H3K27M diffuse midline gliomas (DMG) are characterized by p53 mutations and hypomethylation of MGMT, a DNA-repair enzyme, leading to resistance towards chemotherapeutic agents such as temozolomide (TMZ). As an alternative, we investigated the efficacy of a functionally different DNA-damaging agent, Val-083, on our DMG models. Val-083 is a blood-brain barrier penetrant DNA targeting agent that induces DNA N7-guanine interstrand crosslinks, which is unrepairable by MGMT. As Val-083 also triggers S/G2 phase cell cycle arrest for DNA repair, we evaluated its combined efficacy with Wee1 inhibitor, AZD1775. AZD1775 functions by inhibiting Wee1, at G2/M checkpoint to prevent phosphorylation of CDK1 and propel cells into the M phase. This subsequently overrides cell cycle arrest and drives cells with DNA damage into premature mitosis and apoptosis. Our results showed that Val-083 and AZD1775 work additively on a range of p53 mutant and p53 wildtype DMG models to inhibit cell growth, induce DNA damage and alter cell cycle. In addition, the combination drugs led to significant increase in the number of cells undergoing apoptosis, and a decrease in the migration and invasion activity of the cells. In vivo, the combination of both drugs led to significant reduction in tumor growth in zebrafish xenograft models and prolongation of survival in mice xenograft models. Our findings indicate that Val-083 and AZD1775 in combination demonstrate promising efficacy in DMGs, providing a clinical rationale for positioning these arms in future therapies.

Neuronal activity is an energy-intensive process that is largely sustained by instantaneous fuel utilization and ATP synthesis. However, how neurons couple ATP synthesis rate to fuel availability is largely unknown. Here, we demonstrate that the metabolic sensor enzyme O-linked N-acetyl glucosamine (O-GlcNAc) transferase regulates neuronal activity-driven mitochondrial bioenergetics in hippocampal and cortical neurons. We show that neuronal activity upregulates O-GlcNAcylation in mitochondria. Mitochondrial O-GlcNAcylation is promoted by activity-driven glucose consumption, which allows neurons to compensate for high energy expenditure based on fuel availability. To determine the proteins that are responsible for these adjustments, we mapped the mitochondrial O-GlcNAcome of neurons. Finally, we determine that neurons fail to meet activity-driven metabolic demand when O-GlcNAcylation dynamics are prevented. Our findings suggest that O-GlcNAcylation provides a fuel-dependent feedforward control mechanism in neurons to optimize mitochondrial performance based on neuronal activity. This mechanism thereby couples neuronal metabolism to mitochondrial bioenergetics and plays a key role in sustaining energy homeostasis.

Abstract BACKGROUND Diffuse midline gliomas (DMGs) are malignant pediatric brain tumors characterized by H3K27M mutation and global genome hypomethylation. This results in enhanced transcription of MGMT, a DNA-repair enzyme, rendering alkylating chemotherapeutics ineffective. Therefore, we investigated the efficacy of a functionally different DNA damaging agent, Val-083, that induces double strand breaks and triggers S/G2 phase cell cycle arrest for homologous DNA repair. We further evaluated its combined efficacy with Wee1 (G2/M checkpoint) inhibitor, AZD1775, to override cell cycle arrest and propel cells with DNA damage into premature mitosis and apoptosis. METHODS DMG cells were treated with increasing concentration of Val-083 and/or AZD1775 and their viability was evaluated using CellTiter-Glo luminescent assay. Next, the drugs’ mechanisms of action were investigated by immunoblotting for biomarkers involved in DNA damage response and cell cycle arrest. Flow cytometry was used to investigate cell cycle profile and apoptosis. Additionally, in vivo tumor growth inhibition and survival benefit were evaluated using zebrafish and mouse xenograft DMG models. RESULTS The IC50 values of Val-083 range between 0.69 and 4.38 µM while the IC50 values of AZD1775 range between 0.22 to 0.98 µM. Combination of both drugs showed high areas of synergy on multiple DMG lines, DNA double strand breaks and significant increase in cell population at the S (p<0.01) and G2/M (p<0.05) phases. Importantly, on zebrafish xenograft tumor model, combination treatment significantly (p<0.001) inhibited tumor growth in comparison to control and single treatment groups. Furthermore, the combined treatment demonstrated significant (p<0.01) survival benefit (median survival (MS) = 62 days) on tumor-bearing nude mice models, in comparison to vehicle (MS= 44 days), Val-083 (MS= 54.5 days) and AZD1775 (MS= 47 days) treatment groups. CONCLUSION Val-083 in combination with AZD1775 demonstrate promising efficacy in DMG preclinical models, providing a strong rationale for positioning these arms for clinical testing.

