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Hematopoietic stem cell transplantation is a well known treatment of hematologic malignancies wherein nascent stem cells provide a regenerating marrow and immunotherapy against the tumor. The progeny of hematopoietic stem cells also populate a wide spectrum of tissues, including the brain, as bone marrow derived macrophages similar to microglial cells. We developed a sensitive and novel combined IHC and XY FISH assay to detect, quantify and characterize donor cells in the cerebral cortex of 19 female allogeneic stem cell transplant patients. We show that the number of male donor cells ranged from 0.14-3.0% of total cells or 1.2-25% of microglial cells. Using tyramide based fluorescent IHC we found at least 80% of the donor cells express the microglial marker Iba1 consistent with being bone marrow derived macrophages. The percentage of donor cells was related to pretransplant conditioning; donor cells from radiation based myeloablative cases averaged 8.1% of microglial cells, while those from non-myeloablative cases averaged only 1.3%. The number of donor cells in patients conditioned with Busulfan or Treosulfan based myeloablation were similar to TBI based conditioning; donor cells averaged 6.8% of microglial cells. Notably, patients who received multiple transplants and those with the longest post-transplant survival had the highest level of donor engraftment, with donor cells averaging 16.3% of microglial cells. Our work represents the largest study characterizing bone marrow-derived macrophages in post-transplant patients. The efficiency of engraftment observed in our study warrants future research on microglial replacement as a therapeutic option for disorders of the central nervous system.Key PointsWe developed a sensitive Iba1 IHC and XY FISH co-stain assay to detect bone marrow derived donor cells in the brain of HSCT patients.Donor cells in the CNS express Iba1 and average 8% of microglia after myeloablative HSCT; double transplants increase engraftment up to 25%.

In order to better understand the relationship between normal and neoplastic brain, we combined five publicly available large-scale datasets, correcting for batch effects and applying Uniform Manifold Approximation and Projection (UMAP) to RNA-seq data. We assembled a reference Brain-UMAP including 702 adult gliomas, 802 pediatric tumors and 1409 healthy normal brain samples, which can be utilized to investigate the wealth of information obtained from combining several publicly available datasets to study a single organ site. Normal brain regions and tumor types create distinct clusters and because the landscape is generated by RNA seq, comparative gene expression profiles and gene ontology patterns are readily evident. To our knowledge, this is the first meta-analysis that allows for comparison of gene expression and pathways of interest across adult gliomas, pediatric brain tumors, and normal brain regions. We provide access to this resource via the open source, interactive online tool Oncoscape, where the scientific community can readily visualize clinical metadata, gene expression patterns, gene fusions, mutations, and copy number patterns for individual genes and pathway over this reference landscape.

Temporally regulated alternative splicing choices are vital for proper development, yet the wrong splice choice may be detrimental. Here, we highlight a previously unidentified role for the neurotrophin receptor splice variant TrkB.T1 in neurodevelopment, embryogenesis, transformation, and oncogenesis across multiple tumor types in humans and mice. TrkB.T1 is the predominantNTRK2isoform across embryonic organogenesis, and forced overexpression of this embryonic pattern causes multiple solid and nonsolid tumors in mice in the context of tumor suppressor loss. TrkB.T1 also emerges as the predominantNTRKisoform expressed in a wide range of adult and pediatric tumors, including those harboring tropomyosin receptor kinase fusions. Affinity purification–mass spectrometry proteomic analysis reveals distinct interactors with known developmental and oncogenic signaling pathways such as Wnt, transforming growth factor–β, Sonic Hedgehog, and Ras. From alterations in splicing factors to changes in gene expression, the discovery of isoform specific oncogenes with embryonic ancestry has the potential to shape the way we think about developmental systems and oncology.

RNA-sequencing data is widely used to identify disease biomarkers and therapeutic targets using numerical methods such as clustering, classification, regression, and differential expression analysis. Such approaches rely on the assumption that mRNA abundance estimates from RNA-seq are reliable estimates of true expression levels. Here, using data from five RNA-seq processing pipelines applied to 6,690 human tumor and normal tissues, we show that nearly 88% of protein-coding genes have similar gene expression profiles across all pipelines. However, for >12% of protein-coding genes, current best-in-class RNA-seq processing pipelines differ in their abundance estimates by more than four-fold when applied to exactly the same samples and the same set of RNA-seq reads. Expression fold changes are similarly affected. Many of the impacted genes are widely studied disease-associated genes. We show that impacted genes exhibit diverse patterns of discordance among pipelines, suggesting that many inter-pipeline differences contribute to overall uncertainty in mRNA abundance estimates. A concerted, community-wide effort will be needed to develop gold-standards for estimating the mRNA abundance of the discordant genes reported here. In the meantime, our list of discordantly evaluated genes provides an important resource for robust marker discovery and target selection.

Glioma stem-like cells dynamically transition between a chemoradiation-resistant state (preferentially in the perivascular niche) and a chemoradiation-sensitive state (away from blood vessels). However, physical barriers in the tumour microenvironment restrict the delivery of chemotherapy to tumour compartments distant from blood vessels. Here we show that a computational stochastic model of the spatiotemporal dynamics of the perivascular niche that incorporates glioma stem-like cells, differentiated tumour cells, endothelial cells and stromal cells as well as relevant subcellular, cellular and tissue-level phenomena can be used to optimize the treatment schedules of chemoradiation and of standard radiation fractionation with the administration of temozolomide. In mice with platelet-derived-growth-factor-driven glioblastoma, the model-optimized treatment schedule increased the survival of the animals. For standard radiation fractionation in patients, the model predicts that chemotherapy may be optimally administered about an hour before the application of radiation. Massively parallel simulations of the spatiotemporal dynamics of the tumour microenvironment might predict tumour responses to a broader range of treatments and be used to optimize treatment regimens., Reporting summary. Further information on research design is available in the Nature Research Reporting Summary linked to this article.

