bims-malgli Biomed News
on Biology of malignant gliomas
Issue of 2022–05–22
twelve papers selected by
Oltea Sampetrean, Keio University
  1. Chromatin structure predicts survival in glioma patients.
  2. Glioma and the gut-brain axis: opportunities and future perspectives.
  3. A first-in-human Phase I trial of the oral p-STAT3 inhibitor WP1066 in patients with recurrent malignant glioma.
  4. Novel approaches to combat chemoresistance against glioblastomas.
  5. Target receptor identification and subsequent treatment of resected brain tumors with encapsulated and engineered allogeneic stem cells.
  6. Mitochondrial 1555 G>A variant as a potential risk factor for childhood glioblastoma.
  7. Dangerous RNA links pave the way to glioblastoma.
  8. Identification of Implications of Angiogenesis and m6A Modification on Immunosuppression and Therapeutic Sensitivity in Low-Grade Glioma by Network Computational Analysis of Subtypes and Signatures.
  9. H3-K27M-mutant nucleosomes interact with MLL1 to shape the glioma epigenetic landscape.
  10. Major Features of the 2021 WHO Classification of CNS Tumors.
  11. SARS-CoV-2 Permissive glioblastoma cell line for high throughput antiviral screening.
  12. Locally secreted BiTEs complement CAR T cells by enhancing killing of antigen heterogeneous solid tumors.
  1. Sci Rep. 2022 May 17. 12(1): 8221
    Chromatin structure predicts survival in glioma patients.
    Matthew C Garrett, Rebecca Albano, Troy Carnwath, Sanjit Shah, Daniel Woo, Michael Lamba, David R Plas, Aditi Paranjpe, Krishna Roskin, Chuntao Zhao, Richard Lu.
      The pathological changes in epigenetics and gene regulation that accompany the progression of low-grade to high-grade gliomas are under-studied. The authors use a large set of paired atac-seq and RNA-seq data from surgically resected glioma specimens to infer gene regulatory relationships in glioma. Thirty-eight glioma patient samples underwent atac-seq sequencing and 16 samples underwent additional RNA-seq analysis. Using an atac-seq/RNA-seq correlation matrix, atac-seq peaks were paired with genes based on high correlation values (|r2| > 0.6). Samples clustered by IDH1 status but not by grade. Surprisingly there was a trend for IDH1 mutant samples to have more peaks. The majority of peaks are positively correlated with survival and positively correlated with gene expression. Constructing a model of the top six atac-seq peaks created a highly accurate survival prediction model (r2 = 0.68). Four of these peaks were still significant after controlling for age, grade, pathology, IDH1 status and gender. Grade II, III, and IV (primary) samples have similar transcription factors and gene modules. However, grade IV (recurrent) samples have strikingly few peaks. Patient-derived glioma cultures showed decreased peak counts following radiation indicating that this may be radiation-induced. This study supports the notion that IDH1 mutant and IDH1 wildtype gliomas have different epigenetic landscapes and that accessible chromatin sites mapped by atac-seq peaks tend to be positively correlated with expression. The data in this study leads to a new model of treatment response wherein glioma cells respond to radiation therapy by closing open regions of DNA.
    DOI:  https://doi.org/10.1038/s41598-022-11019-9
  2. Neurooncol Adv. 2022 Jan-Dec;4(1):4(1): vdac054
    Glioma and the gut-brain axis: opportunities and future perspectives.
    Antonio Dono, Jack Nickles, Ana G Rodriguez-Armendariz, Braden C McFarland, Nadim J Ajami, Leomar Y Ballester, Jennifer A Wargo, Yoshua Esquenazi.
