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Diffuse midline gliomas are uniformly fatal pediatric central nervous system cancers that are refractory to standard-of-care therapeutic modalities. The primary genetic drivers are a set of recurrent amino acid substitutions in genes encoding histone H3 (H3K27M), which are currently undruggable. These H3K27M oncohistones perturb normal chromatin architecture, resulting in an aberrant epigenetic landscape. To interrogate for epigenetic dependencies, we performed a CRISPR screen and show that patient-derived H3K27M-glioma neurospheres are dependent on core components of the mammalian BAF (SWI/SNF) chromatin remodeling complex. The BAF complex maintains glioma stem cells in a cycling, oligodendrocyte precursor cell–like state, in which genetic perturbation of the BAF catalytic subunit SMARCA4 (BRG1), as well as pharmacologic suppression, opposes proliferation, promotes progression of differentiation along the astrocytic lineage, and improves overall survival of patient-derived xenograft models. In summary, we demonstrate that therapeutic inhibition of the BAF complex has translational potential for children with H3K27M gliomas. Significance: Epigenetic dysregulation is at the core of H3K27M-glioma tumorigenesis. Here, we identify the BRG1–BAF complex as a critical regulator of enhancer and transcription factor landscapes, which maintain H3K27M glioma in their progenitor state, precluding glial differentiation, and establish pharmacologic targeting of the BAF complex as a novel treatment strategy for pediatric H3K27M glioma.

Rhabdomyosarcoma (RMS) is a common childhood cancer that shares features with developing skeletal muscle. Yet, the conservation of cellular hierarchy with human muscle development and the identification of molecularly defined tumor-propagating cells has not been reported. Using single-cell RNA-sequencing, DNA-barcode cell fate mapping and functional stem cell assays, we uncovered shared tumor cell hierarchies in RMS and human muscle development. We also identified common developmental stages at which tumor cells become arrested. Fusion-negative RMS cells resemble early myogenic cells found in embryonic and fetal development, while fusion-positive RMS cells express a highly specific gene program found in muscle cells transiting from embryonic to fetal development at 7-7.75 weeks of age. Fusion-positive RMS cells also have neural pathway-enriched states, suggesting less-rigid adherence to muscle-lineage hierarchies. Finally, we identified a molecularly defined tumor-propagating subpopulation in fusion-negative RMS that shares remarkable similarity to bi-potent, muscle mesenchyme progenitors that can make both muscle and osteogenic cells.

Human tumors are composed of diverse malignant and nonmalignant cells, generating a complex ecosystem that governs tumor biology and response to treatments. Recent technological advances have enabled the characterization of tumors at single-cell resolution, providing a compelling strategy to dissect their intricate biology. Here we describe recent developments in single-cell expression profiling and the studies applying them in clinical settings. We highlight some of the powerful insights gleaned from these studies for tumor classification, stem cell programs, tumor microenvironment, metastasis, and response to targeted and immune therapies.Significance:Intratumor heterogeneity (ITH) has been a major barrier to our understanding of cancer. Single-cell genomics is leading a revolution in our ability to systematically dissect ITH. In this review, we focus on single-cell expression profiling and lessons learned in key aspects of human tumor biology.

Ewing’s Sarcoma Ewing’s sarcoma, an aggressive cancer of bone and soft tissue, primarily affects children and young adults. A t(11;22) translocation is noted in 85 to 90% of cases. Management inclu...

Human tumors are complex ecosystems where diverse cancer and noncancer cells interact to determine tumor biology and response to therapies. Genomic and transcriptomic methods have traditionally profiled these intricate ecosystems as bulk samples, thereby masking individual cellular programs and the variability among them. Recent advances in single-cell profiling have paved the way for studying tumors at the resolution of individual cells, providing a compelling strategy to bridge gaps in our understanding of human tumors. Here, we review methodologies for single-cell expression profiling of tumors and the initial studies deploying them in clinical contexts. We highlight how these studies uncover new biology and provide insights into drug resistance, stem cell programs, metastasis, and tumor classifications. We also discuss areas of technology development in single-cell genomics that provide new tools to address key questions in cancer biology. These emerging studies and technologies have the potential to revolutionize our understanding and management of human malignancies.

The transcriptomic classification of glioblastoma (GBM) has failed to predict survival and therapeutic vulnerabilities. A computational approach for unbiased identification of core biological traits of single cells and bulk tumors uncovered four tumor cell states and GBM subtypes distributed along neurodevelopmental and metabolic axes, classified as proliferative/progenitor, neuronal, mitochondrial and glycolytic/plurimetabolic. Each subtype was enriched with biologically coherent multiomic features. Mitochondrial GBM was associated with the most favorable clinical outcome. It relied exclusively on oxidative phosphorylation for energy production, whereas the glycolytic/plurimetabolic subtype was sustained by aerobic glycolysis and amino acid and lipid metabolism. Deletion of the glucose-proton symporter SLC45A1 was the truncal alteration most significantly associated with mitochondrial GBM, and the reintroduction of SLC45A1 in mitochondrial glioma cells induced acidification and loss of fitness. Mitochondrial, but not glycolytic/plurimetabolic, GBM exhibited marked vulnerability to inhibitors of oxidative phosphorylation. The pathway-based classification of GBM informs survival and enables precision targeting of cancer metabolism.

Ependymoma represents a heterogeneous disease affecting the entire neuraxis. Extensive molecular profiling efforts have identified molecular ependymoma subgroups based on DNA methylation. However, the intratumoral heterogeneity and developmental origins of these groups are only partially understood, and effective treatments are still lacking for about 50% of patients with high-risk tumors. We interrogated the cellular architecture of ependymoma using single cell/single nucleus RNA-sequencing to analyze 24 tumor specimens across major molecular subgroups and anatomic locations. We additionally analyzed ten patient-derived ependymoma cell models and two patient-derived xenografts (PDXs). Interestingly, we identified an analogous cellular hierarchy across all ependymoma groups, originating from undifferentiated neural stem cell-like populations towards different degrees of impaired differentiation states comprising neuronal precursor-like, astro-glial-like, and ependymal-like tumor cells. While prognostically favorable ependymoma groups predominantly harbored differentiated cell populations, aggressive groups were enriched for undifferentiated subpopulations. Projection of transcriptomic signatures onto an independent bulk RNA-seq cohort stratified patient survival even within known molecular groups, thus refining the prognostic power of DNA methylation-based profiling. Furthermore, we identified novel potentially druggable targets such as IGF- and FGF-signaling within poorly prognostic transcriptional programs. Ependymoma-derived cell models/PDXs widely recapitulated the transcriptional programs identified within fresh tumors and are leveraged to validate identified target genes in functional follow-up analyses. Taken together, our analyses reveal a developmental hierarchy and transcriptomic context underlying the biologically and clinically distinct behavior of ependymoma groups. The newly characterized cellular states and underlying regulatory networks could serve as basis for future therapeutic target identification and reveal biomarkers for clinical trials.

Summary H3K27M mutations resulting in epigenetic dysfunction are frequently observed in diffuse intrinsic pontine glioma (DIPGs), an incurable pediatric cancer. We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. Mechanistically, Corin increases H3K27me3 levels suppressed by H3K27M histones, and simultaneously increases HDAC-targeted H3K27ac and LSD1-targeted H3K4me1 at differentiation-associated genes. Corin treatment induces cell death, cell-cycle arrest, and a cellular differentiation phenotype and drives transcriptional changes correlating with increased survival time in DIPG patients. These data suggest a strategy for treating DIPG by simultaneously inhibiting LSD1 and HDACs.

Summary The mesenchymal subtype of glioblastoma is thought to be determined by both cancer cell-intrinsic alterations and extrinsic cellular interactions, but remains poorly understood. Here, we dissect glioblastoma-to-microenvironment interactions by single-cell RNA sequencing analysis of human tumors and model systems, combined with functional experiments. We demonstrate that macrophages induce a transition of glioblastoma cells into mesenchymal-like (MES-like) states. This effect is mediated, both in vitro and in vivo, by macrophage-derived oncostatin M (OSM) that interacts with its receptors (OSMR or LIFR) in complex with GP130 on glioblastoma cells and activates STAT3. We show that MES-like glioblastoma states are also associated with increased expression of a mesenchymal program in macrophages and with increased cytotoxicity of T cells, highlighting extensive alterations of the immune microenvironment with potential therapeutic implications.

