Journal: bioRxiv

Article Title: KDM5-driven transcriptional noise fuels plasticity-led awakening and relapse in paediatric cancer

doi: 10.1101/2025.10.13.682004

Figure Lengend Snippet: (A) Differential transcriptional noise (overdispersion) analysis between BRI and MES cells (left) or BRI and ADRN cells (right). Dots represent individual genes, dashed lines statistical thresholds and numbers percentage of all noisy genes in each cell state. (B) GSEA of BRI-specific noisy genes in (A). ( C) Representative flow cytometry plots of SK-N-SH cells treated for five days with DMSO, IdU or Cisplatin. Coloured boxes represent CD44 gating strategy and numbers represent the percentage of cells in that gate. (D) Representative flow cytometry histograms across conditions and timepoints (Iso, isotype; Cis, cisplatin). (E) Quantification of the percentage of ADRN (CD44low), BRI (CD44int) and MES (CD44high) cells during IdU or cisplatin treatment. (F) Wound healing assay in SK-N-SH treated with the noise inducer IdU or the plasticity inducer TGF-ß. Lines represent average wound area across two replicates and shaded area represents standard error (G) Representative images of patient-derived xenograft (PDX) before and after being treated ex vivo with IdU, TGF-ß or a combination of both. (H) Quantification of the area, roundness and number of fusions between PDX spheroids in (G). (I) Gene Set Enrichment Analysis (GSEA) of genes differentially expressed between spheroids treated with a combination of IdU+TGF-ß and any other treatment. (J) GSEA of public MES and ADRN signatures in the genes differentially expressed spheroids treated with a combination of IdU+TGF-ß and any other treatment. Stars represent statistical significance resulting from a two-way (E) or one-way (F, H) ANOVA test with Tukey’s HSD (‘****’ p <0.0001 ‘***’ p <0.001, ‘**’ p<0.01, ‘*’ p <0.05, ‘ns’ p >0.05’).

Article Snippet: For experiments not including KDM5-C70, cells were stained with 2μL of anti-CD44 APC/Fire 750 antibody (103062, BioLegend, USA) for 30 min at 4°C.

Techniques: Flow Cytometry, Wound Healing Assay, Derivative Assay, Ex Vivo

Journal: bioRxiv

Article Title: Targeting Glioblastoma Cell State Plasticity for Enhanced Therapeutic Efficacy

doi: 10.1101/2025.09.08.674897

Figure Lengend Snippet: a) Schematic overview of GSC-320 inducible over-expression (OE) and GSC-728 inducible knock-down (KD) of FOSL1, followed by panobinostat treament. B) FOSL1 expression levels measured by Western blot. Actin expression level was used as protein loading control (top). Histograms of CD44 (MES-L state marker) expression measured by flow cytometry (bottom). GSC-320 cells transduced with doxycycline-inducible FOSL1 construct; DOX, GSCs treated with 2.5 μg/mL of doxycycline during 72 hours. C) FOSL1 expression levels measured by Western blot. Actin expression level was used as protein loading control (top). Histograms of CD44 (MES-L state marker) expression measured by flow cytometry (bottom). GSC-728 cells transduced with inducible KD FOSL1 construct DOX, GSCs treated with 2.5 μg/mL of doxycycline during 72 hours. D) GSCs growth curves for inducible FOSL1 OE (left) and (KD) cells treated or not with panobinostat. Viable cells were quantified by direct cell count using trypan blue exclusion. E) Transferase dUTP Nick End Labeling (TUNEL) assay for inducible FOSL1 OE (left) and KD cells (right) treated or not with panobinostat. Proportion of positive apoptotic cells, indicated by arrows, were counted per field and normalized to Control.

Article Snippet: GSCs were stained with CD44 antibody coupled to APC (#130–113–338, Miltenyi Biotec) followed the manufacturer’s cell surface flow cytometry staining protocol.

Techniques: Over Expression, Knockdown, Expressing, Western Blot, Control, Marker, Flow Cytometry, Transduction, Construct, Cell Counting, End Labeling, TUNEL Assay