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A broad range of brain pathologies critically relies on the vasculature, and cerebrovascular disease is a leading cause of death worldwide. However, the cellular and molecular architecture of the human brain vasculature remains incompletely understood1. Here we performed single-cell RNA sequencing analysis of 606,380 freshly isolated endothelial cells, perivascular cells and other tissue-derived cells from 117 samples, from 68 human fetuses and adult patients to construct a molecular atlas of the developing fetal, adult control and diseased human brain vasculature. We identify extensive molecular heterogeneity of the vasculature of healthy fetal and adult human brains and across five vascular-dependent central nervous system (CNS) pathologies, including brain tumours and brain vascular malformations. We identify alteration of arteriovenous differentiation and reactivated fetal as well as conserved dysregulated genes and pathways in the diseased vasculature. Pathological endothelial cells display a loss of CNS-specific properties and reveal an upregulation of MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell–cell interaction analyses predict substantial endothelial-to-perivascular cell ligand–receptor cross-talk, including immune-related and angiogenic pathways, thereby revealing a central role for the endothelium within brain neurovascular unit signalling networks. Our single-cell brain atlas provides insights into the molecular architecture and heterogeneity of the developing, adult/control and diseased human brain vasculature and serves as a powerful reference for future studies.

Un pediatre en milieu communautaire a oriente un garcon de 5 mois vers la clinique de genetique de notre etablissement pour un probleme de petite taille et de macrocephalie. L'accouchement [...]

A 5-month-old boy was referred by a community pediatrician to clinical genetics at our facility for short stature and macrocephaly. His delivery had been normal, although his parents had noticed [...]

Cancer stem cells (CSCs) established from surgical biopsies closely mimic the human context and can be used to investigate disease mechanisms, genetic fitness, and therapeutic evaluation. Here, we present a protocol for the derivation of primary patient-derived CSC lines from ependymal tumors. We describe the necessary steps, from surgical intervention and biopsy to the dissociation of ependymomas to derive cultures. We then detail procedures for cell line propagation and define the characteristics of these primary cancer cell lines.

Abstract: Moyamoya vasculopathy is a rare, progressive neurovascular condition that may cause recurrent transient ischemic attacks, ischemic strokes, hemorrhagic strokes, or neurologic decline in children. Children with moyamoya disease have [...]

Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal neoplasms of the hindbrain with strong links to early development of the hindbrain1–4. Mutations that activate Sonic hedgehog signalling lead to Sonic hedgehog MB in the upper rhombic lip (RL) granule cell lineage5–8. By contrast, mutations that activate WNT signalling lead to WNT MB in the lower RL9,10. However, little is known about the more commonly occurring group 4 (G4) MB, which is thought to arise in the unipolar brush cell lineage3,4. Here we demonstrate that somatic mutations that cause G4 MB converge on the core binding factor alpha (CBFA) complex and mutually exclusive alterations that affect CBFA2T2, CBFA2T3, PRDM6, UTXand OTX2. CBFA2T2is expressed early in the progenitor cells of the cerebellar RL subventricular zone in Homo sapiens, and G4 MB transcriptionally resembles these progenitors but are stalled in developmental time. Knockdown of OTX2in model systems relieves this differentiation blockade, which allows MB cells to spontaneously proceed along normal developmental differentiation trajectories. The specific nature of the split human RL, which is destined to generate most of the neurons in the human brain, and its high level of susceptible EOMES+KI67+unipolar brush cell progenitor cells probably predisposes our species to the development of G4 MB.

Cancers arising from germline DNA mismatch repair deficiency or polymerase proofreading deficiency (MMRD and PPD) in children harbour the highest mutational and microsatellite insertion–deletion (MS-indel) burden in humans. MMRD and PPD cancers are commonly lethal due to the inherent resistance to chemo-irradiation. Although immune checkpoint inhibitors (ICIs) have failed to benefit children in previous studies, we hypothesized that hypermutation caused by MMRD and PPD will improve outcomes following ICI treatment in these patients. Using an international consortium registry study, we report on the ICI treatment of 45 progressive or recurrent tumors from 38 patients. Durable objective responses were observed in most patients, culminating in a 3 year survival of 41.4%. High mutation burden predicted response for ultra-hypermutant cancers (>100 mutations per Mb) enriched for combined MMRD + PPD, while MS-indels predicted response in MMRD tumors with lower mutation burden (10–100 mutations per Mb). Furthermore, both mechanisms were associated with increased immune infiltration even in ‘immunologically cold’ tumors such as gliomas, contributing to the favorable response. Pseudo-progression (flare) was common and was associated with immune activation in the tumor microenvironment and systemically. Furthermore, patients with flare who continued ICI treatment achieved durable responses. This study demonstrates improved survival for patients with tumors not previously known to respond to ICI treatment, including central nervous system and synchronous cancers, and identifies the dual roles of mutation burden and MS-indels in predicting sustained response to immunotherapy.

Embryonal tumours with multi-layered rosettes (ETMRs) are a newly recognised, rare paediatric brain tumour with alterations of the C19MCmicroRNA locus. Due to varied diagnostic practices and scarce clinical data, disease features and determinants of outcomes for these tumours are poorly defined. We did an integrated clinicopathological and molecular analysis of primary ETMRs to define clinical phenotypes, and to identify prognostic factors of survival and key treatment modalities for this orphan disease.