Independent scientific achievements have led to the discovery of aberrant splicing patterns in oncogenesis, while more recent advances have uncovered novel gene fusions involving neurotrophic tyrosine receptor kinases (NTRKs) in gliomas. The exploration of NTRK splice variants in normal and neoplastic brain provides an intersection of these two rapidly evolving fields. Tropomyosin receptor kinase B (TrkB), encoded NTRK2, is known for critical roles in neuronal survival, differentiation, molecular properties associated with memory, and exhibits intricate splicing patterns and post-translational modifications. Here, we show a role for a truncated NTRK2 splice variant, TrkB.T1, in human glioma. TrkB.T1 enhances PDGF-driven gliomas in vivo, augments PDGF-induced Akt and STAT3 signaling in vitro, while next generation sequencing broadly implicates TrkB.T1 in the PI3K signaling cascades in a ligand-independent fashion. These TrkB.T1 findings highlight the importance of expanding upon whole gene and gene fusion analyses to include splice variants in basic and translational neuro-oncology research., Tropomyosin receptor kinase B (TrkB), encoded by the neurotrophic tyrosine receptor kinase 2 (NTRK2) gene, exhibits intricate splicing patterns and post-translational modifications. Here, the authors perform whole gene and transcript-level analyses and report the TrkB.T1 splice variant enhances PDGF-driven gliomas in vivo and augments PI3K signaling cascades in vitro.

Radiation therapy is part of the standard of care for gliomas and kills a subset of tumor cells, while also altering the tumor microenvironment. Tumor cells with stem‐like properties preferentially survive radiation and give rise to glioma recurrence. Various techniques for enriching and quantifying cells with stem‐like properties have been used, including the fluorescence activated cell sorting (FACS)‐based side population (SP) assay, which is a functional assay that enriches for stem‐like tumor cells. In these analyses, mouse models of glioma have been used to understand the biology of this disease and therapeutic responses, including the radiation response. We present combined SP analysis and single‐cell RNA sequencing of genetically‐engineered mouse models of glioma to show a time course of cellular response to radiation. We identify and characterize two distinct tumor cell populations that are inherently radioresistant and also distinct effects of radiation on immune cell populations within the tumor microenvironment., Main Points Early after irradiation of murine glioma, FACS‐analysis shows stem‐like cells are enriched, and scRNA‐seq shows the radioresistant tumor cells are progenitors and stem‐like cells. Also, microglia and macrophage populations shift.

Pilocytic astrocytoma is a low-grade glial neoplasm of the central nervous system (CNS) that tends to occur in the pediatric population and less commonly presents in adults. Hereditary pilocytic astrocytoma is often associated with germline genetic alterations in the tumor suppressor NF1, the gene responsible for the syndrome neurofibromatosis type 1. Sporadic pilocytic astrocytoma frequently harbors somatic alterations in BRAF, with rare pilocytic astrocytomas containing alterations in FGFR1 and NTRK2. NTRK2 encodes for the protein tropomyosin receptor kinase B (TrkB), which is a neurotrophin receptor with high affinity for Brain-Derived Neurotrophic Factor (BDNF), and plays a role in several physiological functions of neurons, including cell survival and differentiation. In this report, we describe a novel PML-NTRK2 gene fusion occurring in an adult sporadic pilocytic astrocytoma and review the biology and implications of specific NTRK2 mutations occurring in CNS neoplasms.

Introduction: Hematopoietic stem cell transplantation (HSCT) has had a major impact on the treatment of hematologic malignancies. Recent studies have shown the role HSCT can have in gene therapy by providing long-lived genetically modified cells to treat a variety of human diseases. It is well known that HSC and bone marrow-derived cells can differentiate into long-lived tissue macrophages and populate a wide spectrum of tissues including the brain. These cells are termed bone marrow derived macrophages and are akin to microglial cells in both morphology and function. There is an expanding literature of preclinical animal studies focused on the potential benefits of bone marrow derived-macrophage engraftment into the central nervous system (CNS). In this study we report the detection and characterization of donor bone marrow-derived macrophages in the cerebral cortex of allogeneic transplant patients. Methods: To determine the frequency of donor cell engraftment in post-transplant patients, we selected a cohort of 20 patients who had undergone a sex-mismatched transplant. Formalin fixed paraffin embedded cerebral cortex samples were obtained from the Fred Hutch tissue repository. Samples from male and female autologous transplants were used as controls. Tissue sections were stained by XY fluorescent in situ hybridization (FISH) to identify male and female cells. The XY FISH-stained slides were imaged at 40X magnification on a TissueFAX system. Scanned images were analyzed in blinded fashion using TissueQuest software. Male donor cells were defined by the presence of the Y chromosome within DAPI stained nuclei. Parameters were established using a small area and then applied to a larger area covering 10,000-15,000 cells. Identified donors were confirmed by manual inspection. Adjacent sections were used in Iba1 immunohistochemistry (IHC) studies to quantify the microglia/macrophage population. Select cases were used in double fluorescent Iba1 IHC (tyramide signal amplification)/XY-FISH studies to identify the donor cell type. Results: Intraparenchymal donor bone marrow derived cells were identified in all cerebral cortex sex mismatched samples. To determine the identity of donor cells, select cases were stained with fluorescent tyramide based Iba1 IHC, imaged, stained with XY FISH and re-imaged. The majority of donor cells (>80%) showed strong expression of Iba1, confirming them to be bone marrow-derived macrophages. In parallel Iba1 IHC studies we showed that microglial cells constitute ~12% of the scanned cell population. Thus, when computed as a percentage of the macrophage/microglial population, donor cells from myeloablative transplants range from 4.2-25%. The bone marrow derived cells are stable over time since length of the post-transplant period did not have a major impact on the number of donor cells. Prior animal studies have demonstrated the importance of conditioning (total body irradiation (TBI) or Busulfan) in providing access to the CNS and stimulating engraftment. Consistently, we found that the strength of the conditioning regimen had a significant impact on donor cell engraftment into the CNS. Donor cells in myeloablative cases (>1,000cGy) averaged 8.0% (4.2-14.9%) of microglial cells, while those in non-myeloablative cases ( Conclusion: This, the largest study of bone marrow-derived macrophages in post-transplant patients, shows that donor derived cells from myeloablative transplants account for 4.1-25.1% of microglial cells. Donor engraftment is highest following myeloablative conditioning or in patients receiving multiple transplants, and lowest in non-myeloablative cases. Our studies document the magnitude of donor-derived macrophages in the CNS following a bone marrow transplant and serve as a basis for future gene therapy studies targeting neurodegenerative disorders. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Whole transcriptome sequencing (RNA-seq) is an important tool for understanding genetic mechanisms underlying human diseases and gaining a better insight into complex human diseases. Several ground-breaking projects have uniformly processed RNASeq data from publicly available studies to enable cross-comparison. One noteworthy study is the recount2 pipeline, which in 2017, has reprocessed ~70,0000 samples from Short Read Archive(SRA), The Cancer Genome Atlas (TCGA), and Genotype-Tissue Expression (GTEx). This vast dataset also includes gene expression data for GTEx-defined brain regions, neurological and psychiatric disorders (such as Parkinson's, Alzheimer’s, Huntington’s) and gliomas (such as TCGA, Chinese Glioma Genome Atlas (CGGA)). We apply uniform manifold approximation and projection (UMAP), a non-linear dimension reduction tool, to bulk gene expression data from brain-related diseases to build a BRAIN-UMAP, which allows for visualization of gene expression profiles across datasets. This UMAP shows that while gliomas form a distinct cluster, the neurological and psychiatric diseases are similar to GTEX-defined normal brain regions which exhibit tissue-specific profiles and patterns. Incorporating gliomas from various publicly available datasets also allows for the ability to observe unique clustering of particular subtypes, which can increase our genetic understanding of the disease. We also present a resource where researchers interested in mechanisms, can easily compare, and contrast the expression of a given gene and/or pathway of interest across various diseases, gliomas, and normal brain regions. Our current study, focusing on brain related diseases, offers insight into what may be possible for the broader neuroscientific community if we continually reprocess newly available brain related RNASeq samples using recount2. Additionally, if we build similar uniformly processing pipelines for other kinds of next-generation sequencing data, we would be able to use multi-omic sequencing data to find novel associations between biological entities and increase our mechanistic knowledge of the disease.

