Fig 1: SMARCB1 regulates ferroptosis.a Heatmap showing the KEGG ferroptosis gene signature in SMARCB1 re-expressing RMC2C (left) and RMC219 (right) cells. b Heatmap showing expression of the ferroptosis gene signature in RMC and TAL clusters. c Flow cytometry quantification of Bodipy-C11, ANXA5 and cleaved CASP3 at 72 h in SMARCB1 or mCHERRY expressing cells and using either Ferrostatin-1 (Fer1) or camptothecin (CAMP) as controls. Biological triplicates are plotted as means ± SD and one-sided unpaired t test analyses were performed by Prism 5, ns= p > 0.05; *=p < 0.05; **=p < 0.01; ***=p < 0.001 and ****=p < 0.0001. P values: upper left panel: 0.076, 0.027 0.005, 0.001; lower left: 0.05 0.06, 0.01, 0.02; upper centre panel: 0.12, 0.13, 0.0001 0.001; lower centre panel: 0.37, 0.21 0.000007 0.0004; upper right panel: 0.16, 0.0002, 0.09, 0.0001; lower right panel: 0.09, 2.27 E–09, 0.18 0. 0002. d. Cell viability (IC50) upon increasing concentrations of RSL3, a class II ferroptosis inducer. Biological triplicates are plotted as means ± SEM. e Gene expression changes of known IFNg downstream targets upon treatment of RMC lines with 10 ng/mL recombinant human IFNg. Biological triplicates are plotted as means ± SEM. f Immunoblots showing expression of selected EMT and ferroptosis markers in RMC lines treated either with IFNg or DMSO vehicle control. n = 3 independent biological replicates. Molecular mass markers in kDa are indicated. g Cell death quantified by flow cytometry using annexin-V in RMC lines. Biological triplicates are plotted as means ± SD and one-sided unpaired t test analyses were performed by Prism 5, ns=p > 0.05; *=p < 0.05; **=p < 0.01; ***=p < 0.001. P values: left panel: 0,09 0,01 3,72E-06; right panel: 0.22, 0.17, 0.0001. h Flow cytometry-based quantification of cell death at 72 h upon treatment with IFNg alone, IFNg with Fer1 or DMSO in RMC lines and normal kidney cells as control. Represented values are the mean of 3 biological replicates as means ± SD and unpaired t test analyses were performed with Prism5 by comparing conditions to matched DMSO. P values: ns=p > 0.05; *=p < 0.05; **=p < 0.01; ***=p < 0.001 and ****=p < 0.0001. P values: left panel: 0.21 0.23; centre panel: 0.0004 0.008; right panel 9.98 E–06, 0.037. Source data are provided as a Source Data files.
Fig 2: Tumour-suppressor function of SMARCB1.a Volcano plot revealing up- and down-regulated genes at 12 h after SMARCB1 re-expression in RMC lines. P values were derived using the Wald test and adjusted using Benjamini-Hochberg FDR correction. b Volcano plot revealing up- and down-regulated genes at 48 h after SMARCB1 re-expression in RMC lines. P values were derived using the Wald test and adjusted using Benjamini-Hochberg FDR correction. c GSEA showing top up- and down-regulated pathways upon SMARCB1 re-expression (48 h) with similar ontologies observed in both lines. d Integrative heatmap showing GSEA Hallmarks enrichments (left panel) in SMARCB1 re-expressing RMC lines and 2 cohorts of RMC primary tumours (MDACC: n = 11; Curie: n = 5) and Metascape ontology analysis of genes constituting the GSEA “Heme metabolism” term (right panel). FDR values were derived by GSEA using permutation and Benjamini-Hochberg correction. e Phase-contrast microscopy at ×10 magnification of RMC lines 48 h after re-expression of either SMARCB1 or mCHERRY control. Scale bar: 500 µm. (upper panel) Quantification of cell death in RMC lines at selected time-points upon SMARCB1 re-expression, as assessed by flow cytometry (lower panel). Note that the % of cells staining positive for either ANXA5 or propidium iodide were tagged as “dead”. The remaining unstained cells were tagged “viable”. Biological triplicates are plotted as means ± SD and one-sided unpaired t test analyses were performed by Prism 5 by comparing matched time-points: p values: ns= p > 0.05; *=p < 0.05; **=p < 0.01; ***=p < 0.001, RMC2C: p values 0.074, 0.082, 0.008 0.00006. RMC219: p values 0.046, 0.00008, 0.00001. Source data are provided as a Source Data files.
Supplier Page from BioLegend for FITC Annexin V Apoptosis Detection Kit with PI