Histone mutations occur in approximately 4% of different cancer types. In 2012, mutations were found in the gene encoding histone variant H3.3 (H3F3A gene) in pediatric diffuse intrinsic pontine gliomas and pediatric hemispheric gliomas. Tumors with mutations in the H3F3A gene are generally characterized as histone mutated gliomas (HMGs) or diffuse midline gliomas. HMGs are a rare subtype of glial tumor that is malignant and fast growing, carrying a poor prognosis. In 2017, the Beau Biden Cancer Moonshot Program appropriated $1.7 billion toward cancer care in 10 select areas. The National Cancer Institute (NCI) was granted support to focus specifically on rare central nervous system (CNS) tumors through NCI-CONNECT. Its mission is to address the challenges and unmet needs in CNS cancer research and treatment by connecting patients, providers, researchers, and advocacy organizations to work in partnership. On September 27, 2018, NCI-CONNECT convened a workshop on histone mutated midline glioma, one of the 12 CNS cancers included in its initial portfolio. Three leaders in the field provided an overview of advances in histone mutated midline glioma research. These experts shared observations and experiences related to common scientific and clinical challenges in studying these tumors. Although the clinical focus of this workshop was on adult patients, one important objective was to start a collaborative dialogue between pediatric and adult clinicians and researchers. Meeting participants identified needs for diagnostic and treatment standards, disease biology and biological targets for this cancer, disease-specific trial designs, and developed a list of action items and future direction.

Communication between cancer cells and immune cells is a key determinant of the glioblastoma ecosystem and its response to therapies, but remains poorly understood. Here we leveraged single-cell RNA-sequencing (scRNA-seq) of human samples and mouse models, deconvolution analysis of bulk specimens from The Cancer Genome Atlas (TCGA) and functional approaches to dissect cellular states and cross-talk in glioblastoma. We demonstrate that macrophages induce a transition of glioblastoma cells into mesenchymal-like (MES-like) states. This effect is mediated, both in vitro and in vivo, by macrophage-derived Oncostatin M (OSM) and its cognate receptor OSMR on glioblastoma cells. We show that MES-like glioblastoma states are associated with increased T cells cytotoxicity and potentially with better clinical response to immunotherapies. Overall, our work dissects the cellular interactions within the glioblastoma microenvironment, with potential implications for therapies.

BackgroundRecurrent high-grade glioma (HGG) represents a significant clinical unmet need with expected survival between 6 to 9 months. Oncolytic viruses are a new therapeutic approach for solid tumors that deploy oncolytic activity combined with local and systemic immune activation. CAN-3110 (rQNestin34.5v2) is an oncolytic herpes simplex virus (HSV), modified to encode the HSV1 ICP34.5 protein under control of the nestin promoter. Selective expression of nestin in brain tumors confers tumor-restricted replication of CAN-3110. We conducted an open-label dose-escalation phase 1 clinical trial in patients with recurrent HGG to evaluate safety, tolerability, and immunological changes after CAN-3110 treatment.MethodsThirty patients with biopsy-confirmed recurrent HGG were enrolled from September 2017 to February 2020. CAN-3110 was injected intratumorally starting at 1x106 plaque forming units (pfu) and dose-escalated by half log to 1x1010 pfu. Patients also received standard of care. Peripheral blood mononuclear cells (PBMCs), plasma and tumor samples were collected for analysis at different time-points post treatment. We evaluated HSV antigen expression in tumor tissue. RNA sequencing and T cell receptor (TCR) rearrangement analysis was performed in matched tissue and PBMCs. Cytokine profiling was completed in 29 patients at baseline, day 2, and day 28 post treatment.ResultsEighteen patients were recruited at their first recurrence and 12 at the second recurrence. Three patients presented with multifocal disease. Tumor volume ranged from 357.4 to and 54,036.1mm3 (median 7,733.9mm3, SDV 15,610.2). CAN-3110 was well-tolerated with no dose-limiting toxicity. Median overall survival was 11.7 months. We demonstrated persistence of HSV antigen and CD8+ T cell infiltrates at the site of injected tumor. Preliminary analysis revealed expansion of shared TCR clonotypes and upregulation of pro-inflammatory genes in post-treatment tumors and peripheral blood samples. Longitudinal modeling of cytokine profiling demonstrated increased levels of IL-6, VEGF alpha, CCL2 and IL1-RA and a decrease in GCP-2 levels at day 2 post-treatment (p ConclusionsIntratumoral administration of CAN-3110 appears well-tolerated in recurrent HGG. Histologic, molecular, and cytokine analyses demonstrate persistence of viral antigen as well as local and systemic immune activation after treatment.Ethics ApprovalThe study was approved by the Office for Human Research Studies at Dana-Farber Cancer Institute, Protocol Number 16–557.

Ependymoma represents a heterogeneous disease affecting the entire neuraxis. Extensive molecular profiling efforts have identified molecular ependymoma subgroups based on DNA methylation. However, the intratumoral heterogeneity and developmental origins of these groups are only partially understood, and effective treatments are still lacking for about 50% of patients with high-risk tumors. We interrogated the cellular architecture of ependymoma using single cell/nucleus RNA-sequencing to analyze 24 tumor specimens across major molecular subgroups and anatomic locations. We additionally analyzed ten patient-derived ependymoma cell models and two patient-derived xenografts (PDXs). Interestingly, we identified an analogous cellular hierarchy across all ependymoma groups, originating from undifferentiated neural stem cell-like populations towards different degrees of impaired differentiation states comprising neuronal precursor-like, astro-glial-like, and ependymal-like tumor cells. While prognostically favorable ependymoma groups predominantly harbored differentiated cell populations, aggressive groups were enriched for undifferentiated subpopulations. Projection of transcriptomic signatures onto an independent bulk RNA-seq cohort stratified patient survival even within known molecular groups, thus refining the prognostic power of DNA methylation-based profiling. Furthermore, we identified novel potentially druggable targets including IGF- and FGF-signaling within poorly prognostic transcriptional programs. Ependymoma-derived cell models/PDXs widely recapitulated the transcriptional programs identified within fresh tumors and are leveraged to validate identified target genes in functional follow-up analyses. Taken together, our analyses reveal a developmental hierarchy and transcriptomic context underlying the biologically and clinically distinct behavior of ependymoma groups. The newly characterized cellular states and underlying regulatory networks could serve as basis for future therapeutic target identification and reveal biomarkers for clinical trials.

Glioblastomas are malignant neoplasms composed of diverse cell populations. This intratumoral diversity has an underlying architecture, with a hierarchical relationship through clonal evolution from a common ancestor. Therapies are limited by emergence of resistant subclones from this phylogenetic reservoir. To characterize this clonal ancestral origin of recurrent tumors, we determined phylogenetic relationships using whole exome sequencing of pre-treatment IDH1/2 wild-type glioblastoma specimens, matched to post-treatment autopsy samples (n = 9) and metastatic extracranial post-treatment autopsy samples (n = 3). We identified “truncal” genetic events common to the evolutionary ancestry of the initial specimen and later recurrences, thereby inferring the identity of the precursor cell population. Mutations were identified in a subset of cases in known glioblastoma genes such as NF1(n = 3), TP53(n = 4) and EGFR(n = 5). However, by phylogenetic analysis, there were no protein-coding mutations as recurrent truncal events across the majority of cases. In contrast, whole copy-loss of chromosome 10 (12 of 12 cases), copy-loss of chromosome 9p21 (11 of 12 cases) and copy-gain in chromosome 7 (10 of 12 cases) were identified as shared events in the majority of cases. Strikingly, mutations in the TERT promoter were also identified as shared events in all evaluated pairs (9 of 9). Thus, we define four truncal non-coding genomic alterations that represent early genomic events in gliomagenesis, that identify the persistent cellular reservoir from which glioblastoma recurrences emerge. Therapies to target these key early genomic events are needed. These findings offer an evolutionary explanation for why precision therapies that target protein-coding mutations lack efficacy in GBM., Brain cancer: Non-coding genomic changes fuel glioblastoma growth Non-coding and structural alterations may be early drivers of brain cancer development. A team led by Priscilla Brastianos and Tracy Batchelor from Massachusetts General Hospital, Boston, USA, analyzed the genetic landscape of glioblastoma by comparing pre-treatment and autopsy tumor specimens from 12 patients who died of the aggressive brain cancer. They identified a common set of four genetic events that occurred early in the evolution of nearly every patient’s cancer: three losses or gains of chromosome regions or entire chromosomes, and mutations in the gene-activating promoter of TERT, which encodes an enzyme implicated in the cancer’s growth. The findings help explain why therapies that target protein-coding mutations don’t work in brain cancer when they do in other tumor types. They also point to new drug targets.

Precise classification of nervous system tumors into coherent clinicopathologic entities is the necessary first step for the appropriate management of patients. While this has been traditionally performed by histopathology only, recent accelerations in our understanding of the molecular features of nervous system tumors have led to the integration of molecular characteristics into diagnostic criteria. The updated WHO 2016 classification of tumors of the central nervous system (CNS)1 thus includes both histologic and molecular features—primarily mutational status of individual genes and copy number alterations—facilitating the precise diagnosis of CNS tumors. While this has led to increased objectivity and reproducibility, classification progress is still required, especially for rare and for poorly understood entities.