      The gut-brain axis has presented a valuable new dynamic in the treatment of cancer and central nervous system (CNS) diseases. However, little is known about the potential role of this axis in neuro-oncology. The goal of this review is to highlight potential implications of the gut-brain axis in neuro-oncology, in particular gliomas, and future areas of research. The gut-brain axis is a well-established biochemical signaling axis that has been associated with various CNS diseases. In neuro-oncology, recent studies have described gut microbiome differences in tumor-bearing mice and glioma patients compared to controls. These differences in the composition of the microbiome are expected to impact the metabolic functionality of each microbiome. The effects of antibiotics on the microbiome may affect tumor growth and modulate the immune system in tumor-bearing mice. Preliminary studies have shown that the gut microbiome might influence PD-L1 response in glioma-bearing mice, as previously observed in other non-CNS cancers. Groundbreaking studies have identified intratumoral bacterial DNA in several cancers including high-grade glioma. The gut microbiome and its manipulation represent a new and relatively unexplored area that could be utilized to enhance the effectiveness of therapy in glioma. Further mechanistic studies of this therapeutic strategy are needed to assess its clinical relevance.
    Keywords:  fecal metabolites; glioblastoma; glioma; gut microbiome; gut–brain axis
    DOI:  https://doi.org/10.1093/noajnl/vdac054
  3. CNS Oncol. 2022 May 16. CNS87
    A first-in-human Phase I trial of the oral p-STAT3 inhibitor WP1066 in patients with recurrent malignant glioma.
    John de Groot, Martina Ott, Jun Wei, Cynthia Kassab, Dexing Fang, Hinda Najem, Barbara O'Brien, Shiao-Pei Weathers, Carlos Kamiya Matsouka, Nazanin K Majd, Rebecca A Harrison, Gregory N Fuller, Jason T Huse, James P Long, Raymond Sawaya, Ganesh Rao, Tobey J MacDonald, Waldemar Priebe, Michael DeCuypere, Amy B Heimberger.
      Aim: To ascertain the maximum tolerated dose (MTD)/maximum feasible dose (MFD) of WP1066 and p-STAT3 target engagement within recurrent glioblastoma (GBM) patients. Patients & methods: In a first-in-human open-label, single-center, single-arm 3 + 3 design Phase I clinical trial, eight patients were treated with WP1066 until disease progression or unacceptable toxicities. Results: In the absence of significant toxicity, the MFD was identified to be 8 mg/kg. The most common adverse event was grade 1 nausea and diarrhea in 50% of patients. No treatment-related deaths occurred; 6 of 8 patients died from disease progression and one was lost to follow-up. Of 8 patients with radiographic follow-up, all had progressive disease. The longest response duration exceeded 3.25 months. The median progression-free survival (PFS) time was 2.3 months (95% CI: 1.7 months-NA months), and 6-month PFS (PFS6) rate was 0%. The median overall survival (OS) rate was 25 months (95% CI: 22.5 months-NA months), with an estimated 1-year OS rate of 100%. Pharmacokinetic (PK) data demonstrated that at 8 mg/kg, the T1/2 was 2-3 h with a dose dependent increase in the Cmax. Immune monitoring of the peripheral blood demonstrated that there was p-STAT3 suppression starting at a dose of 1 mg/kg. Conclusion: Immune analyses indicated that WP1066 inhibited systemic immune p-STAT3. WP1066 had an MFD identified at 8 mg/kg which is the target allometric dose based on prior preclinical modeling in combination with radiation therapy and a Phase II study is being planned for newly diagnosed MGMT promoter unmethylated glioblastoma patients.
    Keywords:  Phase I; STAT3 inhibitor; glioblastoma; toxicity
    DOI:  https://doi.org/10.2217/cns-2022-0005
  4. Cancer Drug Resist. 2020 ;3(4): 686-698
    Novel approaches to combat chemoresistance against glioblastomas.
    Rheal A Towner, Michelle Zalles, Debra Saunders, Nataliya Smith.
