, R. Chapman, R.G. Grundy, A. von Deimling, D. Kawauchi, D.T.W. Jones, M. Kool, S.M. Pfister, F. Sahm, K.W. Pajtler. Molecular heterogeneity and novel oncogenic fusions in RELA- and YAP1-negative supratentorial ependymoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B71.

Diffuse glioneuronal tumour with oligodendroglioma-like features and nuclear clusters (DGONC) - a molecularly defined glioneuronal CNS tumour class displaying recurrent monosomy 14

AIMS

DNA methylation-based central nervous system (CNS) tumour classification has identified numerous molecularly distinct tumour types, and clinically relevant subgroups among known CNS tumour entities that were previously thought to represent homogeneous diseases. Our study aimed at characterizing a novel, molecularly defined variant of glioneuronal CNS tumour.

PATIENTS AND METHODS

DNA methylation profiling was performed using the Infinium MethylationEPIC or 450 k BeadChip arrays (Illumina) and analysed using the 'conumee' package in R computing environment. Additional gene panel sequencing was also performed. Tumour samples were collected at the German Cancer Research Centre (DKFZ) and provided by multinational collaborators. Histological sections were also collected and independently reviewed.

RESULTS

Genome-wide DNA methylation data from >25 000 CNS tumours were screened for clusters separated from established DNA methylation classes, revealing a novel group comprising 31 tumours, mainly found in paediatric patients. This DNA methylation-defined variant of low-grade CNS tumours with glioneuronal differentiation displays recurrent monosomy 14, nuclear clusters within a morphology that is otherwise reminiscent of oligodendroglioma and other established entities with clear cell histology, and a lack of genetic alterations commonly observed in other (paediatric) glioneuronal entities.

CONCLUSIONS

DNA methylation-based tumour classification is an objective method of assessing tumour origins, which may aid in diagnosis, especially for atypical cases. With increasing sample size, methylation analysis allows for the identification of rare, putative new tumour entities, which are currently not recognized by the WHO classification. Our study revealed the existence of a DNA methylation-defined class of low-grade glioneuronal tumours with recurrent monosomy 14, oligodendroglioma-like features and nuclear clusters.

PDCT-08. SUPERIOR OUTCOME FOR BRAF V600E PEDIATRIC GLIOMAS TREATED WITH TARGETED BRAF INHIBITION

BACKGROUND

Children with pediatric low grade glioma’s (PLGG) harboring BRAF V600E mutation have poor outcome due to relative resistance to chemo-radiation and higher risk of malignant transformation. However, the role of targeted BRAF inhibition in these tumors is poorly defined.

METHODS

We assembled an international cohort of children with BRAF V600E mutant gliomas treated with BRAF inhibition, from 29 centers participating in the PLGG taskforce, and collected response, survival and molecular parameters.

RESULTS

Sixty-seven patients were treated with BRAFi (56 PLGG and 11 high grade gliomas) for a median time of 17.4 months (6 – 61 months), with 13 PLGG treated upfront. Objective responses was observed in 80% of PLGG patients compared to 28% with conventional chemotherapy (p< 0.001). Rapid responses were observed in most PLGG patients (median of 4 months), sustained in 86% of tumors up to 5 years while on therapy. In contrast, only 36% of PHGG responded to BRAFi with all but one tumor progressing within 18 months. Seventeen patients with PLGG discontinued BRAFi and 76.5% (13/17) progressed rapidly after discontinuation (median time 2.3 months). However, upon re-challenge with BRAFi therapy, 90% achieved an objective response. Poor prognostic factors to conventional therapies such as concomitant homozygous deletion of CDKN2A or H3K27M mutation were not associated with lack of response to BRAFi. Overall these responses translated to 2-year progression-free survival of 0.636 (95%CI 0.505–0.802) and 0.43 (95% CI 0.32–0.57) for BRAFi and chemotherapy treated BRAF V600E PLGG respectively (p=0.003).

CONCLUSION

The use of BRAFi results in objective, robust and durable responses in BRAF V600E PLGG and is associated with favorable survival. Larger prospective studies will be required to determine appropriate regiments, and long-term functional outcomes with BRAFi therapy in childhood gliomas.

