Abstract BACKGROUND Pediatric high-grade gliomas (pHGG) harboring H3.3 K27M/G34R mutations present formidable challenges in treatment due to their aggressiveness and resistance to standard chemotherapy. Our preliminary investigations have shown promising results, indicating that combining 2-deoxyglucose (2DG), a glycolytic inhibitor, with DNA-damaging agents synergistically inhibits pHGG growth. However, prolonged exposure to 2DG induces resistance, necessitating the exploration of alternative therapies. This study aims to investigate the potential of panobinostat, a histone deacetylase inhibitor, in sensitizing 2DG-resistant pHGG with H3.3 K27M/G34R mutations to apoptosis. METHODS Transcriptomic analysis via Illumina NovaSeq 6000 and metabolomic profiling employing Liquid Chromatography-High-Resolution Mass Spectrometry was used to delineate the molecular landscape of naive and 2DG-resistant pHGG cell lines. Functional assays, including the Agilent Seahorse Mito Stress Test and flow cytometry, assessed bioenergetics and mitochondrial dynamics. Intracellular NAD+ and NADH levels were quantified utilizing NAD+/NADH Glo assays, while apoptotic markers and metabolic stress were measured using the Annexin V-FITC Conjugates for Apoptosis Detection kit and western blot. RESULTS Comparative analysis revealed increased transketolase activity in 2DG-resistant cells, augmenting the interaction between the pentose phosphate pathway and glycolysis, resulting in elevated levels of NADPH and ATP. Additionally, these resistant cells displayed enhanced reliance on mitochondrial energy metabolism, as evidenced by substantial increases in mitochondrial membrane potential and mass, coupled with elevated NAD+ levels. Subsequent treatment with panobinostat induced a significant decrease in NAD+ biosynthesis and ATP generation. Furthermore, this intervention triggered the upregulation of pro-apoptotic BCL-2 family proteins, particularly BAX and BAK, concomitant with a notable reduction in mitochondrial membrane potential and the accumulation of reactive oxygen species. Consequently, heightened caspase-3 activity ensued, leading to significantly elevated cell death rates in 2DG-resistant gliomas. CONCLUSION Our findings highlight panobinostat as a promising therapy to resensitize 2DG-resistant pHGG cells to apoptosis, offering hope for treating these aggressive tumors with H3.3 K27M/G34R mutations.

Abstract Background: Human high-grade gliomas are aggressive brain cancers known for their resistance to treatment. Targeted therapies with single agents have shown limited success, and the presence of tumor heterogeneity complicates treatment. Combining multiple chemotherapeutic agents has emerged as a potential strategy to overcome these challenges. 2-deoxy-D-glucose (2-DG) is a glucose analog known for its ability to disrupt glycolysis, protein folding, and the pentose phosphate pathway. This disruption renders cancer cells more susceptible to further damage from reactive oxygen species and DNA damage. Previous studies have demonstrated synergistic effects when combining 2-DG with chemotherapeutic drugs in various cancers. Our study examines combining 2-DG with DNA-damaging agents for high-grade gliomas to uncover potential synergies, theorizing that this combination enhances cell death and metabolic stress, offering insights for better treatments against these tumors. Methods: The cell proliferation, clonogenic growth, and cell migration assays assessed viability, clonogenic formation, and migration. Additionally, the cell cycle and reactive oxygen species analysis were employed to evaluate cell division, oxidative stress, and antioxidant capacity. The Illumina NovaSeq 6000 platform measured transcript levels, and Liquid Chromatography-High-Resolution Mass Spectrometry analyzed metabolite changes in high-grade glioma cell lines following 2-DG treatment. The Agilent Seahorse Mito Stress Test evaluated alterations in cellular bioenergetics. SYNERGYFINDER 3 quantified synergistic effects of 2-DG with DNA-damaging agents, while the Annexin V-FITC Conjugates and a ROS multiplex assay assessed cell death and metabolic stress. Results: Our findings demonstrate that when used as a single agent, 2-DG induces cell senescence and limits cell migration but is insufficient to trigger cell death. Moreover, 2-DG treatment shifts glioma cells towards oxidative phosphorylation for energy production, elevates ROS levels, and hampers DNA synthesis and repair mechanisms. Our synergy study reveals promising synergistic effects when combining 2-DG with DNA-damaging agents, including 5-FU, Methotrexate, Gemcitabine, and Lomustine. This combined therapy leads to significant ROS generation and increased cell death compared to single-agent treatments. Furthermore, prolonged exposure to 2-DG leads to increased levels of both glucogenic and ketogenic amino acids within glioma cells, potentially serving as an alternative energy source. This finding hints at a prospective therapeutic approach for targeting drug-resistant cells. Conclusions: Our results suggest that the anticancer therapeutic effect of 2-DG is enhanced when used in combination with DNA-damaging agents, indicating this strategy as a potential approach for treating human high-grade glioma. Citation Format: Tracy Miller, Esther Jane, Matthew Halbert, Taylor Gatesman, Stacey Wendell, Dinesh Mohanakrishnan, Sameer Agnihotri, Daniel Premkumar, Ian Pollack. Enhanced chemosensitivity to DNA-damaging agents in human high-grade glioma through 2-DG treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2037.

