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Gene expression data from ependymal tumor samples

ABSTRACT: Ependymal tumors across age groups have been classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patient outcome. We aimed at establishing a reliable molecular classification using DNA methylation fingerprints and gene expression data of the tumors on a large cohort of 500 tumors. Nine robust molecular subgroups, three in each anatomic compartment of the central nervous system (CNS), were identified.

ORGANISM(S): Homo sapiens

PROVIDER: GSE64415 | GEO | 2015/05/21

SECONDARY ACCESSION(S): PRJNA270979

REPOSITORIES: GEO

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Gene expression data from ependymal tumor samples

Project description:Ependymal tumors across age groups have been classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patient outcome. We aimed at establishing a reliable molecular classification using DNA methylation fingerprints and gene expression data of the tumors on a large cohort of 500 tumors. Nine robust molecular subgroups, three in each anatomic compartment of the central nervous system (CNS), were identified. Total RNA from 209 ependymal tumor samples were hybridised to the Affymetrix HG U133 Plus 2.0 microarrays.

2015-05-21 | E-GEOD-64415 | biostudies-arrayexpress

Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups.

Project description:Ependymal tumors across age groups are currently classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patients' outcome. We aimed at establishing a uniform molecular classification using DNA methylation profiling. Nine molecular subgroups were identified in a large cohort of 500 tumors, 3 in each anatomical compartment of the CNS, spine, posterior fossa, supratentorial. Two supratentorial subgroups are characterized by prototypic fusion genes involving RELA and YAP1, respectively. Regarding clinical associations, the molecular classification proposed herein outperforms the current histopathological classification and thus might serve as a basis for the next World Health Organization classification of CNS tumors.

2015-05-21 | GSE65362 | GEO

Robust Molecular Classification of Ependymal Tumors Across All Anatomic Compartments

Project description:Ependymal tumors across age groups have been classified solely by histopathology. It is, however, commonly accepted that this classification has limited clinical utility based on its poor reliability. We aimed at establishing a reliable and reproducible molecular classification using DNA methylation fingerprints of the tumors. Studying a cohort of 500 tumors allowed for the delineation of nine robust molecular subgroups, three in each anatomic compartment of the central nervous system (CNS). Two of the supratentorial subgroups are characterized by prototypic fusion genes involving RELA and YAP1, respectively. Regarding clinical associations, the molecular classification proposed herein outperforms the current histopathological classification by far and thus might serve as a basis for the upcoming update of the WHO classification of CNS tumors. DNA methylation patterns in tumors have been shown to represent a very stable molecular memory of the respective cell of origin throughout the disease course, thus making them particularly suitable for tumor classification purposes. Methylation fingerprinting of a large series of ependymal tumors of all grades revealed a highly reliable way of classifying this clinically extremely heterogeneous group of malignancies. In fact, out of nine highly reproducible molecular subgroups identified in the supratentorial, infratentorial and spinal regions, only two harbor the vast majority of clinical high-risk patients (mostly children) for whom novel therapeutic concepts are desperately needed. Since this analysis can be performed from minute amounts of DNA extracted from archived material, it is ideally suited for routine clinical application. We investigated a set of 562 ependymal tumors using the Illumina 450k methylation array.

2015-05-21 | E-GEOD-65362 | biostudies-arrayexpress

Gene expression of LMPC cells of infratentorial ependymomas when compared to LMPC ependymal cells

Project description:Ependymomas are glial tumors that share morphologic similarities with ependymal cells. Here we laser microdissected ependymoma cells of 15 infratentorial tumors and generated gene expression profiles. These profiles were compared to those of 7 laser microdissected ependymal tissues. 10 000 laser microdissected cells of each of the 15 different infratentorial ependymomas and seven ependymal autopsy tissues were lysed and gene expression profiles were generated. Expression profiles of ependymomas were compared to those of ependymal cells.

2010-12-10 | E-GEOD-25604 | biostudies-arrayexpress

Gene expression of LMPC cells of infratentorial ependymomas when compared to LMPC ependymal cells

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Endogenous opioid signalling regulates spinal ependymal cell proliferation

