Enhanced signalling via the epidermal growth factor receptor (EGFR) is a hallmark of multiple human carcinomas. However, in recent years data have accumulated that EGFR might also be hyperactivated in human sarcomas. Aim of this study was to investigate the influence of EGFR inhibition on cell viability and its interaction with chemotherapy response in osteosarcoma cell lines. We have investigated a panel of human osteosarcoma cell lines regarding EGFR expression and downstream signalling. To test its potential applicability as therapeutic target, inhibition of EGFR by gefitinib was combined with osteosarcoma chemotherapeutics and cell viability, migration, and cell death assays were performed. Osteosarcoma cells expressed distinctly differing levels of functional EGFR reaching in some cases high amounts. Functionality of EGFR in osteosarcoma cells was proven by EGF-mediated activation of both MAPK and PI3K/AKT pathway (determined by phosphorylation of ERK1/2, AKT, S6, and GSK3β). The EGFR-specific inhibitor gefitinib blocked EGF-mediated downstream signal activation. At standard in vitro culture conditions, clinically achievable gefitinib doses demonstrated only limited cytotoxic activity, however, significantly reduced long-term colony formation and cell migration. In contrast, under serum-starvation conditions active gefitinib doses were distinctly reduced while EGF promoted starvation survival. Importantly, gefitinib significantly supported the anti-osteosarcoma activities of doxorubicin and methotrexate regarding cell survival and migratory potential. Our data suggest that EGFR is not a major driver for osteosarcoma cell growth but contributes to starvation- and chemotherapy-induced stress survival. Consequently, combination approaches including EGFR inhibitors should be evaluated for treatment of high-grade osteosarcoma patients.

The BRAF gene and the TERT promoter are among the most frequently altered genomic loci in low-grade (LGG) and high-grade-glioma (HGG), respectively. The coexistence of BRAF and TERT promoter aberrations characterizes a subset of aggressive glioma. Therefore, we investigated interactions between those alterations in malignant glioma. We analyzed co-occurrence of BRAFV600E and TERT promoter mutations in our clinical data (n = 8) in addition to published datasets (n = 103) and established a BRAFV600E-positive glioma cell panel (n = 9) for in vitro analyses. We investigated altered gene expression, signaling events and TERT promoter activity upon BRAF- and E-twenty-six (ETS)-factor inhibition by qRT-PCR, chromatin immunoprecipitation (ChIP), Western blots and luciferase reporter assays. TERT promoter mutations were significantly enriched in BRAFV600E-mutated HGG as compared to BRAFV600E-mutated LGG. In vitro, BRAFV600E/TERT promoter double-mutant glioma cells showed exceptional sensitivity towards BRAF-targeting agents. Remarkably, BRAF-inhibition attenuated TERT expression and TERT promoter activity exclusively in double-mutant models, while TERT expression was undetectable in BRAFV600E-only cells. Various ETS-factors were broadly expressed, however, only ETS1 expression and phosphorylation were consistently downregulated following BRAF-inhibition. Knock-down experiments and ChIP corroborated the notion of a functional role for ETS1 and, accordingly, all double-mutant tumor cells were highly sensitive towards the ETS-factor inhibitor YK-4-279. In conclusion, our data suggest that concomitant BRAFV600E and TERT promoter mutations synergistically support cancer cell proliferation and immortalization. ETS1 links these two driver alterations functionally and may represent a promising therapeutic target in this aggressive glioma subgroup.

Diffusely infiltrating gliomas are characterized by a variable clinical course, and thus novel prognostic biomarkers are needed. The heme biosynthesis cycle constitutes a fundamental metabolic pathway and might play a crucial role in glioma biology. The aim of this study was thus to investigate the role of the heme biosynthesis mRNA expression signature on prognosis in a large glioma patient cohort. Glioma patients with available sequencing data on heme biosynthesis expression were retrieved from The Cancer Genome Atlas (TCGA). In each patient, the heme biosynthesis mRNA expression signature was calculated and categorized into low, medium, and high expression subgroups. Differences in progression-free and overall survival between these subgroups were investigated including a multivariate analysis correcting for WHO grade, tumor subtype, and patient age and sex. In a total of 693 patients, progression-free and overall survival showed a strictly monotonical decrease with increasing mRNA expression signature subgroups. In detail, median overall survival was 134.2 months in the low, 79.9 months in the intermediate, and 16.5 months in the high mRNA expression signature subgroups, respectively. The impact of mRNA expression signature on progression-free and overall survival was independent of the other analyzed prognostic factors. Our data indicate that the heme biosynthesis mRNA expression signature might serve as an additional novel prognostic marker in patients with diffusely infiltrating gliomas to optimize postoperative management.