Abstract BACKGROUND H3K27-altered diffuse midline glioma (DMG) is a devastating pediatric brainstem tumor that affects 200-300 individuals in the US per year. Median survival is 9-11 months, and there are virtually no long-term survivors. Despite decades of clinical trials, radiation therapy remains standard of care, extending survival by 2-3 months. Elucidating the mechanisms that drive H3K27-altered DMG pathogenesis in order to uncover therapeutic vulnerabilities is of critical importance. Recent studies implicate MALT1 as a potential therapeutic target in gliomas. MALT1 is the effector molecule of the CARMA-BCL10-MALT1 (CBM) signalosome, a cytoplasmic protein complex that drives downstream pro-survival transcriptional activity. MALT1, which possesses scaffolding and protease functions, promotes cell viability, proliferation, and migration/invasion in multiple cancer types. We aim to evaluate the hypotheses that MALT1 promotes DMG cancer cell proliferation and migration and that MALT1 inhibition will abrogate tumor progression. METHODS/RESULTS We screened a panel of cells including astrocytes, neural stem cells, and DMG cell lines by Western blot and found that CBM complex members BCL10 and MALT1 are present in all cells tested. We next demonstrated that MALT1 is proteolytically active in DMG cell lines SF8628 and HSJD-DIPG-007. Specifically, we showed cleavage of the MALT1 protease substrate HOIL, which was abrogated by treatment with the MALT1 protease inhibitor MLT-748. We next generated multiple dox-inducible MALT1 shRNA DMG cell lines to assess the impact of MALT1 deficiency on DMG biology. Thus far, we find that shRNA knockdown of MALT1 does not impact SF8628 cell proliferation. CONCLUSIONS MALT1 is expressed and proteolytically active in DMG cells. Initial studies show that MALT1 knockdown does not affect proliferation of SF8628 cells. We will next evaluate the effect of MALT1 knockdown on proliferation of additional DMG cell lines, as well as the impact on other malignant features of DMG cells including migration/invasion.