      The poor prognosis of glioblastoma multiforme (GBM) patients is in part due to resistance to current standard-of-care treatments including chemotherapy [predominantly temozolomide (TMZ; Temodar)], radiation therapy and an anti-angiogenic therapy [an antibody against the vascular endothelial growth factor (bevacizumab; Avastin)], resulting in recurrent tumors. Several recurrent GBM tumors are commonly resistant to either TMZ, radiation or bevacizumab, which contributes to the low survival rate for GBM patients. This review will focus on novel targets and therapeutic approaches that are currently being considered to combat GBM chemoresistance. One of these therapeutic options is a small molecule called OKlahoma Nitrone 007 (OKN-007), which was discovered to inhibit the transforming growth factor β1 pathway, reduce TMZ-resistance and enhance TMZ-sensitivity. OKN-007 is currently an investigational new drug in clinical trials for both newly-diagnosed and recurrent GBM patients. Another novel target is ELTD1 (epidermal growth factor, latrophilin and seven transmembrane domain-containing protein 1; alternatively known as ADGRL4, Adhesion G protein-coupled receptor L4), which we used a monoclonal antibody against, where a therapy against it was found to inhibit Notch 1 in a pre-clinical GBM xenograft model. Notch 1 is known to be associated with chemoresistance in GBM. Other potential therapeutic targets to combat GBM chemoresistance include the phosphoinositide 3-kinase pathway, nuclear factor-κB, the hepatocyte/scatter factor (c-MET), the epidermal growth factor receptor, and the tumor microenvironment.
    Keywords:  ELTD1; Glioblastoma; OKlahoma Nitrone 007; magnetic resonance imaging; pre-clinical models; transforming growth factor-β1
    DOI:  https://doi.org/10.20517/cdr.2020.38
  5. Nat Commun. 2022 May 19. 13(1): 2810
    Target receptor identification and subsequent treatment of resected brain tumors with encapsulated and engineered allogeneic stem cells.
    Deepak Bhere, Sung Hugh Choi, Pim van de Donk, David Hope, Kiki Gortzak, Amina Kunnummal, Jasneet Khalsa, Esther Revai Lechtich, Clemens Reinshagen, Victoria Leon, Nabil Nissar, Wenya Linda Bi, Cheng Feng, Hongbin Li, Yu Shrike Zhang, Steven H Liang, Neil Vasdev, Walid Ibn Essayed, Pablo Valdes Quevedo, Alexandra Golby, Naima Banouni, Anna Palagina, Reza Abdi, Brian Fury, Stelios Smirnakis, Alarice Lowe, Brock Reeve, Arthur Hiller, E Antonio Chiocca, Glenn Prestwich, Hiroaki Wakimoto, Gerhard Bauer, Khalid Shah.
      Cellular therapies offer a promising therapeutic strategy for the highly malignant brain tumor, glioblastoma (GBM). However, their clinical translation is limited by the lack of effective target identification and stringent testing in pre-clinical models that replicate standard treatment in GBM patients. In this study, we show the detection of cell surface death receptor (DR) target on CD146-enriched circulating tumor cells (CTC) captured from the blood of mice bearing GBM and patients diagnosed with GBM. Next, we developed allogeneic "off-the-shelf" clinical-grade bifunctional mesenchymal stem cells (MSCBif) expressing DR-targeted ligand and a safety kill switch. We show that biodegradable hydrogel encapsulated MSCBif (EnMSCBif) has a profound therapeutic efficacy in mice bearing patient-derived invasive, primary and recurrent GBM tumors following surgical resection. Activation of the kill switch enhances the efficacy of MSCBif and results in their elimination post-tumor treatment which can be tracked by positron emission tomography (PET) imaging. This study establishes a foundation towards a clinical trial of EnMSCBif in primary and recurrent GBM patients.
    DOI:  https://doi.org/10.1038/s41467-022-30558-3
  6. Neurooncol Adv. 2022 Jan-Dec;4(1):4(1): vdac045
    Mitochondrial 1555 G>A variant as a potential risk factor for childhood glioblastoma.
    Shaobo Li, Xiaowu Gai, Swe Swe Myint, Katti Arroyo, Libby Morimoto, Catherine Metayer, Adam J de Smith, Kyle M Walsh, Joseph L Wiemels.
