Marco Gessi

Subgroup-Specific Prognostic Implications of TP53 Mutation in Medulloblastoma

PURPOSE Reports detailing the prognostic impact of TP53 mutations in medulloblastoma offer conflicting conclusions. We resolve this issue through the inclusion of molecular subgroup profiles. PATIENTS AND METHODS We determined subgroup affiliation, TP53 mutation status, and clinical outcome in a discovery cohort of 397 medulloblastomas. We subsequently validated our results on an independent cohort of 156 medulloblastomas. RESULTS TP53 mutations are enriched in wingless (WNT; 16%) and sonic hedgehog (SHH; 21%) medulloblastomas and are virtually absent in subgroups 3 and 4 tumors (P < .001). Patients with SHH/TP53 mutant tumors are almost exclusively between ages 5 and 18 years, dramatically different from the general SHH distribution (P < .001). Children with SHH/TP53 mutant tumors harbor 56% germline TP53 mutations, which are not observed in children with WNT/TP53 mutant tumors. Five-year overall survival (OS; ± SE) was 41% ± 9% and 81% ± 5% for patients with SHH medulloblastomas with and without TP53 mutations, respectively (P < .001). Furthermore, TP53 mutations accounted for 72% of deaths in children older than 5 years with SHH medulloblastomas. In contrast, 5-year OS rates were 90% ± 9% and 97% ± 3% for patients with WNT tumors with and without TP53 mutations (P = .21). Multivariate analysis revealed that TP53 status was the most important risk factor for SHH medulloblastoma. Survival rates in the validation cohort mimicked the discovery results, revealing that poor survival of TP53 mutations is restricted to patients with SHH medulloblastomas (P = .012) and not WNT tumors. CONCLUSION Subgroup-specific analysis reconciles prior conflicting publications and confirms that TP53 mutations are enriched among SHH medulloblastomas, in which they portend poor outcome and account for a large proportion of treatment failures in these patients.

Embryonal tumor with abundant neuropil and true rosettes (ETANTR), ependymoblastoma, and medulloepithelioma share molecular similarity and comprise a single clinicopathological entity

Three histological variants are known within the family of embryonal rosette-forming neuroepithelial brain tumors. These include embryonal tumor with abundant neuropil and true rosettes (ETANTR), ependymoblastoma (EBL), and medulloepithelioma (MEPL). In this study, we performed a comprehensive clinical, pathological, and molecular analysis of 97 cases of these rare brain neoplasms, including genome-wide DNA methylation and copy number profiling of 41 tumors. We identified uniform molecular signatures in all tumors irrespective of histological patterns, indicating that ETANTR, EBL, and MEPL comprise a single biological entity. As such, future WHO classification schemes should consider lumping these variants into a single diagnostic category, such as embryonal tumor with multilayered rosettes (ETMR). We recommend combined LIN28A immunohistochemistry and FISH analysis of the 19q13.42 locus for molecular diagnosis of this tumor category. Recognition of this distinct pediatric brain tumor entity based on the fact that the three histological variants are molecularly and clinically uniform will help to distinguish ETMR from other embryonal CNS tumors and to better understand the biology of these highly aggressive and therapy-resistant pediatric CNS malignancies, possibly leading to alternate treatment strategies.

Nuclear Exclusion of TET1 Is Associated with Loss of 5-Hydroxymethylcytosine in IDH1 Wild-Type Gliomas

The recent identification of isocitrate dehydrogenase 1 (IDH1) gene mutations in gliomas stimulated various studies to explore the molecular consequences and the clinical implications of such alterations. The Cancer Genome Atlas Research Network showed evidence for a CpG island methylator phenotype in glioblastomas that was associated with IDH1 mutations. These alterations were associated with the production of the oncometabolite, 2-hydroxyglutarate, that inhibits oxygenases [ie, ten-eleven translocation (TET) enzymes involved in the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC)]. We investigated 60 gliomas for 5hmC presence, 5-methylcytosine content, TET1 expression, and IDH1 mutation to gain insight into their relationships on a histological level. Of gliomas, 61% revealed no immunoreactivity for 5hmC, and no correlation was observed between IDH1 mutations and loss of 5hmC. Interestingly, expression of TET1 showed remarkable differences regarding overall protein levels and subcellular localization. We found a highly significant (P = 0.0007) correlation between IDH1 mutations and nuclear accumulation of TET1, but not with loss of 5hmC. Of 5hmC-negative gliomas, 70% showed either exclusive or dominant cytoplasmic expression, or no detectable TET1 protein (P = 0.0122). Our data suggest that the loss of 5hmC is a frequent event in gliomas, independent of IDH1 mutation, and may be influenced by the nuclear exclusion of TET1 from the nuclei of glioma cells.

H3F3A K27M mutation in pediatric CNS tumors: a marker for diffuse high-grade astrocytomas.

