Atypical Teratoid/Rhabdoid Tumours (ATRT) and Group 3 Medulloblastoma (MB) are aggressive paediatric brain tumours which mostly occur in infants and children. Due to the severity of off-target effects associated with chemo/radiotherapy in young patients, there is increasing consideration of more targeted therapies. Astrocytes have previously been shown to support progression and therapy resistance of other brain tumours; our work aims to elucidate this crosstalk in MB and ATRT to identify novel therapeutic targets amenable for localised delivery to resection cavities. We developed a bespoke 3D model which recapitulates the in vivo scenario, whereby human astrocytes and tumour cells were grown for 7-days in a human brain decellularised extracellular matrix hydrogel. RNA sequencing compared tumour cells from monocultures to those co-cultured with astrocytes. Ubiquitous upregulation of S100A10, SERPINE1, COL1A1, and SOCS3 was observed across the MB cell lines (d283, d341 and d425). For ATRT, common genes including MMP2, NOTCH3, TGFBR2 and GAP43 were upregulated in BT12, BT16 and BT37 cells when cultured with astrocytes. Pathway analyses revealed cancer lines had a more proliferative and invasive phenotype in the presence of astrocytes. Based on RNA-seq analyses, 21 repurposed drugs were screened against MB and ATRT cells. Top ranking compounds included: halofuginone, BB-Cl-amidine, Juglone, and AZD8055. We combined these with potential anti-migratory drugs: Tiplaxtinin, T-5224 and an ANX2T inhibitor and selected synergistic or additive combinations based on bliss synergy scores. For ATRT, a combination of AZD8055 (mTor inhibitor) and Tiplaxtinin (SERPINE1 inhibitor) showed high synergy. 3D migration studies found that T-5224 (FOS inhibitor) and AZD8055 significantly reduced migration of spheroids in vitro for MB cells. Delivery of T-5224 and AZD8055 to a d425 resection model demonstrated tolerability. Similarly, delivery of Tiplaxtinin and AZD8055 conferred tolerability in a BT12 resection model and a survival advantage was indicated in groups treated with AZD8055 alone.

BACKGROUND Atypical Teratoid/Rhabdoid Tumours (ATRT) are aggressive paediatric brain tumours which mostly occur in the first three years of life and which rapidly recur after surgical resection. There has been debate over the use of cytotoxic consolidation therapy due to the severity of off target effects associated with chemo/radiotherapy use in young patients. Astrocytes have previously been shown to support progression and therapy resistance of other brain tumours; however, their role in ATRT pathophysiology is yet to be elucidated. METHODS To better understand how adjacent “healthy” brain tissue may be complicit in ATRT recurrence, we have developed a 3D in vitro model in which ATRT cells are co-cultured with astrocytes within a bespoke decellularized human cerebellum extracellular matrix (ECM) hydrogel. RESULTS Immunofluorescence confirmed that human cerebellar ECM hydrogels retain human brain ECM components (hyaluronic acid, laminin, and fibronectin). ATRT-astrocyte co-culture spheroids were formed within the ECM hydrogel and observed to display a distinctive morphology relative to monoculture controls, with no difference in overall viability. Co-cultured tumour cells were successfully harvested from the model and isolated from astrocyte populations using fluorescence activated cell sorting. In both 2D and 3D culture, we have shown that astrocytes labelled with CM-DiI transfer this cell tracker dye to ATRT-MYC (BT12, BT16) and ATRT-TYR (BT37) cells, potentially indicating intercellular trafficking. Furthermore, in 2D culture ATRT-MYC (BT12 and BT16) cells form actin rich cell-cell processes with astrocytes when co-cultured in vitro. CONCLUSIONS This work represents a comprehensively characterised model of ATRT interaction with the healthy brain. Future work will analyse changes in ATRT cell transcriptomes when astrocytes are present in the model. By understanding how the presence of astrocytes in the tumour microenvironment may promote tumour survival and progression, we aim to use this data to identify candidate therapeutics to inhibit crosstalk and improve patient outcomes.