Familiarity with specific imaging morphologic characteristics of pediatric- and adult-type tumors of the central nervous system is essential to provide the best imaging care to adolescents and young adults as both tumor types can occur in this age group.

BackgroundFailure to appreciate deep venous drainage pathways is a major cause of severe complications in the endovascular treatment of vein of Galen aneurysmal malformations (VOGMs).ObjectiveTo report deep venous drainage patterns in patients with VOGM, emphasizing the internal cerebral veins, and to describe the challenges in evaluating these.MethodsPatients with VOGM presenting to our institute between 2000 and 2018 were retrospectively analyzed. Patients with complete and good quality imaging datasets were included in the study. Three neuroradiologists with expertise in the subject independently analyzed the deep venous drainage patterns on multi-sequence MRI and digital subtraction angiography. Follow-up imaging studies were analyzed for alterations in deep venous drainage patterns that occurred following endovascular treatment. Descriptive statistics were used to report findings.ResultsTwenty-three patients had optimal quality MRI imaging and 25 had optimal quality DSA imaging available. In 14/23 (61%) patients, internal cerebral vein (ICV) communication could be reliably identified on MRI and in 8/25 (32%) patients on DSA. Deep venous communication with the VOGM was demonstrated in 8/26 (30.8%) patients. One (3.8%) patient demonstrated ICV communication with the VOGM only on postoperative imaging, while in 2 (8%) patients the ICV drainage route changed from VOGM to alternative pathways after the procedure. Other variant pathways included lateral mesencephalic vein, superior or inferior sagittal sinus, anterior mesencephalic vein, tentorial sinus, deep Sylvian vein, and superior vermian vein.ConclusionICV communication with the VOGM is not uncommon and requires dedicated preprocedural imaging to identify it. However, there are significant challenges in assessing this communication in the presence of high-flow fistulae, vessel tortuosity and size, and contrast limitations in this population.

IMPORTANCE: Major neurological complications from the embolization of vein of Galen malformations (VOGMs) are poorly understood. We provide a detailed analysis of contributors to periprocedural neurological complications and lessons learned. OBJECTIVE: To assess the rate of major periprocedural neurological complications following VOGM embolization with major procedural and strategic contributors. DESIGN, SETTING, AND PARTICIPANTS: This retrospective cohort study was conducted at a quarternary referral pediatric hospital (Hospital for Sick Children; Toronto, Ontario, Canada) from January 1999 to December 2018 with a mean clinical follow-up of 44.7 months; all children with VOGM diagnosed and/or treated were eligible (n = 48). Thirty-three patients who underwent endovascular treatment were included. INTERVENTIONS: Endovascular staged transarterial embolization performed in 33 patients over 91 sessions. MAIN OUTCOMES AND MEASURES: The primary outcome was the rate of periprocedural neurological complications (occurring within 1 week of embolization). The secondary outcomes were mortality, long-term neurological outcomes, and contributing anatomical and management factors to neurological complications. RESULTS: Of 33 patients who underwent embolization (31 boys [64.6%]; 17 girls [35.4%]; median age at first embolization, 4 months [range, 0-29 months]), 10 patients (30.3%) developed major periprocedural neurological complications. Five of these patients died. Univariate logistic regression analyses identified internal cerebral vein drainage to the main venous sac of the VOGM and use of a microcatheter with a distal outer diameter of more than 2.0F as significant predictors of poor neurological outcomes. Lessons learned from our experience include the need to assess the internal cerebral vein drainage pattern on preprocedural magnetic resonance venography, avoidance of excessive embolization into the venous sac, treatment of more distal fistulae before proximal fistulae to avoid a sump effect, and preferably use of smaller (<2.0F outer diameter) microcatheters in neonatal embolization procedures. CONCLUSIONS AND RELEVANCE: In this cohort, 10 patients with VOGM treated with embolization (30.3%) experienced major periprocedural neurological complications, half of whom died. While these outcomes are superior to historic conservative and surgical treatment results, ongoing improvements in treatment and pretreatment diagnostic approaches are needed. Awareness of the lessons learned from our experience can help to avoid similar complications in the future for this vulnerable population.

Childhood brain tumors have suspected prenatal origins. To identify vulnerable developmental states, we generated a single-cell transcriptome atlas of >65,000 cells from embryonal pons and forebrain, two major tumor locations. We derived signatures for 191 distinct cell populations and defined the regional cellular diversity and differentiation dynamics. Projection of bulk tumor transcriptomes onto this dataset shows that WNT medulloblastomas match the rhombic lip-derived mossy fiber neuronal lineage and embryonal tumors with multilayered rosettes fully recapitulate a neuronal lineage, while group 2a/b atypical teratoid/rhabdoid tumors may originate outside the neuroectoderm. Importantly, single-cell tumor profiles reveal highly defined cell hierarchies that mirror transcriptional programs of the corresponding normal lineages. Our findings identify impaired differentiation of specific neural progenitors as a common mechanism underlying these pediatric cancers and provide a rational framework for future modeling and therapeutic interventions.

