BRAF inhibitors in BRAF-V600 mutated primary neuroepithelial brain tumors

INTRODUCTION

Primary neuroepithelial brain tumors encompass a wide variety of glial and glioneuronal neoplasms. Malignant tumors, tumors located in surgically inaccessible locations (e.g., eloquent brain areas, deep structures, brain stem) and recurrent or progressive tumors pose considerable treatment challenges and are candidates for novel therapeutics based on molecular insights. Small kinase inhibitors of v-RAF murine sarcoma viral oncogene homologue B1 (BRAF) have shown considerable antineoplastic activity in some tumor types harboring activating BRAF-V600 mutations (e.g., melanoma) and promising data are emerging on BRAF inhibitor therapy of mutation-bearing primary brain tumors.

AREAS COVERED

This review summarizes the available data on BRAF-V600 point mutations and the antineoplastic activity and toxicity profiles of BRAF inhibitors in neuroepithelial brain tumors including diffuse gliomas (glioblastomas, astrocytomas, oligodendrogliomas), pilocytic astrocytomas, pleomorphic xanthoastrocytomas and gangliogliomas.

EXPERT OPINION

Activating BRAF-V600 mutations are recurrently found in several glial and glioneuronal brain tumors and the available data indicate that BRAF inhibitors are active and well-tolerated in such tumors. Thus, BRAF inhibitors represent a novel and promising therapeutic opportunity that may alter the disease course of molecularly selected CNS neoplasms in a clinically meaningful way. However, so far the evidence is anecdotal and prospective clinical studies should be conducted.

Clinical Neuropathology practice guide 5-2015: MGMT methylation pyrosequencing in glioblastoma: unresolved issues and open questions

O6-methylguanine-methyltransferase (MGMT) promoter methylation status has prognostic and, in the subpopulation of elderly patients, predictive value in newly diagnosed glioblastoma. Therefore, knowledge of the MGMT promoter methylation status is important for clinical decision-making. So far, MGMT testing has been limited by the lack of a robust test with sufficiently high analytical performance. Recently, one of several available pyrosequencing protocols has been shown to be an accurate and robust method for MGMT testing in an intra- and interlaboratory ring trial. However, some uncertainties remain with regard to methodological issues, cut-off definitions, and optimal use in the clinical setting. In this article, we highlight and discuss several of these open questions. The main unresolved issues are the definition of the most relevant CpG sites to analyze for clinical purposes and the determination of a cut-off value for dichotomization of quantitative MGMT pyrosequencing results into "MGMT methylated" and "MGMT unmethylated" patient subgroups as a basis for further treatment decisions.

PIN3 duplication may be partially responsible for TP53 haploinsufficiency

BACKGROUND

Previously we have suggested that cancer cells develop a mechanism(s) which allows for either: silencing of the wild-type TP53 transcription, degradation of the wild-type TP53 mRNA, or selective overproduction of the mutated TP53 mRNA, which is the subject of this article. Sequencing of TP53 on the respective cDNA and DNA templates from tumor samples were found to give discordant results. DNA analysis showed a pattern of heterozygous mutations, whereas the analysis of cDNA demonstrated the mutated template only. We hypothesized that different TP53 gene expression levels of each allele may be caused by the polymorphism within intron 3 (PIN3). The aim of this study was to test if one of the polymorphic variants of PIN3 (A1 or A2) in the heterozygotes is associated with a higher TP53 expression, and therefore, responsible for the haploinsufficiency phenomenon.

METHODS

250 tumor samples were tested. To analyze the involvement of PIN3 polymorphic variant (A1 or A2) on TP53 mRNA expression regulation, bacterial subcloning combined with sequencing analyses, dual luciferase reporter assays and bioinformatic analysis were performed.

