bims-malgli Biomed News
on Biology of malignant gliomas
Issue of 2020‒09‒27
fifteen papers selected by
Oltea Sampetrean
Keio University
  1. Glioblastoma Tissue Slice Tandem-Cultures for Quantitative Evaluation of Inhibitory Effects on Invasion and Growth.
  2. Monotherapy efficacy of blood-brain barrier permeable small molecule reactivators of protein phosphatase 2A in glioblastoma.
  3. Phagocytic glioblastoma-associated microglia and macrophages populate invading pseudopalisades.
  4. Sox2-dependent maintenance of mouse oligodendroglioma involves the Sox2-mediated downregulation of Cdkn2b, Ebf1, Zfp423, and Hey2.
  5. Glutamate is a non-invasive metabolic biomarker of IDH1 mutant glioma response to temozolomide treatment.
  6. Potential Therapeutic Effects of the Neural Stem Cell-Targeting Antibody Nilo1 in Patient-Derived Glioblastoma Stem Cells.
  7. Sphingolipid Metabolism in Glioblastoma and Metastatic Brain Tumors: A Review of Sphingomyelinases and Sphingosine-1-Phosphate.
  8. Quantitative in vivo bioluminescence imaging of orthotopic patient-derived glioblastoma xenografts.
  9. Extracellular proteolysis in glioblastoma progression and therapeutics.
  10. LncRNA BCYRN1 inhibits glioma tumorigenesis by competitively binding with miR-619-5p to regulate CUEDC2 expression and the PTEN/AKT/p21 pathway.
  11. Overview of Current Drug Delivery Methods Across the Blood-Brain Barrier for the Treatment of Primary Brain Tumors.
  12. Separate and not Equal: Sex Differences in JAM-A Tumor Suppression in Glioblastoma.
  13. Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma.
  14. Author Correction: Selective, high-contrast detection of syngeneic glioblastoma in vivo.
  15. Molecular subtyping of glioblastoma based on immune-related genes for prognosis.
  1. Cancers (Basel). 2020 Sep 21. pii: E2707. [Epub ahead of print]12(9):
    Glioblastoma Tissue Slice Tandem-Cultures for Quantitative Evaluation of Inhibitory Effects on Invasion and Growth.
    Vasile Sidorcenco, Luisa Krahnen, Marion Schulz, Janina Remy, Donat Kögel, Achim Temme, Ute Krügel, Heike Franke, Achim Aigner.
      Glioblastomas (GBMs) are the most malignant brain tumors and are essentially incurable even after extensive surgery, radiotherapy, and chemotherapy, mainly because of extensive infiltration of tumor cells into the adjacent normal tissue. Thus, the evaluation of novel drugs in malignant glioma treatment requires sophisticated ex vivo models that approach the authentic interplay between tumor and host environment while avoiding extensive in vivo studies in animals. This paper describes the standardized setup of an organotypic brain tissue slice tandem-culture system, comprising of normal brain tissue from adult mice and tumor tissue from human glioblastoma xenografts, and explore its utility for assessing inhibitory effects of test drugs. The microscopic analysis of vertical sections of the slice tandem-cultures allows for the simultaneous assessment of (i) the invasive potential of single cells or cell aggregates and (ii) the space occupying growth of the bulk tumor mass, both contributing to malignant tumor progression. The comparison of tissue slice co-cultures with spheroids vs. tissue slice tandem-cultures using tumor xenograft slices demonstrates advantages of the xenograft tandem approach. The direct and facile application of test drugs is shown to exert inhibitory effects on bulk tumor growth and/or tumor cell invasion, and allows their precise quantitation. In conclusion, we describe a straightforward ex vivo system mimicking the in vivo situation of the tumor mass and the normal brain in GBM patients. It reduces animal studies and allows for the direct and reproducible application of test drugs and the precise quantitation of their effects on the bulk tumor mass and on the tumor's invasive properties.