Genomic profiling of Acute lymphoblastic leukemia in ataxia telangiectasia patients reveals tight link between ATM mutations and chromothripsis

Recent developments in sequencing technologies led to the discovery of a novel form of genomic instability, termed chromothripsis. This catastrophic genomic event, involved in tumorigenesis, is characterized by tens to hundreds of simultaneously acquired locally clustered rearrangements on one chromosome. We hypothesized that leukemias developing in individuals with Ataxia Telangiectasia, who are born with two mutated copies of the ATM gene, an essential guardian of genome stability, would show a higher prevalence of chromothripsis due to the associated defect in DNA double-strand break repair. Using whole-genome sequencing, fluorescence in situ hybridization and RNA sequencing, we characterized the genomic landscape of Acute Lymphoblastic Leukemia (ALL) arising in patients with Ataxia Telangiectasia. We detected a high frequency of chromothriptic events in these tumors, specifically on acrocentric chromosomes, as compared with tumors from individuals with other types of DNA repair syndromes (27 cases total, 10 with Ataxia Telangiectasia). Our data suggest that the genomic landscape of Ataxia Telangiectasia ALL is clearly distinct from that of sporadic ALL. Mechanistically, short telomeres and compromised DNA damage response in cells of Ataxia Telangiectasia patients may be linked with frequent chromothripsis. Furthermore, we show that ATM loss is associated with increased chromothripsis prevalence in additional tumor entities.

Primary somatosensory contextual modulation is encoded by oscillation frequency change

OBJECTIVE

This study characterized thalamo-cortical communication by assessing the effect of context-dependent modulation on the very early somatosensory evoked high-frequency oscillations (HF oscillations).

METHODS

We applied electrical stimuli to the median nerve together with an auditory oddball paradigm, presenting standard and deviant target tones representing differential cognitive contexts to the constantly repeated electrical stimulation. Median nerve stimulation without auditory stimulation served as unimodal control.

RESULTS

A model consisting of one subcortical (near thalamus) and two cortical (Brodmann areas 1 and 3b) dipolar sources explained the measured HF oscillations. Both at subcortical and the cortical levels HF oscillations were significantly smaller during bimodal (somatosensory plus auditory) than unimodal (somatosensory only) stimulation. A delay differential equation model was developed to investigate interactions within the 3-node thalamo-cortical network. Importantly, a significant change in the eigenfrequency of Brodmann area 3b was related to the context-dependent modulation, while there was no change in the network coupling.

CONCLUSION

This model strongly suggests cortico-thalamic feedback from both cortical Brodmann areas 1 and 3b to the thalamus. With the 3-node network model, thalamo-cortical feedback could be described.

SIGNIFICANCE

Frequency encoding plays an important role in contextual modulation in the somatosensory thalamo-cortical network.

Towards the time varying estimation of complex brain connectivity networks by means of a General Linear Kalman Filter approach

One of the main limitations of the brain functional connectivity estimation methods based on Autoregressive Modeling, like the Granger Causality family of estimators, is the hypothesis that only stationary signals can be included in the estimation process. This hypothesis precludes the analysis of transients which often contain important information about the neural processes of interest. On the other hand, previous techniques developed for overcoming this limitation are affected by problems linked to the dimension of the multivariate autoregressive model (MVAR), which prevents from analysing complex networks like those at the basis of most cognitive functions in the brain. The General Linear Kalman Filter (GLKF) approach to the estimation of adaptive MVARs was recently introduced to deal with a high number of time series (up to 60) in a full multivariate analysis. In this work we evaluated the performances of this new method in terms of estimation quality and adaptation speed, by means of a simulation study in which specific factors of interest were systematically varied in the signal generation to investigate their effect on the method performances. The method was then applied to high density EEG data related to an imaginative task. The results confirmed the possibility to use this approach to study complex connectivity networks in a full multivariate and adaptive fashion, thus opening the way to an effective estimation of complex brain connectivity networks.