Study of the origin and development of cerebellar tumours has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. Here we use single-cell transcriptomics to study more than 60,000 cells from the developing mouse cerebellum and show that different molecular subgroups of childhood cerebellar tumours mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. The Sonic Hedgehog medulloblastoma subgroup transcriptionally mirrors the granule cell hierarchy as expected, while group 3 medulloblastoma resembles Nestin+stem cells, group 4 medulloblastoma resembles unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the prenatal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumours demonstrates that many bulk tumours contain a mixed population of cells with divergent differentiation. Our data highlight cerebellar tumours as a disorder of early brain development and provide a proximate explanation for the peak incidence of cerebellar tumours in early childhood. Sequencing data from the developing cerebellum are compared with bulk sequencing data from paediatric tumours, providing insights into their potential origins and suggesting that many cerebellar tumours have their origins early in utero.

In this study, Rajakulendran et al. investigated the role of Wnt/βcatenin signaling in GBM stem cell renewal and fate decisions. They identify new contexts for Wnt modulation for targeting stem cell differentiation and self-renewal in GBM heterogeneity.

We investigated the role of 3D genome architecture in instructing functional properties of glioblastoma stem cells (GSCs) by generating sub-5-kb resolution 3D genome maps by in situ Hi-C. Contact maps at sub-5-kb resolution allow identification of individual DNA loops, domain organization, and large-scale genome compartmentalization. We observed differences in looping architectures among GSCs from different patients, suggesting that 3D genome architecture is a further layer of inter-patient heterogeneity for glioblastoma. Integration of DNA contact maps with chromatin and transcriptional profiles identified specific mechanisms of gene regulation, including the convergence of multiple super enhancers to individual stemness genes within individual cells. We show that the number of loops contacting a gene correlates with elevated transcription. These results indicate that stemness genes are hubs of interaction between multiple regulatory regions, likely to ensure their sustained expression. Regions of open chromatin common among the GSCs tested were poised for expression of immune-related genes, including CD276. We demonstrate that this gene is co-expressed with stemness genes in GSCs and that CD276 can be targeted with an antibody-drug conjugate to eliminate self-renewing cells. Our results demonstrate that integrated structural genomics data sets can be employed to rationally identify therapeutic vulnerabilities in self-renewing cells.

Low-grade gliomas (LGG) represent the most common form of primary central nervous system tumor arising in childhood. There is growing evidence to support the role of the mitogen-activated protein kinase pathway in driving tumor growth and MEK inhibitors are being investigated in clinical trials for refractory and unresectable LGGs. As MEK inhibitors progress through clinical trials, drug toxicities have been identified. We report on 2 pediatric patients with LGG and known diabetes insipidus who developed severe hyponatraemia associated with significant decreases in desmopressin doses after starting trametinib. We review potential mechanisms for this sodium imbalance by examining the interaction between MEK inhibition and aquaporin channel physiology. We recommend close monitoring of serum sodium levels and clinical status in patients with diabetes insipidus who have optic-hypothalamic gliomas and are started on treatment with MEK inhibitors.

Genomic sequencing has driven precision-based oncology therapy; however, the genetic drivers of many malignancies remain unknown or non-targetable, so alternative approaches to the identification of therapeutic leads are necessary. Ependymomas are chemotherapy-resistant brain tumours, which, despite genomic sequencing, lack effective molecular targets. Intracranial ependymomas are segregated on the basis of anatomical location (supratentorial region or posterior fossa) and further divided into distinct molecular subgroups that reflect differences in the age of onset, gender predominance and response to therapy. The most common and aggressive subgroup, posterior fossa ependymoma group A (PF-EPN-A), occurs in young children and appears to lack recurrent somatic mutations. Conversely, posterior fossa ependymoma group B (PF-EPN-B) tumours display frequent large-scale copy number gains and losses but have favourable clinical outcomes. More than 70% of supratentorial ependymomas are defined by highly recurrent gene fusions in the NF-κB subunit gene RELA (ST-EPN-RELA), and a smaller number involve fusion of the gene encoding the transcriptional activator YAP1 (ST-EPN-YAP1). Subependymomas, a distinct histologic variant, can also be found within the supratetorial and posterior fossa compartments, and account for the majority of tumours in the molecular subgroups ST-EPN-SE and PF-EPN-SE. Here we describe mapping of active chromatin landscapes in 42 primary ependymomas in two non-overlapping primary ependymoma cohorts, with the goal of identifying essential super-enhancer-associated genes on which tumour cells depend. Enhancer regions revealed putative oncogenes, molecular targets and pathways; inhibition of these targets with small molecule inhibitors or short hairpin RNA diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymomas. Through profiling of transcriptional enhancers, our study provides a framework for target and drug discovery in other cancers that lack known genetic drivers and are therefore difficult to treat.

Human glioblastomas harbour a subpopulation of glioblastoma stem cells that drive tumorigenesis. However, the origin of intratumoural functional heterogeneity between glioblastoma cells remains poorly understood. Here we study the clonal evolution of barcoded glioblastoma cells in an unbiased way following serial xenotransplantation to define their individual fate behaviours. Independent of an evolving mutational signature, we show that the growth of glioblastoma clones in vivo is consistent with a remarkably neutral process involving a conserved proliferative hierarchy rooted in glioblastoma stem cells. In this model, slow-cycling stem-like cells give rise to a more rapidly cycling progenitor population with extensive self-maintenance capacity, which in turn generates non-proliferative cells. We also identify rare ‘outlier’ clones that deviate from these dynamics, and further show that chemotherapy facilitates the expansion of pre-existing drug-resistant glioblastoma stem cells. Finally, we show that functionally distinct glioblastoma stem cells can be separately targeted using epigenetic compounds, suggesting new avenues for glioblastoma-targeted therapy.

