Journal: bioRxiv

Article Title: Spatial epigenomic niches underlie glioblastoma cell state plasticity

doi: 10.1101/2025.05.09.653178

Figure Lengend Snippet: (A) Overview of NicheCompass workflow. (B) Spatial plots of NicheCompass-defined cellular niches with regions of interest highlighted. (D) Spatial plot of SOX10 targets gene program across all samples. (E) Spatial plot of VEGFA combined gene program score. (F) Volcano plot of gene activity scores for pixels belonging to niches 3 and 7 (OPC-like) versus niche 0 (MES-like). (G – H) Representative spatial plots of SOX10 and VEGFA gene activity scores highlighting regions of OPC-like niches surrounded by MES-like niches (I) Representative microscopy image from PhenoCycler data showing the presence of MES-like (white arrows) and OPC-like cells (magenta arrowheads) within the core of a GBM tumor. (J) Quantification of cellular identity in PhenoCycler data. MES is defined as VIM positive, OPC as OLIG2 positive, and intermediate as positive for both markers.

Article Snippet: Primary antibody staining was performed overnight at 4 °C using anti-OLIG2 (Cell Signaling, 65915) diluted 1:400 in DPBS supplemented with 1% Bovine Serum Albumin (BSA) and 0.3% Triton™ X-100 (pH 8.0).

Techniques: Activity Assay, Microscopy

Journal: bioRxiv

Article Title: Spatial epigenomic niches underlie glioblastoma cell state plasticity

doi: 10.1101/2025.05.09.653178

Figure Lengend Snippet: (A) Schematic demonstrating how data are portrayed for panels B and C. (B – C) Signaling programs as defined by NicheCompass demonstrating PDGFB signaling within the OPC-like niche and GPI signaling from the MES-like niche to the OPC-like niche. (D) Heatmap of signaling probabilities as defined by CellChat based on snATAC data of malignant GBM cells. (E) Top ligand-receptor pairs contributing to BMP signaling pathway. (F) Violin plots of BMP7 expression in single cell RNA sequencing data from Couturier and colleagues. (G) Violin plot of gene activity score from snATAC dataset. Note the relatively modest difference in gene activity. (H) Coverage plot of the BMP7 gene. Note relatively similar chromatin landscape. (I) Fluorescence microscopy images of GBM cell culture (GSC016) under control conditions and after treatment for 72 hours with recombinant BMP7 (n = 2 – 4 wells per condition). Scale bar indicates 100 µm. (J) Quantification of percent OLIG2 positive cells in (I).

Article Snippet: Primary antibody staining was performed overnight at 4 °C using anti-OLIG2 (Cell Signaling, 65915) diluted 1:400 in DPBS supplemented with 1% Bovine Serum Albumin (BSA) and 0.3% Triton™ X-100 (pH 8.0).

Techniques: Expressing, RNA Sequencing, Activity Assay, Fluorescence, Microscopy, Cell Culture, Control, Recombinant