Medulloblastoma is a malignant childhood cerebellar tumor comprised of distinct molecular subgroups. Whereas genomic characteristics of these subgroups are well defined, the extent to which cellular diversity underlies their divergent biology and clinical behaviour remains largely unexplored. We used single-cell transcriptomics to investigate intra- and inter-tumoral heterogeneity in twenty-five medulloblastomas spanning all molecular subgroups. WNT, SHH, and Group 3 tumors comprised subgroup-specific undifferentiated and differentiated neuronal-like malignant populations, whereas Group 4 tumors were exclusively comprised of differentiated neuronal-like neoplastic cells. SHH tumors closely resembled granule neurons of varying differentiation states that correlated with patient age. Group 3 and Group 4 tumors exhibited a developmental trajectory from primitive progenitor-like to more mature neuronal-like cells, whose relative proportions distinguished these subgroups. Cross-species transcriptomics defined distinct glutamatergic populations as putative cells-of-origin for SHH and Group 4 subtypes. Collectively, these data provide novel insights into the cellular and developmental states underlying subtype-specific medulloblastoma biology.

Pilocytic astrocytoma (PA) is the most common pediatric low-grade glioma. While PAs exhibit a favorable prognosis compared to higher-grade gliomas, treatment morbidity and tumor recurrence still represent major challenges for some PA patients. PAs frequently harbor rearrangements resulting in expression of oncogenic KIAA1549-BRAF fusion transcripts. We performed scRNAseq of both tumor and non-tumor cells in newly-diagnosed PAs that contained KIAA1549-BRAF rearrangements. To confidently distinguish tumor cells from nontumor cells, we sorted cells by glial progenitor marker A2B5 status and profiled KIAA1549-BRAF fusion status of cells using a quantitative PCR-based assay. Results were validated using RNA in situ hybridization and compared to bulk expression data from 151 pediatric low grade gliomas. When compared to higher-grade gliomas, a higher proportion of the PA tumor cells exhibited a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibited a progenitor-like phenotype with evidence of proliferation. These progenitor-like tumor cells expressed a mitogen-activated protein kinase (MAPK) gene program that was absent from higher-grade gliomas. Similar patterns of expression of genes associated with the astrocyte-like and MAPK gene programs were also seen in formalin fixed, paraffin embedded PA tissues using RNA in situ hybridization. Immune cells, especially microglia, comprised almost half of all cells in the PAs and accounted for many differences seen in bulk pediatric low grade glioma expression profiles. These single cell transcriptional data reveal a transcriptional developmental hierarchy in a pediatric low-grade glioma that is skewed towards more mature brain cells compared to higher-grade gliomas. The results indicate that future analyses of bulk PA tissues should attempt to account for considerable infiltration by nontumor cells. Finally, the finding that a MAPK gene program is not uniformly expressed in PA tumor cells has implications for ongoing clinical investigations of therapies directed at the MAPK pathway for the treatment of PA.

2009 Background: Recurrent glioma patients have few therapeutic options and an expected survival of only 7 to 10 months. New treatments to improve the prognosis of this patient population are a dire medical need. Oncolytic viruses (OVs) are emerging as important new agents for cancer treatment. The first FDA approved OV was talimogene laherparepvec (Imlygic, T-Vec) for treatment of melanoma. T-Vec, as most other clinical HSV-1 based OVs, is deleted in the ICP34.5 gene, which is responsible for HSV-1 neurovirulence. However, deletion of ICP34.5 also impedes efficient viral replication. CAN-3110 (rQNestin34.5v2) maintains a copy of the HSV1 ICP34.5 gene under transcriptional control of the tumor-specific promoter for nestin to drive robust tumor-selective replication. CAN-3110 replicates in malignant glioma cells far above levels seen with ICP34.5 deleted viruses. This potency also created the hypothetical risk for increased neurovirulence, thus the regulatory advice to conduct a cautious nine-dose-level Phase-1 dose escalation study in patients with recurrent high-grade glioma (HGG). Methods: From September 2017 to February 2020, thirty patients with biopsy-confirmed recurrent high-grade glioma were treated in an open label clinical trial. Patients with multifocal, multicentric, tumors larger than 5 cm, and tumors that had recurred multiple times were eligible. All patients received best standard of care treatments as indicated by their physician. CAN-3110 was injected intratumorally starting at 1x106 plaque forming units (pfu) and dose-escalating (3+3 design) by half log increments up to 1x1010 pfu. Tissue (when possible) and blood samples were obtained before and during treatment for experimental medicine analyses. Results: CAN-3110 was well tolerated with no dose limiting toxicity observed. The initial tissue diagnosis of the recurrent tumor for the 30 subjects was 26 glioblastoma, 3 anaplastic oligodendroglioma, and 1 anaplastic astrocytoma. The median overall survival (mOS) of the entire study group is 13.25 months. Post-treatment tissue is available for 18/30 subjects and revealed persistence of HSV antigen and CD8+ T cell infiltrates. Additional response, immunologic (including T cell receptor repertoire), transcriptomic and single cell RNA sequencing analyses are ongoing. Conclusions: Administration of CAN-3110 into recurrent glioma was well tolerated without evidence of ICP34.5-induced encephalitis/meningitis. Histological and molecular analyses showed evidence of biological activity and that CAN-3110 injection was associated with immune activation and viral antigen persistence. Although definitive clinical efficacy cannot be determined in this small phase 1 study, OS of CAN-3110 treated subjects compares favorably to historical reports and warrants further clinical studies. Clinical trial information: NCT03152318.

There are ~1,400 oligodendroglioma diagnoses in the U.S. annually, with up to 15,000 persons living with this disease today. However, there have not been any new treatments approved for oligodendroglioma in the past 25 years. A lack of funding and advocacy has contributed to this, but the lack of reagents allowing researchers to study the disease may be the most critical factor. Oligodendroglioma tissue and disease models, including cell lines and xenograft models, are crucial resources needed for researchers to understand oligodendroglioma biology, identify new treatment strategies, and perform preclinical research. Oligo Nation has created a collection of oligo tissue large enough to enable adequately-sized studies and meet the needs of researchers interested in studying Oligodendroglioma. Oligo Nation is also investing in developing new models of the disease as well as acquiring existing models to make them easily accessible to the research community. A number of resources are now available to support academic researchers: An oligodendroglioma biobank with over 100 patient tissue samples; WGS and RNA sequencing data, including long reads for these samples; An oligodendroglioma cell line repository with 3 lines available (to date) to researchers; An oligodendroglioma PDX repository will be available in the coming year through the NCI Patient Derived Model Repository; GEMM models that include both IDH1 (R132) and CIC mutations, two of the most common mutations in oligodendroglioma, will be available by the end of 2020. Extensive analysis including high-throughput and CRISPR knockout screens will be performed on all existing and new cell lines. The data generated on these models will be stored in a public repository and made available to the research community. Making these reagents available to the research community will hopefully increase research in oligodendroglioma, and will set us on a path to discover improved and ultimately curative treatments for this disease.

Immune checkpoint inhibitors (ICI) have revolutionized oncologic treatment for metastatic melanoma. With improved systemic control, there has been increasing prevalence of patients with brain metastases. Recent evidence has demonstrated intracranial responses in a subset of these patients treated with ICI. We hypothesize that the response to ICI in melanoma brain metastases (MBM) is reflective of unique features within the tumor microenvironment of the brain. A cohort of 27 patients, encompassing 8 pre- and 19 post-immunotherapy MBM underwent single cell RNA sequencing (Smart-Seq2). The cohort includes patients with longitudinal cranial resections and simultaneously resected, spatially distinct tumors. Each tumor underwent unsupervised transcriptomic analysis, differential gene expression, inferred copy number variation, and T-cell receptor (TCR) clonotyping. Published extracranial melanoma single cell datasets were used to compare the tumor microenvironment of the brain and periphery in response to ICI. A total of 14,027 cells (6,189 malignant, 7,838 non-malignant) were sequenced. Brain metastases demonstrated a heterogeneous distribution of macrophage states. Intracranial macrophages were found to be more tumor-supportive than their extracranial counterparts. MBM also included a distribution of reactive neutrophils and astrocytes. Analysis across pre- and post-treatment MBM demonstrated an increase in clonally expanded T cells in patients responding to ICI. Across longitudinal brain metastases collected from the same patients, there was evidence of identical T cell clones across timepoints and locations. Single cell sequencing of MBM provides insights into the cellular composition of the tumor and microenvironment. Our data suggest the cellular heterogeneity within MBM is unique when compared to extracranial disease. Additionally, T cell clonal expansion is found following ICI and T cells of the same clonotype infiltrate spatially and temporally separated brain metastases. These findings raise potential therapeutic implications as we learn to target the differential features of the innate and adaptive immune system within brain metastases and their extracranial counterparts.