Abstract BACKGROUND Medulloblastoma (MB) and Atypical Teratoid/ Rhabdoid Tumours (ATRT) represent paediatric cerebellar tumours with a dismal prognosis. For ATRT in particular, 5-year survival remains at less than 32%. We have developed a 3D in vitro model termed ‘tumoursphere matrix’ which recapitulates in vivo crosstalk between tumour and reactive brain. METHODS AND RESULTS We co-cultured D283 (Group 3-MYC amplified MB) and BT12 (ATRT-MYC) cells with primary human cerebellar astrocytes within a PEGDA hydrogel containing decellularised cerebellar extracellular matrix (ECM) derived from non-disease human autopsy brain. Cerebellar ECM was extensively characterised, showing a significant reduction in cellular material whilst retaining ECM ligands. Reduction of DNA content to 174 ng/mg was corroborated by an absence of nuclei in immunohistochemical staining. Colorimetric assays indicated collagen and glycosaminoglycan retention in decellularised ECM, and Immunofluorescence confirmed retention of fibronectin, laminin and hyaluronic acid. Detection of all ECM ligands was cross-validated by Orbitrap-Secondary Ion Mass Spectrometry. A solubilised ECM/PEGDA hydrogel was used to coat an AggreWell™ plate. Primary human cerebellar astrocytes, D283 and BT12 cells were cultured as spheroids within the ECM/PEGDA hydrogel for 7 days with no significant decrease in cellular viability. Cytokine and Human Matrix Metalloproteinase (MMP) Antibody Arrays showed cytokine and MMP expression in all three cell lines was retained in the presence of ECM material. Furthermore, D283 and BT12 cells were co-cultured with primary astrocytes for 7 days prior to separation using fluorescence activated cell sorting to generate individual cell populations. CONCLUSIONS We have developed a 3D in vitro model which can co-culture cells for over 7 days, whilst recapitulating the in vivo tumour environment. RNA sequencing is currently in progress to identify differentially expressed genes in cerebellar tumour cells upon astrocytic and brain ECM crosstalk. We hypothesise that biochemical signalling underlying this communication will reveal putative therapeutic vulnerabilities.

Abstract BACKGROUND Atypical Teratoid/Rhabdoid Tumours (ATRT) are aggressive paediatric brain tumours which mostly occur in the first three years of life and which rapidly recur after surgical resection. There has been debate over the use of cytotoxic consolidation therapy due to the severity of off target effects associated with chemo/radiotherapy use in young patients. Astrocytes have previously been shown to support progression and therapy resistance of other brain tumours; however, their role in ATRT pathophysiology is yet to be elucidated. METHODS To better understand how adjacent “healthy” brain tissue may be complicit in ATRT recurrence, we have developed a 3D in vitro model in which ATRT cells are co-cultured with astrocytes within a bespoke decellularized human cerebellum extracellular matrix (ECM) hydrogel. RESULTS Immunofluorescence confirmed that human cerebellar ECM hydrogels retain human brain ECM components (hyaluronic acid, laminin, and fibronectin). ATRT-astrocyte co-culture spheroids were formed within the ECM hydrogel and observed to display a distinctive morphology relative to monoculture controls, with no difference in overall viability. Co-cultured tumour cells were successfully harvested from the model and isolated from astrocyte populations using fluorescence activated cell sorting. In both 2D and 3D culture, we have shown that astrocytes labelled with CM-DiI transfer this cell tracker dye to ATRT-MYC (BT12, BT16) and ATRT-TYR (BT37) cells, potentially indicating intercellular trafficking. Furthermore, in 2D culture ATRT-MYC (BT12 and BT16) cells form actin rich cell-cell processes with astrocytes when co-cultured in vitro. CONCLUSIONS This work represents a comprehensively characterised model of ATRT interaction with the healthy brain. Future work will analyse changes in ATRT cell transcriptomes when astrocytes are present in the model. By understanding how the presence of astrocytes in the tumour microenvironment may promote tumour survival and progression, we aim to use this data to identify candidate therapeutics to inhibit crosstalk and improve patient outcomes.

