Krzysztof Zakrzewski

Hotspot Mutations in H3F3A and IDH1 Define Distinct Epigenetic and Biological Subgroups of Glioblastoma

Glioblastoma (GBM) is a brain tumor that carries a dismal prognosis and displays considerable heterogeneity. We have recently identified recurrent H3F3A mutations affecting two critical amino acids (K27 and G34) of histone H3.3 in one-third of pediatric GBM. Here, we show that each H3F3A mutation defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and that they are mutually exclusive with IDH1 mutations, which characterize a third mutation-defined subgroup. Three further epigenetic subgroups were enriched for hallmark genetic events of adult GBM and/or established transcriptomic signatures. We also demonstrate that the two H3F3A mutations give rise to GBMs in separate anatomic compartments, with differential regulation of transcription factors OLIG1, OLIG2, and FOXG1, possibly reflecting different cellular origins.

Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR

Embryonal tumors with multilayered rosettes (ETMRs) are rare, deadly pediatric brain tumors characterized by high-level amplification of the microRNA cluster C19MC. We performed integrated genetic and epigenetic analyses of 12 ETMR samples and identified, in all cases, C19MC fusions to TTYH1 driving expression of the microRNAs. ETMR tumors, cell lines and xenografts showed a specific DNA methylation pattern distinct from those of other tumors and normal tissues. We detected extreme overexpression of a previously uncharacterized isoform of DNMT3B originating at an alternative promoter that is active only in the first weeks of neural tube development. Transcriptional and immunohistochemical analyses suggest that C19MC-dependent DNMT3B deregulation is mediated by RBL2, a known repressor of DNMT3B. Transfection with individual C19MC microRNAs resulted in DNMT3B upregulation and RBL2 downregulation in cultured cells. Our data suggest a potential oncogenic re-engagement of an early developmental program in ETMR via epigenetic alteration mediated by an embryonic, brain-specific DNMT3B isoform.

Arrested neural and advanced mesenchymal differentiation of glioblastoma cells-comparative study with neural progenitors

BackgroundAlthough features of variable differentiation in glioblastoma cell cultures have been reported, a comparative analysis of differentiation properties of normal neural GFAP positive progenitors, and those shown by glioblastoma cells, has not been performed.MethodsFollowing methods were used to compare glioblastoma cells and GFAP+NNP (NHA): exposure to neural differentiation medium, exposure to adipogenic and osteogenic medium, western blot analysis, immunocytochemistry, single cell assay, BrdU incorporation assay. To characterize glioblastoma cells EGFR amplification analysis, LOH/MSI analysis, and P53 nucleotide sequence analysis were performed.ResultsIn vitro differentiation of cancer cells derived from eight glioblastomas was compared with GFAP-positive normal neural progenitors (GFAP+NNP). Prior to exposure to differentiation medium, both types of cells showed similar multilineage phenotype (CD44+/MAP2+/GFAP+/Vimentin+/Beta III-tubulin+/Fibronectin+) and were positive for SOX-2 and Nestin. In contrast to GFAP+NNP, an efficient differentiation arrest was observed in all cell lines isolated from glioblastomas. Nevertheless, a subpopulation of cells isolated from four glioblastomas differentiated after serum-starvation with varying efficiency into derivatives indistinguishable from the neural derivatives of GFAP+NNP. Moreover, the cells derived from a majority of glioblastomas (7 out of 8), as well as GFAP+NNP, showed features of mesenchymal differentiation when exposed to medium with serum.ConclusionOur results showed that stable co-expression of multilineage markers by glioblastoma cells resulted from differentiation arrest. According to our data up to 95% of glioblastoma cells can present in vitro multilineage phenotype. The mesenchymal differentiation of glioblastoma cells is advanced and similar to mesenchymal differentiation of normal neural progenitors GFAP+NNP.

Neuroendoscopic techniques in the treatment of arachnoid cysts in children and comparison with other operative methods

Objective: The authors intended to evaluate the application of neuroendoscopic techniques for the treatment of arachnoid cysts in children and compare it with other operative methods. Methods: The analysis covered the results of treatment of 44 children with arachnoid cysts who were subjected to neuroendoscopic procedures and 62 patients who underwent other operations. Results: The neuroendoscopic treatment of arachnoid cysts was very effective because of low rate of reoperative treatment (six out of 44 patients), no need to change the operative method (40 effective out of total 44 operative procedures), and low rate of persistent worsening (none of 44 patients worsened). Conclusions: Summing up all the mentioned aspects of neuroendoscopic techniques, the neuroendoscopic techniques were the most suitable operative procedures in the treatment of arachnoid cysts in the presented group of patients, providing that the connection between the lumen of the arachnoid cyst and the cerebrospinal fluid cisterns was of good quality.

Molecular heterogeneity of meningioma with INI1 mutation

Background: INI1 (hSNF5) mutations are linked to rhabdoid tumours, but mutations in meningiomas with hot spot mutations in position 377 have also been reported. Aims: To analyse the INI1 gene in meningioma. Methods: Exons 1, 4, 5, and 9 of the INI1 gene were analysed by the polymerase chain reaction and direct sequencing in 80 meningiomas. For all cases, western blotting of the INI1 protein was performed. Results: Only one of the 80 samples showed a cytosine insertion in codon 376. This mutation changed the open reading frame in almost the whole exon 9 and resulted in a longer hSNF5 protein. Complex analysis of the above described tumour sample by western blotting, DNA sequencing, and loss of heterozygosity (LOH) analysis showed that this particular meningioma consisted of heterogeneic cellular components. One of these components had a mutated INI1 gene, whereas in the other component INI1 was intact. Conclusions: INI1 mutation is a rare event in the molecular pathology of meningiomas. It is possible for the INI1 gene to be mutated in only a proportion of meningioma cells.