Glioblastoma is an incurable malignancy that remains poorly understood. By large-scale single cell RNA-seq and follow up experiments we found that malignant cells in glioblastoma exist in four main cellular states that recapitulate distinct steps of neural development, are influenced by the tumor microenvironment, and exhibit plasticity. Importantly, we show that while each glioblastoma contains similar cellular states, their relative frequency varies between tumors and is influenced by chromosomal aberrations as well as by the tumor microenvironment. In particular, we demonstrate that macrophages induce a transition of glioblastoma cells into mesenchymal-like (MES-like) states. This effect is mediated, both in vitro and in vivo, by macrophage-derived ligands that interact with receptors on glioblastoma cells. Finally, we show that MES-like glioblastoma states is associated with altered T cells cytotoxicity and response to immunotherapies. Overall, this work dissects the cellular diversity and interactions within the glioblastoma microenvironment, with potential implications for therapies. Citation Format: Toshi Hara, Rony Chanoch, Mario Suva, Itay Tirosh. Dissecting glioblastoma by single cell RNA-seq [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr IA24.

Human diffuse gliomas are incurable malignancies, where cellular state diversity fuels tumor progression and resistance to therapy. Single-cell RNA-sequencing (scRNAseq) studies recently charted the cellular states of the two major categories of human gliomas, IDH-mutant gliomas (IDH-MUT) and IDH-wildtype glioblastoma (GBM), showing that malignant cells partly recapitulate neurodevelopmental trajectories. This raises the central questions of how cell states are encoded epigenetically and whether unidirectional hierarchies or more plastic state transitions govern glioma cellular architectures. To address these questions, we generated multi-omics single-cell profiling, integrating DNA methylation (DNAme), transcriptome and genotyping of 1,728 cells from 11 GBM and IDH-MUT primary patient samples. Direct comparison of the methylomes of distinct glioma cell states revealed Polycomb repressive complex 2 (PRC2) targets DNAme as a key switch in the differentiation of malignant GBM cells. In contrast, dissecting aberrant circuits of hyper-methylation and gene expression in IDH-MUT gliomas, we observed a decoupling of the promoter methylation-expression relationship, with disruption of CTCF insulation and enhancer vulnerability which increases with cellular differentiation. To define cell state transition dynamics directly in patient samples, we generated high-resolution lineage histories of glioma cells using heritable DNAme changes, and projected the scRNAseq-derived cell states onto the lineage trees. This analysis demonstrated that cell states are heritable across malignant gliomas and, while in IDH-MUT differentiation far outpaces de-differentiation, GBM harbors a higher degree of cell state plasticity allowing reversion of GBM cells from a differentiated to a stem-like state. Overall, our work provides detailed insights into gliomagenesis, dissecting the epigenetic encoding, regulatory programs, and dynamics of the cellular states that drive human gliomas. Importantly, it also carries significant translational implication, as the high degree of de-differentiation in GBM challenges the paradigm of therapeutically targeting glioma stem-like cells to deprive tumors of their ability to regenerate.

Human diffuse gliomas are incurable brain tumors, where cellular state diversity fuels tumor progression and resistance to therapy. Single-cell RNA-sequencing (scRNAseq) studies recently charted the cellular states of the two major categories of human gliomas, IDH-mutant gliomas (IDH-MUT) and IDH-wildtype glioblastoma (GBM), showing that malignant cells partly recapitulate neurodevelopmental trajectories. This raises the central questions of how cell states are encoded epigenetically and whether unidirectional hierarchies or more plastic state transitions govern glioma cellular architectures. To address these questions, we generated multi-omics single-cell profiling, integrating DNA methylation (DNAme), transcriptome and genotyping of 1,728 cells from 11 GBM and IDH-MUT primary patient samples. The assessment of DNAme intra-tumoral heterogeneity of malignant cells revealed that single-cell DNAme profiles within tumors span multiple bulk subtypes, are associated with important biological features of malignant cells, and may be confounded by the tumor micro-environment. Such sources of intra-tumoral heterogeneity in bulk profiles are important to recognize, as DNAme profiling is increasingly being utilized for bulk clinical brain tumor classification. The direct comparison of the methylomes of distinct glioma cellular states revealed Polycomb repressive complex 2 (PRC2) targets DNAme as a key switch in the differentiation of malignant GBM cells. In contrast, dissecting aberrant circuits of hypermethylation and gene expression in IDH-MUT gliomas, we observed a decoupling of the promoter methylation-expression relationship, with disruption of CTCF insulation and enhancer vulnerability which increases with cellular differentiation. To define cell state transition dynamics directly in patient samples, we generated high-resolution lineage histories of glioma cells using heritable DNAme changes, and projected the scRNAseq-derived cell states onto the lineage trees. This analysis demonstrated that cell states are heritable across malignant gliomas and, while in IDH-MUT differentiation far outpaces de-differentiation, GBM harbors a higher degree of cellular state plasticity allowing reversion of GBM cells from a differentiated to a stem-like state. Overall, our work provides detailed insights into gliomagenesis, dissecting the epigenetic encoding, regulatory programs, and dynamics of the cellular states that drive human gliomas. Importantly, it also carries significant translational implication, as the high degree of de-differentiation in GBM challenges the paradigm of therapeutically targeting glioma stem-like cells to deprive tumors of their ability to regenerate. Citation Format: Federico Gaiti, Ronan Chaligne, Dana Silverbush, Joshua S. Schiffman, Hannah R. Weisman, Lloyd Kluegel, Simon Gritsch, Sunil D. Deochand, Alyssa R. Richman, Johanna Klughammer, Tommaso Biancalani, Christoph Muus, Caroline Sheridan, Alicia Alonso, Franco Izzo, Orit Rozenblatt-Rosen, Aviv Regev, Mario L. Suvà, Dan A. Landau. Deciphering differentiation hierarchies, heritability and plasticity in human gliomas via single-cell multi-omics [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-019.

In situ transgenesis methods such as virus and electroporation can create somatic transgenic mice quickly, but they lack the exquisite control over copy number, zygosity, and locus specificity. We have recently established mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely-defined chromosomal loci. MADR provides a toolkit of elements for combinatorial labeling, inducible/reversible transgene manipulation, VCre recombinase expression, and genetic manipulation of human cells. Further, we have demonstrated the versatility of MADR by creating glioma models with mixed, reporter-identified zygosity or with “personalized” driver mutations from pediatric glioma. For example, introducing H3f3a mutation variants with MADR regulates the spatiotemporal profile of glioma, and single-cell RNA and ATAC sequencing analysis demonstrates a recapitulation of developmental hierarchy seen in K27M-mutant human glioma. Moreover, we have generated novel models of supratentorial ependymoma using patient-derived oncofusion transgenes. These models display a high degree of fidelity and we now compare these models on a single-cell level with our previous models and human tumor cell transcriptomes. In addition, we now demonstrate the ability to generalize the MADR technology to other non-CNS tissues using local plasmid delivery. Finally, we have engineered human cells to allow for MADR transgenesis and somatic transgenic organoids. These combined approaches will enable researchers to discovery disease mechanisms and test therapeutics in more physiologically relevant cancer models.MADR is extensible to thousands of existing mouse lines and can be adapted to human cells, providing a flexible platform to democratize the generation of somatic transgenic disease models. Citation Format: Gi Bum Kim, David Rincon Fernandez Pacheco, David Saxon, Amy Yang, Sara Sabat, Marina Dutra-Clarke, Rachelle Levy, Ashley Watkins, Hannah Park, Aslam Abbasi Akhtar, Paul W. Linesch, Naomi Kobritz, Swasty S. Shandra, Katie Grausam, Alberto Ayala-Sarmiento, Jessica Molina, Kristyna Sedivakova, Daniel S. Gareau, Mariella G. Filbin, Serguei Bannykh, Jie Tang, Mario L. Suva, Bin Chen, Moise Danielpour, Joshua J. Breunig. MADR: Rapid generation of somatic mosaics to model cancer in mice and human organoids [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr NG01.