Temporally regulated alternative splicing choices are vital for proper development yet the wrong splice choice may be detrimental. Here we highlight a novel role for the neurotrophin receptor splice variant TrkB.T1 in neurodevelopment, embryogenesis, transformation, and oncogenesis across multiple tumor types in both humans and mice. TrkB.T1 is the predominant NTRK2 isoform across embryonic organogenesis and is highly expressed in a wide range of adult and pediatric tumors. Further, forced expression of TrkB.T1 causes multiple solid and non-solid tumors in mice in the context of tumor suppressor loss. These results highlight a unique role for the neurotrophin receptor splicing in development and oncogenesis and underscore the need for considering alternative splicing and transcript level data in neuroscience, developmental biology, and oncology research.

Oncolytic viruses induce local tumor destruction and inflammation. Whether virotherapy can also overcome immunosuppression in noninfected tumor areas is under debate. To address this question, we have explored immunologic effects of oncolytic herpes simplex viruses (oHSVs) in a genetically engineered mouse model of isocitrate dehydrogenase (IDH) wild-type glioblastoma, the most common and most malignant primary brain tumor in adults. Our model recapitulates the genomics, the diffuse infiltrative growth pattern, and the extensive macrophage-dominant immunosuppression of human glioblastoma. Infection with an oHSV that was armed with a UL16-binding protein 3 (ULBP3) expression cassette inhibited distant tumor growth in the absence of viral spreading (abscopal effect) and yielded accumulation of activated macrophages and T cells. There was also abscopal synergism of oHSV(ULBP3) with anti–programmed cell death 1 (anti–PD-1) against distant, uninfected tumor areas; albeit consistent with clinical trials in patients with glioblastoma, monotherapy with anti–PD-1 was ineffective in our model. Arming oHSV with ULBP3 led to upregulation of antigen processing and presentation gene sets in myeloid cells. The cognate ULBP3 receptor NKG2D, however, is not present on myeloid cells, suggesting a noncanonical mechanism of action of ULBP3. Overall, the myeloid-dominant, anti–PD-1–sensitive abscopal effect of oHSV(ULBP3) warrants further investigation in patients with IDH wild-type glioblastoma.

Glioblastoma is the most common and most aggressive primary brain tumour. Standard of care consists of surgical resection followed by radiotherapy and concomitant and maintenance temozolomide (temozolomide/radiotherapy→temozolomide). Corticosteroids are commonly used perioperatively to control cerebral oedema and are frequently continued throughout subsequent treatment, notably radiotherapy, for amelioration of side effects. The effects of corticosteroids such as dexamethasone on cell growth in glioma models and on patient survival have remained controversial. We performed a retrospective analysis of glioblastoma patient cohorts to determine the prognostic role of steroid administration. A disease-relevant mouse model of glioblastoma was used to characterize the effects of dexamethasone on tumour cell proliferation and death, and to identify gene signatures associated with these effects. A murine anti-VEGFA antibody was used in parallel as an alternative for oedema control. We applied the dexamethasone-induced gene signature to The Cancer Genome Atlas glioblastoma dataset to explore the association of dexamethasone exposure with outcome. Mouse experiments were used to validate the effects of dexamethasone on survival in vivo Retrospective clinical analyses identified corticosteroid use during radiotherapy as an independent indicator of shorter survival in three independent patient cohorts. A dexamethasone-associated gene expression signature correlated with shorter survival in The Cancer Genome Atlas patient dataset. In glioma-bearing mice, dexamethasone pretreatment decreased tumour cell proliferation without affecting tumour cell viability, but reduced survival when combined with radiotherapy. Conversely, anti-VEGFA antibody decreased proliferation and increased tumour cell death, but did not affect survival when combined with radiotherapy. Clinical and mouse experimental data suggest that corticosteroids may decrease the effectiveness of treatment and shorten survival in glioblastoma. Dexamethasone-induced anti-proliferative effects may confer protection from radiotherapy- and chemotherapy-induced genotoxic stress. This study highlights the importance of identifying alternative agents such as vascular endothelial growth factor antagonists for managing oedema in glioblastoma patients. Beyond the established adverse effect profile of protracted corticosteroid use, this analysis substantiates the request for prudent and restricted use of corticosteroids in glioblastoma.