    Keywords:  Pim-1; STAT3; ex vivo model; glioblastoma; tissue slice co-cultures; tumor invasion; tumor xenografts
    DOI:  https://doi.org/10.3390/cancers12092707
  2. Brain Commun. 2020 ;2(1): fcaa002
    Monotherapy efficacy of blood-brain barrier permeable small molecule reactivators of protein phosphatase 2A in glioblastoma.
    Joni Merisaari, Oxana V Denisova, Milena Doroszko, Vadim Le Joncour, Patrik Johansson, William P J Leenders, David B Kastrinsky, Nilesh Zaware, Goutham Narla, Pirjo Laakkonen, Sven Nelander, Michael Ohlmeyer, Jukka Westermarck.
      Glioblastoma is a fatal disease in which most targeted therapies have clinically failed. However, pharmacological reactivation of tumour suppressors has not been thoroughly studied as yet as a glioblastoma therapeutic strategy. Tumour suppressor protein phosphatase 2A is inhibited by non-genetic mechanisms in glioblastoma, and thus, it would be potentially amendable for therapeutic reactivation. Here, we demonstrate that small molecule activators of protein phosphatase 2A, NZ-8-061 and DBK-1154, effectively cross the in vitro model of blood-brain barrier, and in vivo partition to mouse brain tissue after oral dosing. In vitro, small molecule activators of protein phosphatase 2A exhibit robust cell-killing activity against five established glioblastoma cell lines, and nine patient-derived primary glioma cell lines. Collectively, these cell lines have heterogeneous genetic background, kinase inhibitor resistance profile and stemness properties; and they represent different clinical glioblastoma subtypes. Moreover, small molecule activators of protein phosphatase 2A were found to be superior to a range of kinase inhibitors in their capacity to kill patient-derived primary glioma cells. Oral dosing of either of the small molecule activators of protein phosphatase 2A significantly reduced growth of infiltrative intracranial glioblastoma tumours. DBK-1154, with both higher degree of brain/blood distribution, and more potent in vitro activity against all tested glioblastoma cell lines, also significantly increased survival of mice bearing orthotopic glioblastoma xenografts. In summary, this report presents a proof-of-principle data for blood-brain barrier-permeable tumour suppressor reactivation therapy for glioblastoma cells of heterogenous molecular background. These results also provide the first indications that protein phosphatase 2A reactivation might be able to challenge the current paradigm in glioblastoma therapies which has been strongly focused on targeting specific genetically altered cancer drivers with highly specific inhibitors. Based on demonstrated role for protein phosphatase 2A inhibition in glioblastoma cell drug resistance, small molecule activators of protein phosphatase 2A may prove to be beneficial in future glioblastoma combination therapies.
    Keywords:  CIP2A; DT-061; E98; PME-1; tricyclic neurological drugs
    DOI:  https://doi.org/10.1093/braincomms/fcaa002
  3. Brain Commun. 2020 ;2(1): fcz043
    Phagocytic glioblastoma-associated microglia and macrophages populate invading pseudopalisades.
    Elena Saavedra-López, Meritxell Roig-Martínez, George P Cribaro, Paola V Casanova, José M Gallego, Ana Pérez-Vallés, Carlos Barcia.
      Hypoxic pseudopalisades are a pathological hallmark of human glioblastoma, which is linked to tumour malignancy and aggressiveness. Yet, their function and role in the tumour development have scarcely been explored. It is thought that pseudopalisades are formed by malignant cells escaping from the hypoxic environment, although evidence of the immune component of pseudopalisades has been elusive. In the present work, we analyse the immunological constituent of hypoxic pseudopalisades using high-resolution three-dimensional confocal imaging in tissue blocks from excised tumours of glioblastoma patients and mimic the hypoxic gradient in microfluidic platforms in vitro to understand the cellular motility. We visualize that glioblastoma-associated microglia and macrophages abundantly populate pseudopalisades, displaying an elongated kinetic morphology across the pseudopalisades, and are oriented towards the necrotic focus. In vitro experiments demonstrate that under hypoxic gradient, microglia show a particular motile behaviour characterized by the increase of cellular persistence in contrast with glioma cells. Importantly, we show that glioblastoma-associated microglia and macrophages utilize fibres of glioma cells as a haptotactic cue to navigate along the anisotropic structure of the pseudopalisades and display a high phagocytic activity at the necrotic border of the pseudopalisades. In this study, we demonstrate that glioblastoma-associated microglia and macrophages are the main immune cells of pseudopalisades in glioblastoma, travelling to necrotic areas to clear the resulting components of the prothrombotic milieu, suggesting that the scavenging features of glioblastoma-associated microglia and macrophages at the pseudopalisades serve as an essential counterpart for glioma cell invasion.