Project description:After injury, mammalian spinal cords develop scars to confine the lesion and prevent further damage. However, excessive scarring can hinder neural regeneration and functional recovery. These competing actions underscore the importance of developing therapeutic strategies to dynamically modulate scar progression. Previous research on scarring has primarily focused on astrocytes, but recent evidence has suggested that ependymal cells also participate. Ependymal cells normally form the epithelial layer encasing the central canal, but they undergo massive proliferation and differentiation into astroglia following certain injuries, becoming a core scar component. However, the mechanisms regulating ependymal proliferation in vivo remain unclear. Here we uncover an endogenous κ-opioid signalling pathway that controls ependymal proliferation. Specifically, we detect expression of the κ-opioid receptor, OPRK1, in a functionally under-characterized cell type known as cerebrospinal fluid-contacting neuron (CSF-cN). We also discover a neighbouring cell population that expresses the cognate ligand prodynorphin (PDYN). Whereas κ-opioids are typically considered inhibitory, they excite CSF-cNs to inhibit ependymal proliferation. Systemic administration of a κ-antagonist enhances ependymal proliferation in uninjured spinal cords in a CSF-cN-dependent manner. Moreover, a κ-agonist impairs ependymal proliferation, scar formation and motor function following injury. Together, our data suggest a paracrine signalling pathway in which PDYN+ cells tonically release κ-opioids to stimulate CSF-cNs and suppress ependymal proliferation, revealing an endogenous mechanism and potential pharmacological strategy for modulating scarring after spinal cord injury.

2024-06-29 | GSE255883 | GEO

Single-cell RNA-sequencing of spinal cord ependymal cells from FOXJ1-EGFP mice

Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. Ependymal cells are, however, heterogeneous and we know little about what this reflects. To gain new insights into ependymal cell heterogeneity, we microdissected the ependymal cell layer from the thoracic spinal cord of 4 FOXJ1-EGFP transgenic mice (2.5-to-3-month old). After after dissociating the tissue into a cell suspension, we sorted single GFP-positive ependymal cells into lysis plates. cDNA synthesis was performed using Smart-seq2 technology.

2022-12-13 | E-MTAB-11563 | biostudies-arrayexpress

Comparative analysis of ependymal cells from the lateral ventricular wall and the spinal cord of adult mice

Project description:In contrast to ependymal cells in the lateral ventricle wall (LVW), spinal cord (SC) ependymal cells possess certain neural stem cell characteristics. Isolated CD133+/CD24+/CD45-/CD34- ependymal cells from the SC displayed in vitro self renewal and differentiation capacity, whereas those from the LVW did not. The molecular basis of this difference is unknown. In this study, antibodies against multiple surface markers were applied to isolate SC and LVW ependymal cells which allowed a direct comparison of their in vitro behavior and gene expression profile. cRNA samples of three independent biological replicates of CD133+/CD24+/CD45-/CD34- LVW ependymal cells, CD133+/CD24+/CD45-/CD34- SC ependymal cells, CD133+/CD24-/CD45-/CD34- radial glial cells, and SC ependymal cell-derived NSPs were hybridized onto Illumina MouseWG-6 v1.1 gene expression arrays

2010-10-01 | E-GEOD-18528 | biostudies-arrayexpress

DNA damage-p53/p21 response contributes to ependymal cell development

Project description:Multiciliated Ependymal Cells and Adult Neural Stem Cells are components of the adult neurogenic niche, essential for brain homeostasis. These cells share a common glial cell lineage regulated by the Geminin family members Geminin and GemC1/Mcidas. Ependymal precursors require GemC1/Mcidas expression to massively amplify centrioles and become multiciliated cells. Here we show that GemC1-dependent differentiation occurs mostly in cycling Radial Glial Cells, in which a DNA damage response, including replicative stress and dysfunctional telomeres, arrests the cell cycle after the G1/S restriction point due to the activation of the p53-p21 pathway, which contributes to centriole amplification. Telomerase expression in Radial Glial Cells impairs ependymal differentiation and favors the Neural Stem Cell fate.

2021-09-21 | GSE184397 | GEO

Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function

Project description:Ependymal cells are multi-ciliated cells that form the brain’s ventricular epithelium and a niche for neural stem cells (NSCs) in the ventricular-subventricular zone (V-SVZ). In addition, ependymal cells are suggested to be latent NSCs with a capacity to acquire neurogenic function. This remains highly controversial due to a lack of prospective in vivo labeling techniques that can effectively distinguish ependymal cells from neighboring V-SVZ NSCs. We describe a transgenic system that allows for targeted labeling of ependymal cells within the V-SVZ. Single-cell RNA-seq revealed that ependymal cells are enriched for cilia-related genes and share several stem-cell-associated genes with neural stem or progenitors. Under in vivo and in vitro neural-stem- or progenitor-stimulating environments, ependymal cells failed to demonstrate any suggestion of latent neural-stem-cell function. These findings suggest remarkable stability of ependymal cell function and provide fundamental insights into the molecular signature of the V-SVZ niche.

2018-05-02 | GSE100320 | GEO

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