RESULTS

Haplotype analysis showed the predominance of the mutated template during the cDNA sequencing in all samples showing a heterozygous TP53 mutation and PIN3 heterozygosity. Out of 30 samples (from the total of 250 tested samples) which carried TP53 mutations and had a bias in allelic expression 6 were heterozygous for the A1/A2 polymorphism, and all 6 (p = 0.04) samples carried the mutation within the PIN3 longer allele (A2). Reporter assays revealed higher luciferase activity in cells transfected with the plasmid containing A2 construct than A1 and control. A2/A1 ratio ranged from 1.16 for AD293 cell line (p = 0.019) to 1.59 for SW962 cell line (p = 0.0019). Moreover, bioinformatic analyses showed that PIN3 duplication stabilized secondary DNA structures - G-quadruplexes.

CONCLUSION

TP53 alleles are not equivalent for their impact on the regulation of expression of TP53 mRNA. Therefore, in PIN3-heterozygous cases a single TP53 mutation of the longer allele might sufficiently destabilize its function. Secondary DNA structures such as quadruplexes can also play a role in PIN3-dependent TP53 haploinsufficiency.

Different mutational characteristics of TSG in cell lines and surgical specimens

One of the most crucial concerns of cancer research pertains to the differences between the neoplastic cells in tumor specimens in vivo and their counterparts in cell lines. The huge amount of results deposited in cancer genetic databases allows to address this issue from a wider perspective. Our analysis of the Sanger Institute Catalog Of Somatic Mutations In Cancer (COSMIC) database v61 showed a lower percentage of homozygous mutations in a group of tumor suppressor genes in surgical samples (in vivo) in comparison to their frequency in cell lines (in vitro). Similarly, the mutations resulting in the lack of protein (e.g., nonsense mutations or whole gene deletions) of several tumor suppressor genes (TSGs) were more frequently observed in vitro than in vivo. In this article, we suggest two potential explanations of these data. Firstly, TSG heterozygous mutations resulting in the modified protein (e.g., missense mutations) may be gradually (when the specific molecular context is achieved) changed to homozygous mutations resulting in the lack of protein during carcinogenesis. Secondly, among different independent pathways of tumorigenesis, those leading to homozygous nonsense mutations are characteristic for cells which are more efficiently stabilized in vitro. To conclude, these observations may be interesting for researchers working with cell line in vitro models illustrating the extent to which they reflect the tumors in vivo.

Spontaneous in vitro senescence of glioma cells confirmed by an antibody against IDH1R132H

BACKGROUND

We have recently suggested that glioblastoma cells become spontaneously senescent in cell culture conditions. The antibody specific against IDH1(R132H) offers the perfect opportunity to verify this hypothesis.

MATERIALS AND METHODS

We analyzed the features of senescence in 8 glioma cell cultures showing the IDH1(R132H) mutation based on combination of immunocytochemistry, enzymo-cytochemistry, BrdU incorporation assay and real-time microscopic observation.

RESULTS

We report that glioma cells showing the IDH1(R132H) mutation become rapidly and spontaneously senescent in vitro. Senescence was observed in both classical and novel serum-free cell culture conditions. Importantly, the senescent IDH1(R132H)-positive cells showed the expression of stemness marker (SOX2).

CONCLUSION

In vitro senescence appeared to be the main reason of the difficulties in any kind culturing of glioma cells. 3D cell cultures prolonged the survival and in vitro proliferation of neoplastic IDH1(R132H)-positive cells, however, did not enhance the stabilization efficiency. Senescence of glioma cells is spontaneously triggered in vitro, which offers the opportunity of potential new therapeutic strategies based on this phenomenon.