    Keywords:  glioblastoma; hypoxia; macrophages; microglia; pseudopalisades
    DOI:  https://doi.org/10.1093/braincomms/fcz043
  4. Glia. 2020 Sep 25.
    Sox2-dependent maintenance of mouse oligodendroglioma involves the Sox2-mediated downregulation of Cdkn2b, Ebf1, Zfp423, and Hey2.
    Cristiana Barone, Mariachiara Buccarelli, Francesco Alessandrini, Miriam Pagin, Laura Rigoldi, Irene Sambruni, Rebecca Favaro, Sergio Ottolenghi, Roberto Pallini, Lucia Ricci-Vitiani, Paolo Malatesta, Silvia K Nicolis.
      Cancer stem cells (CSC) are essential for tumorigenesis. The transcription factor Sox2 is overexpressed in brain gliomas, and is essential to maintain CSC. In mouse high-grade glioma pHGG cells in culture, Sox2 deletion causes cell proliferation arrest and inability to reform tumors after transplantation in vivo; in Sox2-deleted cells, 134 genes are derepressed. To identify genes mediating Sox2 deletion effects, we overexpressed into pHGG cells nine among the most derepressed genes, and identified four genes, Ebf1, Hey2, Zfp423, and Cdkn2b, that strongly reduced cell proliferation in vitro and brain tumorigenesis in vivo. CRISPR/Cas9 mutagenesis of each gene, individually or in combination (Ebf1 + Cdkn2b), significantly antagonized the proliferation arrest caused by Sox2 deletion. The same genes also repressed clonogenicity in primary human glioblastoma-derived CSC-like lines. These experiments identify a network of critical tumor suppressive Sox2-targets whose inhibition by Sox2 is involved in glioma CSC maintenance, defining new potential therapeutic targets.
    Keywords:  Sox2; cancer stem cells; gene regulatory networks; human glioblastoma; mouse oligodendroglioma; transcription factors; tumorigenesis
    DOI:  https://doi.org/10.1002/glia.23914
  5. Cancer Res. 2020 Sep 21. pii: canres.1314.2020. [Epub ahead of print]
    Glutamate is a non-invasive metabolic biomarker of IDH1 mutant glioma response to temozolomide treatment.
    Elavarasan Subramani, Marina Radoul, Chloe Najac, Georgios Batsios, Abigail R Molloy, Donghyun Hong, Anne Marie Gillespie, Romelyn Delos Santos, Pavithra Viswanath, Joseph F Costello, Russell O Pieper, Sabrina M Ronen.
      Although lower-grade gliomas are driven by mutations in the isocitrate dehydrogenase 1 (IDH1) gene and are less aggressive than primary glioblastoma, they nonetheless generally recur. IDH1 mutant patients are increasingly being treated with temozolomide (TMZ), but early detection of response remains a challenge and there is a need for complementary imaging methods to assess response to therapy prior to tumor shrinkage. The goal of this study was to determine the value of magnetic resonance spectroscopy (MRS)-based metabolic changes for detection of response to TMZ in both genetically engineered and patient-derived mutant IDH1 models. Using 1H MRS in combination with chemometrics identified several metabolic alterations in TMZ-treated cells, including a significant increase in steady-state glutamate levels. This was confirmed in vivo, where the observed 1H MRS increase in glutamate/glutamine occurred prior to tumor shrinkage. Cells labeled with [1-13C]glucose and [3-13C]glutamine, the principal sources of cellular glutamate, showed that flux to glutamate both from glucose via the tricarboxylic acid cycle and from glutamine were increased following TMZ treatment. In line with these results, hyperpolarized [5-13C]glutamate produced from [2-13C]pyruvate and hyperpolarized [1-13C]glutamate produced from [1-13C]α-ketoglutarate were significantly higher in TMZ-treated cells compared to controls. Collectively, our findings identify 1H MRS-detectable elevation of glutamate and hyperpolarized 13C MRS-detectable glutamate production from either pyruvate or α-ketoglutarate as potential translatable metabolic biomarkers of response to TMZ treatment in mutant IDH1 glioma.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1314
  6. Front Oncol. 2020 ;10 1665
    Potential Therapeutic Effects of the Neural Stem Cell-Targeting Antibody Nilo1 in Patient-Derived Glioblastoma Stem Cells.