Abstract Introduction: Immune checkpoint inhibitors (ICI) are an important therapeutic option for patients with triple negative breast cancer (TNBC). However, identification of patients most likely to respond is challenging. PD-L1 positivity by immunohistochemistry is the standard biomarker used for ICI therapy selection in TNBC. However, other biomarkers, such as analysis of the tumor microenvironment (TME) may be more accurate in predicting response. The XernaTM TME Panel uses RNA sequencing data and machine learning to analyze the TME, utilizing the angiogenic and immunogenic biology of the TME to classify tumors into four TME subtypes. In this study, the distribution of Xerna TME subtypes and associated genomic alterations in TNBC were investigated for their potential use in therapy selection. Methods: A total of 203 TNBC patient samples underwent tumor-normal whole-exome, whole-transcriptome sequencing testing with the OncoExTraTM assay. The whole-transcriptome expression data were analyzed using the Xerna TME Panel to assign each sample to one of four subtypes: Immune Active (IA), Immune Suppressed (IS), Immune Desert (ID) and Angiogenic (A). The IA and IS subtypes both have high immune scores that may be particularly sensitive to ICI therapy. Actionable alterations, defined as those with FDA-approved matched therapies in any cancer, with matched clinical trials, or with evidence in cancer guidelines or the literature for possible matched therapies, were also identified and associations across Xerna subtypes were explored. Results: Approximately half (100 of 203; 49.3%) of the patient samples had high (IA+IS) immune subtypes (Table 1). Targetable alterations associated with an FDA-approved therapy were present in 114 (56.2%) patients. No biomarkers were significantly associated (p < 0.05) with high (IA+IS) versus low (ID+A) immune scores. Biomarkers associated with ICI response, namely mismatch repair gene alterations (MSH2/3/6, MLH1/3, PMS1/2), high tumor mutational burden (TMB-high) and microsatellite instability were detected in only 6 (3.0%), 3 (1.5%) and 1 (0.5%) patient samples respectively, and all but 1, an MSH6 alteration, were in high immune subtype samples. Conclusions: The Xerna TME Panel classified 49.3% of TNBC patient tumors to IA or IS, suggesting they may respond to ICI therapy. Many (56.2%) patient tumors harbored alterations associated with FDA-approved therapies, providing the potential for novel combination therapies. These findings warrant further study and clinical validation in TNBC patients treated with ICI therapy. Table 1. Frequency of actionable biomarkers that were present in at least 10 (5%) TNBC patient samples. Citation Format: Gargi Basu, Janine Lobello, Snehal Thakkar, Jessica Aldrich, Matthew Halbert, Patrick Eimerman, Cynthia Flannery, Nishitha Therala, David Hall, Daniel Pointing, Lea Vohar, Roman Luštrik, Luka Ausec, Mark Uhlik, Seema Iyer, Laura Benjamin, Frederick Baehner. Prevalence of genomic alterations in Xerna tumor microenvironment subtypes in triple negative breast cancer patients [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-06-10.

Abstract Purpose: This study evaluates MALT1 as a potential therapeutic target in H3K27-altered diffuse midline glioma (DMG). Background: H3K27-altered DMG is a devastating pediatric brain tumor that affects 200-300 individuals in the US per year. Median survival is 9-11 months, and there are virtually no long-term survivors. Despite decades of clinical trials, radiation therapy remains standard of care, extending survival by 2-3 months. Development of effective therapies for H3K27-altered DMG is a critical unmet need. MALT1 is the effector molecule of the CARMA-BCL10-MALT1 (CBM) signalosome, a cytoplasmic protein complex that drives downstream signaling, including activation of the pro-survival NF-kB transcription factor. MALT1, which possesses distinct scaffolding and protease activities, has been best characterized as an oncogenic driver in multiple lymphomas. More recently, MALT1 has been shown to act in multiple solid tumor types (breast, lung, glioblastoma) to promote cell viability, proliferation, and migration/invasion. Based on these studies, we hypothesize that MALT1 promotes H3K27-altered DMG cancer cell proliferation and survival and that MALT1 inhibition will abrogate DMG tumor progression. Methods/Results: We screened a panel of patient-derived DMG cell lines by Western blot and found that the CBM signalosome components BCL10 and MALT1 are present in all cell lines tested. We next optimized a brain-penetrant lipid nanoparticle (LNP) delivery system to achieve efficient siRNA knockdown in non-adherent DMG cells and utilized this approach to knockdown MALT1 in DIPG07, BT245, and DIPG XIII FL cell lines. Preliminary findings indicate that loss of MALT1 leads to a reduction in DMG cell viability. To complement this RNAi-based approach, we utilized the blood brain barrier (BBB)-penetrant small molecule MALT1 inhibitor “M1i-124.” This compound, discovered in our laboratory, is a protein-protein interaction inhibitor that disrupts the binding of BCL10 and MALT1 and blocks both MALT1 scaffold and protease activities (manuscript in revision). M1i-124 treatment, at nanomolar-range doses, reduces the viability of both DIPG07 and BT245 DMG cell lines. Conclusions: We found that both siRNA-mediated MALT1 knockdown and the small molecule MALT1 inhibitor M1i-124 are toxic to DMG cells. These preliminary findings point to the potential for therapeutic targeting of MALT1 in H3K27-altered DMG. Future Directions: We will next evaluate the mechanism by which MALT1 knockdown or pharmacological inhibition impacts DMG cell survival using RNA-sequencing and proteomics approaches. We will also use H3K27-altered DMG xenograft models to evaluate the impact of MALT1 inhibition on H3K27-altered DMG tumor progression in vivo. Citation Format: Hannah Butterfield, Juliana Hofstatter Azambuja, Lisa Maurer, Saigopalakrishna S. Yerneni, Andrea Cruz, Matthew Halbert, Taylor Gatesman, Sameer Agnihotri, Peter C. Lucas, Linda M. McAllister-Lucas. MALT1 as a regulator of tumor progression in H3K27-altered diffuse midline glioma [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr A002.

