scholarly journals Mutant IDH Inhibitors Induce Lineage Differentiation in IDH-mutant Oligodendroglioma

2021 ◽  
Author(s):  
Avishay Spitzer ◽  
Simon Gritsch ◽  
Hannah Weisman ◽  
Nicolas Gonzalez Castro ◽  
Masashi Nomura ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Single Cell ◽  
Clinical Response ◽  
Rna Sequencing ◽  
Treatment Initiation ◽  
Experimental Models ◽  
Low Grade ◽  
Lineage Differentiation ◽  
Single Nucleus ◽  
Sample Pair

Recent data showed promising signs of objective tumor responses in subsets of patients with low grade glioma treated with inhibitors of mutant IDH (IDHi). However, the molecular and cellular underpinnings of such responses are not known. Here, we profiled 6,039 transcriptomes by single-cell or single-nucleus RNA-sequencing isolated from three IDH-mutant oligodendroglioma patients with clinical response to IDHi. Importantly, the tissues were sampled on-drug, four weeks from treatment initiation and our dataset includes a matched pre- and on-treatment sample pair. We integrate our findings with analysis of 8,241 transcriptomes from seven untreated samples, 134 bulk samples from the TCGA and experimental models. We find that IDHi treatment induces a robust differentiation towards glial lineages, accompanied by a depletion of stem-like cells and a reduction of cell proliferation. Our study provides the first evidence in patients of the differentiating potential of IDHi on the cellular hierarchies that drive oligodendrogliomas.

scholarly journals Pro-tumoral Effects of Intra-tumoral Neutrophils in the Glioblastoma Microenvironment

Neurosurgery ◽  
2019 ◽  
Vol 66 (Supplement_1) ◽  
Author(s):  
Sumedh S Shah ◽  
Garima Yagnik ◽  
Alan T Nguyen ◽  
Harsh Wadhwa ◽  
Jordan Spatz ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Stem Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cellular Proliferation ◽  
Flow Cytometric Analysis ◽  
Cell Phenotype ◽  
Low Grade ◽  
Single Cell Rna Sequencing

Abstract INTRODUCTION The glioblastoma microenvironment contains immune cells, particularly well-defined macrophage populations; however, intratumoral neutrophils and their effects on GBM biology are under-characterized. While tumor-associated neutrophils (TANs) were initially thought as passive bystanders due to their short-lived nature, current investigation of TANs in other cancer types revealed distinct pro-tumoral roles. Therefore, we sought to characterize TANs in the glioblastoma microenvironment and define their oncologic effects. METHODS Following informed consent, patient-derived GBM samples were collected for flow cytometry of TANs, which were then used to produce conditioned media (CM) for in Vitro studies on tumor cell proliferation and ELISA quantification of TAN-secreted factors. Single-cell RNA sequencing was performed on TANs to identify pro-tumoral factors. RESULTS Flow cytometric analysis (CD11b+/CD15+ /CD66b+) indicated higher percentages of TAN-infiltration to glioblastoma compared to low-grade gliomas (1.76% [n = 13] vs 0.33% [n = 6], P = .03). Using the Transwell migration assay with glioblastoma tumor CM, we found recruitment of circulating neutrophils to tumor sites is mediated by leukotriene-B4 and that this chemoattraction can be blocked with an LtB4 receptor antagonist, LY293111. We then performed single-cell RNA sequencing of isolated TANs and identified upregulation of osteopontin. Osteopontin is linked to GBM stem cell-like phenotype maintenance, thus, we decided to investigate osteopontin as a possible driver of pro-tumoral signaling. Osteopontin concentration was significantly higher in TAN CM than in patient-matched peripheral blood neutrophil CM (3.2 ng/mL [n = 3] vs 0.02 ng/mL [n = 3], P < .05). In Vitro, TAN CM led to significantly increased GBM cell proliferation and increased stem marker expression (Nanog, Oct4, Sox2) when incubated with neurospheres from an established GBM line. Pro-tumoral effects were lost in presence of osteopontin-neutralizing antibodies. CONCLUSION This study elucidates a possible mechanism of neutrophil-mediated pro-tumoral signaling. We found that neutrophils are recruited to tumor sites and play a biologically relevant role in GBM cellular proliferation and maintenance of a stem cell phenotype via osteopontin secretion.

scholarly journals Single Cell, Single Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity

2021 ◽  
Author(s):  
Tallulah S Andrews ◽  
Jawairia Atif ◽  
Jeff C Liu ◽  
Catia T Perciani ◽  
Xue-Zhong Ma ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Human Liver ◽  
Stellate Cell ◽  
Parenchymal Cell ◽  
Cell Types ◽  
Cell Populations ◽  
Healthy Human ◽  
Single Nucleus