BACKGROUND:Glioblastoma (GBM) is a highly aggressive primary brain tumor with limited treatment success and poor prognosis. Despite surgical resection and adjuvant therapies, GBM often recurs, and resistance to radiotherapy and temozolomide presents significant challenges. This study aimed to elucidate molecular signatures associated with treatment responses, identify potential biomarkers, and enhance personalized treatment strategies for GBM. METHODS:We conducted a comprehensive analysis using the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. The GEO dataset (GSE206225) was used to identify differentially expressed genes (DEGs) between radiation-sensitive/resistant and temozolomide-sensitive/resistant GBM samples. TCGA data were utilized for subsequent analyses, including Lasso-Cox regression, risk score model construction, Kaplan-Meier survival analysis, and gene set enrichment analysis (GSEA). Hub genes were identified through survival analysis, and a gene prognostic nomogram was developed. Additionally, validation of the three-gene risk signature through multiple external cohorts and validation of protein expression levels were performed. RESULTS:DEG analysis identified 111 genes associated with chemoradiotherapy resistance, providing insights into the complex landscape of GBM treatment response. The risk score model effectively stratified patients, showing significant differences in overall survival and progression-free survival. GSEA offered a deeper understanding of pathway activities, emphasizing the intricate molecular mechanisms involved. NNAT, IGFBP6, and CYGB were identified as hub genes, and a gene prognostic nomogram demonstrated predictive accuracy. CONCLUSION:This study sheds light on the molecular intricacies governing GBM treatment response. The identified hub genes and the gene prognostic nomogram offer valuable tools for predicting patient outcomes and guiding personalized treatment strategies. These findings contribute to advancing our understanding of GBM biology and may pave the way for improved clinical management.

BackgroundDiffuse intrinsic pontine glioma (DIPG) usually occurs in children and has poor outcomes despite treatment. Large drug screens have identified the pan-histone deacetylate inhibitor panobinostat as a promising agent, however clinical response might be hampered by limited blood brain barrier penetration. Hyperpolarized 13C magnetic resonance (MR) metabolic imaging has successfully been applied to non-invasively assess metabolic activity of cancer therapies. Here, we use in vitro and in vivo DIPG models to validate the therapeutic efficacy of MTX110, an aqueous form of panobinostat delivered by convection enhanced delivery (CED) and apply metabolic imaging.MethodsMTX110 inhibitory effect was assessed in 11 DIPG cell lines. Caspase 3/7 levels were measured to assess mode of cell death. FACS analysis was utilized to determine impact on cell cycle. Hyperpolarized 13C imaging determined changes in pyruvate and lactate levels after treatment. In vivo activity of CED of MTX110 was assessed in a patient-derived xenograft rat model and tissue half-life of MTX110 was determined using mass spectrometry.ResultsMTX110 showed similar IC50 to panobinostat ranging from 5.34 nM and 47.96 nM. Anti-proliferative effects of MTX110 are mediated by G1 cell cycle arrest and subsequent apoptosis. Drug treatment led to reduced pyruvate to lactate conversion. CED of MTX110 significantly prolonged survival of tumor-bearing rats (p = 0.0372) with no signs of systemic toxicity. Tissue half-life after single CED of MTX110 is 2 h.ConclusionsOur results demonstrate that CED of MTX110, has potent antitumor activity with limited systemic toxicity and that hyperpolarized 13C imaging is able to assess metabolic impact.