In situ transgenesis methods such as virus and electroporation can create somatic transgenic mice quickly, but they lack the exquisite control over copy number, zygosity, and locus specificity. We have recently established mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely defined chromosomal loci. MADR provides a toolkit of elements for combinatorial labeling, inducible/reversible transgene manipulation, VCre recombinase expression, and genetic manipulation of human cells. Further, we have demonstrated the versatility of MADR by creating glioma models with mixed, reporter-identified zygosity or with “personalized” driver mutations from pediatric glioma. For example, introducing H3f3a mutation variants with MADR regulates the spatiotemporal profile of glioma, and single-cell RNA and ATAC sequencing analysis demonstrates a recapitulation of developmental hierarchy seen in K27M mutant human glioma. Moreover, we have generated novel models of supratentorial ependymoma using patient-derived oncofusion transgenes. These models display a high degree of fidelity, and we now compare these models on a single-cell level with our previous models and human tumor cell transcriptomes. In addition, we now demonstrate the ability to generalize the MADR technology to other non-CNS tissues using local plasmid delivery. Finally, we have engineered human cells to allow for MADR transgenesis and somatic transgenic organoids. These combined approaches will enable researchers to discover disease mechanisms and test therapeutics in more physiologically relevant cancer models. MADR is extensible to thousands of existing mouse lines and can be adapted to human cells, providing a flexible platform to democratize the generation of somatic transgenic disease models. This abstract is also being presented as Poster B46. Citation Format: Gi Bum Kim, David Rincon Fernandez Pacheco, David Saxon, Amy Yang, Sara Sabet, Marina Dutra-Clarke, Rachelle Levy, Ashley Watkins, Hannah Park, Aslam Abbasi Akhtar, Paul W. Linesch, Naomi Kobritz, Swasty S. Chandra, Katie Grausam, Alberto Ayala- Sarmiento, Jessica Molina, Kristyna Sedivakova, Daniel S. Gareau, Mariella G. Filbin, Serguei Bannykh, Jie Tang, Mario Suva, Bin Chen, Moise Danielpour, Joshua J. Breunig. MADR: Rapid generation of somatic mosaics with locus-specific, stably integrated transgenic elements for generation of “personalized” mouse models and human organoid tumor models [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR11.

Diffuse gliomas are the most common human primary brain tumors and remain incurable. They are complex entities in which diverse genetic and nongenetic effects determine tumor biology and clinical course. Our current understanding of gliomas in patients is primarily based on genomic and transcriptomic methods that have profiled them as bulk, providing critical information yet masking the diversity of cells within each tumor. Recent advances in single-cell DNA and RNA profiling have paved the way to studying tumors at cellular resolution. Here, we review initial studies deploying single-cell analysis in clinical glioma samples, with a focus on RNA expression profiling. We highlight how these studies provide new insights into glioma biology, tumor heterogeneity, cancer cell lineages, cancer stem cell programs, the tumor microenvironment, and glioma classification.

INTRODUCTION: Diffuse intrinsic pontine glioma (DIPG) remains a devastating and incurable disease. The DIPG-BATs clinical trial incorporates diagnostic biopsy with molecularly determined treatment stratification. Here we present the initial genomic analysis of the DIPG-BATs cohort. METHODS: Children enrolled on the DIPG-BATs clinical trial underwent upfront diagnostic biopsies prior to commencement of therapy. RNA and DNA were extracted from single core biopsies and subjected to whole-genome sequencing (WGS) and RNA-sequencing. Tumor samples were also collected at autopsy if there was parental consent. RESULTS: Fifty-three patients were enrolled on study, of whom 50 underwent biopsy. There were no biopsy-related deaths. A mean of 5ug of RNA and 10ug of DNA were extracted from single frozen cores. WGS on 41 DIPG samples (including eight autopsy samples) revealed a mean mutation rate of 0.753 mutations per Mb. We confirmed TP53, PIK3CA, H3F3A, ACVR1, PPM1D, and HIST1H3B to be recurrently mutated in DIPG. Additional mutations were found in epigenetic modifiers including ASXL1. Copy-number analysis revealed PDGFRA to meet statistical significance as a recurrent amplification peak in DIPG (q

Reversal of immune cell exhaustion through immune checkpoint blockade (ICB) has become a first-line approach for patients with metastatic melanoma due to success in controlling extracranial tumors. However, patients frequently experience discordant responses, with extracranial response and intracranial progression. We hypothesize that ICB exerts selective pressure leading to the clonal evolution of treatment resistant clones that ultimately culminate in disease progression. We collected a cohort of 97 patients, encompassing 312 pre- and post-immunotherapy melanoma tumors, for whole exome sequencing (WES) and included primary, extracranial, or intracranial samples. Each tumor was analyzed for somatic mutations, copy number alterations, neoantigen profile, and patient specific phylogenetic trees were constructed encompassing a tumor’s genetic subclones. Heterogeneity of the tumor microenvironment was evaluated using high multiplicity single-cell immunofluorescent staining (CycIF). Single cell sequencing was performed on fresh tissue from 4 pre-treatment and 14 post-immunotherapy melanoma brain metastases using the Smart-Seq2 protocol. WES of pre- and post-immunotherapy tumors yielded distinct patterns of clonal evolution and immunoediting within brain metastases compared to their extracranial counterparts, including mutations in B2M. In paired pre- and post-immunotherapy samples, CycIF demonstrated decreased in CD8 infiltration and increased CD45RO, FOXP3, and PD-L1 staining suggesting less cytotoxic, terminally differentiated T cells in resistant tumors. Single cell sequencing analysis of 3,974 tumor and immune cells demonstrated patient-specific tumor clustering and gene expression profiles mediating resistance to ICB. In conclusion, we document, for the first time, evidence of ongoing branched evolution during immunotherapy in brain metastases with divergence compared to systemic sites of disease. Next-generation sequencing provides novel insights into clonal evolution mediating discordant responses of intra- and extracranial sites and immunosuppressive features of the intracranial tumor microenvironment. Targeting these mechanisms of resistance provide potential therapeutic avenues for patients with progressive intracranial disease.

High-grade gliomas are a lethal group of cancers whose progression is robustly regulated by neuronal activity. Activity-regulated release of growth factors into the tumor microenvironment represents part of the mechanism by which neuronal activity influences glioma growth, but this alone is insufficient to explain the magnitude of the effect that activity exerts on glioma progression. Here, we report that neuron-glioma interactions include electrochemical communication through both bona fide synapses and activity-dependent potassium flux. Single cell transcriptomic analyses revealed unambiguous expression of synaptic genes by malignant glioma cells, and neuron to glioma synaptic structures were evident by electron microscopy. Whole cell patch clamp electrophysiology demonstrated AMPAR-mediated excitatory neurotransmission between pre-synaptic neurons and post-synaptic glioma cells. Millisecond timescale excitatory post-synaptic currents (EPSCs) were found in a subpopulation of glioma cells, reminiscent of the axon-glial synapses between neurons and normal oligodendrocyte precursor cells (OPCs). Neuronal activity also evokes a second, non-synaptic electrophysiological response characterized by a prolonged (>1 sec) depolarization in a subpopulation of glioma cells. These longer duration currents are blocked by tetrodotoxin or barium and induced by potassium, indicating neuronal activity-dependent potassium flux reminiscent of astrocyte currents. The amplitude of the prolonged currents is reduced by gap junction inhibitors, supporting the concept that gap junction-mediated tumor interconnections can function to amplify evoked potassium currents in an electrically coupled network. As membrane depolarization of normal neural precursor cells can regulate proliferation, differentiation and survival, and glioma cells exhibit two distinct mechanisms of neuronal activity-evoked membrane depolarization, we tested the hypothesis that membrane depolarization promotes glioma growth. Using in vivooptogenetic techniques to depolarize xenografted glioma cells, we found that glioma membrane depolarization robustly promoted proliferation, while pharmacologically or genetically blocking electrochemical signaling inhibited glioma xenograft growth and extended mouse survival. Together, these findings indicate that electrical circuit integration promotes glioma progression.

Single-cell RNA sequencing (scRNAseq) has been performed across a range of intermediate to high-grade gliomas that each harbor multiple driver mutations. Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma. PAs frequently harbor oncogenic KIAA1549-BRAF fusions, and exhibit low rates of other driver mutations. While PAs exhibit a favorable prognosis compared to the higher-grade gliomas, treatment morbidity and tumor recurrence can represent major challenges for some PA patients. We performed scRNAseq of both tumor and non-tumor cells in newly-diagnosed PAs that contained KIAA1549-BRAF rearrangements. To confidently distinguish tumor cells from nontumor cells, we sorted cells by glial progenitor marker A2B5 status and profiled KIAA1549-BRAF fusion status of cells using a sensitive quantitative PCR-based assay. Results were validated using RNA in situ hybridization. When compared to higher-grade gliomas, a higher proportion of the PA tumor cells exhibited a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibited a progenitor-like phenotype with evidence of proliferation. These progenitor-like tumor cells expressed a mitogen-activated protein kinase (MAPK) program that was absent from higher-grade gliomas. Similar patterns of expression of genes associated with the astrocyte-like and MAPK gene programs were also seen in formalin fixed, paraffin embedded PA tissues using RNA in situ hybridization. Immune cells, especially microglia, comprised almost half of all cells in the PAs and accounted for differences in bulk expression profiles between tumor locations and subtypes. These single cell transcriptional data reveal a transcriptional developmental hierarchy in a pediatric low grade glioma that is skewed towards more mature brain cells compared to higher-grade gliomas. The results indicate that future analyses of bulk PA tissues should attempt to account for considerable infiltration by nontumor cells. Finally, the finding that a MAPK gene program is not uniformly expressed in PA tumor cells has implications for ongoing clinical investigations of therapies directed at the MAPK pathway for the treatment of PA. Citation Format: Zachary J. Reitman, Brenton Paolella, Guillaume Bergthold, Kristine Pelton, Robert Jones, Sarah Becker, Claire E. Sinai, Haley Malkin, Ying Huang, Leslie Grimmett, Zachary T. Herbert, Yu Sun, Jessica Weatherbee, John Alberta, John Daley, Orit Rozenblatt-Rosen, Rosalind Segal, Daphne Haas-Kogan, Mariella G. Filbin, Mario L. Suva, Aviv Regev, Charles Stiles, Mark W. Kieran, Liliana Goumnerova, Keith L. Ligon, Alex K. Shalek, Pratiti Bandopadhayay, Rameen Beroukhim. Single cell RNA sequencing reveals mitogenic and progenitor gene programs inBRAF-rearranged pilocytic astrocytomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3647.