Brain tumors are one of the most common childhood malignancies. Diffuse high-grade gliomas represent approximately 10% of pediatric brain tumors. Exon sequencing has identified a mutation in K27M of the histone H3.3 gene (H3F3A K27M and G34R/V) in about 20% of pediatric glioblastomas, but it remains to be seen whether these mutations can be considered specific for pediatric diffuse high-grade astrocytomas or also occur in other pediatric brain tumors. We performed a pyrosequencing-based analysis for the identification of H3F3A codon 27 and codon 34 mutations in 338 pediatric brain tumors. The K27M mutation occurred in 35 of 129 glioblastomas (27.1%) and in 5 of 28 (17.9%) anaplastic astrocytomas. None of the other tumor entities showed H3F3A K27M mutation. Because H3F3A K27M mutations occur exclusively in pediatric diffuse high-grade astrocytomas, analysis of codon 27 mutational status could be useful in the differential diagnosis of these neoplasms.

TERT promoter mutations: a novel independent prognostic factor in primary glioblastomas.

BACKGROUND Activating somatic mutations in the promoter region of the telomerase reverse transcriptase gene (TERT) have been detected in several cancers. In this study we investigated the TERT promoter mutations and their impact on patient survival in World Health Organization grade IV glioblastoma multiforme (GBM). METHODS The TERT core promoter region containing the previously described mutations and a common functional polymorphism (rs2853669) was sequenced in tumors and blood samples from 192 GBM patients. O(6)-methylguanine-DNA methyltransferase (MGMT) promoter methylation status was assessed by pyrosequencing in 177 (92.2%) cases. Relevant clinical data were obtained from a prospectively maintained electronic database. RESULTS We detected specific (-124 C>T and -146 C>T) TERT promoter mutations in 143/178 (80.3%) primary GBM and 4/14 (28.6%) secondary GBM (P < .001). The presence of TERT mutations was associated with poor overall survival, and the effect was confined to the patients who did not carry the variant G-allele for the rs2853669 polymorphism. An exploratory analysis suggested that TERT mutations might be prognostic only in patients who had incomplete resections and no temozolomide chemotherapy. CONCLUSIONS In this study, specific TERT promoter mutations were markers of primary GBM and predicted patient survival in conjunction with a common functional polymorphism. The prognostic impact of TERT mutations was absent in patients with complete resections and temozolomide chemotherapy. If confirmed in additional studies, these findings may have clinical implications, that is, TERT mutations appear to characterize tumors that require aggressive treatment.

High frequency of H3F3A K27M mutations characterizes pediatric and adult high-grade gliomas of the spinal cord

We identified 16 HGG (11 glioblastomas, 3 anaplastic astrocytomas and 2 anaplastic gangliogliomas, 16/30, 53 %) and 1 diffuse astrocytoma harboring H3F3A mutations (Fig. 1a–e). The frequency of mutations among HGG affecting adults and children was similar (52 vs. 54 %). The mean age of adult patients with mutated tumors was lower (34 years) than that observed in patients with wild-type tumors (53 years) (Fig. 1f). All tumors affecting infants were H3F3A wild type. The distributions of mutated and wild-type HGG along the spinal cord appeared similar, but in cervical spine HGG were more frequently mutated (Fig. 1g). Neither H3F3A wild-type HGG nor DA showed immunoreactivity for mutant IDH1 protein (not shown). Histones are nuclear proteins which regulate DNA replication and transcription by modifying the nucleosome structure [9]. H3.3 histone proteins, encoded by H3.3A (H3F3A) and H3.3B, are deposited on chromatin in a replication-independent manner and are enriched at actively transcribed genes and heterochromatic regions [9]. H3F3A mutations occur in a hotspot region (K27 and G34) undergoing posttranslational modifications. Similar to IDH1 mutated gliomas in adults, reduced H3.3K27 trimethylation and deregulated DNA methylation are considered to play a major role in pediatric gliomagenesis [2]. Recently, several groups have highlighted the high frequency of H3F3A mutations in pediatric midline HGG as well as in DIPG [2, 3, 7, 8]. These mutations are not limited to pediatric patients, but can occur, although more rarely, in adults. H3F3A mutations were frequently observed in thalamic HGG affecting young adults [1] and adult DIPG, but rare in supratentorial adult HGG [6]. Notably, the patient’s age did not affect the pattern of methylation in H3F3A mutant tumors [1]. Diffuse high-grade gliomas (HGG) in the spinal cord are rare [5]. It is still undetermined whether they could share genetic alterations with their supratentorial counterparts: in particular, because the spinal cord has to be considered a midline structure, a high incidence of H3F3A mutations could be hypothesized, as reported in diffuse pontine gliomas (DIPG) and in pediatric midline HGG [1–3, 6–8]. In this study, we investigated the H3F3A status of 30 primary spinal HGG affecting pediatric and adult patients. Formalin-fixed paraffin-embedded specimens of 36 primary spinal diffusely infiltrating gliomas, including 30 HGG (18 glioblastomas, WHO IV; 10 anaplastic astrocytomas, WHO III; 2 anaplastic gangliogliomas, WHO III) and 6 diffuse astrocytomas (WHO II) [5] were retrieved from the archives of the Institute of Neuropathology, University of Bonn medical Center and of the DGNN Brain Tumor Reference Center, Bonn, Germany. No brainstem HGG were included. The clinical features are summarized in supplementary Table 1. The H3F3A status was evaluated by immunohistochemistry and/or by pyrosequencing, as described previously [4]. Antibodies against mutant H3.3K27M (Millipore, Temecula, USA), methylated H3.3K27me3 protein (Cell Signaling, Danvers, USA) as well as mutant IDH1 protein (Dianova, Hamburg, Germany) were used.