RNA-sequencing data is widely used to identify disease biomarkers and therapeutic targets. Here, using data from five RNA-seq processing pipelines applied to 6,690 human tumor and normal tissues, we show that for >12% of protein-coding genes, in at least 1% of samples, current best-in-class RNA-seq processing pipelines differ in their abundance estimates by more than four-fold using the same samples and the same set of RNA-seq reads, raising clinical concern.

Recent work has uncovered oncogenic TRK fusions in a wide range of cancer types, including adult and pediatric gliomas. With some exceptions, many of these fusions tend to occur at very low frequencies below 1–2%, with unclear clinical significance, yet they highlight a potentially important and rapidly evolving role for NTRK1, NTRK2, NTRK3 in glioma biology. Basic scientific and clinical investigation surrounding TRKs’ role in cancer has often been hindered due to the nonspecific nature of antibodies and kinase inhibitors, combined with a lack of precise exon-specific expression data from patient populations. Tropomyosin receptor B (TrkB), encoded by the NTRK2 gene, is most known for its established roles in neuronal survival, proliferation, differentiation, apoptosis, learning, and memory. TrkB exerts diverse effects on cellular outcomes through interactions with downstream signaling cascades and has been shown to exhibit complex alternative splicing patterns. Here we show a novel role for a TrkB splice variant in human gliomas via NTRK2 transcript analyses in normal human brain and gliomas using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression Project (GTEx). Using a novel antibody designed against this splice variant, immunostaining shows altered receptor localization within human gliomas compared to normal human brain. This NTRK2 splice variant enhances PDGF-driven gliomas in vivo in an RCAS-TVA mouse model and augments PDGF-induced signaling in vitro. Through the lens of NTRK2, these results highlight the importance of expanding upon whole gene-level and kinase-fusion analyses to explore TRK splicing in basic and translational research.

Breakthroughs in modern medicine have increased pediatric cancer survival rates throughout the last several decades. Despite enhanced cure rates, a subset of pediatric cancer survivors exhibit life-long psychological side effects. A large body of work has addressed potential mechanisms for secondary symptoms of anxiety, post-traumatic stress, impaired emotion regulation and cognitive deficits in adults. Yet, absent from many studies are the ways in which cancer treatment can impact the developing brain. Additionally, it remains less known whether typical neurobiological changes during adolescence and early adulthood may potentially buffer or exacerbate some of the known negative cancer survivorship outcomes. This review highlights genetic, animal, and human neuroimaging research across development. We focus on the neural circuitry associated with aversive learning, which matures throughout childhood, adolescence and early adulthood. We argue that along with other individual differences, the precise timing of oncological treatment insults on such neural circuitry may expose particular vulnerabilities for pediatric cancer patients. We also explore other moderators of treatment outcomes, including genetic polymorphisms and neural mechanisms underlying memory and cognitive control. We discuss how neural maturation extending into young adulthood may also provide a sensitive period for intervention to improve psychological and cognitive outcomes in pediatric cancer survivors.

Glioblastoma is a deadly disease with median survival ranging below one year. T-cell-based immunotherapy approaches failed to prolong survival of glioblastoma patients in two phase III clinical trials, thus reflecting the immunologically inert features of glioblastoma. Pre-clinical efficacy of oncolytic virus therapy in combination with immune checkpoint inhibition was demonstrated in syngeneic glioblastoma models. However, given the extensive spreading of glioblastoma cells throughout the brain, we hypothesized that efficacious immunotherapy approaches in patients will need to elicit abscopal responses, i.e. the secondary targeting of tumor cells at sites distant from treated lesions. We addressed this issue in an immune competent RCAS/tv-a-based genetic glioblastoma model that recapitulates the genotype, gene expression, histology and immune phenotype of human glioblastomas. Spatial distance of virus-treated and untreated glioblastoma lesions was modeled by generating two tumors in both hemispheres of N/tv-a;Ink4a/Arf(-/-);PTEN(fl/fl);Luc(LSL/LSL)mice. One tumor was generated by transduction with RCAS-Pdgfb and RCAS-shPTEN. A second, contralateral tumor was generated with RCAS-Pdgfb and RCAS-Cre, thus enabling additional monitoring of tumor growth through luciferase activity. We infected luciferase-negative tumor lesions with a miR-124-attenuated oncolytic herpes simplex virus 1 (oHSV) armed with the NKG2D ligand ULBP3. oHSV-ULBP3 infection slowed the growth of distant, non-infected glioblastoma lesions and prolonged survival. oHSV-ULBP3 led to influx and activation of T-cells in both, treated and untreated glioblastoma lesions. Massive influx of monocytes yielded an increase of mostly PD1+ macrophages in both tumors. Neutrophils were also increased ubiquitously, whereas NK-cells were suppressed. Treatment with an anti-PD1 antibody alone had no effect, but combination with oHSV-ULBP3 counteracted macrophage and neutrophil influx and enhanced abscopal anti-tumor responses. We conclude that oHSV-ULBP3 in combination with anti-PD-1 is a feasible approach to induce abscopal T-cell-mediated immune responses in glioblastoma. Unraveling the role of myeloid components of the tumor microenvironment may be critical to overcome resistance to such treatment.

