Brian V. Nahed

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

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 Screening individual cancer cells within a brain tumor may help to guide treatment and predict prognosis. Human cancers are complex ecosystems composed of cells with distinct phenotypes, genotypes, and epigenetic states, but current models do not adequately reflect tumor composition in patients. We used single-cell RNA sequencing (RNA-seq) to profile 430 cells from five primary glioblastomas, which we found to be inherently variable in their expression of diverse transcriptional programs related to oncogenic signaling, proliferation, complement/immune response, and hypoxia. We also observed a continuum of stemness-related expression states that enabled us to identify putative regulators of stemness in vivo. Finally, we show that established glioblastoma subtype classifiers are variably expressed across individual cells within a tumor and demonstrate the potential prognostic implications of such intratumoral heterogeneity. Thus, we reveal previously unappreciated heterogeneity in diverse regulatory programs central to glioblastoma biology, prognosis, and therapy.

Roles of the cation-chloride cotransporters in neurological disease.

In the nervous system, the intracellular chloride concentration ([Cl−]i) determines the strength and polarity of γ-aminobutyric acid (GABA)-mediated neurotransmission. [Cl−]i is determined, in part, by the activities of the SLC12 cation–chloride cotransporters (CCCs). These transporters include the Na–K–2Cl cotransporter NKCC1, which mediates chloride influx, and various K–Cl cotransporters—such as KCC2 and KCC3—that extrude chloride. A precise balance between NKCC1 and KCC2 activity is necessary for inhibitory GABAergic signaling in the adult CNS, and for excitatory GABAergic signaling in the developing CNS and the adult PNS. Altered chloride homeostasis, resulting from mutation or dysfunction of NKCC1 and/or KCC2, causes neuronal hypoexcitability or hyperexcitability; such derangements have been implicated in the pathogenesis of seizures and neuropathic pain. [Cl−]i is also regulated to maintain normal cell volume. Dysfunction of NKCC1 or of swelling-activated K–Cl cotransporters has been implicated in the damaging secondary effects of cerebral edema after ischemic and traumatic brain injury, as well as in swelling-related neurodegeneration. CCCs represent attractive therapeutic targets in neurological disorders the pathogenesis of which involves deranged cellular chloride homoestasis.

Molecular Mechanisms of Ischemic Cerebral Edema: Role of Electroneutral Ion Transport

The brain achieves homeostasis of its intracellular and extracellular fluids by precisely regulating the transport of solute and water across its major cellular barriers: endothelia of the blood-brain barrier (BBB), choroid plexus epithelia, and neuroglial cell membranes. Cerebral edema, the pathological accumulation of fluid in the brains intracellular and extracellular spaces, is a major cause of morbidity and mortality following stroke and other forms of ischemic brain injury. Until recently, mechanisms of cerebral edema formation have been obscure; consequently, its treatment has been empiric and suboptimal. Here, we provide a paradigm for understanding ischemic cerebral edema, showing that its molecular pathogenesis is a complex yet step-wise process that results largely from impaired astrocytic cell volume regulation and permeability alterations in the cerebral microvasculature, both of which arise from pathological changes in the activities of specific ion channels and transporters. Recent data has implicated the bumetanide-sensitive NKCC1, an electroneutral cotransporter expressed in astrocytes and the BBB, in cerebral edema formation in several different rodent models of stroke. Pharmacological inhibition or genetic deficiency of NKCC1 decreases ischemia-induced cell swelling, BBB breakdown, cerebral edema, and neurotoxicity. Combination pharmacological strategies that include NKCC1 as a target might thus prove beneficial for the treatment of ischemic, and potentially other types of, cerebral edema.

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

Although human tumours are shaped by the genetic evolution of cancer cells, evidence also suggests that they display hierarchies related to developmental pathways and epigenetic programs in which cancer stem cells (CSCs) can drive tumour growth and give rise to differentiated progeny. Yet, unbiased evidence for CSCs in solid human malignancies remains elusive. Here we profile 4,347 single cells from six IDH1 or IDH2 mutant human oligodendrogliomas by RNA sequencing (RNA-seq) and reconstruct their developmental programs from genome-wide expression signatures. We infer that most cancer cells are differentiated along two specialized glial programs, whereas a rare subpopulation of cells is undifferentiated and associated with a neural stem cell expression program. Cells with expression signatures for proliferation are highly enriched in this rare subpopulation, consistent with a model in which CSCs are primarily responsible for fuelling the growth of oligodendroglioma in humans. Analysis of copy number variation (CNV) shows that distinct CNV sub-clones within tumours display similar cellular hierarchies, suggesting that the architecture of oligodendroglioma is primarily dictated by developmental programs. Subclonal point mutation analysis supports a similar model, although a full phylogenetic tree would be required to definitively determine the effect of genetic evolution on the inferred hierarchies. Our single-cell analyses provide insight into the cellular architecture of oligodendrogliomas at single-cell resolution and support the cancer stem cell model, with substantial implications for disease management.