BACKGROUND:Pediatric diffuse midline gliomas (DMGs) are incurable childhood cancers. The imipridone ONC201 has shown early clinical efficacy in a subset of DMGs. However, the anticancer mechanisms of ONC201 and its derivative ONC206 have not been fully described in DMGs. METHODS:DMG models including primary human in vitro (n = 18) and in vivo (murine and zebrafish) models, and patient (n = 20) frozen and FFPE specimens were used. Drug-target engagement was evaluated using in silico ChemPLP and in vitro thermal shift assay. Drug toxicity and neurotoxicity were assessed in zebrafish models. Seahorse XF Cell Mito Stress Test, MitoSOX and TMRM assays, and electron microscopy imaging were used to assess metabolic signatures. Cell lineage differentiation and drug-altered pathways were defined using bulk and single-cell RNA-seq. RESULTS:ONC201 and ONC206 reduce viability of DMG cells in nM concentrations and extend survival of DMG PDX models (ONC201: 117 days, P = .01; ONC206: 113 days, P = .001). ONC206 is 10X more potent than ONC201 in vitro and combination treatment was the most efficacious at prolonging survival in vivo (125 days, P = .02). Thermal shift assay confirmed that both drugs bind to ClpP, with ONC206 exhibiting a higher binding affinity as assessed by in silico ChemPLP. ClpP activation by both drugs results in impaired tumor cell metabolism, mitochondrial damage, ROS production, activation of integrative stress response (ISR), and apoptosis in vitro and in vivo. Strikingly, imipridone treatment triggered a lineage shift from a proliferative, oligodendrocyte precursor-like state to a mature, astrocyte-like state. CONCLUSION:Targeting mitochondrial metabolism and ISR activation effectively impairs DMG tumorigenicity. These results supported the initiation of two pediatric clinical trials (NCT05009992, NCT04732065).

Abstract Introduction Diffuse midline gliomas (DMGs) are amongst the most unforgiving pediatric brain tumors, characterized by an intrinsic resistance to therapy. Despite major advances in understanding of tumor biology, the prognosis remains exceedingly poor, and treatment options are limited. New therapeutics are being evaluated at a fast rate by different laboratories. In order to prioritize effective drug candidates for DMG treatment, we comprehensively characterized a panel of promising therapeutic agents in in vitro and in different vivo systems. Methods We determined the sensitivity of primary DMG cell lines to a panel of small molecule inhibitors targeting known DMG targets and pathways. Dose response curves were generated for more than 20 different compounds and possible synergistic effects were investigated by SynergieFinder. In an effort to highlight potential toxicities and associated mechanisms at a large scale, we performed a preclinical toxicity evaluation in zebrafish larvae, with a slightly modified version of the official Fish Embryo Acute Toxicity (FET) test. Drug toxicity was tested by continuous exposure of zebrafish larvae to increasing concentrations of the different compounds. Survival curves, morphological analyses and behavioral tests were performed at a maximum tolerated dose (MTD). To confirm the findings obtained in zebrafish, we further performed in vivo studies in mice for promising candidates. Results Among the tested drugs in vitro we found 10 drugs showing promising dose- dependent reduction in cell viability with IC50 in nM to µM range. These were further evaluated for toxicity in zebrafish. The zebrafish larvae toxicities observations strongly correlated with the findings in murine in vivo studies, reinforcing the importance of zebrafish as an accurate investigative toxicology model to assess acute toxicity of molecules in preclinical studies. Conclusions By testing a wide range of drugs, targeting different pathways on DMG cells and in different in vivo systems we identified promising drug candidates for clinical management of children diagnosed with DMG.

Abnormal signaling of the RAS/RAF and mTOR pathways predominates in pediatric low-grade gliomas (PLGGs). MLN0128 is a second-generation pan-mTOR inhibitor (TORC1/2). Rapalink-1, a third-generation bivalent mTOR inhibitor that combines rapamycin with MLN0128 by an inert chemical linker, shows potent anti-tumor effects in preclinical adult glioma models. MEK inhibition with e.g. AZD6244 shows promising anti-tumor effects in PLGGs and the type II generation pan-RAF inhibitor TAK580 is currently under clinical investigation in PLGG. In this study, we evaluate the effects of MLN0128 and Rapalink-1 in preclinical models of PLGGs, for both mono- and combination therapy with AZD6244 and TAK580. These inhibitors were used to treat glioma cell lines carrying wild-type BRAF (SF188 and LN229), and isogenic systems of KIAA1549-BRAF expressing NIH/3T3 cell line. Using CellTiter-Glo Luminescent Cell Viability Assay, we found that mTOR inhibition monotherapy reduces cell viability in a dose dependent manner while Rapalink-1 (IC50 between 3.5–8.2nM) is more effective than MLN0128 (IC50 between 22.9–120.2nM). Combined with AZD6244, both inhibitors synergistically increase the suppression of cell viability (combination index value ndgeneration pan-RAF inhibitor TAK580 in combination with mTOR inhibition.