The failure in the stabilization of glioblastoma-derived cell lines: spontaneous in vitro senescence as the main culprit

Cell line analysis is an important element of cancer research. Despite the progress in glioblastoma cell culturing, the cells isolated from the majority of specimens cannot be propagated infinitely in vitro. The aim of this study was to identify the processes responsible for the stabilization failure. Therefore, we analyzed 56 primary GB cultures, 7 of which were stabilized. Our results indicate that senescence is primarily responsible for the glioblastoma cell line stabilization failure, while mitotic catastrophe and apoptosis play a minor role. Moreover, a new technical approach allowed for a more profound analysis of the senescent cells in primary cultures, including the distinction between tumor and normal cells. In addition, we observed that glioblastoma cells in primary cultures have a varied potential to undergo spontaneous in vitro senescence, which is often higher than that of the normal cells infiltrating the tumor. Thus, this is the first report of GB cells in primary cell cultures (including both monolayer and spheroid conditions) rapidly and spontaneously becoming senescent. Intriguingly, our data also suggest that nearly half of GB cell lines have a combination of TP53 mutation and CDKN2A homozygous deletion, which are considered as mutually exclusive in glioblastoma. Moreover, recognition of the mechanisms of senescence and mitotic catastrophe in glioblastoma cells may be a step towards a potential new therapeutic approach.

EGFRvIII--a stable target for anti-EGFRvIII therapy

BACKGROUND

Epidermal growth factor receptor (EGFR) gene alterations play important roles in pathogenesis of glioblastoma. Antibodies against EGFRvIII have been recently developed. Their efficacy depends on numerous factors, including the co-existence of EGFRvIII with other genetic alterations, and especially with point mutations of EGFR.

MATERIALS AND METHODS

We examined 91 patients diagnosed with glioblastoma in order to determine the prevalence and mutual relationships between EGFR alterations. Real-time polymerase chain reaction (real-time PCR), fluorescent in situ hybridization (FISH), and sequencing were used to analyze prevalence of the amplification of EGFR gene, polysomy of chromosome 7, EGFRvIII mutation, and point mutations in exons 7-8 and 15 of EGFR.

RESULTS

We revealed that all these alterations can occur independently from each other. Nevertheless, the co-existence of EGFRvIII mutation and excessive copies of EGFR gene was observed in most cases (10/14). Similarly, the point mutations in exons 7-8 and 15 co-existed with an excessive number of EGFR copies in nearly all cases.

CONCLUSION

EGFRvIII is a reliable and stable target for anti-EGFRvIII therapy.

Limited importance of the dominant-negative effect of TP53 missense mutations

BACKGROUND

Heterozygosity of TP53 missense mutations is related to the phenomenon of the dominant-negative effect (DNE). To estimate the importance of the DNE of TP53 mutations, we analysed the percentage of cancer cases showing a single heterozygous mutation of TP53 and searched for a cell line with a single heterozygous mutation of this gene. This approach was based on the knowledge that genes with evident DNE, such as EGFR and IDH1, represent nearly 100% of single heterozygous mutations in tumour specimens and cell lines.

METHODS

Genetic analyses (LOH and sequencing) performed for early and late passages of several cell lines originally described as showing single heterozygous TP53 mutations (H-318, G-16, PF-382, MOLT-13, ST-486 and LS-123). Statistical analysis of IARC TP53 and SANGER databases. Genetic analyses of N-RAS, FBXW7, PTEN and STR markers to test cross-contamination and cell line identity. Cell cloning, fluorescence-activated cell sorting and SSCP performed for the PF-382 cell line.

RESULTS

A database study revealed TP53 single heterozygous mutations in 35% of in vivo (surgical and biopsy) samples and only 10% of cultured cells (in vitro), although those numbers appeared to be overestimated. We deem that published in vivo TP53 mutation analyses are not as rigorous as studies in vitro, and we did not find any cell line showing a stable, single heterozygous mutation. G16, PF-382 and MOLT-13 cells harboured single heterozygous mutations temporarily. ST-486, H-318 and LS-123 cell lines were misclassified. Specific mutations, such as R175H, R273H, R273L or R273P, which are reported in the literature to exert a DNE, showed the lowest percentage of single heterozygous mutations in vitro (about 5%).