Hypertension, Age, and Location Predict Rupture of Small Intracranial Aneurysms

BACKGROUND:Although current guidelines for the management of unruptured intracranial aneurysms (IAs) suggest aneurysms larger than 7 mm should be considered for treatment, a significant number of subarachnoid hemorrhages are caused by IAs 7 mm or smaller. Thus, we sought to identify risk factors associated with the rupture of IAs 7 mm or smaller. METHODS:We identified 100 patients with subarachnoid hemorrhage resulting from IAs 7 mm or smaller between January 2001 and 2004. Patients were compared with controls (n = 51) with unruptured IAs 7 mm or smaller, diagnosed by conventional angiography or three-dimensional computerized angiography, with respect to aneurysm characteristics (size, location, and age of presentation) and risk factors (hypertension, smoking, cocaine use, and family history). RESULTS:Hypertensive patients with IAs 7 mm or smaller were 2.6 times more likely to experience rupture (P = 0.01; 95% confidence interval, 1.21–5.53) than patients with normal blood pressure. Posterior circulation aneurysms were 3.5 times more likely to rupture than anterior circulation aneurysms (P = 0.048; 95% confidence interval, 0.95–19.4). After adjustment for location and hypertension, the age of patient on presentation was associated with a trend toward inverse correlation with aneurysmal rupture risk (P = 0.07). Hypertension and posterior location remained significant independent predictors in the logistic regression model. CONCLUSION:Among patients with small aneurysms (≤7 mm), hypertension, relatively young age, and posterior circulation were significant risk factors for rupture. Given the minimal long-term morbidity and mortality of treatment of unruptured aneurysms in large, tertiary medical centers, management of unruptured aneurysms 7 mm or smaller should be governed by factors other than size, specifically age, history of hypertension, and location.

Mapping a Mendelian Form of Intracranial Aneurysm to 1p34.3-p36.13

The identification of pathways that underlie common disease has been greatly impacted by the study of rare families that segregate single genes with large effect. Intracranial aneurysm is a common neurological problem; the rupture of these aneurysms constitutes a frequently catastrophic neurologic event. The pathogenesis of these aneurysms is largely unknown, although genetic and environmental factors are believed to play a role. Previous genomewide studies in affected relative pairs have suggested linkage to several loci, but underlying genes have not been identified. We have identified a large kindred that segregates nonsyndromic intracranial aneurysm as a dominant trait with high penetrance. Genomewide analysis of linkage was performed using a two-stage approach: an analysis of ~10,000 single-nucleotide polymorphisms in the 6 living affected subjects, followed by the genotyping of simple tandem repeats across resulting candidate intervals in all 23 kindred members. Analysis revealed significant linkage to a single locus, with a LOD score of 4.2 at 1p34.3-p36.13 under a dominant model with high penetrance. These findings identify a Mendelian form of intracranial aneurysm and map the location of the underlying disease locus.

Genetics of intracranial aneurysms.

DESPITE ADVANCES IN the treatment of intracranial aneurysms (IA) in recent years, the overall outcome of patients with aneurysmal subarachnoid hemorrhage has shown only modest improvement. Given this poor prognosis, diagnosis of IA before rupture is of paramount importance. Currently, there are no reliable methods other than screening imaging studies of high-risk individuals to diagnose asymptomatic patients. Multiple levels of evidence suggest that environmental factors acting in concert with genetic susceptibilities lead to the formation, growth, and rupture of aneurysms in these patients. Epidemiological studies have already identified aneurysm-specific risk factors such as size and location, as well as patient-specific risk factors, such as age, sex, and presence of medical comorbidities, such as hypertension. In addition, exposure to certain environmental factors such as smoking have been shown to be important in the formation of IA. Furthermore, substantial evidence proves that certain loci contribute genetically to IA pathogenesis. Genome-wide linkage studies using relative pairs or rare families that are affected with the Mendelian forms of IA have already shown genetic heterogeneity of IA, suggesting that multiple genes, alone or in combination, are important in the disease pathophysiology. The linkage results, along with association studies, will ultimately lead to the identification of IA susceptibility genes. Identification of the genes important in IA pathogenesis will not only provide novel insights into the primary determinants of IA, but will also result in new opportunities for early diagnosis in the preclinical setting. Ultimately, novel therapeutic strategies based on biology will be developed, which will target these newly elucidated genetic susceptibilities.