We have developed a simple and generalizable in vivo method for brain tumor modeling, mosaic analysis by dual recombinase-mediated cassette exchange (MADR). MADR allows for stable labeling of mutant cells expressing transgenic elements from a precisely-defined chromosomal locus. We have demonstrated the power and versatility of MADR by creating novel glioma models with mixed, reporter-defined zygosity, or with “personalized” H3. 3-containing driver mutation signatures from pediatric glioma--each manipulation altering the spatiotemporal profile of resulting tumors. Further we have generated ependymoma models by employing patient-derived fusion driver mutations. Notably, each model displays divergent spatiotemporal tumor expansion profiles and cellular phenotypes. Now, we use single-cell RNA-seq to compare these models to their cells of mutation and to human datasets to elucidate the fundamental transcriptional programs and markers within and across these tumor types. This investigation will assess and credential these models against their clinical counterparts by scrutinizing the resulting datasets and validating their clinical relevance as pre-clinical models for therapeutic discovery and testing.

Pediatric high-grade gliomas (pHGGs) are a lethal group of cancers whose progression is robustly regulated by neuronal activity. Activity-regulated release of growth factors into the tumor microenvironment represents part of the mechanism by which neuronal activity influences pHGG growth, but this alone is insufficient to explain the magnitude of the effect that activity exerts on glioma progression. Here, we report that neuron-glioma interactions include bona fide synaptic communication. Single cell transcriptomic analyses of primary pediatric and adult glioma samples reveal unambiguous expression of synaptic genes by malignant glioma cells. Whole cell patch clamp recordings from xenografted, pediatric patient-derived glioma cells revealed the existence of AMPAR-mediated excitatory neurotransmission between pre-synaptic glutamatergic neurons and post-synaptic glioma cells. Millisecond timescale excitatory post-synaptic currents (EPSCs) that are depolarizing were observed in a subpopulation of pHGG cells and are associated with activity-induced glioma cell calcium transients. These excitatory axon-glioma synapses are reminiscent of the axon-glial synapses formed between neurons and oligodendrocyte precursor cells. A second electrophysiological response characterized by a prolonged (>1 sec) depolarization in response to neuronal activity was also observed. These longer duration currents are blocked by gap junction inhibitors, supporting the concept that gap junction-mediated tumor interconnections, such as observed with tumor microtubes, can function as an electrically coupled network. As neurotransmitter-mediated depolarization of normal neural precursor cells can profoundly affect precursor cell proliferation, differentiation and survival, we tested the hypothesis that depolarizing currents in pediatric glioma cells promote tumor growth. Using in vivooptogenetic techniques to depolarize xenografted pHGG cells expressing channelrhodopsin-2 (ChR2), we found that glioma depolarization robustly promoted proliferation, while expression of a dominant-negative AMPAR subunit (GluA2) that blocks neuron-glioma signaling inhibited pHGG xenograft growth and extended mouse survival. These findings suggest that integration of pediatric glioma into neural circuits promotes tumor progression.

BACKGROUND: The impact of individualized neoepitope vaccination targeting neoantigens arising from tumor-specific mutations for GBM, a low mutation burden tumor with an immunologically cold tumor microenvironment, as well as that of concurrently administered dexamethasone (dex), are unknown. METHODS: Individualized vaccination of up to 20 synthetic, long neoepitope peptides with high predicted HLA binding affinity admixed with poly-ICLC, were administered subcutaneously using a prime-boost schedule after RT to newly diagnosed, MGMT unmethylated, at least partially resected, GBM patients without progression after radiation (RT) in our phase 1b study. RESULTS: 9 of 10 screened patients had sufficient (10) identified neoepitope peptides. 8 patients without progression after RT received vaccine consisting of a median of 12 peptides (range, 7–20) beginning a median of 19.9 wks (range 17.1–24.7) after surgery. Adverse events were limited to infrequent grade 1/2 local reactions and fatigue. Median PFS and OS were 7.5 mths (90% CI: 6.2, 9.7) and 16.8 mths (90% CI: 9.6, 21.3). Evaluation of neoepitope-specific immune responses and tumor immune infiltrate analyses were performed on five patients with pre- and post-vaccination samples. Three patients on dex for post-RT edema during vaccine had no immune responses and no change in tumor infiltrating effector cells. In contrast 2 patients not on dex had robust, de novo immune responses against multiple predicted personal neoantigens including polyfunctional neoantigen-specific CD4+ and CD8+ T cell responses that were enriched for memory and activated phenotypes as well as increased numbers of tumor-infiltrating CD4+ and CD8+ T cells. T cell receptor analysis from one patient identified identical clonotypes isolated from post-vaccination tumor tissue and peripheral blood including two clonotypes specific for ARHGAP35, a neoantigen targeted by vaccination. CONCLUSIONS: Individualized, multi-neoepitope vaccines are feasible, safe and capable of generating systemic and intra-tumoral immune responses in GBM patients that appear to be abrogated by dex.

Personal vaccines directed at neoantigens arising from tumor mutations can induce neoepitope-specific T cell responses in patients with highly mutated tumors such as melanoma. It remains unknown if this approach can be successfully applied in tumors with low mutation frequency. We conducted a phase 1/1b study to determine the safety and feasibility of patient-specific neoantigen-targeting vaccination in patients with newly diagnosed, methylguanine methyltransferase (MGMT) unmethylated glioblastoma, administered following maximum surgical resection and conventional radiotherapy. Tumor-specific mutations were identified by whole-exome sequencing. Each vaccine, composed of up to 20 synthetic long peptides containing predicted tumor neoepitopes admixed with poly-ICLC, was administered subcutaneously on a prime-boost schedule. Among 8 treated patients, adverse events were limited to mild injection site reactions. Seven patients (88%) received a vaccine with ≥10 neoepitope peptides (median 12, range, 7-20), with median time to vaccine initiation of 18.6 weeks from surgery. All patients died from progressive disease. Median progression-free and overall survival was 7.5 months (95% CI: 6.2, 9.7) and 16.8 months (90% CI: 9.6, 21.3), respectively. 3 patients dropped out of the study due to disease progression. We analyzed vaccine responses on 5 patients that got at least one booster immunization. All 3 patients who required dexamethasone during vaccine priming failed to generate interferon-γ responses in peripheral blood mononuclear cells. In contrast, 2 patients who did not receive dexamethasone during vaccine priming, generated robust de novo immune responses against multiple personal neoantigens. Circulating vaccine-induced polyfunctional neoantigen-specific CD4+ and CD8+ T cell responses were enriched for memory and activated phenotypes, and increased numbers of tumor-infiltrating CD4+ and CD8+ T cells were detected in these 2 patients. T cell receptor analysis identified identical clonotypes isolated from post-vaccination glioblastoma tissue and peripheral blood including a clonotype specific for ARHGAP35, a neoantigen targeted by vaccination. To our knowledge we provide the first evidence that tumor specific T cells can traffic from the periphery into glioblastoma tumors and that neoantigen-targeting vaccines can favorably alter the tumor immune milieu of glioblastoma. In conclusion, individualized, multi-neoepitope vaccination is feasible, safe, and generates neoantigen-specific T cell responses in the periphery and intracranial tumors of patients with glioblastoma. Citation Format: Derin B. Keskin, Itay Tirosh, Annabelle Anandappa, Jing Sun, Nathan D. Mathewson, Sachet A. Shukla, Evisa Gjini, Shuqiang Li, Letitia Li, Anita Giobbie-Hurder, Phuong M. Le, Zhuting Hu, Wandi Zhang, Oriol Olive, Christine McCluskey, Heather Daley, Patrick Y. Wen, Antonio E. Chiocca, Maegan Harden, Niall Lennon, Stacey Gabriel, Gad Getz, Donna Neuberg, Jerome Ritz, Eric S. Lander, Aviv Regev, Kai Wucherpfennig, Mario Suva, Edward F. Fritsch, Rodig Scott, Keith L. Ligon, Kenneth J. Livak, Hacohen Nir, Patrick A. Ott, Catherine J. Wu, David A. Reardon. Personal neoantigen-targeting vaccination generates neoepitope-specific T cell responses in tumors of patients with glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5631.