Abstract Metabolic reprogramming in pediatric diffuse midline glioma is driven by gene expression changes induced by the hallmark histone mutation H3K27M, which results in aberrantly permissive activation of oncogenic signaling pathways. Previous studies of diffuse midline glioma with altered H3K27 (DMG-H3K27a) have shown that the RAS pathway, specifically through its downstream kinase, extracellular-signal-related kinase 5 (ERK5), is critical for tumor growth. However, there remains a knowledge gap in identifying effectors of ERK signaling and their roles in DMG-H3K27a. Leveraging several patient multi-omic datasets, we identified a unique relationship between ERK5 and brain tumor glycolysis. We establish that ERK5 is a critical regulator of cell proliferation and glycolysis in DMG-H3K27a, where ERK5 knockdown leads to decreases in glycolysis and increases in mitochondrial metabolism. We demonstrate through loss of function and overexpression studies that ERK5 mediates glycolysis through regulation of glycolytic enzyme Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3). PFKFB3 is a protein that catalyzes the synthesis or degradation of fructose-2,6-bisphosphate (F2,6BP). Furthermore, we establish a novel mechanism, in which ERK5 mediates PFKFB3 expression via activation of MEF2A, an oncogenic transcription factor. DMG-H3K27a cells are sensitive to the loss or inhibition of PFKFB3 both in vitro and in orthotopic mouse models. However, monotherapy is ineffective in heterogenous diseases such as gliomas, including DMG-H3K27a. To combat this, we show multi-targeted therapy against the ERK5-PFKFB3 axis is synergistic in vitro and in vivo. Multi-targeted drug therapy against the ERK5-PFKFB3 axis, such as with small-molecule inhibitors, may represent a promising therapeutic approach in patients with pediatric diffuse midline glioma. Moreover, we have identified resistance to our dual therapy using several systems biology approaches, which we are currently investigating and validating. Collectively, our study defines a novel, targetable axis in DMG-H3K27a and highlights the importance of tumor cell metabolism in defining therapeutic vulnerabilities.

Abstract BACKGROUND Diffuse Midline Glioma (DMG) is a highly aggressive (CNS WHO Grade IV) pediatric brain tumor characterized by the histone mutation H3K27M, resulting in global hypomethylation of histones. H3K27M mutant cells are highly dependent on methionine and methionine Adenosyltransferase 2A (MAT2A), a central regulator of the methionine cycle, representing a key vulnerability in H3K27M gliomas. MAT2A is upregulated by methyltransferase-like protein 16 (METTL16), which deposits N6-methyladenosine (m6A) on a subset of RNA residues to regulate gene expression. MAT2A is a sensor of methyl group donor S-adenosylmethionine (SAM) that, when placed, increases MAT2A intron splicing to compensate for a decrease in MAT2A function. METHODS To investigate our hypothesis, H3K27M histone mutation knockout cell lines were established using CRISPR Cas9 (Jabado lab) in DIPG4 cells. shRNA-mediated knockdown was used to attenuate METTL16 expression in DIPG4 H3K27M cells, and growth was assessed via sulforhodamine B (SRB) assay. RESULTS In silico analysis of normal brain tissue compared to low-grade glioma and high-grade glioma demonstrated increased METTL16 at both the RNA and protein levels (p=<0.0001). Therefore, we postulated that targeting METTL16 would affect H3K27M growth. Results showed increased cell death compared to control cells by day 4 (p=0.0034) and day 8 (p=<0.0001). Furthermore, knockdown of METTL16 in DMG cells with H3K27M decreased m6A levels on poly (A) RNA (p=0.049). CONCLUSIONS Our study highlights the vulnerability of H3K27M mutant cells to METTL16 modulation, elucidating underlying molecular mechanisms and paving the way for innovative therapeutic strategies targeting this axis.

