Fig. 7: macroH2A1.1 drives TOP1i resistance in cancer cells.

a Western blot for the indicated proteins in MDA-MB-453 (gray) and NCI60 (black) breast cancer cell lines. TNBC cell lines are italicized. A representative of two independent experiments is shown. b Drug activity levels in NCI60 breast cancer cell lines based on data from the National Cancer Institute NCI60 drug screening program, arranged by increasing macroH2A1.1 expression, n: number of compounds tested per drug target. Box plots depict average compound activity Z score distributions for each cell line, each data point represents one drug. The majority of compounds were tested in at least two independent experiments, see https://discover.nci.nih.gov/cellminer/ for details. Box limits represent upper and lower quartiles, whiskers the 10 to 90 percentile range, and center lines the median. P values are based on the two-sided Pearson’s Correlation Coefficient of median drug activity scores. c Cell viability of the indicated cell lines in response to CPT treatment measured by MTT assay, macroH2A1.1^high cells are in gray, macroH2A1.1^low cells in blue. Data are presented as mean and SD (n = 4 independent replicates); p values are based on two-sided Student’s t-test. d TOP1 RADAR assay for the indicated cell lines as in Fig. 2f. Similar results were obtained in three independent experiments. e Western blot in MCF7 cells expressing siRNAs against macroH2A1.1 (si-1.1), macroH2A1.2 (si-1.2) or a control sRNA (si-ctrl). A representative of two independent experiments is shown. f Clonogenic survival of cells from (e) in response to the indicated drug combinations. Survival was normalized to untreated cells for each siRNA transfection. Representative images are shown, scale bar: 1 cm. Data are presented as mean and SD (n = 3 independent replicates); p values are based on two-sided Student’s t-test. g Cell viability in the indicated cell lines in response to CPT treatment in the presence or absence of PARPi, measured by MTT after 10 days of clonogenic growth, data are presented as mean and SD (n = 3 independent replicates); p values are based on two-sided Student’s t-test. Source data for a-g are provided as a Source Data file. h Kaplan–Meier survival analysis of TCGA ovarian cancer patient subgroups where treatment regimens contained Topotecan (n = 119 patients) or taxol (n = 821 patients). Patients were stratified by macroH2A1.1 mRNA expression based on an isoform-specific Affymetrix microarray probe (214500_at), the bottom 25% were considered macroH2A1.1 low expressors.