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Organizational principles in glioblastoma: decoded by ptalign and targeted via SFRP1 [GBM]

ABSTRACT: Organizational principles in glioblastoma: decoded by ptalign and targeted via SFRP1 [GBM]

PROVIDER: PRJNA1004603 | ENA |

REPOSITORIES: ENA

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Organizational principles in glioblastoma: decoded by ptalign and targeted via SFRP1

Project description:Organizational principles in glioblastoma: decoded by ptalign and targeted via SFRP1

| PRJNA1004600 | ENA

Organizational principles in glioblastoma: decoded by ptalign and targeted via SFRP1 [GBM]

Project description:Cancer research has largely focused on understanding mutations driving uncontrolled growth, leaving the organization of cellular hierarchies that sustain tumor progression less explored. We address this gap with ptalign, a tool that decodes such hierarchies in glioblastoma. By introducing the concept of pseudolineages mirroring adult neural stem cell lineages, we establish a correspondence between tumor pseudolineage and patient survival, devising biomarkers enabling cost-effective pseudolineage-based patient stratification. Comparing tumor pseudolineages to adult neural stem cell lineages, we identify the recurrent loss of the secreted Wnt antagonist SFRP1 in glioblastoma. This Wnt antagonist is expressed after the transition from dormant to quiescent neural stem cells, regulating their activation. Introducing SFRP1 into glioblastoma induced the generation of dormant astrocyte-like tumor cells, thereby increasing the quiescent tumor cell fraction and suggesting its potential as a target to arrest tumor progression. The insights facilitated by ptalign offer a new perspective on glioblastoma's cellular organization, providing a framework for understanding and treating glioblastomas and other solid tumors.

2023-12-01 | GSE240675 | GEO

Organizational principles in glioblastoma: decoded by ptalign and targeted via SFRP1

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-12-01 | GSE240676 | GEO

Genetically defined human GBM organoids reveal principles of GBM development and actionable targets

Project description:Genetically defined human GBM organoids reveal principles of GBM development and actionable targets

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Proteogenomic anlalysis of glioblastoma (GBM)

Project description:Proteogenomic anlalysis of glioblastoma (GBM)

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In vitro models of glioblastoma (GBM)

Project description:Characterization of gene expression for a panel of 50 in vitro and in vivo models of glioblastoma (GBM). Models include subcutaneously established xenograft lines, orthotopically grown subcutaneously established xenograft lines, serum derived cell lines and stem cell media derived cell lines. Multiple replicates of each line were run on different dates to determine the effect of batch and processing date on reproducibility of gene expression profiles 117 samples analyzed from 50 distinct GBM xenografts or cell lines. Biological replicates from the same passage number were included for many, but not all, of the lines.

2011-12-01 | E-GEOD-26344 | biostudies-arrayexpress

Genome-wide methylation analyses in glioblastoma multiforme (GBM)

Project description:Our main objective was to study genome-wide differential methylation in de novo glioblastoma multiforme (GBM, grade IV glioma). We evaluated CpG sites in gene promoters of 26,000+ genes using an array-based chip. We retrieved 54 GBM from biorepositories of two institutions(40 from Columbia University and 14 from Case Western Reserve University) and 24 control brain tissues from the New York Brain Bank, which collected control brain tissues from consented subjects without history of neurological diseases at autopsy. Bisulfite modified DNA was extracted from 54 GBM and 24 control brain tissue. The HumanMethylation27 Analysis Bead-Chips (Illumina) were used to interrogate 26,486 informative CpG sites in the autosomes.

2013-10-18 | E-GEOD-50923 | biostudies-arrayexpress

Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins

Project description:This SuperSeries is composed of the following subset Series: GSE39579: Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins (Chip-Seq data) GSE39580: Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins (expression data) Refer to individual Series

2012-07-30 | E-GEOD-39581 | biostudies-arrayexpress

Proteogenomic anlalysis of glioblastoma (GBM)

Project description:To examine patterns associated with survival, we assembled a cohort of GBM patients whose survival ranges from less than 3 months and up to 10 years, most of which are not bearing isocitrate-dehyderogenase (IDH)-1 mutation and did not undergo prior treatment. We integrated high-resolution mass-spectrometry proteomics and RNA sequencing to examine the yet unresolved proteomic contribution to poor patient outcome, and compared it to the more established transcriptomic contribution and to published single-cell data. Discovering both layer-specific and shared processes, we found that long and short survival are distinguished by immune, metabolic and developmental processes. Additionally, we observed a significant discrepancy in tumor classification between expression layers. Overall, our integrative findings establish proteomic heterogeneity in GBM as a gateway to explaining poor survival.

2021-03-02 | GSE149009 | GEO

Gene expression in glioblastoma (GBM) tissues, glioblastoma stem-like cell (GSC) cultures and neural foetal cell line (NFC)

Project description:This microarray contains expression data for two GBM tissue samples, four GSC cultures grown as spheres and one NFC culture grown as spheres Total RNA was isolated from GSC cultures and GBM tissues

2015-11-26 | E-GEOD-60705 | biostudies-arrayexpress

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