Abstract Diffuse Midline gliomas (DMGs) are grade IV tumors by the World Health Organization. They are inoperable and resistant to chemo/radiotherapies resulting in a median survival of 8-11 months and a 5-year survival of <2%. DMG is an epigenetic disease characterized by mutations on histone H3.3 K27M resulting in global transcriptional reprogramming. This disease lacks appropriate models to predict disease biology and response to treatment. Therefore, we developed a novel syngeneic H3K27M mouse model using clinically relevant co-alterations in Olig2+ neural progenitor cells (NPCs). Using an unbiased systems biology approach, we identified a reliance of H3K27M but not isogenic controls to the amino acid methionine, and the enzymes methionine adenosyltransferase 2A (MAT2A), and adenosylmethionine decarboxylase 1 (AMD1). MAT2A is a master regulator of methionine metabolism that converts methionine into the universal methyl donor S-adenosylmethionine (SAM) which is later converted into decarboxylated SAM (dcSAM) by AMD1 for polyamine metabolism. We postulated that targeting methionine regulator MAT2A through genetic/pharmacological abrogation would selectively alter DMG viability by disrupting the methylome. We discovered a novel mechanism demonstrating H3K27M cells are sensitive to MAT2A loss independent of methylthioadenosine phosphorylase (MTAP) deletions but rather through AMD1 overexpression. The current paradigm shows that MAT2A protein expression is inversely correlated with cellular SAM concentrations as sensed by splicing complex and m6A reader methyltransferase-like protein 16 (METTL16). To investigate the molecular mechanism by which H3K27M represses MAT2A, we postulated that dcSAM, the resultant metabolite of AMD1, promote(s) high turnover of METTL16–MAT2A transcript interactions like SAM, thereby diminishing MAT2A transcript and protein expression. We found that exogenous dcSAM promoted MAT2A intron retention and lower mature transcript levels. Our findings demonstrate that H3K27M leads to increased AMD1 protein expression resulting in diminished MAT2A expression. Combinatorial treatments inhibiting MAT2A and AMD1 may presents exploitable therapeutic vulnerabilities in these gliomas.

Glioblastoma is the most common primary, malignant brain tumor that remains uniformly lethal in nearly all cases as a result of extreme cellular heterogeneity, treatment resistance, and recurrence. A major hurdle in therapeutic delivery to brain tumors is the blood–brain barrier (BBB), which is the tightly regulated vascular barrier between the brain parenchyma and systemic circulation that prevents distribution of otherwise beneficial chemotherapeutics to central nervous system tumors. To overcome the obstacle of drug delivery beyond the BBB, nanoparticle formulations have come to the forefront, having demonstrated success in preclinical observations, but have not translated well into the clinical setting. In summary, this review article discusses brain tumors and challenges for drug delivery caused by the BBB, explores the benefits of nanoparticle formulations for brain tumor delivery, describes the characteristics these formulations possess that make them attractive therapeutic strategies, and provides preclinical examples that implement nanoparticles within glioma treatment regimens. Additionally, we explore the pitfalls associated with clinical translation and conclude with remarks geared toward overcoming these issues.