Abstract AIMS Group-3 medulloblastoma (MB) is a paediatric cerebellar tumour with a dismal prognosis. Our objective was to establish a 3D in vitro model termed ‘tumoursphere matrix’ to recapitulate physiologically-relevant communication between tumour cells and reactive brain elements, aiming to discern differential gene expression in cancer cells upon co-culture with astrocytes and human brain extracellular matrix (ECM). METHOD Non-disease human autopsy brain was decellularised to generate ECM and extensively characterised to show DNA reduction, ECM ligand retention and compatibility with different cell lines. D283, D341 and D425 cells were co-cultured with primary human cerebellar astrocytes within a PEGDA hydrogel containing decellularised ECM. Following 7 days of culture, co-cultured cells were separated using fluorescence activated cell sorting to generate individual cell populations for transcriptomic analysis. RESULTS ECM characterisation showed a significant reduction in cellular material whilst retaining ECM ligands. Reduction of DNA content to 174 ng/mg was corroborated by an absence of nuclei in immunohistochemical staining. Colorimetric assays indicated collagen and glycosaminoglycan retention in decellularised ECM, and immunofluorescence confirmed retention of fibronectin, laminin and hyaluronic acid. Detection of all ECM ligands was cross-validated by Orbitrap-Secondary Ion Mass Spectrometry. Primary human cerebellar astrocytes, D283, D341 and D425 cells were cultured as spheroids within the ECM/PEGDA hydrogel for 7 days with no significant decrease in cellular viability. Cytokine and Human Matrix Metalloproteinase (MMP) Antibody Arrays showed retained cytokine and MMP expression in all three cell lines in the presence of ECM material. CONCLUSION We have developed a bespoke 3D model which can co-culture cells for over 7 days, whilst recapitulating the in vivo tumour environment. RNA sequencing on all 3 cell lines in mono and co-culture is currently in progress to identify differentially expressed genes in medulloblastoma cells upon astrocytic and brain ECM crosstalk. We hypothesise that biochemical signalling underlying this communication network will reveal putative therapeutic vulnerabilities.

Abstract AIMS Atypical Teratoid Rhabdoid Tumours (ATRT) and Medulloblastoma are embryonal brain tumours arising in the cerebellum. Many in vitro models of paediatric brain tumours fail to recapitulate key pathophysiological characteristics. We aim to address this gap by developing a bespoke model incorporating cellular and acellular aspects of the TME. METHOD Cerebellar tissue from a healthy human autopsy donor brain was decellularized to form cerebellar ECM and incorporated into a “blank slate” hydrogel. Spheroid-forming multi-well plates were coated with the hydrogel and used to culture patient-derived Medulloblastoma and ATRT cells in co-culture with primary human cerebellar astrocytes. RESULTS Tissue decellularization and retention of ECM components was demonstrated using colorimetric assays and Orbitrap Secondary Ion Mass Spectrometry. Biocompatibility of the ECM hydrogel was shown in 2D and 3D culture conditions using the CellTiter-Glo® 3D cell viability assay. Furthermore, the size and morphology of spheroids grown on the hydrogel was characterised using a high-throughput imaging and analysis methodology. Cell lines were labelled to facilitate discrimination between tumour cells and astrocytes. Optical sections of co-culture spheroids generated using confocal microscopy showed cell-cell contact between tumour cells and astrocytes. Finally, co-culture spheroids were separated by fluorescence activated cell sorting to facilitate downstream analyses on individual cell types. CONCLUSIONS This work presents a highly characterised model of medulloblastoma and ATRT interactions with healthy brain tissue, mimicking the immediate post-surgical microenvironment. Future work will utilise transcriptomics to assess the tumour-astrocyte crosstalk modelled using this system.

The lack of treatment options for high-grade brain tumors has led to searches for alternative therapeutic modalities. Electrical field therapy is one such area. The Optune™ system is an FDA-approved novel device that delivers continuous alternating electric fields (tumor treating fields—TTFields) to the patient for the treatment of primary and recurrent Glioblastoma multiforme (GBM). Various mechanisms have been proposed to explain the effects of TTFields and other electrical therapies. Here, we present the first study of genome-wide expression of electrotherapy (delivered via TTFields or Deep Brain Stimulation (DBS)) on brain tumor cell lines. The effects of electric fields were assessed through gene expression arrays and combinational effects with chemotherapies. We observed that both DBS and TTFields significantly affected brain tumor cell line viability, with DBS promoting G0-phase accumulation and TTFields promoting G2-phase accumulation. Both treatments may be used to augment the efficacy of chemotherapy in vitro. Genome-wide expression assessment demonstrated significant overlap between the different electrical treatments, suggesting novel interactions with mitochondrial functioning and promoting endoplasmic reticulum stress. We demonstrate the in vitro efficacy of electric fields against adult and pediatric high-grade brain tumors and elucidate potential mechanisms of action for future study.