       Background: Childhood glioblastoma multiforme (GBM) is a highly aggressive disease with low survival, and its etiology, especially concerning germline genetic risk, is poorly understood. Mitochondria play a key role in putative tumorigenic processes relating to cellular oxidative metabolism, and mitochondrial DNA variants were not previously assessed for association with pediatric brain tumor risk.
    Methods: We conducted an analysis of 675 mitochondrial DNA variants in 90 childhood GBM cases and 2789 controls to identify enrichment of mitochondrial variant associated with GBM risk. We also performed this analysis for other glioma subtypes including pilocytic astrocytoma. Nuclear-encoded mitochondrial gene variants were also analyzed.
    Results: We identified m1555 A>G was significantly associated with GBM risk (adjusted OR 29.30, 95% CI 5.25-163.4, P-value 9.5 X 10-4). No association was detected for other subtypes. Haplotype analysis further supported the independent risk contributed by m1555 G>A, instead of a haplogroup joint effect. Nuclear-encoded mitochondrial gene variants identified significant associations in European (rs62036057 in WWOX, adjusted OR = 2.99, 95% CI 1.88-4.75, P-value = 3.42 X 10-6) and Hispanic (rs111709726 in EFHD1, adjusted OR = 3.57, 95% CI 1.99-6.40, P-value = 1.41 X 10-6) populations in ethnicity-stratified analyses.
    Conclusion: We report for the first time a potential role played by a functional mitochondrial ribosomal RNA variant in childhood GBM risk, and a potential role for both mitochondrial and nuclear-mitochondrial DNA polymorphisms in GBM tumorigenesis. These data implicate cellular oxidative metabolic capacity as a contributor to the etiology of pediatric glioblastoma.
    Keywords:  mitochondrial genome; pediatric glioblastoma; risk factor; variant
    DOI:  https://doi.org/10.1093/noajnl/vdac045
  7. Mol Cell. 2022 May 19. pii: S1097-2765(22)00392-6. [Epub ahead of print]82(10): 1783-1785
    Dangerous RNA links pave the way to glioblastoma.
    Magda Bienko.
      A new study by Deforzh et al. (2022) demonstrates how two long non-coding RNAs (lncRNAs) link a distal enhancer to the HOXD3/D4/miR-10b gene promoter, leading to transcriptional activation of the therapeutic target miR-10b in glioblastoma multiforme.
    DOI:  https://doi.org/10.1016/j.molcel.2022.04.029
  8. Front Immunol. 2022 ;13 871564
    Identification of Implications of Angiogenesis and m6A Modification on Immunosuppression and Therapeutic Sensitivity in Low-Grade Glioma by Network Computational Analysis of Subtypes and Signatures.
    Bo Li, Fang Wang, Nan Wang, Kuiyuan Hou, Jianyang Du.
      Angiogenesis is a complex process in the immunosuppressed low-grade gliomas (LGG) microenvironment and is regulated by multiple factors. N6-methyladenosine (m6A), modified by the m6A modification regulators ("writers" "readers" and "erasers"), can drive LGG formation. In the hypoxic environment of intracranial tumor immune microenvironment (TIME), m6A modifications in glioma stem cells are predominantly distributed around neovascularization and synergize with complex perivascular pathological ecology to mediate the immunosuppressive phenotype of TIME. The exact mechanism of this phenomenon remains unknown. Herein, we elucidated the relevance of the angiogenesis-related genes (ARGs) and m6A regulators (MAGs) and their influencing mechanism from a macro perspective. Based on the expression pattern of MAGs, we divided patients with LGG into two robust categories via consensus clustering, and further annotated the malignant related mechanisms and corresponding targeted agents. The two subgroups (CL1, CL2) demonstrated a significant correlation with prognosis and clinical-pathology features. Moreover, WGCNA has also uncovered the hub genes and related mechanisms of MAGs affecting clinical characters. Clustering analysis revealed a synergistic promoting effect of M6A and angiogenesis on immunosuppression. Based on the expression patterns of MAGs, we established a high-performance gene-signature (MASig). MASig revealed somatic mutational mechanisms by which MAGs affect the sensitivity to treatment in LGG patients. In conclusion, the MAGs were critical participants in the malignant process of LGG, with a vital potential in the prognosis stratification, prediction of outcome, and therapeutic sensitivity of LGG. Findings based on these strategies may facilitate the development of objective diagnosis and treatment systems to quantify patient survival and other outcomes, and in some cases, to identify potential unexplored targeted therapies.