CONCLUSION

We suggest that the currently reported percentage of TP53 single heterozygous mutations in tumour samples and cancer cell lines is overestimated. Thus, the magnitude of the DNE of TP53 mutations is questionable. This scepticism is supported by database investigations showing that retention of the wild-type allele occurs with the same frequency as either nonsense or missense TP53 mutations.

Glioma cells showing IDH1 mutation cannot be propagated in standard cell culture conditions

BACKGROUND

It has recently been reported by several sources that original (i.e., present in vivo) glioma cell phenotypes or genotypes cannot be maintained in vitro. For example, glioblastoma cell lines presenting EGFR amplification cannot be established.

METHODS AND RESULTS

IDH1 sequencing and loss of heterozygosity analysis was performed for 15 surgery samples of astrocytoma and early and late passages of cells derived from those and for 11 archival samples. We were not able to culture tumour cells presenting IDH1 mutations originating from currently proceeded 10 tumours; the same results were observed in 7 samples of archival material.

CONCLUSION

The IDH1 mutation is expected to be almost mutually exclusive with EGFR amplification, so glioma cells with IDH1 mutations seem to represent a new group of tumour cells, which cannot be readily analysed in vitro because of their elimination. The reasons for this intriguing phenomenon should be investigated since its understanding can help to define a new therapeutic approach based on simulating in vivo conditions, responsible for tumour cells elimination in vitro. Moreover, a new model for culturing glioma cells in vitro should be designed since the current one does not provide conditions corresponding to in vivo growth.

Detection of P53 mutations in different cancer types is improved by cDNA sequencing

Recently published data show discrepancies between P53 cDNA and DNA sequencing results in glioblastoma, colorectal cancer and pleomorphic xanthoastrocytoma. We hypothesized that similar discrepancies are observed in other types of human cancers. Using DNA and cDNA direct sequencing, we analyzed 40 cases of invasive breast duct carcinoma, 23 cases of acute myeloblastic leukaemia, 12 cases of astrocytoma and 40 cases of soft tissue sarcoma for P53 mutations. Additionally, we used real-time quantitative PCR to estimate the normalized relative P53 expression. In the comparative study, the P53 mutation was detected more frequently when using cDNA sequencing than DNA sequencing in all of the cancer types. Furthermore, several samples presented missense P53 mutations, with visible wild-type nucleotide on the DNA sequence. In contrast, elimination of the wild-type allele or selective overproduction of the mutated allele was observed on the cDNA sequence. P53 expression was not significantly different between the cases with or without P53 mutations. These results indicate that cDNA sequencing improves the detection of P53 mutations in these cancers. We suggest that the true incidence of P53 mutations in these cancers is underestimated at the DNA level, and evaluation of the alteration should be carried out using cDNA analysis.

IL-1 receptor antagonist (IL-1ra) expression, function, and cytokine-mediated regulation during mycobacterial and schistosomal antigen-elicited granuloma formation

Granulomas (GR) mediated predominantly by Th1/type 1 (IFN-gamma) and Th2/type 2 (IL-4, IL-5, IL-10) cytokines were induced by i.v. injection of sensitized CBA/J mice with carbohydrate beads coated with Mycobacterium tuberculosis or Schistosoma mansoni egg Ags, respectively. GR macrophages (Mphi) from types 1 and 2 GR both produced IL-1ra, but the former showed accelerated IL-1ra-producing capacity, releasing two- to threefold greater amounts on day 4 than those of type 2 GR, as measured by sandwich ELISA. In vivo depletion of IL-1ra exacerbated GR size and augmented regional cytokine production in both types of responses. To determine the critical cytokines mediating IL-Ira expression, oil-elicited peritoneal Mphi were exposed to graded doses (0.1 to 10 ng/ml) of cytokines (IL-1beta, IL-2, IL-4, IL-10, IL-12, IFN-gamma, and TNF-alpha) for 24 h, then stimulated with opsonized zymosan. Of the cytokines tested, IFN-gamma and TNF-alpha were the best costimuli for IL-1ra production in the presence of zymosan, whereas IL-1beta, IL-10, and IL-12 were not active. In vivo depletion of IL-4, IL-10, IL-12, IFN-gamma, or TNF-alpha with 5 mg of cytokine-specific neutralizing rabbit IgG revealed that IFN-gamma and TNF-alpha were required for maximal IL-1ra production by Mphi. Furthermore, the delayed IL-1ra production by type 2 GR Mphi could be related to later TNF-alpha production. Our findings indicate that IL-1ra is a common regulatory product of inflammatory Mphi and is particularly promoted by type 1 cytokines, IFN-gamma, and TNF-alpha.