With an unsurpassed capacity for invasion into normal brain tissue, glioblastoma multiforme is the most lethal primary brain tumor. New research suggests that altering a subset of extracellular matrix factors, including interferon regulatory factor 3 (IRF3) and casein kinase 2 (CK2), may decrease the migratory potential of these aggressive tumors.

The capacity to learn to associate cues with negative outcomes is a highly adaptive process that appears to be conserved across species. However, when the cue is no longer a valid predictor of danger, but the emotional response persists, this can result in maladaptive behaviors, and in humans contribute to debilitating emotional disorders. Over the past several decades, work in neuroscience, psychiatry, psychology, and biology have uncovered key processes underlying, and structures governing, emotional responding and learning, as well as identified disruptions in the structural and functional integrity of these brain regions in models of pathology. In this review, we highlight some of this elegant body of work as well as incorporate emerging findings from the field of developmental neurobiology to emphasize how development contributes to changes in the ability to learn and express emotional responses, and how early experiences, such as stress, shape the development and functioning of these circuits.

Glioblastoma is the most common adult primary brain tumor and has a dismal median survival. Radiation is a mainstay of treatment and significantly improves survival, yet recurrence is nearly inevitable. Better understanding the radiation response of glioblastoma will help improve strategies to treat this devastating disease. Here, we present a comprehensive study of the in vivo radiation response of glioma cells in a mouse model of proneural glioblastoma. These tumors are a heterogeneous mix of cell types with differing radiation sensitivities. To explicitly study the gene expression changes comprising the radiation response of the Olig2(+) tumor bulk cells, we used translating ribosome affinity purification (TRAP) from Olig2-TRAP transgenic mice. Comparing both ribosome-associated and total pools of mRNA isolated from Olig2(+) cells indicated that the in vivo gene expression response to radiation occurs primarily at the total transcript level. Genes related to apoptosis and cell growth were significantly altered. p53 and E2F were implicated as major regulators of the radiation response, with p53 activity needed for the largest gene expression changes after radiation. Additionally, radiation induced a marked shift away from a proneural expression pattern toward a mesenchymal one. This shift occurs in Olig2(+) cells within hours and in multiple genetic backgrounds. Targets for Stat3 and CEBPB, which have been suggested to be master regulators of a mesenchymal shift, were also up-regulated by radiation. These data provide a systematic description of the events following radiation and may be of use in identifying biological processes that promote glioma radioresistance.

Brain-derived neurotrophic factor (BDNF) is a growth factor that plays key roles in regulating higher-order emotional and cognitive processes including fear learning and memory. A common single-nucleotide polymorphism (SNP) has been identified in the human BDNF gene (BDNF Val66Met) that leads to decreased BDNF secretion and impairments in specific forms of fear learning in adult humans and genetically modified mice containing this SNP. As the emergence of anxiety and other fear-related disorders peaks during adolescence, we sought to better understand the impact of this BDNF SNP on fear learning during the transition through adolescence in BDNF Val66Met knock-in mice. Previously, we have shown that contextual fear expression is temporarily suppressed in wild-type mice during a distinct period in adolescence, but re-emerges at later, postadolescent ages. Until recently, it was unclear whether BDNF-TrkB signaling is involved in the modulation of hippocampal-dependent contextual fear learning and memory during this adolescent period. Here we show that in BDNF Val66Met mice, the presence of the Met allele does not alter contextual fear expression during adolescence, but when previously conditioned BDNFMet/Met mice are tested in adulthood, they fail to display the delayed expression of contextual fear compared to wild-type BDNFVal/Val controls, indicating that the Met allele may permanently alter hippocampal function, leading to persistent functioning that is indistinguishable from the adolescent state. Conversely, truncated TrkB receptor (TrkB.T1)-deficient (TrkB.T1-/-) mice, a genetic mouse model with increased BDNF-TrkB signaling through full-length TrkB receptors, exhibit an accelerated expression of contextual fear during adolescence compared to wild-type controls. Our results point to a critical function for BDNF-TrkB signaling in fear regulation in vivo, particularly during a potentially sensitive period in adolescence.

Most known for their essential roles in the development and maintenance of the nervous system, the neurotrophins consist of nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), NT-3, NT-4 and their respective tropomyosin receptor kinases (TRKs) TrkA, TrkB, and TrkC along with the low affinity nerve growth factor receptor, p75. In addition to known roles in neuronal survival, proliferation, differentiation, and apoptosis, TRKs exert diverse effects on cellular outcomes through their interactions with downstream signaling cascades. Prior to TRKs’ established roles in neurobiology, oncogenic TRK was discovered as tropomysoin 3 (TPM3)-TrkA fusion and as a result, oncological studies of the neurotrophin family have identified additional TRK fusions. Putative oncogenic TRK fusions have been observed in various cancer types, but their clinical significance remains unclear and these fusions tend to occur at very low frequencies below 1–2%. The low incidence of these fusions combined with significant overexpression of various TRKs in a multitude of cancers raises the possibility that another aspect of TRK biology, in addition to kinase-domain fusions, may be relevant. Basic scientific and clinical investigation surrounding TRKs’ role in cancer has often been hindered due to the nonspecific nature of antibodies and kinase inhibitors, combined with a lack of precise exon-specific expression data from patient populations. Tropomyosin receptor B (TrkB), encoded by the NTRK2 gene, exhibits complex alternative splicing patterns. Here we show a novel role for a TrkB splice variant in gliomas via NTRK2 transcript analyses and immunostaining using a novel antibody engineered specifically to this variant. This NTRK2 splice variant enhances PDGF-driven gliomas in vivo and augments PDGF-induced signaling in vitro. Through the lens of NTRK2, these results highlight the importance of expanding upon whole gene-level and kinase-fusion analyses to explore TRK splicing in basic and translational research.