Poor outcomes associated with diffuse high-grade gliomas occur in both adults and children, despite substantial progress made in the molecular characterisation of the disease. Targeting the metabolic requirements of cancer cells represents an alternative therapeutic strategy to overcome the redundancy associated with cell signalling. Cholesterol is an integral component of cell membranes and is required by cancer cells to maintain growth and may also drive transformation. Here, we show that removal of exogenous cholesterol in the form of lipoproteins from culture medium was detrimental to the growth of two paediatric diffuse glioma cell lines, KNS42 and SF188, in association with S-phase elongation and a transcriptomic program, indicating dysregulated cholesterol homeostasis. Interrogation of metabolic perturbations under lipoprotein-deficient conditions revealed a reduced abundance of taurine-related metabolites and cholesterol ester species. Pharmacological reduction in intracellular cholesterol via decreased uptake and increased export was simulated using the liver X receptor agonist LXR-623, which reduced cellular viability in both adult and paediatric models of diffuse glioma, although the mechanism appeared to be cholesterol-independent in the latter. These results provide proof-of-principle for further assessment of liver X receptor agonists in paediatric diffuse glioma to complement the currently approved therapeutic regimens and expand the options available to clinicians to treat this highly debilitating disease.

Abstract INTRODUCTION Childhood medulloblastoma (MB) and atypical teratoid/rhabdoid tumours (AT/RT) are malignant brain tumours occurring in the posterior fossa, for which prognoses remains particularly poor for the MB Group 3 subtype characterised by amplification of the Myc oncogene and for AT/RT in general. Current in vitro models for these neoplasms rely on non-coated plastic, various hydrogels, or animal-derived extracellular matrix (ECM), which fail to recapitulate the physiological environment from which the cells are derived from. METHODS We have developed a method to decellularize ex vivo human brain tissue from different anatomical locations for the use in 3D in vitro models. Human cerebellar brain tissue was harvested from autopsy brain and sectioned into small cubes before bathing in a sodium dodecyl sulfate/phosphate-buffered saline mixture for several days, before washing and lyophilising. RESULTS The optimised method for generation of decellularized human brain ECM successfully removes nuclei as confirmed by histological staining and DNA quantification (DNA reduction of ≥ 60%). Orbitrap-Secondary Ion Mass Spectrometry analysis confirmed the retention of the ECM components laminin (C9H11N3O2Na+), fibronectin (C9H14N4O2Na+ and C20H33N7O5Na+) and collagen (C4H5N2O2+), with a reduction in cell membrane lipid components (glycerophosphocholine, C9H19NPO4+; phosphocholine, C5H15NPO4+; and choline, C5H14NO+) relative to control tissue, with a < 2 ppm accuracy, which was further corroborated by glycosaminoglycan and collagen assays. Multiple molecular subtype-specific AT/RT and MB cell lines have been successfully grown on decellularized cerebellar-ECM/PEGDA hydrogel, showing no reduction in metabolic viability using PrestoBlue and Cell Titer Glo assays. CONCLUSIONS This methodology offers an innovative human-only high-throughput 3D drug screening model, whereby patient-derived MB or AT/RT cells are co-cultured with healthy human cerebellar astrocytes upon decellularized cerebellar ECM, which we term ‘Tumoursphere Matrices’.