Effectiveness of neuroendoscopic procedures in the treatment of complex compartmentalized hydrocephalus in children

ObjectiveThe main object of the work is to assess the suitability of neuroendoscopic techniques for the treatment of complex compartmentalized hydrocephalus.MethodsFor this purpose the authors compared two groups of children treated in the Research Institute of the Polish Mothers Memorial Hospital from March 1997 to January 2002. The first group of 47 children, treated using neuroendoscopic procedures, was compared with the second, which comprised 80 children treated conventionally by complicated shunt implantations.ResultsThe children treated neuroendoscopically needed on average 1.7660 procedures during the entire therapy, and 1.0232 operations a year. The same parameters in the conventionally-treated group were as follows: the total number of procedures was 7.050, and the rate of reoperation was 3.949 procedures a year. The proportion of patients who suffered from complications connected with operative treatment and who had a bad outcome was higher in the conventionally-treated group than in the neuroendoscopic one.

Primitive Neuroectodermal Tumors: Ultrastructural and Immunohistochemical Studies

We report here ultrastructural and immunohistochemical studies of neuroblastic differentiation in the retrospective (n = 17) and prospective (n = 26) series of primitive neuroectodermal tumors (PNETs). By electron microscopy, neuritelike structures containing parallel-oriented microtubules, adhesive plaque junctions, and pleomorphic dense-core vesicles were found in the majority of tumor specimens while synaptic specializations were very rare. By immunohistochemistry, synaptophysin appeared to be the most reliable marker for neuroblastic differentiation present in the most reliable marker for neuroblastic differentiation present in the majority of tumors, while 200 kDa neurofilament protein was immunovisualized in a lower proportion of tumors. Glial fibrillary acidic protein (GFAP) was expressed in both reactive astrocytes and in a small proportion of otherwise typical neoplastic cells. We conclude that the majority of PNETs revealed diverse differentiation and that electron microscopy is still the most reliable tool for its detection followed by immunohistochemistry for synaptophysin.

Cytogenetic Changes in Two Cases of Subependymal Giant-Cell Astrocytoma

Cytogenetic analysis of subependymal giant-cell astrocytomas (SEGAs) from two patients presenting the clinical symptoms of tuberous sclerosis complex (TSC) revealed clonal chromosomal changes, resulting in the partial loss of chromosome 22q in both tumors. Immunohistochemically, tumors exhibited features of glial differentiation, while ultrastructural studies identified the characteristic paracrystalline inclusions within the tumor cells. To our knowledge, it is the first cytogenetic description of SEGAs associated with TSC.

Prevalence of mutated TP53 on cDNA (but not on DNA template) in pleomorphic xanthoastrocytoma with positive TP53 immunohistochemistry

Pleomorphic xanthoastrocytoma (PXA) is a tumor of astrocytic lineage that may have anaplastic features; such a phenotype usually correlates with a less favorable outcome. The molecular profile of PXA differs from other astrocytic tumors, but the molecular mechanisms of its formation and progression are still undefined. We analyzed a loss of heterozygosity and mutations of the SMARCB1 (also known as SNF5 or INI1) and TP53 genes in four cases of PXA. In just one case a TP53 mutation (Cys238Tyr) was readily detectable at the mRNA level, but it was almost undetectable during DNA sequencing. This case was also the only one exhibiting anaplastic features and TP53 overexpression as defined by immunohistochemistry. This observation supports our earlier findings on discrepancies in TP53 status in glioblastomas. We suggest that the incidence of TP53 mutations in pleomorphic xanthoastrocytoma may be underestimated and that molecular approaches should be used for greater diagnostic precision.

Altered MicroRNA Expression Is Associated with Tumor Grade, Molecular Background and Outcome in Childhood Infratentorial Ependymoma

Background Ependymal tumors are the third most common group of brain tumors in children, accounting for about 10% of all primary brain neoplasms. According to the current WHO classification, they comprise four entities with the most frequent ependymoma and anaplastic ependymoma. The most of pediatric tumors are located within the posterior fossa, with a tendency to infiltrate the vital brain structures. This limits surgical resection and poses a considerable clinical problem. Moreover, there are no appropriate outcome prognostic factors besides the extent of surgical resection. Despite definition of molecular subgroups, the majority of childhood ependymomas present a balanced genome, which makes it difficult to establish molecular prognostic factors. Methods The purpose of our study was to explore whether miRNA expression could be used as prognostic markers in pediatric infratentorial ependymomas. We also performed a mRNA expression pattern analysis of NELL2 and LAMA2 genes, with immunohistochemical illustrations of representative cases. The miRNA and mRNA expression was measured in 53 pediatric infratentorial ependymomas using a real-time quantitative PCR. Results Three miRNAs were shown to efficiently differentiate between grade II and III ependymomas: miR-17-5p, miR-19a-3p, and miR-106b-5p. Survival analysis showed that the probabilities of overall (p = 0.036) and event-free survival (p = 0.002) were reduced with higher than median miRNA expression levels of miR-17-5p. Using multivariate analysis adjusted for patients age, sex, tumor grade and localization, we showed statistically significant associations with event-free survival (p = 0004) and borderline statistical significance with overall survival (p = 0.057) for miR-17-5p. Correlation analysis of miR-19a, miR-17-5p, miR-106b revealed that their expression levels were significantly correlated with EZH2 expression, suggested marker of PFA ependymomas. Furthermore, lower expression level of LAMA2 mRNA was shown to be associated with an increased risk of death in covariate-adjusted analyses. Conclusions Our data provide a better understanding of pediatric ependymoma and suggests the presence of plausible molecular biomarkers connected with the outcome.