The critical functions of the human liver are coordinated through the interactions of hepatic parenchymal and non-parenchymal cells. Recent advances in single cell transcriptional approaches have enabled an examination of the human liver with unprecedented resolution. However, dissociation related cell perturbation can limit the ability to fully capture the human liver's parenchymal cell fraction, which limits the ability to comprehensively profile this organ. Here, we report the transcriptional landscape of 73,295 cells from the human liver using matched single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq). The addition of snRNA-seq enabled the characterization of interzonal hepatocytes at single-cell resolution, revealed the presence of rare subtypes of hepatic stellate cells previously only seen in disease, and detection of cholangiocyte progenitors that had only been observed during in vitro differentiation experiments. However, T and B lymphocytes and NK cells were only distinguishable using scRNA-seq, highlighting the importance of applying both technologies to obtain a complete map of tissue-resident cell-types. We validated the distinct spatial distribution of the hepatocyte, cholangiocyte and stellate cell populations by an independent spatial transcriptomics dataset and immunohistochemistry. Our study provides a systematic comparison of the transcriptomes captured by scRNA-seq and snRNA-seq and delivers a high-resolution map of the parenchymal cell populations in the healthy human liver.

scholarly journals LGG-05. SINGLE-CELL RNA SEQUENCING OF PEDIATRIC LOW-GRADE GLIOMAS REVEALS INTRATUMORAL HETEROGENEITY

2017 ◽  
Vol 19 (suppl_4) ◽  
pp. iv33-iv34
Author(s):  
Brenton Paolella ◽  
Pratiti Bandopadhayay ◽  
Guillaume Bergthold ◽  
Alex Shalek ◽  
Kristine Pelton ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Intratumoral Heterogeneity ◽  
Low Grade ◽  
Low Grade Gliomas ◽  
Single Cell Rna Sequencing

scholarly journals Complementary Roles for Single-Nucleus and Single-Cell RNA Sequencing in Kidney Disease Research

2019 ◽  
Vol 30 (4) ◽  
pp. 712-713 ◽  
Author(s):  
Eoin D. O’Sullivan ◽  
Katie J. Mylonas ◽  
Jeremy Hughes ◽  
David A. Ferenbach
Keyword(s):  
Kidney Disease ◽  
Single Cell ◽  
Rna Sequencing ◽  
Disease Research ◽  
Single Cell Rna Sequencing ◽  
Single Nucleus

scholarly journals The novel BET inhibitor UM-002 reduces glioblastoma cell proliferation and invasion

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anna M. Jermakowicz ◽  
Matthew J. Rybin ◽  
Robert K. Suter ◽  
Jann N. Sarkaria ◽  
Zane Zeier ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Single Cell ◽  
Rna Sequencing ◽  
Ex Vivo ◽  
Adult Brain ◽  
Bet Inhibitor ◽  
Bet Inhibitors ◽  
Single Cell Rna Sequencing

AbstractBromodomain and extraterminal domain (BET) proteins have emerged as therapeutic targets in multiple cancers, including the most common primary adult brain tumor glioblastoma (GBM). Although several BET inhibitors have entered clinical trials, few are brain penetrant. We have generated UM-002, a novel brain penetrant BET inhibitor that reduces GBM cell proliferation in vitro and in a human cerebral brain organoid model. Since UM-002 is more potent than other BET inhibitors, it could potentially be developed for GBM treatment. Furthermore, UM-002 treatment reduces the expression of cell-cycle related genes in vivo and reduces the expression of invasion related genes within the non-proliferative cells present in tumors as measured by single cell RNA-sequencing. These studies suggest that BET inhibition alters the transcriptional landscape of GBM tumors, which has implications for designing combination therapies. Importantly, they also provide an integrated dataset that combines in vitro and ex vivo studies with in vivo single-cell RNA-sequencing to characterize a novel BET inhibitor in GBM.

scholarly journals A survey of the mouse hindbrain in the fed and fasted state using single-nucleus RNA sequencing

2021 ◽  
Author(s):  
Georgina K.C. Dowsett ◽  
Brian Y.H. Lam ◽  
John Tadross ◽  
Irene Cimino ◽  
Debra Rimmington ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Area Postrema ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Fasted State ◽  
Single Nucleus ◽  
Human Use ◽  
Obesity Drugs

AbstractObjectiveThe area postrema (AP) and the nucleus tractus solitaris (NTS), located in the hindbrain, are key nuclei that sense and integrate peripheral nutritional signals and, consequently, regulate feeding behaviour. While single cell transcriptomics have been used in mice to reveal the gene expression profile and heterogeneity of key hypothalamic populations, similar in-depth studies have not yet been performed in the hindbrain.MethodsUsing single-nucleus RNA sequencing, we provide a detailed survey of 16,034 cells within the AP and NTS of the mouse, in the fed and fasted state.ResultsOf these, 8910 are neurons that group into 30 clusters, with 4289 coming from mice fedad libitumand 4621 from overnight fasted mice. 7124 nuclei are from non-neuronal cells, including oligodendrocytes, astrocytes and microglia. Interestingly, we identified that the oligodendrocyte population was particularly transcriptionally sensitive to an overnight fast. The receptors GLP1R, GIPR, GFRAL and CALCR, which bind GLP1, GIP, GDF15 and amylin respectively, are all expressed in the hindbrain and are major targets for anti-obesity therapeutics. We characterise the transcriptomes of these four populations and show that their gene expression profiles are not dramatically altered by an overnight fast. Notably, we find that roughly half of cells that express GIPR are oligodendrocytes. Additionally, we profile POMC expressing neurons within the hindbrain and demonstrate that 84% of POMC neurons express either PCSK1, PSCK2 or both, implying that melanocortin peptides are likely produced by these neurons.ConclusionWe provide a detailed single-cell level characterisation of AP and NTS cells expressing receptors for key anti-obesity drugs that are either already approved for human use or are in clinical trials. This resource will help delineate the mechanisms underlying the effectiveness of these compounds, and also prove useful in the continued search for other novel therapeutic targets.