IL-1 receptor antagonist (IL-1ra) expression, function, and cytokine-mediated regulation during mycobacterial and schistosomal antigen-elicited granuloma formation

Granulomas (GR) mediated predominantly by Th1/type 1 (IFN-gamma) and Th2/type 2 (IL-4, IL-5, IL-10) cytokines were induced by i.v. injection of sensitized CBA/J mice with carbohydrate beads coated with Mycobacterium tuberculosis or Schistosoma mansoni egg Ags, respectively. GR macrophages (Mphi) from types 1 and 2 GR both produced IL-1ra, but the former showed accelerated IL-1ra-producing capacity, releasing two- to threefold greater amounts on day 4 than those of type 2 GR, as measured by sandwich ELISA. In vivo depletion of IL-1ra exacerbated GR size and augmented regional cytokine production in both types of responses. To determine the critical cytokines mediating IL-Ira expression, oil-elicited peritoneal Mphi were exposed to graded doses (0.1 to 10 ng/ml) of cytokines (IL-1beta, IL-2, IL-4, IL-10, IL-12, IFN-gamma, and TNF-alpha) for 24 h, then stimulated with opsonized zymosan. Of the cytokines tested, IFN-gamma and TNF-alpha were the best costimuli for IL-1ra production in the presence of zymosan, whereas IL-1beta, IL-10, and IL-12 were not active. In vivo depletion of IL-4, IL-10, IL-12, IFN-gamma, or TNF-alpha with 5 mg of cytokine-specific neutralizing rabbit IgG revealed that IFN-gamma and TNF-alpha were required for maximal IL-1ra production by Mphi. Furthermore, the delayed IL-1ra production by type 2 GR Mphi could be related to later TNF-alpha production. Our findings indicate that IL-1ra is a common regulatory product of inflammatory Mphi and is particularly promoted by type 1 cytokines, IFN-gamma, and TNF-alpha.

Endogenous IL-1 receptor antagonist protein (IRAP) regulates schistosome egg granuloma formation and the regional lymphoid response

This study examined the role of IL-1 receptor antagonist protein (IRAP) in the regulation of the immune/inflammatory response to schistosome eggs. Initial screening for IRAP-specific mRNA transcripts by reverse transcriptase and primer-directed polymerase chain reactions suggested significant endogenous IRAP synthesis in lungs with Schistosoma mansoni egg-induced hypersensitivity granulomas but not in normal lungs or lungs with non-immune bead granulomas. Direct detection using mIRAP-specific antibodies corroborated the RNA studies. Both ELISA and immunohistochemical studies revealed significant spontaneous IRAP production in cultures of isolated egg granulomas and regional reactive lymphoid tissue that could be localized largely but not exclusively to macrophages. Synchronously developing secondary schistosome egg granulomas showed accelerated and augmented IRAP production compared with primary lesions, paralleling granuloma cellularity and growth kinetics. Nonimmune T cell-independent bead lesions produced the least amounts of IRAP. In draining lymphoid tissue the onset of IRAP production corresponded with local cell proliferation in both primary and secondary egg responses. Next, the in vivo role of IRAP was tested by administration of anti-IRAP antisera which caused 40-50% increases in egg granuloma area. Moreover, treatment increased (50-100%) IL-2, IL-4, IL-10, and IFN-gamma production in the primary response and all but IFN in secondary response lymph node cultures. Our results suggest that IRAP is an endogenous regulatory protein and may limit the activity of IL-1 during the Ag-specific granulomatous response to schistosome eggs. Furthermore, our findings provide in vivo support for the notion that Ag-elicited lymphocyte-derived products probably augment IRAP production and block the action of IL-1.

