Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells

Abstract

Homologous recombination (HR)-deficient cancers are sensitive to poly-ADP ribose polymerase inhibitors (PARPi), which have shown clinical efficacy in the treatment of high-grade serous cancers (HGSC). However, the majority of patients will relapse, and acquired PARPi resistance is emerging as a pressing clinical problem. Here we generated seven single-cell clones with acquired PARPi resistance derived from a PARPi-sensitive TP53−/− and BRCA1−/− epithelial cell line generated using CRISPR/Cas9. These clones showed diverse resistance mechanisms, and some clones presented with multiple mechanisms of resistance at the same time. Genomic analysis of the clones revealed unique transcriptional and mutational profiles and increased genomic instability in comparison with a PARPi-sensitive cell line. Clonal evolutionary analyses suggested that acquired PARPi resistance arose via clonal selection from an intrinsically unstable and heterogenous cell population in the sensitive cell line, which contained preexisting drug-tolerant cells. Similarly, clonal and spatial heterogeneity in tumor biopsies from a clinical patient with BRCA1-mutant HGSC with acquired PARPi resistance was observed. In an imaging-based drug screening, the clones showed heterogenous responses to targeted therapeutic agents, indicating that not all PARPi-resistant clones can be targeted with just one therapy. Furthermore, PARPi-resistant clones showed mechanism-dependent vulnerabilities to the selected agents, demonstrating that a deeper understanding on the mechanisms of resistance could lead to improved targeting and biomarkers for HGSC with acquired PARPi resistance. Significance: This study shows that BRCA1-deficient cells can give rise to multiple genomically and functionally heterogenous PARPi-resistant clones, which are associated with various vulnerabilities that can be targeted in a mechanism-specific manner.

REV7/FANCV Binds to CAMP and Promotes Homologous Recombination Repair

“…5d) 23 . These cells exhibited multiple independent mechanisms of PARPi resistance, including downregulation of the Shieldin Complex or upregulation of ATR/CHK1 pathway activity 23 . Interestingly, one of these PARPi-resistant clones (NA5) exhibited high CAMP mRNA expression compared to the parental PARPi-sensitive cell line (Extended Data Fig.…”

“…We used a panel of BRCA1-deficient cell lines with acquired PARPiresistance, collected through serial selection in increasing concentrations of PARPi (Extended Data Fig. 5d) 23 . These cells exhibited multiple independent mechanisms of PARPi resistance, including downregulation of the Shieldin Complex or upregulation of ATR/CHK1 pathway activity 23 .…”

PARP inhibition in ovarian cancer: what is still missing?

“…Drugs showing promise in overcoming these mechanisms of resistance (extensively reviewed by Paes Dias et al [12]) include suppression of alternative HR pathways and cell-cycle checkpoint signalling, and the implementation of immunotherapy. The mechanisms of resistance might be overall driven or by clonal selection of preexisting drug-tolerant cells (genetic route) [13] or by the effect of the interplay of these HRD cells within the tumour microenvironment.…”

REV7/FANCV Binds to CHAMP1 and Promotes Homologous Recombination Repair

“…We next sought additional evidence that CHAMP1 upregulation correlates with PARP inhibitor resistance. We used a panel of BRCA1-deficient cell lines with acquired PARPiresistance, collected through serial selection in increasing concentrations of PARPi (Figure 6A) (Farkkila et al, 2021). These cells exhibited multiple independent mechanisms of PARPi resistance, including downregulation of the Shieldin Complex or upregulation of ATR/CHK1 pathway activity (Farkkila et al, 2021).…”

“…We used a panel of BRCA1-deficient cell lines with acquired PARPiresistance, collected through serial selection in increasing concentrations of PARPi (Figure 6A) (Farkkila et al, 2021). These cells exhibited multiple independent mechanisms of PARPi resistance, including downregulation of the Shieldin Complex or upregulation of ATR/CHK1 pathway activity (Farkkila et al, 2021). Interestingly, one of these PARPi-resistant clones (NA5) exhibited high CHAMP1 protein expression compared to the parental PARPi-sensitive cell line (Figure S6A).…”