Supplementary Figure S4. Cell cycle distributions for veliparib, olaparib, and talazoparib, in A) HCC1143, B) MDAMB231, and C) HCC1806; Supplementary Figure S5. Cell cycle histograms for veliparib, olaparib, and talazoparib, in A) HCC1143, B) MDAMB231, and C) HCC1806 at selected concentrations; Supplementary Figure S6. Cleaved-PARP expression; Supplementary Figure S7. Representative EC50 dose-response curves of normalized percentage of cells positive for 53BP1 for veliparib, olaparib, and talazoparib in A) HCC1143, B) MDAMB231, C) HCC1806, D) HCC1395, and E) MDAMB436; Supplementary Figure S8. IC50 and EC50 values compiled for 8 breast cancer cell lines, for veliparib, olaparib, and talazoparib; Supplementary Figure S9. For each PARP inhibitor, correlations between IC50 values and A) EC50 values for % positive 53BP1, B) EC50 values for 53BP1 foci, C) EC50 values for % positive for cleaved-PARP; Supplementary Figure S10. Summary of Gene Set Enrichment Analysis (GSEA); Supplementary Figure S11. Enrichment plots after gene set enrichment analysis; Supplementary Figure S12. A) Presence of mutations in 63 gene-set in triple-negative breast cancer patients; B) Mutational frequency of 63 pathway enriched genes in triple-negative breast cancer (TNBC), ER-negative, ER-positive, basal, luminal B, and luminal A breast cancer subtypes.
Funding
TELUS-Canadian Breast Cancer Foundation National Fellowship
Canadian Institutes of Health Research
Ontario Institute for Cancer Research
Conquer Cancer Foundation
Evelyn H. Lauder Family
Breast Cancer Research Foundation
NIH, NCI
ARTICLE ABSTRACT
Effective treatment of patients with triple-negative (ER-negative, PR-negative, HER2-negative) breast cancer remains a challenge. Although PARP inhibitors are being evaluated in clinical trials, biomarkers are needed to identify patients who will most benefit from anti-PARP therapy. We determined the responses of three PARP inhibitors (veliparib, olaparib, and talazoparib) in a panel of eight triple-negative breast cancer cell lines. Therapeutic responses and cellular phenotypes were elucidated using high-content imaging and quantitative immunofluorescence to assess markers of DNA damage (53BP1) and apoptosis (cleaved PARP). We determined the pharmacodynamic changes as percentage of cells positive for 53BP1, mean number of 53BP1 foci per cell, and percentage of cells positive for cleaved PARP. Inspired by traditional dose–response measures of cell viability, an EC50 value was calculated for each cellular phenotype and each PARP inhibitor. The EC50 values for both 53BP1 metrics strongly correlated with IC50 values for each PARP inhibitor. Pathway enrichment analysis identified a set of DNA repair and cell cycle–associated genes that were associated with 53BP1 response following PARP inhibition. The overall accuracy of our 63 gene set in predicting response to olaparib in seven breast cancer patient-derived xenograft tumors was 86%. In triple-negative breast cancer patients who had not received anti-PARP therapy, the predicted response rate of our gene signature was 45%. These results indicate that 53BP1 is a biomarker of response to anti-PARP therapy in the laboratory, and our DNA damage response gene signature may be used to identify patients who are most likely to respond to PARP inhibition. Mol Cancer Ther; 16(12); 2892–901. ©2017 AACR.