Phase I/II intra-patient dose escalation study of vorinostat in children with relapsed solid tumor, lymphoma or leukemia

Members of the histone deacetylase (HDAC) family exhibit great promise as potential drug targets in pediatric tumors including neuroblastoma, medulloblastoma, ependymoma and Ewing's sarcoma. HDAC inhibitors of various structural classes have shown anti-tumoral effects in pre-clinical pediatric tumor models as single agents or in combination treatments. Suberoylanilidehydroxamic acid (SAHA=vorinostat) is the most clinical advanced compound of the class and was approved by the US FDA in October 2006 for the treatment of refractory cutaneous T-cell lymphoma. In this phase I/II trial, pediatric patients with relapsed solid tumors, lymphoma or leukemias are treated according to an individualized dose escalation concept ensuring each individual patient to receive his optimal dose with respect to toxicity and efficacy. The study is accompanied by an extensive pharmacokinetic, pharmacodynamic and biomarker program.

Time-variant partial directed coherence in analysis of the cardiovascular system. A methodological study

Time-variant partial directed coherence (tvPDC) is used for the first time in a multivariate analysis of heart rate variability (HRV), respiratory movements (RMs) and (systolic) arterial blood pressure. It is shown that respiration-related HRV components which also occur at other frequencies besides the RM frequency (= respiratory sinus arrhythmia, RSA) can be identified. These additional components are known to be an effect of the 'half-the-mean-heart-rate-dilemma' ('cardiac aliasing' CA). These CA components may contaminate the entire frequency range of HRV and can lead to misinterpretation of the RSA analysis. TvPDC analysis of simulated and clinical data (full-term neonates and sedated patients) reveals these contamination effects and, in addition, the respiration-related CA components can be separated from the RSA component and the Traube-Hering-Mayer wave. It can be concluded that tvPDC can be beneficially applied to avoid misinterpretations in HRV analyses as well as to quantify partial correlative interaction properties between RM and RSA.

Targeting histone deacetylases in neuroblastoma

Histone deacetylases (HDACs) are an emerging class of novel anti-cancer drug targets. Recently, studies in adult cancers and in neuroblastoma have shown that individual HDAC family members are aberrantly expressed in tumors and correlate with disease stage and prognosis. In neuroblastoma, knockdown of individual HDAC family members causes distinct phenotypes ranging from differentiation to apoptosis. HDACs are involved in controlling MYCN function and are upregulated in chemotherapy-resistant neuroblastoma cells. Treatment with unselective pan-HDAC inhibitors causes cell cycle arrest, differentiation, apoptosis, and inhibition of clonogenic growth of neuroblastoma cells, and restores susceptibility to chemotherapy treatment. The molecular mechanisms mediating the anti-cancer effects of HDAC inhibitors on neuroblastoma cells are incompletely understood and involve targeting of aberrant epigenetic repression of tumor suppressor genes, activation of developmental differentiation pathways, as well as changing the acetylation level and function of non-histone proteins. In neuroblastoma mouse models, unselective HDAC inhibitors demonstrate anti-tumoral effects. First phase I clinical trials in children with refractory cancers using HDAC inhibitors depsipeptide and the recently approved vorinostat are underway. This review summarizes our current knowledge about classical HDAC family members as novel drug targets for neuroblastoma therapy and discusses the potential role of next generation, selective HDAC inhibitors.

[Evaluation of results after arthroscopic reconstruction of the anterior cruciate ligament with a free graft of the patellar ligament]

From among 312 patients treated with arthroscopic anterior cruciate ligament reconstruction (one-incision, transtibial with the use of ipsilateral bone-patellar tendon-bone autograft) between 1992 and 1994 256 (82%) were reviewed with a mean follow-up of 26.4 months. An aggressive rehabilitative protocol advocated by Shelbourne has been employed. Stability of the knee has been assessed with KT-1000 arthrometer and IKDC and OAK forms served to evaluate the results. In 77% of the cases nearly normal function of the knee has been restored (87% excellent and good results in OAK form). Arthroscopic technique and aggressive rehabilitation decreased the number of patients with peripatellar pain and improved patient's acceptance of the management. Competitive athletes seem to achieve best end-results.