    Gorjana Rackov, Giorgia Iegiani, Daniel Uribe, Claudia Quezada, Cristóbal Belda-Iniesta, Carmen Escobedo-Lucea, Augusto Silva, Pere Puig, Víctor González-Rumayor, Ángel Ayuso-Sacido.
      Glioblastoma (GBM) is the most devastating and least treatable brain tumor with median survival <15 months and extremely high recurrence rates. Promising results of immune checkpoint blockade obtained from pre-clinical studies in mice did not translate to clinic, and new strategies are urgently needed, particularly those targeting GBM stem cells (GSCs) that are held responsible for drug resistance and tumor recurrence. Patient-derived GSC cultures are critical for finding effective brain tumor therapies. Here, we investigated the ability of the recently described monoclonal antibody Nilo1 to specifically recognize GSCs isolated from GBM surgical samples. We employed five patient-derived GSC cultures with different stemness marker expression and differentiation potential, able to recapitulate original tumors when xenotransplanted in vivo. To answer whether Nilo1 has any functional effects in patient-derived GSCs lines, we treated the cells with Nilo1 in vitro and analyzed cell proliferation, cell cycle, apoptosis, sphere formation, as well as the expression of stem vs. differentiation markers. All tested GSCs stained positively for Nilo1, and the ability of Nilo1 to recognize GSCs strongly relied on their stem-like phenotype. Our results showed that a subset of patient-derived GSCs were sensitive to Nilo1 treatment. In three GSC lines Nilo1 triggered differentiation accompanied by the induction of p21. Most strikingly, in one GSC line Nilo1 completely abrogated self-renewal and led to Bax-associated apoptosis. Our data suggest that Nilo1 targets a molecule functionally relevant for stemness maintenance and pinpoint Nilo1 as a novel antibody-based therapeutical strategy to be used either alone or in combination with cytotoxic drugs for GSC targeting. Further pre-clinical studies are needed to validate the effectiveness of GSC-specific Nilo1 targeting in vivo.
    Keywords:  Nilo1; antibody; glioblastoma; glioma stem cells; immunotherapy; neural stem cells
    DOI:  https://doi.org/10.3389/fonc.2020.01665
  7. Biomolecules. 2020 Sep 23. pii: E1357. [Epub ahead of print]10(10):
    Sphingolipid Metabolism in Glioblastoma and Metastatic Brain Tumors: A Review of Sphingomyelinases and Sphingosine-1-Phosphate.
    Cyntanna C Hawkins, Tomader Ali, Sasanka Ramanadham, Anita B Hjelmeland.
      Glioblastoma (GBM) is a primary malignant brain tumor with a dismal prognosis, partially due to our inability to completely remove and kill all GBM cells. Rapid tumor recurrence contributes to a median survival of only 15 months with the current standard of care which includes maximal surgical resection, radiation, and temozolomide (TMZ), a blood-brain barrier (BBB) penetrant chemotherapy. Radiation and TMZ cause sphingomyelinases (SMase) to hydrolyze sphingomyelins to generate ceramides, which induce apoptosis. However, cells can evade apoptosis by converting ceramides to sphingosine-1-phosphate (S1P). S1P has been implicated in a wide range of cancers including GBM. Upregulation of S1P has been linked to the proliferation and invasion of GBM and other cancers that display a propensity for brain metastasis. To mediate their biological effects, SMases and S1P modulate signaling via phospholipase C (PLC) and phospholipase D (PLD). In addition, both SMase and S1P may alter the integrity of the BBB leading to infiltration of tumor-promoting immune populations. SMase activity has been associated with tumor evasion of the immune system, while S1P creates a gradient for trafficking of innate and adaptive immune cells. This review will explore the role of sphingolipid metabolism and pharmacological interventions in GBM and metastatic brain tumors with a focus on SMase and S1P.