Central nervous system high-grade neuroepithelial tumor with BCL6-corepressor alteration (CNS HGNET-BCOR) is a recently discovered molecular brain tumor entity characterized by genomic alterations of BCOR, a central component of a non-canonical polycomb repressive complex. However, the underlying oncogenic mechanisms and their consequences for tumor-specific anti-cancer therapy remain widely enigmatic. We systematically analyzed genomics, transcriptomics, and drug-sensitivity patterns in three tumor-derived models (two cell-lines, one primary cell-culture) from three consecutive intracranial CNS HGNET-BCOR metastases of one patient. All models harbored a unique frameshift mutation within BCOR resulting in a truncated protein lacking functionally important c-terminal protein domains. Re-expression of BCOR wild-type in our CNS HGNET-BCOR cell-models resulted in decreased cell proliferation and increased apoptosis. Interestingly, genes downregulated upon re-expression of BCOR wild-type were also derepressed in CNS HGNET-BCOR tumor tissues harboring BCOR-alterations different from our case (e.g. internal tandem duplication in BCOR). Via comparison with a chromatin immunoprecipitation DNA-sequencing dataset, we determined that a significant proportion of the corresponding gene promoters are occupied by BCOR in BCOR wild-type cancer cells. An additional drug-screen demonstrated hypersensitivity of CNS HGNET-BCOR cells against histone deacetylase inhibitors and histone methyltransferase inhibitors. Matching of drug sensitivity patterns to upregulated target-genes determined bortezomib, dasatinib, and crizotinib as promising tumor-specific therapeutics against CNS HGNET-BCOR. Taken together, our results suggest that dysfunction of BCOR-mediated gene repression determines the oncogenic behavior and transcriptomic profile of CNS HGNET-BCOR. Moreover, we provide preliminary results for potential pharmacological interventions against this aggressive tumor type.

High-risk ependymomas (EPN) arise throughout the neuroaxis, with aggressive posterior fossa group A (PFA EPN) and supratentorial tumors harboring zinc finger translocation-associated protein fusions (ST-ZFTA) predominating in pediatric patients. Among these, PFA EPN are characterized by distinctly poor overall survival based on high tumor recurrence rates and limited response to therapies. This underscores an urgent need to identify molecular drivers and mechanisms underlying the aggressive behavior of this high-risk EPN subtype. Besides a high abundance of stem- and progenitor-like cell populations, EZH2 inhibitory protein (EZHIP) is suggested to act as a driver of PFA EPN-associated epigenetic reprogramming. However, the impact of EZHIP on cellular differentiation during PFA EPN progression remains to be elucidated. In this study, we explored the interaction between EZHIP and cilia-associated as well as mesenchymal-like marker genes through integrative analysis of RNA expression ( n = 58), DNA methylation ( n = 37), ChIP sequencing profiling of H3K27me3, H3K27ac, and EZHIP ( n = 4), and multiplex immunohistochemistry ( n = 15) in a cohort of PFA EPN tissue specimens complemented by publicly available datasets. Here, we demonstrate increased expression of cilia-related genes, particularly CAPS and DNAAF1 , in PFA EPN compared to ST-ZFTA. Notably, EZHIP binds to CAPS gene loci, resulting in significantly reduced CAPS levels upon EZHIP knockdown in PFA EPN cells. This suggests an association of EZHIP with neuro-epithelial differentiation programs. Even further, a strong correlation between CAPS and EZHIP and the chromosome 1q gain was identified, and this association was particularly enriched in progressive diseases. During PFA EPN progression, tissue reorganization led to layered pseudorosette structures in which CA9-positive mesenchymal compartments encircled CAPS-positive ciliated cells, with both cell types being positive for EZHIP. Summarizing, our study advances the understanding of PFA EPN tumor biology by uncovering epigenetic and spatial mechanisms associated with EZHIP and neuro-epithelial- as well as mesenchymal-like differentiation during PFA EPN progression.

We introduce TRAM, a triple acquisition strategy on high-speed, time-of-flight mass spectrometry for merging non-targeted and targeted metabolomics into one run. TRAM stands for “quasi-simultaneous” acquisition of (1) a full scan MS1, (2) top 30 data-dependent MS2 (DDA), and (3) targeted scheduled MS2 for multiple reaction monitoring (MRM) within measurement cycles of ~ 1 second. TRAM combines the selectivity and sensitivity of state-of-the-art targeted MRM-based methods with the full scope of non-targeted analysis enabled by high-resolution mass spectrometry. In this work, we deploy a workflow based on hydrophilic interaction chromatography (HILIC). For a broad panel of metabolites, we provide chromatographic retention times, and opti-mized conditions as a basis for targeted MRM experiments, listing accurate masses and sum formulas for fragment ions (including fully 13C labelled analogs). Validation experiments showed that TRAM offered (1) linear working ranges and limits of quantifica-tion comparable to MRM-only methods, (2) enabled accurate quantification in SRM 1950 human plasma reference material, and (3) was equivalent to DDA-only approaches in non-targeted metabolomics. Metabolomics in human cerebrospinal fluid showcased the power of the strategy, emphasizing the need for high coverage/high throughput metabolomics in clinical studies. Acquiring up to 30 data-dependent spectra per MS cycle while still offering gold-standard absolute quantification, TRAM allows in-depth pro-filing and reduces required sample volume, time, cost, and environmental impact.