Spatial heterogeneity of transcriptional and genetic markers between physically isolated biopsies of a single tumor poses major barriers to the identification of biomarkers and the development of targeted therapies that will be effective against the entire tumor. We analyzed the spatial heterogeneity of multiregional biopsies from 35 patients, using a combination of transcriptomic and genomic profiles. Medulloblastomas (MBs), but not high-grade gliomas (HGGs), demonstrated spatially homogeneous transcriptomes, which allowed for accurate subgrouping of tumors from a single biopsy. Conversely, somatic mutations that affect genes suitable for targeted therapeutics demonstrated high levels of spatial heterogeneity in MB, malignant glioma, and renal cell carcinoma (RCC). Actionable targets found in a single MB biopsy were seldom clonal across the entire tumor, which brings the efficacy of monotherapies against a single target into question. Clinical trials of targeted therapies for MB should first ensure the spatially ubiquitous nature of the target mutation.

The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon–driven, functional genomic mouse model of medulloblastoma with ‘humanized’ in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy.

Neural stem cell biology took off in 1992 when Brent Reynolds and Samuel Weiss, working at the University of Calgary, discovered that culturing mammalian brain cells in serum-free conditions (in [...]

In a retrospective review of 24 metastatic medulloblastoma patients whose treatment included craniospinal irradiation, 5 patients presented with gross residual abnormalities at completion of therapy. This report describes 2 medulloblastoma patients with persistent residual abnormalities on serial follow-up imaging studies. The patients aged 2 and 2.5 years old at the time of diagnosis underwent surgery followed by multiagent chemotherapy. One patient progressed on therapy and underwent salvage craniospinal radiation. The second showed residual tumor on end of treatment imaging and received low-dose craniospinal irradiation. Despite persistent magnetic resonance imaging findings, the patients are alive and well 13 and 7 years after diagnosis with no further treatment applied. The nature of these residual abnormalities is discussed.

Background:Moyamoya is a progressive arteriopathy condition characterized by steno-occlusion of the arteries of the circle of Willis. MRI performed with hypercapnic challenge can image blood-oxygen-level-dependent cerebrovascular reactivity (BOLD-CVR) thereby assessing cerebrovascular reserve. MRI studies of children <7 years of age, or with significant behavioural challenges require anesthesia. The purpose of this study was to validate the use of ventilator-induced hypercapnic challenge under general anaesthesia (GA).Methods:Children with moyamoya underwent two BOLD-CVR imaging in the same session under GA (GA-CVR). Differences in CVR estimates and intraclass correlation coefficient (ICC) between repeated scans were examined to determine repeatability across grey and white matter tissue and vascular territories. Bland-Altman plots were used to visulaize the overall variation between the scans. The associations with age, moyamoya types, and stroke presentation were also examined. Qualitative scoring by visual inspection was also conducted by trained neurologists.Results:Thirty-two paired GA-CVR studies (sixty-four scans in total) were analyzed (mean age: 7.07 (2.74 -17.95) years, 13 females). Forty-one percent (41%) were under 7 and 77%, under 10. No significant differences between repeated scans were found for any of the CVR estimates, when summarized by tissue and vascular territory. Of the paired studies, repeatability (ICC) for the whole-brain CVR estimates was excellent (≥0.74) in 14 (43.8%), good (≤0.59, >0.74) in 7 (21.9%), fair (≤0.41, >0.59) in 6 (18.8%) and poor (<0.41) in 5 (15.6%). Bland-Altman plots illustrated the overall variation of whole-brain CVR within 95% confidence interval level. Repeatability indices were not affected by children’s age and other clinical factors. On qualitative scoring, the Cohen weighted kappa showed substantial agreement in both right (0.75) and left (0.81) hemispheres.Conclusion:Our study support the clinical use of GA-CVR across all ages and disease conditions. The GA-CVR provides a feasible, repeatable, and reliably interpretable tool for the assessment of cerebrovascular reserve of very young and behaviourally challenged children with moyamoya.

Introduction:Moyamoya is a progressive cerebral arteriopathy affecting the arteries in the circle of Willis. Suzuki grade for moyamoya using catheter angiogram has been gold standard for the evaluation of moyamoya both in children and adults. Suzuki grade evaluates the amount of stenosis and collateral formation in the cerebral arteries. Magnetic resonance angiography (MRA) non-luminal imaging can overestimate stenosis and underestimate collaterals. With greater use of MRA for diagnosis and follow-up, it is important to understand MRA staging is truly comparable to catheter angiogram.Methods:Study neurologist and interventional radiologist reviewed both catheter angiograms and MRAs without clinical information. The modified Suzuki stage was used to evaluate the MRA. Median time from MRA to catheter angiogram was calculated. Cohen’s Kappa was used to compare modalities of Suzuki grade based on catheter angiogram to modified Suzuki grade by MRA on the same patients.Results:A total of 29 patients with moyamoya were reviewed. Median time between MRA and catheter angiogram was 2.4 months with interquartile range from 0.6-5.3 months. Unweighted Cohen’s Kappa was 0.34 (p<0.0001) which is considered fair correlation. When we calculated a weighted Cohen’s Kappa it improved but only to 0.49 (p<0.0001) which is moderate correlation.Conclusion:Using Cohen’s kappa to compare two methods of evaluating cerebral artery stenosis in children with moyamoya, we demonstrated that there is only moderate correlation between catheter angiogram Suzuki staging compared to modified Suzuki staging with MRA. In conclusion, we suggest caution in the reliance of MRA for diagnosis and follow-up of children with moyamoya. We recommend consideration catheter angiograms at time of diagnosis and with surgical planning.