Glioblastoma is the most malignant primary brain tumor, the prognosis of which remains dismal even with aggressive surgical, medical, and radiation therapies. Glioblastoma stem cells (GSCs) promote therapeutic resistance and cellular heterogeneity due to their self-renewal properties and capacity for plasticity. To understand the molecular processes essential for maintaining GSCs, we performed an integrative analysis comparing active enhancer landscapes, transcriptional profiles, and functional genomics profiles of GSCs and non-neoplastic neural stem cells (NSCs). We identified sorting nexin 10 (SNX10), an endosomal protein sorting factor, as selectively expressed in GSCs compared with NSCs and essential for GSC survival. Targeting SNX10 impaired GSC viability and proliferation, induced apoptosis, and reduced self-renewal capacity. Mechanistically, GSCs utilized endosomal protein sorting to promote platelet-derived growth factor receptor β (PDGFRβ) proliferative and stem cell signaling pathways through posttranscriptional regulation of the PDGFR tyrosine kinase. Targeting SNX10 expression extended survival of orthotopic xenograft–bearing mice, and high SNX10 expression correlated with poor glioblastoma patient prognosis, suggesting its potential clinical importance. Thus, our study reveals an essential connection between endosomal protein sorting and oncogenic receptor tyrosine kinase signaling and suggests that targeting endosomal sorting may represent a promising therapeutic approach for glioblastoma treatment.

Background In advanced colorectal cancer (CRC), analysis of the tumor microenvironment (TME) may be useful as a predictive biomarker, particularly supporting the use of immunotherapies and anti-angiogenic therapies.1 The XernaTM TME Panel utilizes RNA sequencing data and machine learning to analyze the angiogenic and immunogenic biology of the TME to classify tumors into four TME subtypes.2 In this study, we investigated the distribution of Xerna TME subtypes and associated genomic alterations in CRC for their potential use in therapy selection. Methods A total of 336 CRC patient samples underwent testing with the OncoExTraTM assay. This assay utilizes whole-exome, whole-transcriptome sequencing to identify actionable alterations, defined as those with FDA-approved matched therapies in any cancer, with matched clinical trials, or with evidence in cancer guidelines or the literature for possible matched therapies. The whole-transcriptome expression data were analyzed using the Xerna TME Panel to assign each sample to one of four subtypes: Immune Active (IA), Immune Suppressed (IS), Immune Desert (ID) and Angiogenic (A). Biomarker associations were explored. Results Approximately half (49.4%) of the patient samples had high (IA+IS) versus low (ID+A) immune subtypes, and 247 (73.5%) harbored targetable alterations associated with an FDA-approved therapy. Several biomarkers were significantly associated (p<0.05) with Xerna subtypes, most of which were over-represented in high immune subtypes (19 of 21), with 13 indicative of defective DNA repair (table 1). Microsatellite instability (MSI-high) and high tumor mutational burden (TMB-high) were detected in 30 (8.9%) and 37 (11.0%) patient samples, with 28 (16.9%) and 33 (19.9%) occurring within high immune subtypes (IA+IS), respectively. Some MSI-high and TMB-high samples occurred in low immune subtypes (ID+A), perhaps indicating a lower propensity for response to ICI therapy. Of note, 138 of 306 (45.1%) MSI-low and 133 of 299 (44.5%) TMB-low samples were in the high immune subtypes, suggestive of possible sensitivity to ICI therapy. Actionable KRAS/NRAS, and BRAF alterations were detected in 162 (48.2%) and 23 (6.8%) patients respectively, though none were significantly associated with TME subtypes. Conclusions The Xerna TME Panel classified 49.4% of CRC patients to IA or IS subtypes who may benefit from ICI therapy, including many lacking biomarkers currently used for this therapy decision. Most (73.5%) patients harbored alterations associated with FDA-approved therapies, providing the potential for novel combination therapies.3 These findings warrant further study and clinical validation in CRC patients treated with ICI therapy. References Huyghe N, Benidovskaya E, Stevens P, Van den Eynde M. Biomarkers of Response and Resistance to Immunotherapy in Microsatellite Stable Colorectal Cancer: Toward a New Personalized Medicine. Cancers (Basel). 2022 Apr 29;14(9):2241. doi: 10.3390/cancers14092241. PMID: 35565369; PMCID: PMC9105843. Uhlik M, Pointing D, Iyer S, Ausec L, Štajdohar M, Cvitkovič R, Žganec M, Culm K, Santos VC, Pytowski B, Malafa M, Liu H, Krieg AM, Lee J, Rosengarten R, Benjamin L. Xerna™ TME Panel is a machine learning-based transcriptomic biomarker designed to predict therapeutic response in multiple cancers. Front Oncol. 2023 May 12;13:1158345. doi: 10.3389/fonc.2023.1158345. PMID: 37251949; PMCID: PMC10213262. Yang Z, Wu G, Zhang X, Gao J, Meng C, Liu Y, Wei Q, Sun L, Wei P, Bai Z, Yao H, Zhang Z. Current progress and future perspectives of neoadjuvant anti-PD-1/PD-L1 therapy for colorectal cancer. Front Immunol. 2022 Sep 9;13:1001444. doi: 10.3389/fimmu.2022.1001444. PMID: 36159842; PMCID: PMC9501688. Ethics Approval The study was approved by WCG IRB Ethics Board, approval number 20181863.