Throughout the past several decades, studies have uncovered a wealth of information about the neural circuitry underlying fear learning and extinction that has helped to inform treatments for fear-related disorders such as post-traumatic stress and anxiety. Yet, up to 40% of people do not respond to such treatments. Adolescence, in particular, is a developmental stage during which anxiety disorders peak, yet little is known about the development of fear-related neural circuitry during this period. Moreover, pharmacological and behavioral therapies that have been developed are based on mature circuitry and function. Here, we review neural circuitry implicated in fear learning and data from adolescent mouse and human fear learning studies. In addition, we propose a developmental model of fear neural circuitry that may optimize current treatments and inform when, during development, specific treatments for anxiety may be most effective.

Fear learning is an adaptive, evolutionarily conserved process that allows people to respond appropriately to threats in the environment. These threats can vary across different contexts and across the life course. Taking into account the high degree of neural and behavioral conservation across species in fear regulation and its underlying neural circuitry, we examined how fear learning changes across contexts and over the course of development, focusing specifically on the environmentally changing and challenging period of adolescence. We show two surprising developmental findings specific to adolescents, relative to older and younger individuals: (a) diminished fear to previously aversive contexts and (b) heightened fear to previously aversive cues. These behavioral changes are paralleled by developmental changes in frontolimbic circuitry. We discuss how these evolutionarily conserved mechanisms may be essential to survival of the species, given the changing environmental demands (social, sexual, and physical) of adolescence. Our findings also have important implications for unremitting forms of fear at the core of anxiety-related disorders, which peak during adolescence, and for when during development specific treatments for these disorders may be most effective.

Fear extinction learning, the ability to reassess a learned cue of danger as safe when it no longer predicts aversive events, is often dysregulated in anxiety disorders. Selective serotonin reuptake inhibitors (SSRI's) enhance neural plasticity and their ability to enhance fear extinction learning may explain their anxiolytic properties. Caloric restriction (CR) has SSRI-like effects on neural plasticity and anxiety-related behavior. We implemented CR in mice to determine its effects on conditioned-fear responses. Wild type and serotonin transporter (SERT) knockout mice underwent CR for 7 days leading to significant weight loss. Mice were then tested for cued fear learning and anxiety-related behavior. CR markedly enhanced fear extinction learning and its retention in adolescent female mice, and adults of both sexes. These effects of CR were absent in SERT knockout mice. Moreover, CR phenocopied behavioral and molecular effects of chronic fluoxetine, but there was no additive effect of CR in fluoxetine-treated mice. These results demonstrate that CR enhances fear extinction learning through a SERT-dependent mechanism. These results may have implications for eating disorders such as anorexia nervosa (AN), in which there is a high prevalence of anxiety before the onset of dietary restriction and support proposals that in AN, CR is a motivated effort to control dysregulated fear responses and elevated anxiety.

Fear can be highly adaptive in promoting survival, yet it can also be detrimental when it persists long after a threat has passed. Flexibility of the fear response may be most advantageous during adolescence when animals are prone to explore novel, potentially threatening environments. Two opposing adolescent fear-related behaviours—diminished extinction of cued fear and suppressed expression of contextual fear—may serve this purpose, but the neural basis underlying these changes is unknown. Using microprisms to image prefrontal cortical spine maturation across development, we identify dynamic BLA-hippocampal-mPFC circuit reorganization associated with these behavioural shifts. Exploiting this sensitive period of neural development, we modified existing behavioural interventions in an age-specific manner to attenuate adolescent fear memories persistently into adulthood. These findings identify novel strategies that leverage dynamic neurodevelopmental changes during adolescence with the potential to extinguish pathological fears implicated in anxiety and stress-related disorders., Flexible fear-related responses may be advantageous in adolescence. Here the authors use microprisms to image prefrontal cortical spine maturation across development and report that plasticity in adolescent fear extinction responses is associated with dynamic reorganization in the amygdalahippocampal-PFC circuit.

The only evidence-based behavioral treatment for anxiety and stress-related disorders involves desensitization techniques that rely on principles of extinction learning. However, 40% of patients do not respond to this treatment. Efforts have focused on individual differences in treatment response, but have not examined when, during development, such treatments may be most effective. We examined fear-extinction learning across development in mice and humans. Parallel behavioral studies revealed attenuated extinction learning during adolescence. Probing neural circuitry in mice revealed altered synaptic plasticity of prefrontal cortical regions implicated in suppression of fear responses across development. The results suggest a lack of synaptic plasticity in the prefrontal regions, during adolescence, is associated with blunted regulation of fear extinction. These findings provide insight into optimizing treatment outcomes for when, during development, exposure therapies may be most effective.

Highly conserved neural circuitry between rodents and humans has allowed for in-depth characterization of behavioral and molecular processes associated with emotional learning and memory. Despite increased prevalence of affective disorders in adolescent humans, few studies have characterized how associative-emotional learning changes during the transition through adolescence or identified mechanisms underlying such changes. By examining fear conditioning in mice, as they transitioned into and out of adolescence, we found that a suppression of contextual fear occurs during adolescence. Although contextual fear memories were not expressed during early adolescence, they could be retrieved and expressed as the mice transitioned out of adolescence. This temporary suppression of contextual fear was associated with blunted synaptic activity in the basal amygdala and decreased PI3K and MAPK signaling in the hippocampus. These findings reveal a unique form of brain plasticity in fear learning during early adolescence and may prove informative for understanding endogenous mechanisms to suppress unwanted fear memories.