BACKGROUND:Glioblastoma (GBM) is a highly aggressive brain tumor with rapid subclonal diversification, harboring molecular abnormalities that vary temporospatially, a contributor to therapy resistance. Fluorescence-guided neurosurgical resection utilizes the administration of 5-aminolevulinic acid (5-ALA) generating individually fluorescent tumor cells within a background population of non-neoplastic cells in the invasive tumor region. The aim of the study was to specifically isolate and interrogate the invasive GBM cell population using a novel 5-ALA-based method.METHODS:We have isolated the critical invasive GBM cell population by developing 5-ALA-based metabolic fluorescence-activated cell sorting. This allows purification and study of invasive cells from GBM without an overwhelming background "normal brain" signal to confound data. The population was studied using RNAseq, real-time PCR, and immunohistochemistry, with gene targets functionally interrogated on proliferation and migration assays using siRNA knockdown and known drug inhibitors.RESULTS:RNAseq analysis identifies specific genes such as SERPINE1 which is highly expressed in invasive GBM cells but at low levels in the surrounding normal brain parenchyma. siRNA knockdown and pharmacological inhibition with specific inhibitors of SERPINE1 reduced the capacity of GBM cells to invade in an in vitro assay. Rodent xenografts of 5-ALA-positive cells were established and serially transplanted, confirming tumorigenicity of the fluorescent patient-derived cells but not the 5-ALA-negative cells.CONCLUSIONS:Identification of unique molecular features in the invasive GBM population offers hope for developing more efficacious targeted therapies compared to targeting the tumor core and for isolating tumor subpopulations based upon intrinsic metabolic properties.

Abstract Glioblastoma therapeutic challenges are in considerable part due to myriad survival adaptations and mechanisms, which allow malignant cells to repurpose signalling pathways within discreet microenvironments. These Darwinian adaptations facilitate invasion into brain parenchyma and perivascular space or promote evasion from repressive factors that represent anti-cancer defence mechanisms. We hypothesised that pre-clinical modelling of glioma invasion by recapitulating early events occurring immediately after surgery at the glioblastoma invasive margin, could reveal the cross-talk between malignant cells and the surrounding healthy astrocytes, which facilitates tumour recurrence. We first generated transgenic H1-derived neural stem cells using CRISPR/Cas9-mediated knock-in of the YFP reporter gene under the control of the GFAP promoter. Reproducible ultrahigh-throughput AggreWells™ (19,200 micro-wells per 24-well plate) were used to create astrocyte-glioblastoma organoids, which we term ‘Gliomasphere Matrices’. YFP-labelled astrocytes were co-cultured with 10 treatment-naïve patient-derived cell lines isolated from the 5-aminolevulinic (5ALA)-determined glioblastoma invasive margin. Co-cultures were seeded upon on a sequentially constructed, time-of-flight secondary ion mass spectrometry (ToF-SIMS)-characterised 3D scaffold, composed of decellularised human brain extract with defined PEGDA hydrogel. YFP-astrocytes were purified from each of the 10 Gliomasphere Matrices using fluorescence-activated cell sorting (FACS) after 6- and 10-days co-culture. RNAseq profiling to address both putative astrocytic reprogramming by invasive glioblastoma cells and gene expression changes intrinsic to tumour cells will be discussed in relation to RNAseq data from patient-derived 5ALA FACS-purified glioblastoma invasive margin tissue. This novel multi-faceted model offers a unique opportunity to recapitulate early molecular cross-talk which facilitates glioblastoma recurrence and may be utilised for high-throughput drug screening.

Glioblastoma therapeutic challenges are in considerable part due to myriad survival mechanisms which allow malignant cells to repurpose signalling pathways within discreet microenvironments. These Darwinian adaptations facilitate invasion into brain parenchyma and perivascular space. We hypothesised that pre-clinical modelling of glioma invasion by recapitulating early events occurring immediately after surgery at the glioblastoma invasive margin, could reveal the cross-talk between malignant cells and surrounding healthy astrocytes. We first generated transgenic H1-derived neural stem cells using CRISPR/Cas9-mediated knock-in of the YFP reporter gene under the control of the GFAP promoter at the AAVS1 safe harbour locus. Reproducible ultrahigh-throughput AggreWells™ (7200 mini-wells per plate) were used to create astrocyte-glioblastoma organoids, which we term ‘Gliomasphere Matrices’. YFP-labelled astrocytes were co-cultured with 10 treatment-naïve patient-derived cell lines isolated from the 5-aminolevulinic (5ALA)-determined glioblastoma invasive margin. Co-cultures were seeded upon a sequentially constructed, time-of-flight secondary ion mass spectrometry (ToF-SIMS)-characterised decellularised human brain extract. YFP-astrocytes were purified from each of the 10 Gliomasphere Matrices using fluorescence-activated cell sorting (FACS) after 6- and 10-days co-culture. RNA-sequencing of the putatively reprogrammed YFP-astrocytes showed the characteristic expression of canonical key regulators of multiple malignant diseases including high-grade glioma such as SND1 and EFNB2 in addition to the identification of a single novel marker located at chromosome 1 (C1orf61), highly expressed in malignant glioma when compared to somatic cancers according to TCGA RNA-sequencing data. Differentiated YFP-astrocytes also overexpressed IFITM2 and IFITM10, known to be involved in priming resistance against pathogenic microorganisms. This ultimately suggests a fluctuating state between malignant transformation imposed by the highly infiltrative glioma cells and the counter-action of the normal astrocytes to these deleterious invasive cells. This multi-faceted model offers a unique opportunity to recapitulate early molecular cross-talk which facilitates glioblastoma recurrence and may be utilised for high-throughput drug screening.