    Keywords:  glioblastoma; metastasis; sphingolipid; sphingomyelin; sphingomyelinase; sphingosine-1-phosphate
    DOI:  https://doi.org/10.3390/biom10101357
  8. Sci Rep. 2020 Sep 21. 10(1): 15361
    Quantitative in vivo bioluminescence imaging of orthotopic patient-derived glioblastoma xenografts.
    Anna L Koessinger, Dominik Koessinger, Katrina Stevenson, Catherine Cloix, Louise Mitchell, Colin Nixon, Natividad Gomez-Roman, Anthony J Chalmers, Jim C Norman, Stephen W G Tait.
      Despite extensive research, little progress has been made in glioblastoma therapy, owing in part to a lack of adequate preclinical in vivo models to study this disease. To mitigate this, primary patient-derived cell lines, which maintain their specific stem-like phenotypes, have replaced established glioblastoma cell lines. However, due to heterogenous tumour growth inherent in glioblastoma, the use of primary cells for orthotopic in vivo studies often requires large experimental group sizes. Therefore, when using intracranial patient-derived xenograft (PDX) approaches, it is advantageous to deploy imaging techniques to monitor tumour growth and allow stratification of mice. Here we show that stable expression of near-infrared fluorescent protein (iRFP) in patient-derived glioblastoma cells enables rapid, direct non-invasive monitoring of tumour development without compromising tumour stemness or tumorigenicity. Moreover, as this approach does not depend on the use of agents like luciferin, which can cause variability due to changing bioavailability, it can be used for quantitative longitudinal monitoring of tumour growth. Notably, we show that this technique also allows quantitative assessment of tumour burden in highly invasive models spreading throughout the brain. Thus, iRFP transduction of primary patient-derived glioblastoma cells is a reliable, cost- and time-effective way to monitor heterogenous orthotopic PDX growth.
    DOI:  https://doi.org/10.1038/s41598-020-72322-x
  9. Biochim Biophys Acta Rev Cancer. 2020 Sep 18. pii: S0304-419X(20)30147-5. [Epub ahead of print] 188428
    Extracellular proteolysis in glioblastoma progression and therapeutics.
    Agathe Quesnel, George S Karagiannis, Panagiota S Filippou.
      Gliomas encompass highly invasive primary central nervous system (CNS) tumours of glial cell origin with an often poor clinical prognosis. Of all gliomas, glioblastoma is the most aggressive form of primary brain cancer. Current treatments in glioblastoma are insufficient due to the invasive nature of brain tumour cells, which typically results in local tumour recurrence following treatment. The latter represents the most important cause of mortality in glioblastoma and underscores the necessity for an in-depth understanding of the underlying mechanisms. Interestingly, increased synthesis and secretion of several proteolytic enzymes within the tumour microenvironment, such as matrix metalloproteinases, lysosomal proteases, cathepsins and kallikreins for extracellular-matrix component degradation may play a major role in the aforementioned glioblastoma invasion mechanisms. These proteolytic networks are key players in establishing and maintaining a tumour microenvironment that promotes tumour cell survival, proliferation, and migration. Indeed, the targeted inhibition of these proteolytic enzymes has been a promisingly useful therapeutic strategy for glioblastoma management in both preclinical and clinical development. We hereby summarize current advances on the biology of the glioblastoma tumour microenvironment, with a particular emphasis on the role of proteolytic enzyme families in glioblastoma invasion and progression, as well as on their subsequent prognostic value as biomarkers and their therapeutic targeting in the era of precision medicine.
