P300-mediated adaptive conversion of glioma stem cells to vascular-like cells in response to therapeutic stress promotes tumor recurrence [scRNA-seq in vivo]
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ABSTRACT: Purpose: The goal of the study is to determine the phenotypic and functional states of glioma cells induce in response to a standard glioblastoma therapy, ionizing radiation. Methods: We performed single-cell RNA-sequencing on non-radiated and radiated tumor cells isolated from patient-derived xenografts. Tumor-bearing mice were exposed to a single dose of radiation ( 8 Gy) and cells were isolated and FACS sorted to obtain cell suspensions for assessing gene expression. Single cell suspensions and cDNA library preparation was done using 10x Genomics Chromium single cell reagent kit v3 according to manufacturer's protocol. cDNA samples were sequenced on 1 lane of NovaSeq 6000 S2 flowcell. Reads were mapped to HumanGRCh38 genome using Cell Ranger v.3.0.2. Seurat package v3.1.1 was used for integrated analysis by Canonical correlation analysis method with 75 dimensions . PCA was used for dimensional reduction, and Cell clustering was performed using shared nearest neighbor method. Each cell cluster was annotated by a combination of the following methods 1) canonical marker expression 2) Gene Set Enrichment Analysis (GSEA) of cluster specific markers determined by Find Markers function in Seurat and 3) Co-expression modules obtained by Louvain community detection clustering method. Trajectory analysis was done with monocle 3 (version 0.2.1.3) by converting Seurat object to monocle. Results: We identified 14 clusters in non-radiated tumors and 15 clusters in radiated tumors.
ORGANISM(S): Homo sapiens
PROVIDER: GSE207726 | GEO | 2022/09/09
REPOSITORIES: GEO
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