Figure 6. Aneuploidy-activated CEBPB transcription factor suppresses PARP1.

(A) Top: Strategy to identify transcription factors (TFs) regulating PARP1 expression in aneuploid cells. Bottom: Heatmap showing PARP1-promoting and PARP1-suppressing TFs and their expression changes across lysosome-deficient and aneuploid models. p<0.05. (B) CEBPB ChIP-Seq data (ENCODE) near the PARP1 transcription start site. (C) CEBPB RNA and protein levels in acute aneuploidy models. (D) Nuclear CEBPB in hCECs with acute and chronic aneuploidy. Left: representative images (scale bar, 10 μm). Right: quantification of nuclear CEBPB. n>50 cells/condition. (E) CEBPB RNA (left) and protein (right) correlation with aneuploidy score in aneuploid clones. (F) CEBPB RNA in Baf A1-treated cells (published dataset). (G) Normalized sgCEBPB read counts in sorted samples versus unsorted samples. (H) PARP1 protein after CEBPB overexpression. (I) CRISPR activation (CRISPRa) Perturb-Seq analysis of PARP1 regulation by CEBPB. (Left) CEBPB and PARP1 levels in cells with CEBPB CRISPRa (sgCEBPB-1) versus control (sgNC). (Right) PARP1 expression heatmap following CEBPB activation. (J) scRNA-seq analysis of malignant colorectal cancer cells. UMAP plots displaying cell density for cells with top 30% of CEBPB expression (upper left), top 30% of PARP1 expression (upper right), aneuploidy score >5 (lower left), and top 30% of KEGG lysosome signature score (lower right). Cell density is weighted by the respective scores. Populations with high CEBPB expression, high aneuploidy, and high lysosomal activity (red arrows) overlap but are distinct from populations with high PARP1 expression (blue arrows). (K) CEBPB and PARP1 RNA level correlation in pan-cancer cell lines. (L) Viability after H₂O₂ in CEBPB-OE versus EV cells (40 μM for TP53-KO hCEC, 2 mM for DLD1, 24h). One-way ANOVA with Dunnett’s test (hCEC in C, G); with Tukey’s test (hCEC clones in D). Unpaired t-test (RPE1, RPE1-TP53KO and HCT116 in C, acute aneuploidy in D, F, H, I, L).