Fig 2: Computational design of peptide targeting FOXO4. a, Domains of FOXO4 and TP53 (p53). FOXO4FH (PDB ID: 3L2C), in its closed state, interacts with FOXO4CR3. TP53DBD (PDB ID: 3KMD), disrupts this intramolecular interaction and binds both FOXO4FH and FOXO4CR3. The FH epitope (87-120) which was used to design the senolytic peptide ES2 is coloured red and framed with dashed lines. Protein-protein docking analysis of b, FOXO4CR3-TP53DBD, c, FOXO4FH-TP53DBD and d, FOXO4FH-CR3. The TP53DBD is colored gray, FOXO4FH is green and FOXO4CR3 is blue. The FOXO4 epitope used to design the senolytic peptide ES2 is coloured red. For b, c and d the binding free energy (?Gbind) of the complexes which were predicted by MM-GBSA is given. See also Fig. S1 and S2 and Table S1 and S2.

Fig 3: Senolytic activity of ES2 in different cell lines, different senescence inducers and different TP53 status. a-h, Line plots of relative viability of seven different cell lines on dividing cells (black) or senescent cells from different senescence inducers: Doxorubicin (red), Dabrafenib (grey), and Palbociclib (blue). Solid lines are best fit polynomial. a-b, Normal epithelial cell line, MCF10a, and fibroblast cell line, IMR90. c-d, Melanoma cell lines A375 and B16F10 (mouse). e, Breast cancer cell line MCF7. f, Colorectal cancer cell line HCT116. g-h, TP53 mutant colorectal cancer cell lines DLD1 and SW480.

Fig 4: Increased expression of miR-34a-activating pathways in cortical tubers. (A) Relative protein expression of pathological markers in cortical tubers compared with autopsy-derived controls; (B) representative western blots; (C–F) in situ hybridisation with double-labelling: (C) P-S6 was expressed by giant cells (arrowheads) and co-localised with miR-34a in situ hybridisation signal (IHS) to various extent; (D) expression of p53 with nuclear localisation in giant cells co-localised with miR-34a IHS (arrowhead); (E) expression of c-Myc co-localised with miR-34a IHS (arrowhead); (F) expression of p-JNK in control white matter (arrowhead), in giant cells in tuberous sclerosis complex (TSC) white matter (arrow), as well as in astrocytes in TSC grey matter (arrowheads); blue +/- sign indicate miR-34a IHS presence; red +/- indicate maker expression presence; scale bar in each panel is as indicated at the closest panel to the left, WM, white matter, GM, grey matter

Fig 5: ES2 rapidly destroys TP53-FOXO4 foci leading to TP53 mediated apoptosis. a, Annexin V live staining showing that rapid induction of apoptosis is greater in senescent (Sen) compared to dividing (Div) cells (p=0.001) (n=5 for each time point). b, Proximity Ligation Assay showing increased FOXO4-TP53 and FOXO4-53BP1 foci (red) in senescent cells (n=41 for each) compared to dividing cells (n=41 and 36, respectively) (p<0.001). In addition, FOXO4-TP53 foci and FOXO4-53BP1 foci are reduced 1 hour after ES2 treatment in senescent cells (n=33 and 47 respectively) (p<0.01) but not dividing cells (n=41 and 44). c, ddPCR expression analysis shows that ES2 does not increase TP53 target genes in dividing cells, but shows a statistically significant increase after 30 minutes of ES2 treatment in senescent cells (n=6 for each time point) (p<0.001). d, Line plot of relative viability of MCF10a dividing (black) and senescent (red) cells with or without TP53 following a range of ES2 treatments. e, Bio-layer Interferometry analysis reveals ES2 preferentially binds FOXO4. Representative sensorgrams of FOXO4 binding to biotinylated ES2 peptide immobilized on streptavidin sensors. Representative sensorgrams of TP53 binding to biotinylated ES2 peptide immobilized on streptavidin sensors. See also Fig. S4 and S5.