Where DNA Copying Fails Can Decide How Cancer Cells Respond to PARP Inhibitors

Not all DNA damage is equal. During cell division, cells must replicate their DNA, but some regions of the genome are harder to copy than others. Cancer cells rely on a protective response to overcome these difficulties. A new study identifies where problems occur on chromosomes and demonstrates that blocking this response with PARP inhibitors leads to the accumulation of damage at those sites, reducing the cancer cells' survival.

The research, led by NYU Langone Health’s Perlmutter Cancer Center, is published in Nature Cell Biology as "Positional replication fork instability drives PARP inhibitor cytotoxicity." Co-corresponding authors Eli Rothenberg, PhD, and Dipika Gupta, PhD, conducted the study. They started with CRISPR screens in breast and small cell lung cancer models, which highlighted ESCO2, a protein that holds newly copied chromosomes together, as a key factor in sensitivity to PARP inhibitors.

Even a partial loss of ESCO2 made colorectal, ovarian, and lung cancer cells more sensitive to the drugs. Despite the BRCA-mutated cancers, typically treated with PARP inhibitors, having impaired DNA repair pathways, the ESCO2-depleted cells still retained the homologous recombination response. The researchers used quantitative single-molecule imaging to distinguish different types of replication-associated damage sites that standard methods cannot easily separate.

They found that reducing ESCO2 led to an increase in G-quadruplexes, or G4s, which are folded DNA structures that can interfere with copying. This increase was localized to a small subset of replication sites, especially in repetitive pericentromeric regions close to centromeres. The imaging allowed them to detect subtle replication issues, pinpoint the affected sites, and identify the protective response the cells relied on.

This response depended on PARP1 activity and involved two additional proteins. Timeless helps protect DNA replication, and DDX11 is an enzyme that can unwind G4 structures. When PARP inhibitors were used in ESCO2-depleted cells, the protective response was disrupted. G4s accumulated, DNA synthesis decreased, and damage increased near centromeres, explaining the cells' sensitivity to the drugs.

Rothenberg emphasized that while one might think that more DNA damage generally means a higher chance of killing a cancer cell, the findings suggest that location is more important. The results offer a foundation for developing biomarkers of cancer drug sensitivity and suggest that other DNA-damaging treatments might work because they are more likely to hit these sensitive genomic sites.

The study was conducted on cancer cell models, so further preclinical and clinical research is needed to confirm whether these features can guide treatment decisions.