Cancer at single-cell resolution: Single-cell sequencing can illuminate the genetic properties of brain cancers and reveal heterogeneity within a tumor. Patel et al. examined the genome sequence of single cells isolated from brain glioblastomas. The findings revealed shared chromosomal changes but also extensive transcription variation, including genes related to signaling, which represent potential therapeutic targets. The authors suggest that the variation in tumor cells reflects neural development and that such variation among cancer cells may prove to have clinical significance. Science , this issue p. 1396

An epigenetic mechanism in which gain-of-function IDH mutations promote gliomagenesis by disrupting chromosomal topology is presented, with IDH mutations causing the binding sites of the methylation-sensitive insulator CTCF to become hypermethylated; disruption of a CTCF boundary near the glioma oncogene PDGFRA allows a constitutive enhancer to contact and activate the oncogene aberrantly. Cancer genome sequencing studies have identified recurrent IDH mutations in brain tumours and other cancers. IDH mutant gliomas have altered DNA methylation landscapes, such as hypermethylation of CpG island promoters. Here, Brad Bernstein and colleagues show that the effects of IDH1 mutation in gliomas are not limited to CpG islands, and the binding sites of the methylation-sensitive insulator CTCF are also hypermethylated. Disruption of a CTCF boundary near the glioma oncogene PDGFRA allows a constitutive enhancer to aberrantly contact and activate it. IDH mutations can therefore promote gliomagenesis by disrupting chromosomal topology and allowing aberrant gene regulatory interactions. Gain-of-function IDH mutations are initiating events that define major clinical and prognostic classes of gliomas1,2. Mutant IDH protein produces a new onco-metabolite, 2-hydroxyglutarate, which interferes with iron-dependent hydroxylases, including the TET family of 5′-methylcytosine hydroxylases3,4,5,6,7. TET enzymes catalyse a key step in the removal of DNA methylation8,9. IDH mutant gliomas thus manifest a CpG island methylator phenotype (G-CIMP)10,11, although the functional importance of this altered epigenetic state remains unclear. Here we show that human IDH mutant gliomas exhibit hypermethylation at cohesin and CCCTC-binding factor (CTCF)-binding sites, compromising binding of this methylation-sensitive insulator protein. Reduced CTCF binding is associated with loss of insulation between topological domains and aberrant gene activation. We specifically demonstrate that loss of CTCF at a domain boundary permits a constitutive enhancer to interact aberrantly with the receptor tyrosine kinase gene PDGFRA, a prominent glioma oncogene. Treatment of IDH mutant gliomaspheres with a demethylating agent partially restores insulator function and downregulates PDGFRA. Conversely, CRISPR-mediated disruption of the CTCF motif in IDH wild-type gliomaspheres upregulates PDGFRA and increases proliferation. Our study suggests that IDH mutations promote gliomagenesis by disrupting chromosomal topology and allowing aberrant regulatory interactions that induce oncogene expression.

Single-cell RNA sequencing identifies a common origin for specific types of human glioma brain tumors.

The growth of adult and paediatric brain tumours depends on a microenvironmental signalling pathway involving the activity-regulated secretion of neuroligin-3 (NLGN3) from normal neurons and oligodendrocyte precursor cells, highlighting the potential of NLGN3 as a therapeutic target. The growth of brain tumours is influenced by the microenvironment of the normal brain. Here, the authors unravel a microenvironmental signalling pathway involving secretion of neuroligin-3 (NLGN3) by normal neurons. NLGN3 is cleaved by extracellular proteases, stimulates oncogenic signalling in glioma cells and induces transcriptional changes. Inhibition of NLGN3 cleavage in the tumour microenvironment impairs the growth of brain tumour xenografts in vivo, suggesting that interfering with this pathway and with microenvironmental signalling in general is a potential therapeutic strategy for brain tumours. High-grade gliomas (HGG) are a devastating group of cancers, and represent the leading cause of brain tumour-related death in both children and adults. Therapies aimed at mechanisms intrinsic to glioma cells have translated to only limited success; effective therapeutic strategies will need also to target elements of the tumour microenvironment that promote glioma progression. Neuronal activity promotes the growth of a range of molecularly and clinically distinct HGG types, including adult and paediatric glioblastoma (GBM), anaplastic oligodendroglioma, and diffuse intrinsic pontine glioma (DIPG)1. An important mechanism that mediates this neural regulation of brain cancer is activity-dependent cleavage and secretion of the synaptic adhesion molecule neuroligin-3 (NLGN3), which promotes glioma proliferation through the PI3K–mTOR pathway1. However, the necessity of NLGN3 for glioma growth, the proteolytic mechanism of NLGN3 secretion, and the further molecular consequences of NLGN3 secretion in glioma cells remain unknown. Here we show that HGG growth depends on microenvironmental NLGN3, identify signalling cascades downstream of NLGN3 binding in glioma, and determine a therapeutically targetable mechanism of secretion. Patient-derived orthotopic xenografts of paediatric GBM, DIPG and adult GBM fail to grow in Nlgn3 knockout mice. NLGN3 stimulates several oncogenic pathways, such as early focal adhesion kinase activation upstream of PI3K–mTOR, and induces transcriptional changes that include upregulation of several synapse-related genes in glioma cells. NLGN3 is cleaved from both neurons and oligodendrocyte precursor cells via the ADAM10 sheddase. ADAM10 inhibitors prevent the release of NLGN3 into the tumour microenvironment and robustly block HGG xenograft growth. This work defines a promising strategy for targeting NLGN3 secretion, which could prove transformative for HGG therapy.