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A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snATAC_data_tissue]

ABSTRACT: Atypical teratoid rhabdoid tumors (ATRTs), characterized by the loss of SMARCB1, are among the most lethal pediatric brain tumors. Three molecular subtypes have been identified, each defined by distinct molecular and clinical features. Still, no subtype-specific treatments are available, highlighting the need to understand their inter and intra-subtype heterogeneity. Here, we generated a single-nucleus transcriptome atlas of ATRTs, validated with single-cell ATAC-seq and spatial transcriptomics, to study subtype-specific differentiation trajectories. We identified retained brain progenitor expression profiles within unique subtype-specific differentiation lineages. A shared cycling, progenitor-like cell population, interspersed throughout tumors, was observed across all ATRT patients. Finally, we demonstrate that subtype-specific differentiation trajectories can be induced pharmacologically in ATRT tumoroids directing tumor cells towards a non-proliferative, mature phenotype. Our study reveals that ATRT subtypes exhibit signaling trajectories mirroring normal fetal brain development, potentially enabling the development of maturation therapies tailored towards ATRTs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE283836 | GEO | 2025/07/24

REPOSITORIES: GEO

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A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [bulk RNA-Seq]

Project description:Atypical teratoid rhabdoid tumors (ATRTs), characterized by the loss of SMARCB1, are among the most lethal pediatric brain tumors. Three molecular subtypes have been identified, each defined by distinct molecular and clinical features. Still, no subtype-specific treatments are available, highlighting the need to understand their inter and intra-subtype heterogeneity. Here, we generated a single-nucleus transcriptome atlas of ATRTs, validated with single-cell ATAC-seq and spatial transcriptomics, to study subtype-specific differentiation trajectories. We identified retained brain progenitor expression profiles within unique subtype-specific differentiation lineages. A shared cycling, progenitor-like cell population, interspersed throughout tumors, was observed across all ATRT patients. Finally, we demonstrate that subtype-specific differentiation trajectories can be induced pharmacologically in ATRT tumoroids directing tumor cells towards a non-proliferative, mature phenotype. Our study reveals that ATRT subtypes exhibit signaling trajectories mirroring normal fetal brain development, potentially enabling the development of maturation therapies tailored towards ATRTs.

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Gene expression data from ATRT tumor samples

Project description:Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants. Although the prognosis of ATRT patients is poor, some patients respond favorably to current treatments, suggesting molecular inter-tumor heterogeneity. To investigate this further, we genetically and epigenetically analyzed a large series of human ATRTs. Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location, and type of SMARCB1 alterations, were identified. Whole-genome DNA and RNA sequencing found no recurrent mutations in addition to SMARCB1 that would explain the differences between subgroups. Whole-genome bisulfite sequencing and H3K27Ac chromatin-immunoprecipitation sequencing of primary tumors, however, revealed clear differences, leading to the identification of subgroup-specific regulatory networks and potential therapeutic targets. 49 ATRT samples were selected for RNA extraction and hybridization on Affymetrix Affymetrix Human Genome U133 Plus 2.0 Arrays. ---------------------------------------- This submission consists of the expression data for 49 of 170 samples only

2016-03-02 | E-GEOD-70678 | biostudies-arrayexpress

Gene expression data from ATRT tumor samples

2016-03-02 | GSE70678 | GEO

The genomic and epigenomic landscape of atypical teratoid rhabdoid tumors

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Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities

Project description:Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically defined by mutations in SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be subdivided in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subtype-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT subgroups. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing representative pre-clinical models allowing for the development of subtype-specific therapies.

| EGAS00001006422 | EGA

Integrative analyses of rhabdoid tumors across all anatomical sites reveal subgroups with possible immune modulation through epigenetic dysregulation

Project description:Extra-cranial malignant rhabdoid tumors (MRTs) and cranial atypical teratoid RTs (ATRTs) are pediatric cancers driven by SMARCB1 loss. To understand biological relationships between MRTs and ATRTs, we performed integrative data analyses of 140 MRTs and 161 ATRTs, and detected features conserved between MRTs and the MYC subgroup of ATRTs, including global DNA hypomethylation and over-expression of HOX and mesenchymal development genes, thereby distinguishing them from other ATRT subgroups that exhibit neural-like features. Our analyses revealed five DNA-methylation subgroups associated with distinct anatomical sites, SMARCB1 alteration patterns, and distinct gene-expression and enhancer profiles. We also report on RT subgroups with expression patterns indicative of both increased immune infiltration and expression of immune checkpoint genes, which were confirmed using immunohistochemical techniques.

2019-06-01 | GSE123601 | GEO

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