FGFR1 mutations in Rosette-forming glioneuronal tumors of the fourth ventricle.

Rosette-forming glioneuronal tumors (RGNTs) are rare glioneuronal tumors of the fourth ventricle region that preferentially affect young adults. Despite their histologic similarity with pilocytic astrocytomas (PAs), RGNTs do not harbor KIAA1549-BRAF fusions or BRAF mutations, which represent the most common genetic alteration in PAs. Recently, mutations affecting the hotspot codons Asn546 and Lys656 of fibroblast growth factor receptor 1 (FGFR1) have been described in PAs. They are considered to be the most frequent mechanism of mitogen-activated protein kinase activation, alternative to KIAA1549-BRAF fusion and BRAF mutations. To uncover possible molecular similarities between RGNTs and PAs, we performed a mutational study of FGFR1 in 8 RGNTs. An FGFR1 N546K mutation and an FGFR1 K656E mutation were found in the tumors of 2 patients. Notably, the patient with an FGFR1 K656E mutated RGNT had undergone a resection of a diencephalic pilocytic astrocytoma with pilomyxoid features 5 years before the discovery of the fourth ventricle tumor; the mutational analysis uncovered the presence of the same FGFR1 K656E mutation in the diencephalic tumor. These results indicate that, in addition to histologic similarities, at least a subgroup of RGNTs may show close molecular relationships with PAs. Whether FGFR1 mutated RGNTs represent a specific subset of this rare tumor entity remains to be determined.

Evidence of H3 K27M mutations in posterior fossa ependymomas.

be excluded a priori. We report here the very unexpected finding of H3K27M mutations in two Group A posterior fossa ependymomas (PF-EPN-A), an aggressive subgroup of tumors with relatively stable genomes and no well-characterized oncogenic driving event [9, 10]. The first patient was a 1.5 year-old female. MRI scans revealed a large tumor in the posterior fossa, highly suggestive of an ependymoma (Suppl. Fig. 1a–c). To avoid the high risk of severe morbidity associated with gross total resection (GTR), a biopsy was performed. Neuropathological analysis showed an anaplastic ependymoma (WHO grade III) (Fig. 1a–d). Next-generation sequencing (NGS) of a custom gene panel [12] from the tumor tissue performed within the German Molecular Neuropathology 2.0 study (http://pediatric-neurooncology.dkfz.de/index. php/en/diagnostics/molecular-neuropathology) detected an H3F3A K27M mutation (not shown). The presence Histone 3 (H3) K27M mutations are considered to be a genetic hallmark of diffuse midline gliomas, including high-grade astrocytomas and diffuse intrinsic pontine gliomas (DIPG) [3]. Similar to IDH-mutated gliomas in adults, these mutations are associated with alterations in the epigenetic profile of tumor cells, and are thought to represent a main driving factor in gliomagenesis [2, 8]. In diffuse midline gliomas, H3K27M mutations have been demonstrated to induce de–repression of pro-oncogenic transcription factors by global reduction of histone 3 K27 trimethylation (H3K27me3) [2, 8]. Reportedly, H3K27M mutations are exceedingly rare in tumors other than in diffuse midline gliomas [6, 7, 14]. The possibility of an H3K27M mutation occurring in other brain neoplasms cannot, however,

Absence of KIAA1549-BRAF fusion in rosette-forming glioneuronal tumors of the fourth ventricle (RGNT)

Rosette-forming glioneuronal tumors (RGNT) of the fourth ventricle are rare mixed glioneuronal tumors included in the revised WHO classification of central nervous system tumors, showing partial histological similarities to pilocytic astrocytomas. To evaluate potential similarities at the molecular level between these tumors, we analysed a series of 10 RGNT for the presence of KIAA1549-BRAF fusions using interphase fluorescence in situ hybridisation. However, we found no cases showing KIAA1549-BRAF gene fusion or BRAFV600E mutation. Our data support the hypothesis that RGNT may represent a distinct entity among the glioneuronal tumors of the central nervous system, with molecular features different from pilocytic astrocytomas.

Analysis of KIAA1549-BRAF fusion status in a case of rosette-forming glioneuronal tumor of the fourth ventricle (RGNT)

Rosette‐forming glioneuronal tumors (RGNT) of the fourth ventricle are rare mixed glio‐neuronal tumors included in the revised WHO classification of CNS tumors and show histopathological features similar to pilocytic astrocytomas. To evaluate at molecular level potential affinities between these tumors, we investigated a case of RGNT, arising in the cerebellum of a young patient, for the presence of transcriptional products originating from the KIAA1549‐BRAF fusion. However, the analysis did not show any fusion. Further studies in larger RGNT case series are needed in order to demonstrate the possible presence of KIAA1549‐BRAF fusion and better delineate its relationship with pilocytic astrocytomas.