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.

Single-cell RNA sequencing identifies a common origin for specific types of human glioma brain tumors. Effects of the tumor microenvironment Glioma brain tumors that carry mutant copies of the IDH gene can be subdivided into two major classes. However, the development of and differences between these two classes are not well characterized. Venteicher et al. coupled bulk sequencing and publicly available data with single-cell RNA sequencing data on glioma patient tissue samples. They identified a common lineage program that is shared between glioma subtypes. This suggests that the observed differences between the two glioma classes originate from lineage-specific genetic changes and the tumor microenvironment. Science, this issue p. eaai8478 INTRODUCTION Tumor fitness, evolution, and resistance to therapy are governed by selection of malignant cells with specific genotypes, by expression programs related to cellular phenotypes, and by influences of the tumor microenvironment (TME). Although bulk tumor analysis can interrogate the genetic state of tumor cells with high precision, bulk expression profiles average the diverse cells within each tumor, thereby masking critical differences and providing limited insight into cancer cell programs and TME influences. Single-cell RNA sequencing (scRNA-seq) can help to address those challenges but incurs financial and logistic considerations, including the time required to accrue large cohorts of fresh tumor specimen for single-cell analysis. RATIONALE We reasoned that scRNA-seq of a limited number of representative tumors could be combined with bulk data from large cohorts to decipher differences between tumor subclasses. In this approach, bulk samples collected for large cohorts, such as from The Cancer Genome Atlas (TCGA), are first used to define the combined effects of differences in cancer cell genotypes, phenotypes, and the composition of the TME. Single-cell analysis of a limited set of representative tumors is then used to distinguish those effects. We applied this approach to understand the differences between two types of isocitrate dehydrogenase (IDH)–mutant gliomas: astrocytoma (IDH-A) and oligodendroglioma (IDH-O). IDH-A and IDH-O are distinguished by co-occurring signature genetic events and by histopathology and are thought to recapitulate distinct glial lineages. By combining 9879 scRNA-seq profiles from 10 IDH-A tumors, 4347 scRNA-seq profiles from six IDH-O tumors, and 165 TCGA bulk RNA profiles, we could decipher differences between these two tumor types at single-cell resolution. RESULTS We find that differences in bulk expression profiles between IDH-A and IDH-O are primarily explained by the impact of signature genetic events and TME composition, but not by distinct expression programs of glial lineages in the malignant cells. We infer that both IDH-A and IDH-O share the same developmental hierarchy, consisting in each case of three subpopulations of malignant cells: nonproliferating cells differentiated along the astrocytic and oligodendrocytic lineages, and proliferative undifferentiated cells that resemble neural stem/progenitor cells. By analyzing tumors of different clinical grades, we observe that higher-grade tumors present enhanced proliferation, larger pools of undifferentiated glioma cells, and an increase in macrophage over microglia programs in the TME. CONCLUSION Our approach provides a general framework to decipher differences between classes of human tumors by decoupling cancer cell genotypes, phenotypes, and the composition of the TME. The shared glial lineages and developmental hierarchies observed in IDH-A and IDH-O suggest a common progenitor for all IDH-mutant gliomas, shedding light on a long-standing debate in gliomagenesis. In contrast to the similarity in glial lineages, IDH-A and IDH-O differ significantly in their TME, and in particular in the abundance of microglia/macrophage cells. Microglia and macrophages also differ between IDH-A tumors of different grades. Our study redefines the cellular composition of human IDH-mutant gliomas, with important implications for disease management. Single-cell RNA-seq of IDH-mutant gliomas reveals tumor architecture. (Top) Human samples were dissociated and analyzed by scRNA-seq. (Bottom) IDH-O and IDH-A differ in genetics and TME but are both primarily composed of three main types of malignant cells: cycling stem-like cells and noncycling astrocyte-like and oligodendrocyte-like cells. Tumor progression is associated with increased proliferation, decreased differentiation, and increase in macrophages over microglia in the TME. Tumor subclasses differ according to the genotypes and phenotypes of malignant cells as well as the composition of the tumor microenvironment (TME). We dissected these influences in isocitrate dehydrogenase (IDH)–mutant gliomas by combining 14,226 single-cell RNA sequencing (RNA-seq) profiles from 16 patient samples with bulk RNA-seq profiles from 165 patient samples. Differences in bulk profiles between IDH-mutant astrocytoma and oligodendroglioma can be primarily explained by distinct TME and signature genetic events, whereas both tumor types share similar developmental hierarchies and lineages of glial differentiation. As tumor grade increases, we find enhanced proliferation of malignant cells, larger pools of undifferentiated glioma cells, and an increase in macrophage over microglia expression programs in TME. Our work provides a unifying model for IDH-mutant gliomas and a general framework for dissecting the differences among human tumor subclasses.