Background and objectiveTo date, there have been few published studies examining the relationship between arteriovenous malformation (AVM) angioarchitecture and hemorrhagic presentation among children with cerebral AVMs. This study examines this relationship in this unique population, in whom symptomatic presentation of cerebral AVM is the norm rather than the exception.MethodsA cohort of children with AVMs from 2000 to 2011 were included. Predictors studied included patient age, gender and angioarchitectural features, including AVM location, nidus size and morphology, venous drainage, presence of venous outflow lesions and associated aneurysms. Predictors of hemorrhagic presentation were assessed using multivariate logistic regression.Results135 children (70 males, mean age 10.1 years) were included. 86/135 (63.7%) children presented with hemorrhage, 18 (13.3%) with seizures, 17 (12.6%) with headaches or neurological deficits and 14 (10.4%) were asymptomatic. AVM location, morphology and the presence of associated aneurysm, venous ectasia, draining vein stenosis and single draining vein were not significantly associated factors. After multivariate analysis, AVM size (OR 0.57, 95% CI 0.43 to 0.77; p<0.01), exclusive deep venous drainage (OR 4.94, 95% CI 1.30 to 18.8; p=0.02) and infratentorial location (OR 9.94, 95% CI 1.71 to 51.76; p=0.01) were independently associated with hemorrhagic presentation.ConclusionSmaller AVM size, exclusive deep venous drainage and infratentorial location are specific angioarchitectural factors independently associated with initial hemorrhagic presentation in children with AVMs.

The Institute of Medicine calls for the use of clinical guidelines and practice parameters to promote “best practices” and improve patient outcomes. In 2006, The Trauma Association of Canada Pediatric Committee set out to create an evidence-based, national pediatric cervical spine (c-spine) clearance guideline based on the literature, existing algorithms from each pediatric trauma center and from expert opinion from across Canada.

Long non-coding RNAs (lncRNAs) are increasingly recognized as functional units in cancer and powerful biomarkers; however, most remain uncharacterized. Here, we analyze 5,592 prognostic lncRNAs in 9,446 cancers of 30 types using machine learning. We identify 166 lncRNAs whose expression correlates with survival and improves the accuracy of common clinical variables, molecular features, and cancer subtypes. Prognostic lncRNAs are often characterized by switch-like expression patterns. In low-grade gliomas, HOXA10-ASactivation is a robust marker of poor prognosis that complements IDH1/2mutations, as validated in another retrospective cohort, and correlates with developmental pathways in tumor transcriptomes. Loss- and gain-of-function studies in patient-derived glioma cells, organoids, and xenograft models identify HOXA10-ASas a potent onco-lncRNA that regulates cell proliferation, contact inhibition, invasion, Hippo signaling, and mitotic and neuro-developmental pathways. Our study underscores the pan-cancer potential of the non-coding transcriptome for identifying biomarkers and regulators of cancer progression.

Patients and methods The clinical, radiological, surgical, and pathological findings of 16 children with a primary central nervous system (CNS) sarcoma are reported. There were 8 (50%) girls and 8 (50%) boys ranging in age from 4 months to 14 years (mean age 4.8 years). Four patients (23%) were in their 1st year of life. Fourteen children (87%) had an intracranial sarcoma, and 2 (13%) had intraspinal tumors. Nine intracranial tumors (60%) were supratentorial. The parietal and temporal regions were the most frequently involved sites. Results Characteristic imaging findings included tumor cysts in 7 patients and marked tumoral enhancement in 9 (69%) with intratumoral calcification and hemorrhage. All patients underwent at least one operation to surgically remove the tumor with the aim of maximal resection and 3 patients underwent a second resection due to a recurrent tumor. Resection was total in 9 (53%) patients and subtotal in another 7 (41%). Dural attachment by tumor was confirmed in 7 (44%) patients and parenchymal invasion was present in 9 (56%). In one-third of the patients there was a well-defined plane of dissection around the tumor. Postoperative radiation was used in 10 patients. Postoperative chemotherapy was used in all but 2 patients. Immunohistochemical studies were available in 13 patients with the most consistent finding being strong vimentin positivity. Five out of the 6 patients in whom the proliferation markers were obtained demonstrated a high proliferation index (Ki-67 labeling index, 20–50%). The mean length of survival in the group was 4.6 years (range 1 month to 16 years). Children who presented in the 1st year of life had shorter survival than those who presented at an older age. Six patients (40%) had cerebrospinal fluid (CSF) dissemination of the tumor. CSF dissemination was associated with a shorter mean survival of 1.9 years. Conclusions Our review of this series of patients indicates the requirement for adjuvant therapy and for continued efforts to classify tumor subtypes aimed at optimizing future treatments for patients with a primary CNS sarcoma.

