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Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin [snATAC-seq]

ABSTRACT: Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin [snATAC-seq]

PROVIDER: PRJNA1209099 | ENA |

REPOSITORIES: ENA

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Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin [snATAC-seq]

Project description:Glioblastoma (GBM) remains an untreatable disease. Understanding of GBM’s infiltrative biology at the resection margin is limited, despite causing disease recurrence and progression. To address this, we generated a high-throughput single-nucleus (sn)RNA-seq and snATAC-seq multi-omic dataset from six tumors with distinct genomic drivers and combined it with spatial transcriptomics to characterize the unique molecular phenotype of GBM near the margin. By contrasting GBM-specific biology in matching “Core” vs. “Margin” dissections, we define unique, shared “GBM infiltration” and chromatin accessibility signatures near the margin. We prioritize EGFR as a top differentially expressed and accessible “Margin” marker across GBM subtypes, show its dynamic expression along a core-to-margin infiltration trajectory, and validate its role in migration through CRISPR/Cas9 deletion in two patient-derived models. ChIP-seq studies furthermore corroborate preferential TEAD1 binding at EGFR’s accessible regulatory elements. This validated multi-omic dataset enables further studies into tumor and microenvironment biology in the context of residual GBM disease.

2025-07-14 | GSE286415 | GEO

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Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin [10x Spatial]

Project description:Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin [10x Spatial]

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Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin [RNA-seq]

Project description:Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin [RNA-seq]

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Glioblastoma cell fate is differentially regulated by the microenvironments of the tumour bulk and infiltrative margin.

Project description:Glioblastoma recurrence originates from invasive cells that escape surgical resection, but their biology remains poorly understood. Here we generated three somatic mouse models recapitulating the main driver mutations of the human disease to characterise the infiltrative tumour margin. We find that, regardless of genetics, tumours are fuelled by highly proliferative glioma stem-like cells (GSCs) resembling active neural stem cells (NSCs), which recapitulate normal and injury-induced neurogenesis in both bulk and margin. Surprisingly, GSCs are evenly distributed across both regions, suggesting that invasive potential is uncoupled from stemness. However, tumour region influences fate choice, with margin cells progressing towards astrocyte-like, and bulk cells towards injured NSC-like (iNSCs) fates. iNSCs account for a significant proportion of dormant glioblastoma cells and are induced by interferon signalling within T-cell-rich niches that form selectively in the bulk. These findings identify key differences between bulk and margin and indicate that glioblastoma cell fate is under cell-extrinsic control.

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Glioblastoma cell fate is differentially regulated by the microenvironments of the tumour bulk and infiltrative margin.

Project description:Glioblastoma cell fate is differentially regulated by the microenvironments of the tumour bulk and infiltrative margin.

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Glioblastoma intra-tumour transcriptomics

Project description:Gene expression microarray profiling on glioblastoma intra-tumour regions, where the study hypothesis states that the infiltrative tumour margin harbours a distinct transcriptomic profile from all non-infiltrative tumour regions. Data is from three patients (patient 9, 14 and 15) where regions 1-4 per patient were obtained from non-infiltrative intra-tumour regions, and region 5 was obtained from the infiltrative margin. All patients underwent craniotomy with intra-operative image guidance and visualization of 5ALA induced fluorescence to obtain infiltrative margin biopsies.

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snATAC-seq data from single cell multiomics (paired snRNA-seq+snATAC-seq) of human colorectal cancer liver metastatic samples

Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Tumour microenvironment cell types and cancer cell states were identified using 10x Genomics Multiome (paired snRNA-seq + snATAC-seq). snATAC-seq data is uploaded here.

2025-04-22 | E-MTAB-13652 | biostudies-arrayexpress

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