Malpractice Liability and Defensive Medicine: A National Survey of Neurosurgeons

Background Concern over rising healthcare expenditures has led to increased scrutiny of medical practices. As medical liability and malpractice risk rise to crisis levels, the medical-legal environment has contributed to the practice of defensive medicine as practitioners attempt to mitigate liability risk. High-risk specialties, such as neurosurgery, are particularly affected and neurosurgeons have altered their practices to lessen medical-legal risk. We present the first national survey of American neurosurgeons’ perceptions of malpractice liability and defensive medicine practices. Methods A validated, 51-question online-survey was sent to 3344 practicing U.S. neurosurgeon members of the American Association of Neurological Surgeons, which represents 76% of neurosurgeons in academic and private practices. Results A total of 1028 surveys were completed (31% response rate) by neurosurgeons representing diverse sub-specialty practices. Respondents engaged in defensive medicine practices by ordering additional imaging studies (72%), laboratory tests (67%), referring patients to consultants (66%), or prescribing medications (40%). Malpractice premiums were considered a “major or extreme” burden by 64% of respondents which resulted in 45% of respondents eliminating high-risk procedures from their practice due to liability concerns. Conclusions Concerns and perceptions about medical liability lead practitioners to practice defensive medicine. As a result, diagnostic testing, consultations and imaging studies are ordered to satisfy a perceived legal risk, resulting in higher healthcare expenditures. To minimize malpractice risk, some neurosurgeons have eliminated high-risk procedures. Left unchecked, concerns over medical liability will further defensive medicine practices, limit patient access to care, and increase the cost of healthcare delivery in the United States.

Predictors of cranioplasty complications in stroke and trauma patients

OBJECT Decompressive craniectomy mandates subsequent cranioplasty. Complications of cranioplasty may be independent of the initial craniectomy, or they may be contingent upon the craniectomy. Authors of this study aimed to identify surgery- and patient-specific risk factors related to the development of surgical site infection and other complications following cranioplasty. METHODS A consecutive cohort of patients of all ages and both sexes who had undergone cranioplasty following craniectomy for stroke or trauma at a single institution in the period from May 2004 to May 2012 was retrospectively established. Patients who had undergone craniectomy for infectious lesions or neoplasia were excluded. A logistic regression analysis was performed to model and predict determinants related to infection following cranioplasty. RESULTS Two hundred thirty-nine patients met the study criteria. The overall rate of complication following cranioplasty was 23.85% (57 patients). Complications included, predominantly, surgical site infection, hydrocephalus, and new-onset seizures. Logistic regression analysis identified previous reoperation (OR 3.25, 95% CI 1.30-8.11, p = 0.01) and therapeutic indication for stroke (OR 2.45, 95% CI 1.11-5.39, p = 0.03) as significantly associated with the development of cranioplasty infection. Patient age, location of cranioplasty, presence of an intracranial device, bone flap preservation method, cranioplasty material, booking method, and time interval > 90 days between initial craniectomy and cranioplasty were not predictive of the development of cranioplasty infection. CONCLUSIONS Cranioplasty complications are common. Cranioplasty infection rates are predicted by reoperation following craniectomy and therapeutic indication (stroke). These variables may be associated with patient-centered risk factors that increase cranioplasty infection risk.