Journal: Oncogene

Article Title: Multicellular tumor-stromal interactions recapitulate aspects of therapeutic response and human oncogenic signaling in a 3D disease model for H3K27M-altered DIPG

doi: 10.1038/s41388-025-03533-7

Figure Lengend Snippet: A Volcano plots display p-values of proteins differentially expressed in TTA (TEM-6) versus DIPG-only neurospheres (T-6) (expressed as -Log 10 p Value), plotted against log 2 fold change. Data from pellet (left) and supernatant (right) are presented separately. Mass spectrometric data was pooled over cultures at multiple points in time (5, 10, and 15 days of culture). Red data points indicate proteins with a p -value < 0.05 and a log 2 fold change ≥ or ≤1.5. Grey data points have p > 0.05. B RNA seq analysis as -log 10 of the false discovery rate (FDR) for differentially expressed transcripts in flow-sorted GFP-expressing DIPG cells (TEM-6 −13 combined vs. T-6 −13 combined) plotted against log 2 fold change at day 5. Red data points indicate differentially expressed genes with FDR < 0.05 and log 2 fold change ≥ or ≤1.0. Grey data points have FDR > 0.05 and are not significant in the sample sets compared. C Heatmap visualization and hierarchical clustering of differential expression in select proteins identified by mass spectrometric analysis in the supernatant and pellet of TTA (TEM-6) and tumor cell-only cultures (T-6) (results shown from 5,10, and 15 days in culture). D Heatmap visualization of the directed gene set in flow-sorted DIPG cells that are statistically significant (black) and also contribute to pathway enrichment (red) observed by RNA seq analysis. Data displayed are from GFP-expressing DIPG cells from the TTA (TEM-6 & TEM-13 shown independently) and GFP-expressing DIPG cells cultured alone as neurospheres (T-6 & T-13). Color key illustrates the relative expression across all samples. E Schematic representation of potential interactions among the differentially expressed select genes/proteins from the proteomic and transcriptomic datasets. F Scatter plots of relative staining positivity (% positivity) and histology score (H-score) analyzed from banked human glioma tissue samples (purple) and reference normal tissue samples (blue) from The Human Protein Atlas public database, pertaining to the identified transcripts. p-values from the omics datasets are identified as **** p ≤ 0.0001, *** p ≤ 0.001, ** p ≤ 0.01, * p ≤ 0.05, identified as described above. G Representative 1 mm diameter immunohistochemical slices from glioma/ GBM (Upper panel) and normal brain tissue (Lower panel) from THPA were used to perform the quantitative analysis in F.

Article Snippet: F Scatter plots of relative staining positivity (% positivity) and histology score (H-score) analyzed from banked human glioma tissue samples (purple) and reference normal tissue samples (blue) from The Human Protein Atlas public database, pertaining to the identified transcripts. p-values from the omics datasets are identified as **** p ≤ 0.0001, *** p ≤ 0.001, ** p ≤ 0.01, * p ≤ 0.05, identified as described above.

Techniques: RNA Sequencing, Expressing, Quantitative Proteomics, Cell Culture, Staining, Immunohistochemical staining