Neural stem cells have recently come to the forefront in neurobiology because of the possibilities for CNS repair by transplantation. Further understanding of the biology of these cells is critical for making their use in CNS repair possible. It is likely that these discoveries will also have spin-offs for neuro-oncology as primary brain tumors may arise from a CNS progenitor cell. An understanding of the normal migratory ability of these cells is also likely to have a very important impact on the knowledge of brain tumor invasion.

The unique INK4A/ARFlocus at chromosome 9p21 encodes two distinct proteins that intimately link the pRB and p53 tumour suppressor pathways. p16INK4Ahas been identified as an inhibitor of the cell cycle, capable of inducing arrest in G1 phase. p14/p19ARFon the other hand can induce both G1 and G2 arrest due to its stabilizing effects on the p53 transcription factor. In addition to their roles in growth arrest, both proteins are involved in cellular senescence and apoptosis. The frequent mutation or deletion of INK4A/ARF in human tumours as well as the occurence of tumours in the murine knockout models have identified both p16 and ARF as bona fide tumour suppressors.

The cell cycle is a precisely controlled cellular program that ensures normal cellular proliferation and development. The cyclin-dependant kinases (CDK) are molecules central to the continued progression through the cell-cycle checkpoints and as such are regulated by various mechanisms including cyclin levels, phosphorylation/dephosphorylation and cyclin-dependant kinase inhibitors (CKI). The CKIs are grouped into two families based on their structure and function, four Ink4 CKIs and three Cip/Kip CKIs. Abnormalities in these proteins can give rise to developmental defects and cancer. In this review, we will discuss the biochemistry and cell biology of the each of the Cip/Kip CKIs, their role in development as evidenced by targeted mutations in mice, and their role as possible tumor suppressor genes.

Astrocytic tumors frequently exhibit defects in the expression or activity of proteins that control cell-cycle progression. Inhibition of kinase activity associated with cyclin/cyclin-dependent kinase co-complexes by cyclin-dependent kinase inhibitors is an important mechanism by which the effects of growth signals are down-regulated. We undertook the present study to determine the role of p57KIP2(p57) in human astrocytomas. We demonstrate here that whereas p57 is expressed in fetal brain tissue, specimens of astrocytomas of varying grade and permanent astrocytoma cell lines do not express p57, and do not contain mutations of the p57gene by multiplex-heteroduplex analysis. However, the inducible expression of p57 in three well-characterized human astrocytoma cell lines (U343 MG-A, U87 MG, and U373 MG) using the tetracycline repressor system leads to a potent proliferative block in G1as determined by growth curve and flow cytometric analyses. After the induction of p57, retinoblastoma protein, p107, and E2F-1 levels diminish, and retinoblastoma protein is shifted to a hypophosphorylated form. Morphologically, p57-induced astrocytoma cells became large and flat with an expanded cytoplasm. The inducible expression of p57 leads to the accumulation of senescence-associated β-galactosidase marker within all astrocytoma cell lines such that ∼75% of cells were positive at 1 week after induction. Induction of p57 in U373 astrocytoma cells generated a small population of cells (∼15%) that were nonviable, contained discrete nuclear fragments on Hoechst 33258 staining, and demonstrated ultrastructural features characteristic of apoptosis. Examination of bax and poly-(ADP ribose) polymerase levels showed no change in bax, but decreased expression of poly-(ADP ribose) polymerase after p57 induction in all astrocytoma cell lines. These data demonstrate that the proliferative block imposed by p57 on human astrocytoma cells results in changes in the expression of a number of cell cycle regulatory factors, cell morphology, and a strong stimulus to cell senescence.

Across the animal kingdom, adult tissue homeostasis is regulated by adult stem cell activity, which is commonly dysregulated in human cancers. However, identifying key regulators of stem cells in the milieu of thousands of genes dysregulated in a given cancer is challenging. Here, using a comparative genomics approach between planarian adult stem cells and patient-derived glioblastoma stem cells (GSCs), we identify and demonstrate the role of DEAD-box helicase DDX56 in regulating aspects of stemness in four stem cell systems: planarians, mouse neural stem cells, human GSCs, and a fly model of glioblastoma. In a human GSC line, DDX56 localizes to the nucleolus, and using planarians, when DDX56 is lost, stem cells dysregulate expression of ribosomal RNAs and lose nucleolar integrity prior to stem cell death. Together, a comparative genomic approach can be used to uncover conserved stemness regulators that are functional in both normal and cancer stem cells.

Verotoxin 1 (VT1) is an E. coli toxin comprising an A subunit with N-glycanase activity, and five smaller B subunits capable of binding to the functional receptor globotriaosylceramide (Galα1-4-Galβ1-4-Glcceramide-Gb3). VT is implicated in hemorrhagic colitis and the more serious hemolytic uremic syndrome. VT1 is active against various tumor cell lines in vitro and in vivo. To extend the anti-cancer spectrum of activity of VT to human brain tumors, in the present analysis we studied the effects of VT on the growth of 6 permanent human astrocytoma cell lines. All astrocytoma cell lines analyzed express Gb3 and were sensitive to VT-1 at a dose of 50 ng/ml, but sensitivity was not proportional to the relative Gb3 concentration. VT induced apoptosis in these cells was shown by electron microscopy. Morphological evidence (nuclear shrinkage and chromatin condensation) of apoptosis could be clearly distinguished 1.5 hrs after toxin addition. Ultrastructural preservation of organelles was observed in conjunction with blebbing of the plasma membrane, condensation of chromatin within the nucleus and nuclear shrinkage. Apoptosis was also induced by the recombinant toxin B subunit alone, suggesting that the ligation of Gb3 is the primary induction mechanism. These studies indicate that verotoxin/Gb3 targetting may provide a novel basis for the inhibition of astrocytoma tumour cell growth.