    Keywords:  angiogenesis; immunosuppression; low-grade glioma; m6A RNA modification; tumor immune microenvironment
    DOI:  https://doi.org/10.3389/fimmu.2022.871564
  9. Cell Rep. 2022 May 17. pii: S2211-1247(22)00609-X. [Epub ahead of print]39(7): 110836
    H3-K27M-mutant nucleosomes interact with MLL1 to shape the glioma epigenetic landscape.
    Noa Furth, Danielle Algranati, Bareket Dassa, Olga Beresh, Vadim Fedyuk, Natasha Morris, Lawryn H Kasper, Dan Jones, Michelle Monje, Suzanne J Baker, Efrat Shema.
      Cancer-associated mutations in genes encoding histones dramatically reshape chromatin and support tumorigenesis. Lysine to methionine substitution of residue 27 on histone H3 (K27M) is a driver mutation in high-grade pediatric gliomas, known to abrogate polycomb repressive complex 2 (PRC2) activity. We applied single-molecule systems to image individual nucleosomes and delineate the combinatorial epigenetic patterns associated with H3-K27M expression. We found that chromatin marks on H3-K27M-mutant nucleosomes are dictated both by their incorporation preferences and by intrinsic properties of the mutation. Mutant nucleosomes not only preferentially bind PRC2 but also directly interact with MLL1, leading to genome-wide redistribution of H3K4me3. H3-K27M-mediated deregulation of repressive and active chromatin marks leads to unbalanced "bivalent" chromatin, which may support a poorly differentiated cellular state. This study provides evidence for a direct effect of H3-K27M oncohistone on the MLL1-H3K4me3 pathway and highlights the capability of single-molecule tools to reveal mechanisms of chromatin deregulation in cancer.
    Keywords:  CP: Cancer; CP: Molecular biology; DIPG; H3-K27M; chromatin; histone modifications; oncohistone; single molecule
    DOI:  https://doi.org/10.1016/j.celrep.2022.110836
  10. Neurotherapeutics. 2022 May 16.
    Major Features of the 2021 WHO Classification of CNS Tumors.
    Heather L Smith, Nitin Wadhwani, Craig Horbinski.
      Advances in the understanding of the molecular biology of central nervous system (CNS) tumors prompted a new World Health Organization (WHO) classification scheme in 2021, only 5 years after the prior iteration. The 2016 version was the first to include specific molecular alterations in the diagnoses of a few tumors, but the 2021 system greatly expanded this approach, with over 40 tumor types and subtypes now being defined by their key molecular features. Many tumors have also been reconceptualized into new "supercategories," including adult-type diffuse gliomas, pediatric-type diffuse low- and high-grade gliomas, and circumscribed astrocytic gliomas. Some entirely new tumors are in this scheme, particularly pediatric tumors. Naturally, these changes will impact how CNS tumor patients are diagnosed and treated, including clinical trial enrollment. This review addresses the most clinically relevant changes in the 2021 WHO book, including diffuse and circumscribed gliomas, ependymomas, embryonal tumors, and meningiomas.
    Keywords:  Astrocytoma; Embryonal; Ependymoma; Glioma; Meningioma; WHO
    DOI:  https://doi.org/10.1007/s13311-022-01249-0
  11. Antiviral Res. 2022 May 17. pii: S0166-3542(22)00111-5. [Epub ahead of print] 105342
    SARS-CoV-2 Permissive glioblastoma cell line for high throughput antiviral screening.
    Emiel Vanhulle, Joren Stroobants, Becky Provinciael, Anita Camps, Sam Noppen, Piet Maes, Kurt Vermeire.