There has been a dramatic rise in geneenvironment studies of human behavior over the past decade that have moved the field beyond simple nature versus nurture de- bates. These studies offer promise in accounting for more variability in behavioral and biological phenotypes than stud- ies that focus on genetic or experiential factors alone. They also provide clues into mechanisms of modifying genetic risk or resilience in neurodevelopmental disorders. Yet, it is rare that these studies consider how these interactions change over the course of development. In this paper, we describe research that focuses on the impact of a polymorphism in a brain-derived neurotrophic factor (BDNF) gene, known to be involved in learning and development. Specifically we present findings that assess the effects of genotypic and environmental loadings on neuroanatomic and behavioral phenotypes across development. The findings illustrate the use of a genetic mouse model that mimics the human poly- morphism, to constrain the interpretation of gene-environ- ment interactions across development in humans. © 2009

Fear learning is an adaptive, evolutionarily conserved process that allows us to respond appropriately to threats in the environment. These threats can vary across different contexts (e.g., a lion in your yard versus a lion in a zoo) and by age (e.g., a dentist viewed by a child before cavities versus by an adult after cavities). Using the high degree of neural and behavioral conservation across species in fear regulation and the underlying neural circuitry, we examined how fear learning changes across contexts and development, focusing specifically on the environmentally changing and challenging period of adolescence. We show two surprising developmental findings specific to adolescents relative to older and younger ages: 1) diminished fear to previously aversive contexts; and 2) heightened fear to previously aversive cues. These behavioral changes are paralleled by developmental changes in frontolimbic circuitry. We discuss how these evolutionarily conserved mechanisms may be essential to survival of the species with the changing environmental demands (social, sexual and physical) of adolescence. Our findings also have important implications for unremitting forms of fear at the very core of anxiety related disorders that peak during the period of adolescence and when, during development, specific treatments for these disorders may be most effective.

The transition into and out of adolescence represents a unique developmental period during which neuronal circuits are particularly susceptible to modification by experience. Adolescence is associated with an increased incidence of anxiety disorders in humans,1–3 and an estimated 75% of adults with fear-related disorders met diagnostic criteria as children and adolescents.4,5 Conserved neural circuitry between rodents and humans has facilitated neurodevelopmental studies of behavioral and molecular processes associated with fear learning and memory, which lie at the heart of many anxiety disorders. Here, we review the non-linear developmental aspects of fear learning and memory during a transition period into and out of adolescence and provide a discussion of the molecular mechanisms that may underlie these alterations in behavior. We provide a model that may help to inform novel treatment strategies for children and adolescents with fear-related disorders.

To the Editor: Anxiety disorders are the most common psychiatric conditions, affecting as many as 1 in 10 individuals. The diagnosis of anxiety disorders peak during adolescence, a period characterized by pronounced changes in the ability to regulate emotional thoughts and behavior. These changes occur in parallel with development of frontolimbic circuitry captured by the “imbalance model” of adolescence (Figure 1A). Clarifying the nature of neurobehavioral changes during this developmental phase may provide important insight into both the etiology and treatment of anxiety disorders. Figure 1 Fear extinction learning and improvement of anxiety by age. (A) Representative illustration of frontolimbic circuitry, highlighting the earlier developing limbic areas (red) and later developing prefrontal cortex (green) suggested by the imbalance model ...

Fear learning is an adaptive, evolutionarily conserved process that allows one to respond appropriately to threats within the environment. In the case of psychiatric disorders, however, fear may persist long after an environmental threat has passed. This unremitting and often debilitating form of fear is a core component of many anxiety disorders, including post-traumatic stress disorder (PTSD), and involves exaggerated and inappropriate fear responses. The normative developmental trajectory of fear responsiveness is continually modified and sculpted throughout ontogeny to fit the dynamic needs of an organism across the lifespan. In this chapter, we review neural circuitry implicated in fear learning and present data from rodent and human fear learning studies spanning infancy to adulthood. In addition, we propose a developmental model of fear neural circuitry that may optimize current treatments and inform when, during development, specific treatments for anxiety may be most effective.

Adolescence represents a uniquely sensitive developmental stage in the transition from childhood to adulthood. During this transition, neuronal circuits are particularly susceptible to modification by experience. In addition, adolescence is a stage in which the incidence of anxiety disorders peaks in humans and over 75% of adults with fear-related disorders met diagnostic criteria as children and adolescents. While postnatal critical periods of plasticity for primary sensory processes, such as in the visual system are well established, less is known about potential critical or sensitive periods for fear learning and memory. Here, we review the non-linear developmental aspects of fear learning and memory during a transition period into and out of adolescence. We also review the literature on the non-linear development of GABAergic neurotransmission, a key regulator of critical period plasticity. We provide a model that may inform improved treatment strategies for children and adolescents with fear-related disorders.

A fundamental issue in psychiatric medicine is the lack of empirical evidence indicating when, during development, a treatment will be most effective for a patient. We review behavioral and brain changes that occur across development, focusing on the period of adolescence, when there is a peak in diagnosis of many psychiatric disorders. We use anxiety disorders as an example because of their high prevalence in youth (affecting as many as 1 in 10). Basic forms of fear learning, which are at the core of anxiety disorders and are the targets of behavioral therapeutics, are examined as a function of age. We also discuss how fear learning has been genetically modulated in mice and humans. Based on these findings, we provide future directions for determining the efficacy of innovative therapies and preventive strategies for anxiety disorders as a function of age and potential genetic effects inferred from mice and humans.

Throughout the past several decades, studies have uncovered a wealth of information about the neural circuitry underlying fear learning and extinction that has helped to inform treatments for fear-related disorders such as post-traumatic stress and anxiety. Yet, up to 40 percent of people do not respond to such treatments. Adolescence, in particular, is a developmental stage during which anxiety disorders peak, yet little is known about the development of fear-related neural circuitry during this period. Moreover, pharmacological and behavioral therapies that have been developed are based on mature circuitry and function. Here, we review neural circuitry implicated in fear learning and data from adolescent mouse and human fear learning studies. In addition, we propose a developmental model of fear neural circuitry that may optimize current treatments and inform when, during development, specific treatments for anxiety may be most effective.