Glioblastoma, a WHO grade IV astrocytoma, is a highly aggressive and heterogeneous tumour that infiltrates deeply into surrounding brain parenchyma, making complete surgical resection impossible. Despite chemo-radiotherapy, the residual cell population within brain parenchyma post-surgery causes inevitable recurrence. Previously, the tumour core has been the focus of research and the basis for targeted therapeutic regimes, which have failed to improve survival in clinical trials. Here, we focus on the invasive margin as defined by the region with 5-aminolevulinic acid (5ALA) (GliolanTM) fluorescence at surgery beyond the T1 enhancing region on magnetic resonance imaging (MRI). This area is hypothesized to constitute unique microenvironmental pressures, and consequently be molecularly distinct to tumour core and enhancing rim regions. We conducted hematoxylin and eosin (H&E), array real time polymerase chain reaction (PCR), and immunohistochemistry staining on various intra-tumour regions of glioblastoma to determine molecular heterogeneity between regions. We analyzed 73 tumour samples from 21 patients and compared cellular density, cell proliferation, and the degree of vascularity. There is a statistically significant difference between the core, invasive margin and other regions for cell density (p < 0.001), cell proliferation (p = 0.029), and vascularity (p = 0.007). Aldehyde dehydrogenase 1 (ALDH1) and Nestin immunohistochemistry were used as a measure of stem-like properties, showing significantly decreased Nestin expression (p < 0.0001) in the invasive margin. Array PCR of the core, rim, and invasive regions showed significantly increased fibroblast growth factor (FGF) and ALDH1 expression in the invasive zone, with elevated hypoxia inducing factor 1-alpha (HIF1α) in the rim region, adjacent to the hypoxic core. The influence of varying microenvironments in the intra-tumour regions is a major key to understanding intra-tumour heterogeneity. This study confirms the distinct molecular composition of the heterogeneous invasive margin and cautions against purported therapy strategies that target candidate glioblastoma stem-like genes that are predominantly expressed in the tumour core. Full characterization of tumour cells in the invasive margin is critical, as these cells may more closely resemble the residual cell population responsible for tumour recurrence. Their unique nature should be considered when developing targeted agents for residual glioblastoma multiforme (GBM).

Gliomas are devastating brain cancers that have poor prognostic outcomes for their patients. Short overall patient survival is due to a lack of durable, efficacious treatment options. Such therapeutic difficulties exist, in part, due to several glioma survival adaptations and mechanisms, which allow glioma cells to repurpose paracrine signalling pathways and ion channels within discreet microenvironments. These Darwinian adaptations facilitate invasion into brain parenchyma and perivascular space or promote evasion from anti-cancer defence mechanisms. Ultimately, this culminates in glioma repopulation and migration at distances beyond the original tumour site, which is a considerable obstacle for effective treatment. After an era of failed phase II trials targeting individual signalling pathways, coupled to our increasing knowledge of glioma sub-clonal divergence, combinatorial therapeutic approaches which target multiple molecular pathways and mechanisms will be necessary for better treatment outcomes in treating malignant gliomas. Furthermore, next-generation therapy which focuses on infiltrative tumour phenotypes and disruption of the vascular and perivascular microenvironments harbouring residual disease cells offers optimism for the localised control of malignant gliomas.