Intermediate filaments (IFs) are highly diverse intracytoplasmic proteins within the cytoskeleton which exhibit cell type specificity of expression. A growing body of evidence suggests that IFs may be involved as collaborators in complex cellular processes controlling astrocytoma cell morphology, adhesion and proliferation. As the co-expression of different IF subtypes has been linked to enhanced motility and invasion in a number of different cancer subtypes, we undertook the present study to examine the expression of vimentin and nestin in a panel of human astrocytoma cell lines whose tumorigenicity, invasiveness and cytoskeletal protein profiles are well known. Astrocytoma cells were examined for IF protein expression by immunofluorescence confocal and immunoelectron microscopy. The motility of all cell lines was determined by computerized time-lapse videomicroscopy. Invasive potential of astrocytoma cells was determined using Matrigel as a barrier to astrocytoma cell invasion in vitro. Vimentin was expressed by all astrocytoma cell lines. On the other hand, nestin was variably expressed among the different cell lines. The most motile and invasive astrocytoma cell line in our study was antisense GFAP-transfected U251 (asU251) astrocytoma cells which showed marked up-regulation of nestin expression compared to the U251 parental cell line and controls. The U87 astrocytoma cell line also demonstrated high nestin expression levels and was associated with an increased basal motility rate and a high degree of invasiveness through Matrigel. U343 astrocytoma cells did not express nestin, but had high levels of GFAP. It had the lowest motility rate and invasiveness of all the astrocytoma cell lines examined. Taken together, these data suggest that for the astrocytoma cell lines examined in this study, nestin and vimentin co-expression may serve as a marker for an astrocytoma cell type with enhanced motility and invasive potential. Further studies are required to determine the mechanism by which dual-IF protein expression alters other cytoskeletal or cell surface receptor protein components important in the process of astrocytoma invasion.

Genetic evidence from retinoblastoma patients and experiments describing the mechanism of cellular transformation by the DNA tumor viruses have defined a central role for the retinoblastoma protein (pRB) family of tumor suppressors in the normal regulation of the eukaryotic cell cycle. These proteins, pRB, p107, and p130, act in a cell cycle-dependent manner to regulate the activity of a number of important cellular transcription factors, such as the E2F-family, which in turn regulate expression of genes whose products are important for cell cycle progression. In addition, inhibition of E2F activity by the pRB family proteins is required for cell cycle exit after terminal differentiation or nutrient depletion. The loss of functional pRB, due to mutation of both RBI alleles, results in deregulated E2F activity and a predisposition to specific malignancies. Similarly, inac-tivation of the pRB family by the transforming proteins of the DNA tumor viruses overcomes cellular quiescence and prevents terminal differentiation by blocking the interaction of pRB, p107, and p130 with the E2F proteins, leading to cell cycle progression and, ultimately, cellular transformation. Together these two lines of evidence implicate the pRB family of negative cell cycle regulators and the E2F family of transcription factors as central components in the cell cycle machinery.

In a wide variety of tumor types, the expression of stromelysin 1 which is one of the matrix metalloproteinases (MMPs) has been shown to correlate with tumor invasion. However, little is known about the distribution of stromelysin in human brain tumors. We have previously shown that a correlation exists between the type IV collagenases, tissue inhibitor of metalloproteinase (TIMP)-1 and TIMP-2 transcripts and in vitro invasiveness among 7 human astrocytoma cell lines. In the present study, we analyzed the expression of stromelysin 1 among the same panel of human astrocytoma cell lines and human fibroblasts by northern blot analyses and in situ hybridization. Northern blot analysis demonstrated that SF-126 and U87 MG expressed high level stromelysin 1 transcripts. Following heat shock stimulation, the stromelysin 1 transcript was up-regulated in U87 MG astrocytoma cells. In situ hybridization analysis showed specific intracytoplasmic localization of mRNA for stromelysin in these astrocytoma cell lines. By casein zymography, we have determined that both SF-126 and U87 MG secreted stromelysin 1 protein. We conclude that stromelysin 1 is expressed by certain human astrocytoma cell lines, and this study confirms the importance of continuing to characterize the proteolytic enzyme profile of these tumors to fully understand the molecular mechanisms involved in astrocytoma invasiveness.