Endogenous IL-1 receptor antagonist protein (IRAP) regulates schistosome egg granuloma formation and the regional lymphoid response

This study examined the role of IL-1 receptor antagonist protein (IRAP) in the regulation of the immune/inflammatory response to schistosome eggs. Initial screening for IRAP-specific mRNA transcripts by reverse transcriptase and primer-directed polymerase chain reactions suggested significant endogenous IRAP synthesis in lungs with Schistosoma mansoni egg-induced hypersensitivity granulomas but not in normal lungs or lungs with non-immune bead granulomas. Direct detection using mIRAP-specific antibodies corroborated the RNA studies. Both ELISA and immunohistochemical studies revealed significant spontaneous IRAP production in cultures of isolated egg granulomas and regional reactive lymphoid tissue that could be localized largely but not exclusively to macrophages. Synchronously developing secondary schistosome egg granulomas showed accelerated and augmented IRAP production compared with primary lesions, paralleling granuloma cellularity and growth kinetics. Nonimmune T cell-independent bead lesions produced the least amounts of IRAP. In draining lymphoid tissue the onset of IRAP production corresponded with local cell proliferation in both primary and secondary egg responses. Next, the in vivo role of IRAP was tested by administration of anti-IRAP antisera which caused 40-50% increases in egg granuloma area. Moreover, treatment increased (50-100%) IL-2, IL-4, IL-10, and IFN-gamma production in the primary response and all but IFN in secondary response lymph node cultures. Our results suggest that IRAP is an endogenous regulatory protein and may limit the activity of IL-1 during the Ag-specific granulomatous response to schistosome eggs. Furthermore, our findings provide in vivo support for the notion that Ag-elicited lymphocyte-derived products probably augment IRAP production and block the action of IL-1.

Cytochrome P450c17 (steroid 17 alpha-hydroxylase/17,20 lyase): cloning of human adrenal and testis cDNAs indicates the same gene is expressed in both tissues

P450c17 is the single enzyme mediating both 17 alpha-hydroxylase (steroid 17 alpha-monooxygenase, EC 1.14.99.9) and 17,20 lyase activities in the synthesis of steroid hormones. It has been suggested that different P450c17 isozymes mediate these activities in the adrenal gland and testis. We sequenced 423 of the 509 amino acids (83%) of the porcine adrenal enzyme; based on this partial sequence, a 128-fold degenerate 17-mer was synthesized and used to screen a porcine adrenal cDNA library. This yielded a 380-base cloned cDNA, which in turn was used to isolate several human adrenal cDNAs. The longest of these, lambda hac17-2, is 1754 base pairs long and includes the full-length coding region, the complete 3'-untranslated region, and 41 bases of the 5'-untranslated region. This cDNA encodes a protein of 508 amino acids having a predicted molecular weight of 57,379.82. High-stringency screening of a human testicular cDNA library yielded a partial clone containing 1303 identical bases. RNA gel blots and nuclease S1-protection experiments confirm that the adrenal and testicular P450c17 mRNAs are indistinguishable. These data indicate that the testis possesses a P450c17 identical to that in the adrenal. The human amino acid sequence is 66.7% homologous to the corresponding regions of the porcine sequence, and the human cDNA and amino acid sequences are 80.1 and 70.3% homologous, respectively, to bovine adrenal P450c17 cDNA. Both comparisons indicate that a central region comprising amino acid residues 160-268 is hypervariable among these species of P450c17. Comparison of the amino acid sequence of P450c17 with two other human steroidogenic cytochromes P450 show much greater homology with P450c21 (28.9%), another microsomal enzyme, than with P450scc (12.3%), a mitochondrial enzyme.