The brain-derived neurotrophic factor (BDNF) Val66Met polymorphism is a common human single nucleotide polymorphism (SNP) that affects the regulated release of BDNF, and has been implicated in affective disorders and cognitive dysfunction. A decreased activation of the infralimbic medial prefrontal cortex (IL-mPFC), a brain region critical for the regulation of affective behaviors, has been described in BDNFMetcarriers. However, it is unclear whether and how the Val66Met polymorphism affects the IL-mPFC synapses. Here, we report that spike timing-dependent plasticity (STDP) was absent in the IL-mPFC pyramidal neurons from BDNFMet/Metmice, a mouse that recapitulates the specific phenotypic properties of the human BDNF Val66Met polymorphism. Also, we observed a decrease in NMDA and GABA receptor-mediated synaptic transmission in the pyramidal neurons of BDNFMet/Metmice. While BDNF enhanced non-NMDA receptor transmission and depressed GABA receptor transmission in the wild-type mice, both effects were absent in BDNFMet/Metmice after BDNF treatment. Indeed, exogenous BDNF reversed the deficits in STDP and NMDA receptor transmission in BDNFMet/Metneurons. BDNF-mediated selective reversal of the deficit in plasticity and NMDA receptor transmission, but its lack of effect on GABA and non-NMDA receptor transmission in BDNFMet/Metmice, suggests separate mechanisms of Val66Met polymorphism upon synaptic transmission. The effect of the Val66Met polymorphism on synaptic transmission and plasticity in the IL-mPFC represents a mechanism to account for this impact of SNP on affective disorders and cognitive dysfunction.

Recently, a single-nucleotide polymorphism (SNP) in the brain-derived neurotrophic factor (BDNF) gene (BDNF Val66Met) has been linked to the development of multiple forms of neuropsychiatric illness. This SNP, when genetically introduced into mice, recapitulates core phenotypes identified in human BDNF Val66Met carriers. In mice, this SNP also leads to elevated expression of anxiety-like behaviors that are not rescued with the prototypic selective serotonin reuptake inhibitor (SSRI), fluoxetine. A prominent hypothesis is that SSRI-induced augmentation of BDNF protein expression and the beneficial trophic effects of BDNF on neural plasticity are critical components for drug response. Thus, these mice represent a potential model to study the biological mechanism underlying treatment-resistant forms of affective disorders. To test whether the BDNF Val66Met SNP alters SSRI-induced changes in neural plasticity, we used wild-type (BDNF(Val/Val)) mice, and mice homozygous for the BDNF Val66Met SNP (BDNF(Met/Met)). We assessed hippocampal BDNF protein levels, survival rates of adult born cells, and synaptic plasticity (long-term potentiation, LTP) in the dentate gyrus either with or without chronic (28-day) fluoxetine treatment. BDNF(Met/Met) mice had decreased basal BDNF protein levels in the hippocampus that did not significantly increase following fluoxetine treatment. BDNF(Met/Met) mice had impaired survival of newly born cells and LTP in the dentate gyrus; the LTP effects remained blunted following fluoxetine treatment. The observed effects of the BDNF Val66Met SNP on hippocampal BDNF expression and synaptic plasticity provide a possible mechanistic basis by which this common BDNF SNP may impair efficacy of SSRI drug treatment.

Of Mice and Men Just how closely must mouse models replicate the known features of human disorders to be accepted as useful for mechanistic and therapeutic studies? Soliman et al. (p. 863 , published online 14 January) compared mice that vary only in their allelic composition at one position within the gene encoding brain-derived neurotrophic factor (BDNF) with humans exhibiting the same range of allelic variation. Individuals (mice and humans) carrying the allele that codes for a methionine-containing variant of BDNF retained a fearful response to a threatening stimulus even after its removal in comparison to those with the valine variant. Furthermore, in both cases, this linkage was mediated by diminished activity in the ventral-medial region of the prefrontal cortex. This deficit in extinction learning may contribute to differential responses to extinction-based therapies for anxiety disorders.

The characterization of adolescence as a time of “storm and stress” remains an open debate. Intense and frequent negative affect during this period has been hypothesized to explain the increased rates of affective disorders, suicide, and accidental death during this time of life. Yet some teens emerge from adolescence with minimal turmoil. We provide a neurobiological model of adolescence that proposes an imbalance in the development of subcortical limbic (e.g., amygdala) relative to prefrontal cortical regions as a potential mechanism for heightened emotionality during this period. Empirical support for this model is provided from recent behavioral and human imaging studies on the development of emotion regulation. We then provide examples of environmental factors that may exacerbate imbalances in amygdala-ventrofrontal function increasing risk for anxiety related behaviors. Finally we present data from human and mouse studies to illustrate how genetic factors may enhance or diminish this risk. Together, these studies provide a converging methods approach for understanding the highly variable stress and turmoil experienced in adolescence.

Brain-derived neurotrophic factor (BDNF) plays important roles in activity-dependent plasticity processes, such as long-term potentiation, learning, and memory. The recently reported human BDNF Val66Met (BDNFMet) polymorphism has been shown to lead to altered hippocampal volume and impaired hippocampal-dependent memory and is associated with a variety of neuropsychiatric disorders. There are few studies, however, that investigate the effect of the BDNFMetpolymorphism on hippocampal-independent memory processes. A conditioned taste aversion (CTA) task was used for studying the mechanisms of long-term, hippocampal-independent, nondeclarative memory in the mammalian brain. Using the CTA paradigm, we found a novel impairment in extinction learning, but not acquisition or retention, of aversive memories resulting from the variant BDNFMet. BDNFMetmice were slower to extinguish an aversive CTA memory compared with wild-type counterparts. Moreover, the BDNFMetwas associated with smaller volume and decreased neuronal dendritic complexity in the ventromedial prefrontal cortex (vmPFC), which plays a significant role in extinction of CTA. Finally, this delay in extinction learning could be rescued pharmacologically with a cognitive enhancer,d-cycloserine (DCS). To our knowledge, this is the first evidence that the BDNFMetpolymorphism contributes to abnormalities in memory extinction. This abnormality in extinction learning may be explained by alterations in neuronal morphology, as well as decreased neural activity in the vmPFC. Importantly, DCS was effective in rescuing this delay in extinction, suggesting that when coupled with behavior therapy, DCS may be an effective treatment option for anxiety disorders in humans with this genetic variant BDNF.