    Keywords:  Extracellular proteolysis; Glioblastoma; Invasion; Matrix metalloproteinases; Therapeutic targets
    DOI:  https://doi.org/10.1016/j.bbcan.2020.188428
  10. Oncogene. 2020 Sep 25.
    LncRNA BCYRN1 inhibits glioma tumorigenesis by competitively binding with miR-619-5p to regulate CUEDC2 expression and the PTEN/AKT/p21 pathway.
    Maolin Mu, Wanxiang Niu, Xiaoming Zhang, Shanshan Hu, Chaoshi Niu.
      Glioma is the most common malignant tumor in the central nervous system. Altered long noncoding RNAs (lncRNAs) are playing regulatory roles in physiological and pathogenic processes in cancer. Here, we uncovered a differentially expressed lncRNA called brain cytoplasmic RNA 1 (BCYRN1), and elucidated its function and molecular mechanism in the progression and development of glioma. Three fresh tumor tissues from glioma patients and three normal brain tissues from craniocerebral trauma patients were prepared for high-throughput RNA sequencing. Differential RNA transcripts and BCYRN1 were identified by RT-qPCR in glioma samples and controls. CCK-8, colony formation assays, flow cytometry, TUNEL assays, cell migration assays, wound-healing assays, and xenograft model were established to investigate the biological function of BCYRN1 both in vitro and in vivo. Various bioinformatics analysis, dual-luciferase reporter assays, biotinylated RNA pulldown assays, and rescue experiments were conducted to reveal the underlying mechanisms of competitive endogenous RNAs (ceRNAs). 183 lncRNAs were identified with significant dysregulation in glioma and randomly selected differential RNAs were further confirmed by RT-qPCR. Among them, BCYRN1 was the most downregulated lncRNA, and its low expression positively correlated with glioma progression. Functionally, BCYRN1 overexpression inhibited cell proliferation, migration in glioma cell lines, whereas BCYRN1 depletion resulted in the opposite way. MiR-619-5p was further confirmed as the direct target of BCYRN1. Mechanistically, miR-619-5p specifically targeted the CUE domain containing protein 2 (CUEDC2), and BCYRN1/miR-619-5p suppressed glioma tumorigenesis by inactivating PTEN/AKT/p21 pathway in a CUEDC2-dependent manner. Overall, our data presented that the reduced expression of BCYRN1 was associated with poor patient outcome in glioma. BCYRN1 functioned as a ceRNA to inhibit glioma progression by sponging miR-619-5p to regulate CUEDC2 expression and PTEN/AKT/p21 pathway. Our results indicated that BCYRN1 exerted tumor suppressor potential and might be a candidate in the diagnosis and treatment of glioma.
    DOI:  https://doi.org/10.1038/s41388-020-01466-x
  11. CNS Drugs. 2020 Sep 23.
    Overview of Current Drug Delivery Methods Across the Blood-Brain Barrier for the Treatment of Primary Brain Tumors.
    Rianne Haumann, Jessica Carvalho Videira, Gertjan J L Kaspers, Dannis G van Vuurden, Esther Hulleman.
      Existing drug delivery methods have not led to a significant increase in survival for patients with malignant primary brain tumors. While the combination of conventional therapies consisting of surgery, radiotherapy, and chemotherapy has improved survival for some types of brain tumors (e.g., WNT medulloblastoma), other types of brain tumors (e.g., glioblastoma and diffuse midline glioma) still have a poor prognosis. The reason for the differences in response can be largely attributed to the blood-brain barrier (BBB), a specialized structure at the microvasculature level that regulates the transport of molecules across the blood vessels into the brain parenchyma. This structure hampers the delivery of most chemotherapeutic agents for the treatment of primary brain tumors. Several drug delivery methods such as nanoparticles, convection enhanced delivery, focused ultrasound, intranasal delivery, and intra-arterial delivery have been developed to overcome the BBB in primary brain tumors. However, prognosis of most primary brain tumors still remains poor. The heterogeneity of the BBB in primary brain tumors and the distinct vasculature of tumors make it difficult to design a drug delivery method that targets the entire tumor. Drug delivery methods that combine strategies such as focused ultrasound and nanoparticles might be a more successful approach. However, more research is needed to optimize and develop new drug delivery techniques to improve survival of patients with primary brain tumors.
