Extended Data Fig. 9: +1q and +8q associated gene expression changes in HMECs and breast tumors.
From: Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns
(a) HMEC lines were grouped according to +1q (top) or +8q (bottom) status and differential gene expression analysis was performed. mRNA log2 fold changes are plotted for all expressed genes across the genome. Panels on the right show the distributions of log2FCs for resident genes on 1q (top) or 8q (bottom) compared to all other genes. (b) Same analysis as in (a) but for TCGA breast cancer samples. (c) Gene set enrichment analysis of +1q and +8q tumors in each major breast cancer subtype, and across the entire cohort (‘All’). Genes were ranked based on their differential expression in +1q or +8q tumors within each subtype. The Hallmarks gene sets were used. Colors indicated signed negative log10 P values from GSEA. (d) Top: +1q or WT 1q HMECs were exposed to ligand (DLL1 + DLL4 combined 2.5 µg/ml + fibronectin, coated plates), or ligand + GSI (2 μM L-685,458) for 20 h. Control plates (no ligand) were coated with 2.5 µg/ml human IgG + fibronectin. RNA-seq analysis was performed and average log2FC of Notch Activation gene set is plotted for each condition relative to diploid control conditions. +1q HMECs display increased Notch activation capacity when incubated for 20 h on ligand-coated plates, and increased residual Notch activation when GSIs are added. P values calculated from two-sided t-test. Bottom: WT 1q and +1q cell lines used in this experiment. (e) Correlation between mRNA log2FC and DNA log2FC in matched tumor-normal breast cancer TCGA data for the three γ-secretase genes on 1q. P values calculated from linear regression analysis. Dashed lines indicate linear regression models of the data. (f) Expression levels for resident 1q γ-secretase genes APH1A, PSEN2, and NCSTN in +1q and WT 1q HMECs. P values calculated from two-sided t-test. (g) A total of four replicate experiments were performed comparing NCSTN knockdown in WT 1q and +1q HMEC lines. NCSTN (first and third panels) and N1ICD (second and fourth panels) were blotted from lysates of cells treated with EGTA for 10 min. N1ICD imaging required 10x longer exposure.