Diffuse Midline gliomas (DMGs) are grade IV tumors by the World Health Organization. They are inoperable and resistant to chemo/radiotherapies resulting in a median survival of 8-11 months and a 5-year survival of <2%. DMG is an epigenetic disease characterized by mutations on histone H3.3 K27M resulting in global transcriptional reprogramming. This disease lacks appropriate models to predict disease biology and response to treatment. Therefore, we developed a novel syngeneic H3K27M mouse model using clinically relevant co-alterations in Olig2+ neural progenitor cells (NPCs). Using an unbiased systems biology approach, we identified a reliance of H3K27M but not isogenic controls to the amino acid methionine, and the enzymes methionine adenosyltransferase 2A (MAT2A), and adenosylmethionine decarboxylase 1 (AMD1). MAT2A is a master regulator of methionine metabolism that converts methionine into the universal methyl donor S-adenosylmethionine (SAM) which is later converted into decarboxylated SAM (dcSAM) by AMD1 for polyamine metabolism. We postulated that targeting methionine regulator MAT2A through genetic/pharmacological abrogation would selectively alter DMG viability by disrupting the methylome. We discovered a novel mechanism demonstrating H3K27M cells are sensitive to MAT2A loss independent of methylthioadenosine phosphorylase (MTAP) deletions but rather through AMD1 overexpression. The current paradigm shows that MAT2A protein expression is inversely correlated with cellular SAM concentrations as sensed by splicing complex and m6A reader methyltransferase-like protein 16 (METTL16). To investigate the molecular mechanism by which H3K27M represses MAT2A, we postulated that dcSAM, the resultant metabolite of AMD1, promote(s) high turnover of METTL16–MAT2A transcript interactions like SAM, thereby diminishing MAT2A transcript and protein expression. We found that exogenous dcSAM promoted MAT2A intron retention and lower mature transcript levels. Our findings demonstrate that H3K27M leads to increased AMD1 protein expression resulting in diminished MAT2A expression. Combinatorial treatments inhibiting MAT2A and AMD1 may presents exploitable therapeutic vulnerabilities in these gliomas.

Abstract Histone 3 lysine27-to-methionine mutations (H3-K27M) frequently occur in childhood diffuse midline gliomas (DMGs) of the pons, thalamus, and spinal cord, presumed to be driven by the specific spatiotemporal context of these midline locations during postnatal development. While most common in the pons and at mid-childhood ages, the same oncohistone mutation is recurrently detected in adult DMGs and throughout different midline regions. The potential heterogeneity of tumors at different ages and in different anatomical locations of the midline are vastly understudied. Through dissecting the transcriptomic, epigenomic and spatial architectures of a comprehensive cohort of patient H3-K27M DMGs - spanning the age range from 2-68 years and locations from spinal cord to thalamus - at single cell resolution, we delineate how age- and location-dependent contexts shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We identify that oligodendrocyte precursor (OPC)-like cells constitute the stem-like compartment in H3-K27M DMGs across all clinico-anatomical groups, however, depending on location, display varying levels of maturity resembling less differentiated pre-OPCs or more mature OPCs further differentiated along the oligodendroglial lineage. We further demonstrate increased mesenchymal cell states in adult tumors, which we link to age-related differences in glioma-associated immune cell compartments, in particular an increase of macrophages in adult compared to pediatric tumors. Furthermore, we resolve the spatial organization of H3-K27M DMG cell types and states in intact patient tissues, identifying a local niche of the oligodendroglial lineage. Our study provides a powerful resource for rational modeling and therapeutic frameworks taking into account determinants of age and location in this lethal glioma group.