Obtaining paired alpha- and beta-chain information of the T cell receptor (TCR) enables identification of which TCR binds to a particular antigen, providing critical knowledge for understanding how a tumor interacts with its immune microenvironment and for monitoring responses to immunotherapy. We have developed a rapid, cost-effective single-cell TCR sequencing protocol (scTCRseq) that processes single T cells flow sorted into 384-well plates. Exploiting the added specificity provided by RNase H-dependent PCR (rhPCR; Dobosy et al., BMC Biotechnology 11:80, 2011), our scTCRseq protocol mixes primers for all known productive alpha and beta TCR alleles and obtains specific amplification of only the alleles present in a single-cell lysate (typically one alpha allele and one beta allele) without the use of nested PCR. Applying this protocol to T cell samples from normal donors, we detect TCRs arising from all productive TRAV and TRBV genes, and observe the expected highly diverse repertoires. Our method also includes targeted sequencing of 96 (or more) marker transcripts in order to obtain cell phenotype information. Our scTCRseq protocol has been adapted to analyze low-input samples (100 pg-10 ng) of PBMC RNA for characterization of the TCR repertoire and to improve the sensitivity of paired TCR detection in Smart-seq2 libraries prepared from single-cell RNA. We recently applied this approach to analyze T cell clonality in the T cell infiltrate from a glioblastoma patient receiving neoantigen-specific peptide vaccination. Fresh tumor obtained post-vaccination at the time of recurrence was dissociated and single CD3+ T cells were isolated by flow cytometry. Smart-seq2 analysis suggested the presence of clones, but this was based largely on inference from one-chain data. Using our scTCRseq protocol to re-amplify the TCR segments, paired alpha- and beta-chain information was obtained from 277 of 363 (76%) single cells that passed quality control. Out of 231 distinct clonotypes detected, 25 were identified as clones, where a clone is defined as two or more cells with identical alpha- and beta-CDR3 segments. GLIPH analysis (Glanville et al., Nature 547:94-98, 2017) was used to cluster infiltrate TCRs by specificity. A representative TCR from each specificity cluster was cloned in a TCR-negative Jurkat cell line. Cellular assays were used to determine which specificity groups react with epitopes from peptides used in the vaccination. TCRs specific for neoantigens included in the vaccine were detected. We have demonstrated a robust workflow that combines sensitive detection of paired alpha- and beta-chain TCR sequences with TCR cloning and expression to determine which TCRs in a tumor infiltrate have neoantigen specificity. Citation Format: Shuqiang Li, Jing Sun, Annabelle Anandappa, Oliver Spiro, Ignaty Leshchiner, Krishnalekha Datta, Yun Bao, Zhuting Hu, Nir Hacohen, Nathan D. Mathewson, Itay Tirosh, Kai Wucherpfennig, Aviv Regev, Mario Suva, Derin B. Keskin, Catherine J. Wu, Kenneth J. Livak. Novel targeted single-cell TCR sequencing method used for analysis of a T cell infiltrate from a glioblastoma patient [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5387.

High-grade gliomas represent the leading cause of brain tumor-associated death in children. We have recently discovered that active neurons robustly regulate glioma growth through activity-regulated secreted factors that critically include neuroligin-3. Secreted neuroligin-3, in addition to activating multiple oncogenic signaling pathways, induces glioma cell expression of numerous synapse-associated genes. Here, we report that neuron-glioma interactions include bona fide synaptic communication. Glioma cell expression of synapse-related genes was confirmed at the single cell level in primary glioma samples. Structural synapses between presynaptic neurons and post-synaptic glioma cells were identified by high-resolution confocal and electron microscopy. Voltage clamp recordings from patient-derived DIPG cells xenografted to the CA1 region of the hippocampus demonstrates AMPAR-mediated excitatory neurotransmission between presynaptic neurons and post-synaptic glioma cells with local electrode stimulation of inputs to the CA1 region. Millisecond timescale excitatory post-synaptic currents (EPSCs) were observed in approximately 10% of DIPG cells. A subpopulation of glioma cells exhibit a second electrophysiological profile with longer, ~1 sec depolarization in response to neuronal activity. As depolarization of normal neural precursor cells during development affects neural stem cell proliferation, we tested the hypothesis that neuron to glioma synapse-mediated depolarization promotes glioma growth. Using in vivo optogenetic techniques to depolarize patient-derived DIPG cells, we found that DIPG cell depolarization robustly promotes proliferation. These findings define an unexpected integration of glioma cells into neural circuitry, identify excitatory synaptic neurotransmission as a mechanism driving glioma growth and elucidate the previously unexplored potential to target glioma circuit dynamics for therapy of these lethal cancers.

Pilocytic astrocytoma (PAs) are pediatric low grade gliomas that frequently harbor oncogenic KIAA1549-BRAF fusions and exhibit low rates of other somatic genetic alterations. Previous transcriptomic profiling of bulk PA tissues sought to uncover gene expression programs that distinguish PA from other tumor types and which may underlie the unique biological features of PA. However, bulk PA transcriptomic data is often confounded by gene signatures thought to be contributed by normal, non-tumor cells. Also, analysis of bulk PA tissue provides incomplete information on whether distinct cell populations exist among the tumor cells. To resolve the cell types contributing to PA transcriptional profiles and to identify gene expression programs that distinguish PA tumor cells from those of higher-grade tumors, we performed RNA sequencing of >1000 single cells (scRNA-seq) collected from six PAs. To confidently distinguish tumor cells from non-tumor cells, we sorted cells by glial progenitor marker A2B5 status and also profiled KIAA1549-BRAF fusion status for every cell. This scRNA-seq approach revealed unique tumor and non-tumor cell populations within PAs. We identified tumor cell populations expressing oligodendrocyte precursor and radial glia gene signatures. Non-tumor cells consisted of populations expressing microglia, T lymphocyte, and endothelial cell gene signatures which accounted for many of the expression patterns seen in bulk PA transcriptional data. In summary, scRNA-seq has revealed the cellular ecosystem and population structure of PA.

Human cancers are composed of cells with heterogeneous genetic and epigenetic states, resulting in substantial phenotypic diversity. Medulloblastoma (MB), a clinically challenging, malignant childhood brain tumor, is no exception. A better understanding of its cellular heterogeneity is urgently needed in order to develop more efficacious therapeutic strategies that eliminate all tumor subclones underlying MB initiation, maintenance, progression, and relapse. We used single-cell RNA sequencing to assess intratumoral heterogeneity in 20 MB samples representing all four molecular subgroups. Fresh surgical biopsies were dissociated and flow sorted into single cells prior to full-length transcriptome sequencing using the Smart-seq2 protocol. Computational analyses conducted on >6,000 single cells identified cellular hierarchies ranging from proliferative, undifferentiated cell types to more differentiated neural- and astrocyte-like progeny. Transcriptional differences in undifferentiated cell populations between MB subgroups suggested distinct cellular origins, and informed oncogenic pathways believed to promote MB pathogenesis. Identification of transcriptional programs active in single cells aided the deconvolution of published bulk RNA-seq profiles, providing a deeper understanding of the heterogeneity characteristic of Group 3/4 subtypes. Lastly, inference of copy-number variations and probable driver-gene mutations from the single-cell data provided evidence for genetic subclones in a subset of patients. Overlaying transcriptional profiles on MB genetic subclones unveiled how oncogenic programs adapted during tumor evolution. These interim results provide unparalleled insights into the cellular heterogeneity of MB subgroups. Analyses aimed at further resolving molecular substructure in Group 3/4, verifying the developmental origins of MB subgroups, and implicating defined cell populations driving tumorigenesis are ongoing.

DIPG is the leading cause of pediatric brain tumor-related death and remains without effective clinical treatment. Through numerous genomic studies, the H3K27M mutation has emerged as the molecular hallmark of DIPG. While this mutation causes global chromatin remodeling and a broadly oncogenic transcriptional signature, the core molecular pathways driving DIPG pathobiology remain to be defined. In this study, we characterize the active chromatin epigenomic landscape of DIPG in a large cohort of primary tumor samples and identify novel epigenetic subgroups within histone-mutant DIPG. We uncover distinct signaling pathways controlling oncogenic state for each subgroup, elucidating novel mechanisms mediating proliferation and treatment resistance. Utilizing a human iPSC developmental model introducing the histone mutation at progressive stages of neural precursor differentiation, we will describe the developmental cell state most closely resembling DIPG tumors from each genomic subgroup and identify the specific molecular pathways by which the H3K27M mutant drives transformation. Taken together, this study identifies functional molecular heterogeneity between primary DIPG tumors and characterizes novel targets for potential therapeutic development.

2020Background: The impact of individualized neoepitope vaccination targeting neoantigens arising from tumor-specific mutations for GBM, a low mutation burden tumor with an immunologically cold tum...