scholarly journals Adversarial domain translation networks enable fast and accurate large-scale atlas-level single-cell data integration

2021 ◽  
Author(s):  
Jia Zhao ◽  
Gefei Wang ◽  
Jingsi Ming ◽  
Zhixiang Lin ◽  
Yang Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Large Scale ◽  
Superior Performance ◽  
Brain Atlas ◽  
Unified Framework ◽  
Fine Grained ◽  
Wide Range ◽  
Shared Information ◽  
Single Nucleus

The rapid emergence of large-scale atlas-level single-cell RNA-sequencing (scRNA-seq) datasets from various sources presents remarkable opportunities for broad and deep biological investigations through integrative analyses. However, harmonizing such datasets requires integration approaches to be not only computationally scalable, but also capable of preserving a wide range of fine-grained cell populations. We created Portal, a unified framework of adversarial domain translation to learn harmonized representations of datasets. With innovation in model and algorithm designs, Portal achieves superior performance in preserving biological variation during integration, while having significantly reduced running time and memory compared to existing approaches, achieving integration of millions of cells in minutes with low memory consumption. We demonstrate the efficiency and accuracy of Portal using diverse datasets ranging from mouse brain atlas projects, the Tabula Muris project, and the Tabula Microcebus project. Portal has broad applicability and in addition to integrating multiple scRNA-seq datasets, it can also integrate scRNA-seq with single-nucleus RNA-sequencing (snRNA-seq) data. Finally, we demonstrate the utility of Portal by applying it to the integration of cross-species datasets with limited shared-information between them, and are able to elucidate biological insights into the similarities and divergences in the spermatogenesis process between mouse, macaque, and human.

scholarly journals Equivalent high-resolution identification of neuronal cell types with single-nucleus and single-cell RNA-sequencing

2017 ◽  
Author(s):  
Trygve E. Bakken ◽  
Rebecca D. Hodge ◽  
Jeremy M. Miller ◽  
Zizhen Yao ◽  
Thuc N. Nguyen ◽  
...  
Keyword(s):  
High Resolution ◽  
Single Cell ◽  
Rna Sequencing ◽  
Transcriptional Profiling ◽  
Neuronal Cell ◽  
Cell Types ◽  
Matched Pair ◽  
Rna Seq ◽  
Nuclear Rna ◽  
Single Nucleus

AbstractTranscriptional profiling of complex tissues by RNA-sequencing of single nuclei presents some advantages over whole cell analysis. It enables unbiased cellular coverage, lack of cell isolation-based transcriptional effects, and application to archived frozen specimens. Using a well-matched pair of single-nucleus RNA-seq (snRNA-seq) and single-cell RNA-seq (scRNA-seq) SMART-Seq v4 datasets from mouse visual cortex, we demonstrate that similarly high-resolution clustering of closely related neuronal types can be achieved with both methods if intronic sequences are included in nuclear RNA-seq analysis. More transcripts are detected in individual whole cells (∼11,000 genes) than nuclei (∼7,000 genes), but the majority of genes have similar detection across cells and nuclei. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively. Together, these results illustrate the high information content of nuclear RNA for characterization of cellular diversity in brain tissues.

scholarly journals Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Marta Olah ◽  
Vilas Menon ◽  
Naomi Habib ◽  
Mariko F. Taga ◽  
Yiyi Ma ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Single Cell ◽  
Rna Sequencing ◽  
Independent Set ◽  
Neurosurgical Procedures ◽  
Human Microglia ◽  
Single Cell Rna Sequencing ◽  
Single Nucleus ◽  
Disease Related Genes

AbstractThe extent of microglial heterogeneity in humans remains a central yet poorly explored question in light of the development of therapies targeting this cell type. Here, we investigate the population structure of live microglia purified from human cerebral cortex samples obtained at autopsy and during neurosurgical procedures. Using single cell RNA sequencing, we find that some subsets are enriched for disease-related genes and RNA signatures. We confirm the presence of four of these microglial subpopulations histologically and illustrate the utility of our data by characterizing further microglial cluster 7, enriched for genes depleted in the cortex of individuals with Alzheimer’s disease (AD). Histologically, these cluster 7 microglia are reduced in frequency in AD tissue, and we validate this observation in an independent set of single nucleus data. Thus, our live human microglia identify a range of subtypes, and we prioritize one of these as being altered in AD.

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