In previous studies, we demonstrated that panobinostat, a histone deacetylase inhibitor, and bortezomib, a proteasomal inhibitor, displayed synergistic therapeutic activity against pediatric and adult high-grade gliomas. Despite the remarkable initial response to this combination, resistance emerged. Here, in this study, we aimed to investigate the molecular mechanisms underlying the anticancer effects of panobinostat and marizomib, a brain-penetrant proteasomal inhibitor, and the potential for exploitable vulnerabilities associated with acquired resistance. RNA sequencing followed by gene set enrichment analysis (GSEA) was employed to compare the molecular signatures enriched in resistant compared with drug-naïve cells. The levels of adenosine 5'-triphosphate (ATP), nicotinamide adenine dinucleotide (NAD)+ content, hexokinase activity, and tricarboxylic acid (TCA) cycle metabolites required for oxidative phosphorylation to meet their bioenergetic needs were analyzed. Here, we report that panobinostat and marizomib significantly depleted ATP and NAD+ content, increased mitochondrial permeability and reactive oxygen species generation, and promoted apoptosis in pediatric and adult glioma cell lines at initial treatment. However, resistant cells exhibited increased levels of TCA cycle metabolites, which required for oxidative phosphorylation to meet their bioenergetic needs. Therefore, we targeted glycolysis and the electron transport chain (ETC) with small molecule inhibitors, which displayed substantial efficacy, suggesting that resistant cell survival is dependent on glycolytic and ETC complexes. To verify these observations in vivo, lonidamine, an inhibitor of glycolysis and mitochondrial function, was chosen. We produced two diffuse intrinsic pontine glioma (DIPG) models, and lonidamine treatment significantly increased median survival in both models, with particularly dramatic effects in panobinostat- and marizomib-resistant cells. These data provide new insights into mechanisms of treatment resistance in gliomas.

Abstract Diffuse midline glioma is an aggressive brain tumor with a median age at diagnosis of 6.3 years and 5-year survival rate of 2.2%.The defining histone mutation H3K27M precludes docking of a protein responsible for epigenetic modification resulting in erroneously accessible chromatin and subsequent transcription of oncogenic pathways, including the RAS-MERK5-ERK5 signaling cascade. To determine which oncogenic processes are regulated by extracellular signal-regulated kinase 5 (ERK5), gene-set enrichment analysis of patient-derived datasets demonstrated gene networks involved in glycolysis to be enriched with ERK5 expression. In confirmation, loss of ERK5 via shRNA interference reduced cell proliferation and glycolysis in DIPG IV and SF8628 cells. Reintroduction of ERK5 wildtype (WT) into ERK5 knockdown lines rescued cell proliferation and glycolysis, while the addition of ERK5 kinase dead domain (KDD) only partially rescued these survival and metabolic defects. Targeted evaluation of glycolysis enzyme expression via qRT-PCR revealed a direct relationship between ERK5 and proglycolytic enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). Mechanistically, ERK5 activation of PFKFB3 was mediated by activation of transcriptional factor myocyte enhancer factor 2A (MEF2A) as demonstrated by coimmunoprecipitation and luciferase promoter assays. Expression of PFKFB3 was elevated at both the mRNA and protein level in DMG patient-derived samples. Genetic knockdown of PFKFB3 via shRNA interference resulted in reduced proliferation and glycolysis in DIPG IV and SF8628 cells. Similarly, pharmacologic inhibition of PFKFB3 with small molecule inhibitor PFK-158 capitulated these results. This inhibitor demonstrated blood brain barrier penetrance in silico and extended survival of in vivo mouse models. Multitargeted drug therapy against both ERK5 and PFKFB3 produced a synergetic in vitro response with increased sensitivity of these cells to apoptosis compared to single treatment alone. In conclusion, these results support ERK5 regulation of glycolysis through the critical metabolic effector PFKFB3. Multitargeted drug therapy against this axis represents a therapeutic vulnerability in pediatric diffuse midline glioma.