The role that glial filaments play in cells and tumors of glial origin is not well understood. We therefore undertook the present study to determine the relationships between glial and vimentin intermediate filaments (IFs), actin microfilaments, and CD44, a cell surface glycoprotein important in cell migration and invasion, in human astrocytoma cells. Three astrocytoma cell lines, U343 MG-A (U343), U251. MG (U251.), and antisense GFAP-transfected U251. (asU251.) were studied using immunoftuorescence confocal and immunoelectron microscopy. Furthermore, we studied the phenotypic behaviour of these astrocytoma cell lines by analyzing their migration through Matrigel in vitro. U343 astrocytoma ceUs had the highest expression levels of glial fibrillary acidic protein (GFAP), whereas asU251 had virtually no expression of GFAP. Parental U251 cells had intermediate expression levels of GFAP. The elimination of GFAP expression in as U251 cells was accompanied by a marked increase in vimentin, actin microfilaments and CD44 levels. Gold labeling density counts of cytoskeletal and cell surface elements demonstrated that the differences between GFAP, actin, CD44 and vimentin levels in the different astrocytoma cell lines were statistically significant (p < 0.05). Results from the in vitro invasion assay revealed that U343 cells demonstrated the least invasive potential, whereas as U251. astrocytoma cells demonstrated the most. Our results show that elimination of GFAP expression by antisense leads to marked alterations in cell morphology and phenotypic behaviour. These data imply that GFAP may be linked spatially and functionally to cytoskeletal elements which may be altered when this IF is deleted in astrocytomas.

A retrospective review of 36 children diagnosed with a supratentorial primitive neuroectodermal tumor (PNET) at the Hospital for Sick Children was performed for the period 1970-1995. All children but one received their initial treatment at our institution. There were 18 males and 18 females and the median age at diagnosis was 35 months. Twenty-two PNETs were lobar, 3 were deep in the hemisphere, and 10 were located in the pineal region. One child presented with intracranial leptomeningeal disseminated disease. The tumors were mostly undifferentiated although 22 had some evidence of differentiation along one or more neuroepithelial lines. Five children had a biopsy, 24 had subtotal resection, and 7 had gross total resection. Twenty-six children had adjuvant radiotherapy and 13 had chemotherapy. At last follow-up 30 patients were dead and 6 were alive. The median survival was 23 months and the 2, 3, and 5 year survivals were 50%, 34%, and 18% respectively. All of the survivors received craniospinal radiation and 4 received chemotherapy. There was a statistically significantly worse survival in young children. There was a trend to better survival in children treated since 1984, and in children undergoing gross total resection. Because of the extremely poor survival, we recommended that all children undergo gross total resection followed by chemotherapy. For children older than 3 years of age craniospinal radiation should also be given.

The cell of origin for malignant brain tumors remains uncertain, but de-differentiation from mature cells in the CNS has always been considered a strong possibility. In this issue of Nature Neuroscience, Alcantara Llaguno and colleagues report that differentiated neurons resist transformation by glioblastoma-associated mutations, pointing to neural stem cells or immature progenitors as the most likely cells of origin for these tumors, rather than cells of a relatively mature neuronal lineage.

Medulloblastoma (MB) is a neoplasm linked to dysregulated cerebellar development. Previously, we demonstrated that the Sonic Hedgehog (SHH) subgroup grows hierarchically, with Sox2+cells at the apex of tumor progression and relapse. To test whether this mechanism is rooted in a normal developmental process, we studied the role of Sox2 in cerebellar development. We find that the external germinal layer (EGL) is derived from embryonic Sox2+precursors and that the EGL maintains a rare fraction of Sox2+cells during the first postnatal week. Through lineage tracing and single-cell analysis, we demonstrate that these Sox2+cells are within the Atoh1+lineage, contribute extensively to adult granule neurons, and resemble Sox2+tumor cells. Critically, constitutive activation of the SHH pathway leads to their aberrant persistence in the EGL and rapid tumor onset. We propose that failure to eliminate this rare but potent developmental population is the tumor initiation mechanism in SHH-subgroup MB.

Human neural stem cell cultures provide progenitor cells that are potential cells of origin for brain cancers. However, the extent to which genetic predisposition to tumor formation can be faithfully captured in stem cell lines is uncertain. Here, we evaluated neuroepithelial stem (NES) cells, representative of cerebellar progenitors. We transduced NES cells with MYCN, observing medulloblastoma upon orthotopic implantation in mice. Significantly, transcriptomes and patterns of DNA methylation from xenograft tumors were globally more representative of human medulloblastoma compared to a MYCN-driven genetically engineered mouse model. Orthotopic transplantation of NES cells generated from Gorlin syndrome patients, who are predisposed to medulloblastoma due to germline-mutated PTCH1, also generated medulloblastoma. We engineered candidate cooperating mutations in Gorlin NES cells, with mutation of DDX3Xor loss of GSE1both accelerating tumorigenesis. These findings demonstrate that human NES cells provide a potent experimental resource for dissecting genetic causation in medulloblastoma.

Glioblastoma therapies have remained elusive due to limitations in understanding mechanisms of growth and survival of the tumorigenic population. Using CRISPR-Cas9 approaches in patient-derived GBM stem cells (GSCs) to interrogate function of the coding genome, we identify actionable pathways responsible for growth, which reveal the gene-essential circuitry of GBM stemness and proliferation. In particular, we characterize members of the SOX transcription factor family, SOCS3, USP8, and DOT1L, and protein ufmylation as important for GSC growth. Additionally, we reveal mechanisms of temozolomide resistance that could lead to combination strategies. By reaching beyond static genome analysis of bulk tumors, with a genome-wide functional approach, we reveal genetic dependencies within a broad range of biological processes to provide increased understanding of GBM growth and treatment resistance.