      Despite the great success of the administered vaccines against SARS-CoV-2, the virus can still spread, as evidenced by the current circulation of the highly contagious Omicron variant. This emphasizes the additional need to develop effective antiviral countermeasures. In the context of early preclinical studies for antiviral assessment, robust cellular infection systems are required to screen drug libraries. In this study, we reported the implementation of a human glioblastoma cell line, stably expressing ACE2, in a SARS-CoV-2 cytopathic effect (CPE) reduction assay. These glioblastoma cells, designated as U87.ACE2+, expressed ACE2 and cathepsin B abundantly, but had low cellular levels of TMPRSS2 and cathepsin L. The U87.ACE2+ cells fused highly efficiently and quickly with SARS-CoV-2 spike expressing cells. Furthermore, upon infection with SARS-CoV-2 wild-type virus, the U87.ACE2+ cells displayed rapidly a clear CPE that resulted in complete cell lysis and destruction of the cell monolayer. By means of several readouts we showed that the U87.ACE2+ cells actively replicate SARS-CoV-2. Interestingly, the U87.ACE2+ cells could be successfully implemented in an MTS-based colorimetric CPE reduction assay, providing IC50 values for Remdesivir and Nirmatrelvir in the (low) nanomolar range. Lastly, the U87.ACE2+ cells were consistently permissive to all tested SARS-CoV-2 variants of concern, including the current Omicron variant. Thus, ACE2 expressing glioblastoma cells are highly permissive to SARS-CoV-2 with productive viral replication and with the induction of a strong CPE that can be utilized in high-throughput screening platforms.
    Keywords:  Antiviral screen; CPE; Glioblastoma; Omicron; SARS-CoV-2; U87 cell line
    DOI:  https://doi.org/10.1016/j.antiviral.2022.105342
  12. Mol Ther. 2022 May 14. pii: S1525-0016(22)00309-4. [Epub ahead of print]
    Locally secreted BiTEs complement CAR T cells by enhancing killing of antigen heterogeneous solid tumors.
    Yibo Yin, Jesse L Rodriguez, Nannan Li, Radhika Thokala, MacLean P Nasrallah, Li Hu, Logan Zhang, Jiasi Vicky Zhang, Meghan T Logun, Devneet Kainth, Leila Haddad, Yang Zhao, Tong Wu, Emily X Johns, Yu Long, Hongsheng Liang, Jiping Qi, Xiangtong Zhang, Zev A Binder, Zhiguo Lin, Donald M O'Rourke.
      Bispecific T-cell engagers (BiTEs) are bispecific antibodies that redirect T cells to target antigen-expressing tumors. We hypothesized that BiTE-secreting T cells could be a valuable therapy in solid tumors, with distinct properties in mono- or multi-valent strategies incorporating chimeric antigen receptor (CAR) T cells. Glioblastomas represent a good model for solid tumor heterogeneity, representing a significant therapeutic challenge. We detected expression of tumor-associated epidermal growth factor receptor (EGFR), EGFR variant III (EGFRvIII), and interleukin-13 receptor alpha 2 (IL13Rα2) on glioma tissues and cancer stem cells. These antigens formed the basis of a multivalent approach, using a conformation-specific tumor-related EGFR targeting antibody (806) and Hu08, an IL13Rα2-targeting antibody, as the scFvs to generate new BiTE molecules. Compared with CAR T cells, BiTE T cells demonstrated prominent activation, cytokine production, and cytotoxicity in response to target-positive gliomas. Superior response activity was also demonstrated in BiTE secreting bivalent T cells compared with bivalent CAR T cells in a glioma mouse model at early phase, but not in the long-term. In summary, BiTEs secreted by mono- or multi- valent T cells have potent anti-tumor activity in vitro and in vivo with significant sensitivity and specificity, demonstrating a promising strategy in solid tumor therapy.
    DOI:  https://doi.org/10.1016/j.ymthe.2022.05.011
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