    DOI:  https://doi.org/10.1007/s40263-020-00766-w
  12. Neuro Oncol. 2020 Sep 22. pii: noaa218. [Epub ahead of print]
    Separate and not Equal: Sex Differences in JAM-A Tumor Suppression in Glioblastoma.
    Jack M Shireman, Atique U Ahmed.
      
    DOI:  https://doi.org/10.1093/neuonc/noaa218
  13. Mol Syst Biol. 2020 Sep;16(9): e9506
    Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma.
    Yunpeng Liu, Ning Shi, Aviv Regev, Shan He, Michael T Hemann.
      Glioblastoma multiforme (GBM) is a highly malignant form of cancer that lacks effective treatment options or well-defined strategies for personalized cancer therapy. The disease has been stratified into distinct molecular subtypes; however, the underlying regulatory circuitry that gives rise to such heterogeneity and its implications for therapy remain unclear. We developed a modular computational pipeline, Integrative Modeling of Transcription Regulatory Interactions for Systematic Inference of Susceptibility in Cancer (inTRINSiC), to dissect subtype-specific regulatory programs and predict genetic dependencies in individual patient tumors. Using a multilayer network consisting of 518 transcription factors (TFs), 10,733 target genes, and a signaling layer of 3,132 proteins, we were able to accurately identify differential regulatory activity of TFs that shape subtype-specific expression landscapes. Our models also allowed inference of mechanisms for altered TF behavior in different GBM subtypes. Most importantly, we were able to use the multilayer models to perform an in silico perturbation analysis to infer differential genetic vulnerabilities across GBM subtypes and pinpoint the MYB family member MYBL2 as a drug target specific for the Proneural subtype.
    Keywords:  cell state plasticity; gene essentiality inference; glioblastoma multiforme; subtype-specific gene regulation; transcription regulatory networks
    DOI:  https://doi.org/10.15252/msb.20209506
  14. Sci Rep. 2020 Sep 24. 10(1): 16011
    Author Correction: Selective, high-contrast detection of syngeneic glioblastoma in vivo.
    Richard B Banati, Paul Wilcox, Ran Xu, Grace Yin, Emily Si, Eric Taeyoung Son, Mauricio Shimizu, R M Damian Holsinger, Arvind Parmar, David Zahra, Andrew Arthur, Ryan J Middleton, Guo-Jun Liu, Arnaud Charil, Manuel B Graeber.
      An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    DOI:  https://doi.org/10.1038/s41598-020-72364-1
  15. Sci Rep. 2020 Sep 23. 10(1): 15495
    Molecular subtyping of glioblastoma based on immune-related genes for prognosis.
    Xueran Chen, Xiaoqing Fan, Chenggang Zhao, Zhiyang Zhao, Lizhu Hu, Delong Wang, Ruiting Wang, Zhiyou Fang.
      Glioblastoma (GBM) is associated with an increasing mortality and morbidity and is considered as an aggressive brain tumor. Recently, extensive studies have been carried out to examine the molecular biology of GBM, and the progression of GBM has been suggested to be correlated with the tumor immunophenotype in a variety of studies. Samples in the current study were extracted from the ImmPort and TCGA databases to identify immune-related genes affecting GBM prognosis. A total of 92 immune-related genes displaying a significant correlation with prognosis were mined, and a shrinkage estimate was conducted on them. Among them, the 14 most representative genes showed a marked correlation with patient prognosis, and LASSO and stepwise regression analysis was carried out to further identify the genes for the construction of a predictive GBM prognosis model. Then, samples in training and test cohorts were incorporated into the model and divided to evaluate the efficiency, stability, and accuracy of the model to predict and classify the prognosis of patients and to identify the relevant immune features according to the median value of RiskScore (namely, Risk-H and Risk-L). In addition, the constructed model was able to instruct clinicians in diagnosis and prognosis prediction for various immunophenotypes.
    DOI:  https://doi.org/10.1038/s41598-020-72488-4
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