Gliomas comprise heterogeneous malignant glial and stromal cells. While blood vessel co-option is a potential mechanism to escape anti-angiogenic therapy, the relevance of glial phenotype in this process is unclear. We show that Olig2+ oligodendrocyte precursor-like glioma cells invade by single-cell vessel co-option and preserve the blood-brain barrier (BBB). Conversely, Olig2-negative glioma cells form dense perivascular collections and promote angiogenesis and BBB breakdown, leading to innate immune cell activation. Experimentally, Olig2 promotes Wnt7b expression, a finding that correlates in human glioma profiling. Targeted Wnt7a/7b deletion or pharmacologic Wnt inhibition blocks Olig2+ glioma single-cell vessel co-option and enhances responses to temozolomide. Finally, Olig2 and Wnt7 become upregulated after anti-VEGF treatment in preclinical models and patients. Thus, glial-encoded pathways regulate distinct glioma-vascular microenvironmental interactions.

Human tumors are complex systems containing cells with diverse phenotypes, genotypes and epigenetic states; but current treatment strategies and models do not adequately reflect tumor composition in patients. High-grade gliomas are particularly heterogeneous tumors and currently represent the most common cause of cancer-related death in children. Increasing evidence indicates that treatment failure and resistance are at least in part due to this heterogeneity. We used single-cell RNA sequencing (scRNA-seq) to profile the transcriptome of thousands of single cells in pediatric high-grade glioma and reconstructed their cellular architecture. We found restricted expression of neural stem/progenitor expression programs in distinct subsets of cells, and observed that cellular programs evolve during genetic evolution. This suggests that both genetic and superimposed developmental programs contribute to tumor heterogeneity. These results provide unparalleled insight into the cellular composition of pediatric high-grade gliomas at the level of single-cell resolution, and open up new avenues for discovering novel therapeutic targets.

Ewing's sarcoma is a member of Ewing's family tumors (EFTs) and the second most common solid bone and soft tissue malignancy of children and young adults. It is associated in 85% of cases with the t(11;22)(q24:q12) chromosomal translocation that generates fusion of the 5′ segment of the EWS gene with the 3′ segment of the ETS family gene FLI-1. The EWS-FLI-1 fusion protein behaves as an aberrant transcriptional activator and is believed to contribute to EFT development. However, EWS-FLI-1 induces growth arrest and apoptosis in normal fibroblasts, and primary cells that are permissive for its putative oncogenic properties have not been discovered, hampering basic understanding of EFT biology. Here, we show that EWS-FLI-1 alone can transform primary bone marrow–derived mesenchymal progenitor cells and generate tumors that display hallmarks of Ewing's sarcoma, including a small round cell phenotype, expression of EFT-associated markers, insulin like growth factor-I dependence, and induction or repression of numerous EWS-FLI-1 target genes. These observations provide the first identification of candidate primary cells from which EFTs originate and suggest that EWS-FLI-1 expression may constitute the initiating event in EFT pathogenesis. (Cancer Res 2005; 65(24): 11459-68)

Schwannomas are found either sporadically or as part of a syndrome. Genetic alterations found in schwannomas include those in NF2 and SMARCB1 (implicated in schwannomatosis), and BRAF V600E. Reduced copy number of chromosome 22q can be the mechanism for loss of the unaltered allele ofNF2 and/orSMARCB1in some schwannomas. We analyzed a cohort of 57 vestibular and non-vestibular schwannomas from three clinical subtypes (Neurofibromatosis 2, schwannomatosis, and sporadic) for reduced copy number (NF2 and SMARCB1), and mutations (NF2, SMARCB1, LZTR1, NF1 and BRAF). Tumors were histologically classified as conventional/classic, or hybrid. Genomic DNA was extracted from FFPE biopsies. Full coding regions of genes NF1, NF2, LZTR1, SMARCB1 and BRAF were enriched by anchored multiplex-PCR (AMP). Resulting libraries were quantitated and sequenced on the Illumina MiSeq System. Bioinformatics analyses were performed using custom scripts. Copy number alteration was detected using a read depth approach after consolidation of single molecule derived reads. INI1 immunohistochemistry was performed. RNA ISH for SMARCB1 was performed. Five tumors were of hybrid histology, and all five were syndromic. Reduced copy number for NF2 was identified in 33% of vestibular schwannomas and 18% of non-vestibular schwannomas. There was no significant difference in reduced copy number of NF2 between sporadic and syndromic forms. BRAF V600E and NF1 mutations were not identified in any case. For most INI1 mosaics, there was no molecular event explaining the partial loss of INI1 IHC. This study confirms the association of hybrid histology with syndromic schwannomas. NF1 mutations did not explain hybrid histology. We did not find BRAF V600E mutations in this series. INI1 mosaic pattern was not explained by reduced copy number or mutation of SMARCB1 as this was found in only a small number of the cases. These results suggest that loss of INI1 expression could be the result of epigenetic alterations.

While human tumors are shaped by the genetic evolution of cancer cells, evidence also suggests that they display superimposed hierarchies reminiscent of normal development. Yet, relating the genetic and hierarchical models of cancer organization has been limited by technical challenges. Here, studying H3 K27M-mutant diffuse midline gliomas we profiled thousands of single cells from fresh tumors by RNA-seq and reconstructed the genetic and epigenetic cellular architecture of tumors in patients. We identified a subset of cancer cells that are differentiated along specialized glial programs while a distinct subset expresses neural stem/progenitor expression programs. By identifying distinct genetic clones, we show that these cellular architectures evolve during the progression of the tumors, suggesting that developmental programs and genetic influences coordinately determine tumor architecture. These results provide unprecedented insight into the cellular composition of midline brain tumors at single-cell resolution and may help harmonize the cancer stem cell and the genetic models of cancer, with critical implications for disease management.

Background: Glioma stem cells (GSCs) have been identified as the predominant contributor to the therapy resistance, recurrence, and progression of malignant glioma, particularly glioblastoma multiforme (GBM). However, GSCs are elusive therapeutic targets across the blood brain barrier, underscoring the urgent need to develop novel therapeutic targeting strategies. Further impeding the discovery of effective anti-GSC therapies, the complex intratumoral heterogeneity, identified via single cell RNAseq and transcriptome research, as well as the genomic adaptations by GSCs that evade therapeutic pressure, limit therapeutic efficacy of individual gene targeting. With recent breakthrough discoveries of genetic and epigenetic signatures of GSC mediated tumorigenesis, RNAi emerges as a promising anti-GSC therapeutic strategy to counteract tumorigenic genetic elements. HYPOTHESIS: We hypothesize that multiplexed RNAi using GSC targeting nanoparticles are effective counter measures against genetic drivers of GSC phenotypes. Methods: Based on a panel of qPCR and Western blotting analysis, we selected 2 suitable GSC candidates from patient derived glioma as therapeutic model targets. We then identified the novel lipopolymeric nanoparticle 7C1 as a pilot siRNA encapsulation candidate, and characterized its uptake dynamics in comparison with mouse brain endothelial cells and astrocytes. 7C1 demonstrates a striking affinity for GSCs, and multiplexed siRNA encapsulation in 7C1 was achieved using a microfluidic mixing device invented in our group. Results: In this report, we establish that 7C1 nano-encapsulation of multiplexed GSC RNAi is a flexible GSC targeting strategy when delivered directly to the brain tumor microenvironment. In vitro and in vivo GSC growth arrest is accomplished via concurrent siRNA knockdown of four transcription factors that engender the proneural GSC phenotype, namely SOX2, OLIG2, SALL2, and POU3F2. The therapeutic potential was most evident when the 7C1 multiplexed RNAi was delivered to mouse models of GBM created via intracranial xenograft of candidate GSCs via an AlzetTM osmotic pump (Durect Corp., Cupertino, CA, USA), which demonstrates a significant extension of median survival in patient derived GSC xenograft mouse models of aggressive GBM (9 days, log rank test, ***p=0.003). CONCLUSION: This pilot study validates an encouraging non-viral gene therapy platform to target GSCs, and demonstrates the potential capacity to channel infinite combinations of multiplexed RNAi schemes to address the intratumoral heterogeneity championed by GSCs. Future engineering to enhance the intratumoral distribution and enable long term delivery are underway to improve performance.

SummaryThe aberrant transcription factor EWS-FLI1 drives Ewing sarcoma, but its molecular function is not completely understood. We find that EWS-FLI1 reprograms gene regulatory circuits in Ewing sarcoma by directly inducing or repressing enhancers. At GGAA repeat elements, which lack evolutionary conservation and regulatory potential in other cell types, EWS-FLI1 multimers induce chromatin opening and create de novo enhancers that physically interact with target promoters. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild-type ETS transcription factors. These divergent chromatin-remodeling patterns repress tumor suppressors and mesenchymal lineage regulators while activating oncogenes and potential therapeutic targets, such as the kinase VRK1. Our findings demonstrate how EWS-FLI1 establishes an oncogenic regulatory program governing both tumor survival and differentiation.