Pathway-Enriched Gene Signature Associated with 53BP1 Response to PARP Inhibition in Triple-Negative Breast Cancer

Abstract

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 that will most benefit from anti-PARP therapy. We determined the response 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 in 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 for 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 not treated with 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.

53BP1 Accumulation in Circulating Tumor Cells Identifies Chemotherapy-Responsive Metastatic Breast Cancer Patients

“…Present treatments of MBC patients include conventional chemotherapeutics such as anthracyclines and taxanes, but hopefully in the near future, more effective and/or better tolerable drugs will be available [27,39]. Though not addressed in our present study, monitoring 53BP1 in CTCs may also identify resistance to PARP inhibitors as previously suggested from preclinical investigations [40]. Here, we demonstrate the feasibility of detecting nuclear 53BP1 in CTCs from MBC patients.…”

The human HELLS chromatin remodelling protein promotes end resection to facilitate homologous recombination within heterochromatin

“…We uncovered not only impaired accumulation of HR pathway proteins in HELLS downregulated cells, but also defects in some readouts of HR repair, specifically reduced sister chromatid exchange following irradiation and sensitivity to PARP inhibition. In agreement with the PARPi sensitivity that we observed, the HELLS gene was identified in a genome-wide shRNA screen for olaparib sensitivity in MCF7 cells, and as part of a gene signature associated with response to PARP inhibition in a panel of triple-negative breast cancer cell lines (Bajrami et al, 2014;Hassan et al, 2017). Rather that acting as a core HR protein, we suggest that HELLS facilitates recombination at a subset of DSBs, namely those located within heterochromatin.…”

Increased PARP1‐DNA binding due to autoPARylation inhibition of PARP1 on DNA rather than PARP1‐DNA trapping is correlated with PARP1 inhibitor's cytotoxicity

“…Thus, these findings do not support a strong correlation between PARP1-DNA trapping and cytotoxicity of PARPis, which is in contrast with previous reports. 9,10,13 We then took a second strategy to further examine the correlation: Using 2 PARPis simmiparib and talazoparib to treat 4 different human cancer cells including MDA-MB-436 (BRCA1 −/− ), UWB1.289 (BRCA1 −/− ), Capan-1 (BRCA2 −/− ) and HCT-15 (BRCA2 −/− ) that are sensitive to PARPis [5][6][7][8][27][28][29] and detecting their PARP1-DNA trapping. Both PARPis enhanced PARP1-DNA trapping but showed no apparent concentration-dependency in MDA-MB-436, Capan-1 and HCT-15 cells ( Fig.…”

“…5,6 However, the results of this approach show a very low correlation with their ability to induce cytotoxicity in HR-deficient cancer cells. 6,13,[27][28][29]38,39 Our analyses also revealed no significant correlation (r = 0.3898; p = 0.4245) between the IC 50 values of 6 known PARPis (olaparib, niraparib, rucaparib, talazoparib, simmiparib and veliparib) in inhibiting the polymerase activity of PARP1 and their respective average IC 50 values in killing 17 PARPi-sensitive cell lines ( Fig. 5e, right; Supporting Information Table 2 [The used IC 50 values for the cell lines except SK-ES-1 and RD-ES were from References 6,13,27 -29,38,39, respectively]).…”