RATIONALE: One of the major hurdles in developing effective treatment for children with DIPG includes the lack of extensive combinatorial studies targeting major driver oncogenic pathways. Combination of H3K27M and TP53 mutations are found in over 50% of DIPG tumors, however, there is a lack of effective combinatorial precision therapy. METHODS: Tissue specimens obtained from subjects with DIPG were used to generate preclinical models. Subjects were enrolled in a prospective molecular diagnostic clinical trial and specimens were obtained by surgical biopsy both at initial diagnosis, and at the time of progression. RESULTS: Fourteen primary neurosphere cell lines and nine xenograft mouse models were successfully generated. The success rate of generating primary neurospheres and xenograft models was 45% and 75%, respectively. Among the 14 cell lines, one was derived from a biopsy performed after tumor progression, and one from washing a biopsy needle. Whole genome analysis of three biopsy-derived primary neurospheres revealed that these samples shared genomic alterations when compared to the primary tumors. All cell lines retained major oncogenic driver mutations in genes such as H3F3A, HIST1H3B, TP53, PPM1D, PIK3R1, and ACVR1. The needle-wash derived cell line was immortalized with hTERT, and exhibited the most deviation in mutation profiles and copy number alterations compared to primary tumor. Global DNA methylation profiling of seven primary tumor biopsies and matched primary neurospheres revealed similar epigenetic profiles. Primary neurospheres derived from biopsies were treated with the same specialized panel of agents recommended by a personalized medicine tumor board, which was based on the mutational profiles of the original tumor. SIGNIFICANCE: All cell lines exhibited varying levels of sensitivity to single agent indicating patterns of intertumor heterogeneity. The use of these model systems allows testing of combinatorial precision therapy for patients with DIPG, where there is a need for rapid translation into clinical trials.

Mutation of either the intracellular catalytic domain or the extracellular domain of the receptor for epidermal growth factor (EGFR) drives oncogenicity. Extracellular domain EGFR mutations are highly expressed in patients with glioblastoma. Despite clinical success with targeting EGFR catalytic site mutants, no drugs have proven effective in glioblastoma patients expressing extracellular EGFR mutations. Herein, we define the molecular mechanism for oncogenic activation of families of extracellular EGFR mutations and reveal how this mechanism renders current generation small molecule ATP-site inhibitors ineffective. We demonstrate that a group of the most commonly expressed extracellular domain EGFR mutants expressed in glioblastomas is activated by disulfide-bond mediated covalent homodimerization, collectively referred to as locked dimerization (LoDi-EGFR oncogenes). Strikingly, current generation small molecules binding to the active kinase conformation potently inhibit catalytic site mutants, but induce covalent dimerization and activate LoDi-EGFR receptors, manifesting in paradoxical acceleration of proliferation. These data demonstrate how the locked-dimer mechanism of EGFR oncogenesis has profound impact on the activity of small molecules acting at the distal catalytic site, providing further evidence for “inside-out” allosteric signaling in EGFR. This provides a mechanistic understanding for the failure of current generation EGFR inhibitors to effectively treat LoDi-EGFR mutants in GBM and sets guidelines for discovery of selective LoDi-EGFR inhibitors. Citation Format: Matthew O'Connor, Theodore Nicolaides, Jie Zhang, Alexander Flohr, Roberto Iacone, Alexander V. Mayweg, David M. Epstein, Elizabeth Buck. Epidermal growth factor receptor oncogenes expressed in glioblastoma are activated as covalent dimers and exhibit unique pharmacology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-111.

Mutation of both the intracellular catalytic domain and the extracellular domain of the receptor for epidermal growth factor (EGFR) can drive oncogenicity. Despite clinical success with targeting EGFR catalytic site mutations, no drugs have proven effective in patients expressing allosteric extracellular domain EGFR mutations, including glioblastomas (GBM) where these mutations are highly expressed. We define the molecular mechanism for oncogenic activation of families of extracellular EGFR mutations and reveal how this mechanism renders current generation small molecule ATP-site inhibitors ineffective. We demonstrate that a group of commonly expressed extracellular domain EGFR mutants expressed in GBM is activated by disulfide-bond mediated covalent dimerization, collectively referred to as locked dimerization (LoDi) EGFR oncogenes. Strikingly, small molecules binding to the active kinase conformation (Type I), but not those binding to the inactive kinase conformation (Type II), potently inhibit catalytic site mutants, but induce covalent dimerization and activate LoDi-EGFR oncogenes, manifesting in paradoxical acceleration of proliferation. Significance Our data demonstrate how the locked-dimer mechanism of EGFR oncogenesis has a profound impact on the activity of small molecule inhibitors. This provides a mechanistic understanding for the failure of current generation EGFR inhibitors to effectively treat LoDi-EGFR mutants in GBM, and sets guidelines for discovery of selective LoDi-EGFR inhibitors.