DNA-copying overload may reveal which cancer cells respond to ATR-inhibitor drugs

Too many DNA-copying sites can overwhelm cancer cells

The researchers studied several breast cancer cell lines with different levels of sensitivity to the ATR inhibitor ceralasertib. But the differences in sensitivity could not be explained by broad measures of replication stress.

The team combined analyses of proteins, gene-expression data, and measurements of DNA replication activity to search for a more specific explanation. They found that sensitive cancer cells had higher levels and activity of proteins involved in initiating DNA replication. When ATR was blocked, these cells activated abnormally large numbers of replication origins.

Starting DNA replication at too many sites at once appears to overwhelm the cell’s replication machinery, leading to widespread DNA damage and cell death. Resistant cells appeared better able to limit the number of origins activated and avoid lethal damage to their genomes.

Experiments in breast and colorectal cancer cells showed that reducing cells’ ability to activate replication origins made sensitive cells less responsive to ATR inhibition, while increasing this ability made resistant cells more vulnerable. These results suggest that the capacity to activate replication origins helps determine whether a cancer cell responds to ATR inhibition.

Could origin firing help predict treatment response?

The team examined whether patterns of gene and protein activity linked to DNA replication origin firing could help predict sensitivity across different cancers. They found that genes involved in starting DNA replication were more active in cells that are sensitive to ATR-inhibitors from a range of cancer types. Similar effects were also present in acute myeloid leukaemia samples and in pancreatic cancer cells from patients.

However, the strength of the prediction varied between cancer types. Future biomarkers may need to be tailored to particular cancer types and combine several types of information, such as gene activity, protein levels and the activity of enzymes involved in origin firing.

While this work provides a proof-of-principle, larger studies using samples linked to clinical responses will be needed to determine whether these measurements can predict how patients respond to ATR inhibitors. Ultimately, this could help direct treatment towards those most likely to benefit while sparing others from a drug that may be ineffective and cause unnecessary side effects.

Collaborative research across disciplines

This work drew on expertise from several research groups and core facilities at Barts Cancer Institute, alongside collaborators at the University of Cambridge, the University of Oxford and AstraZeneca.

Expert input on mass spectrometry, proteomic analysis and RNA sequencing from collaborators in other teams within BCI was crucial in revealing differences in replication-related proteins and activity between sensitive and resistant cells. A sequencing approach developed by collaborators in Cambridge also allowed the researchers to study how quickly DNA was being copied, where replication stalled and how frequently new origins were activated.

Professor McClelland highlighted Dr Lumeau’s role in leading the project and building the collaborations needed to follow the emerging evidence.

“Audrey drove this study by following the biology wherever it led,” she says. “She identified the expertise she needed, learnt new analytical approaches and brought together colleagues across BCI and beyond.

“We would not have developed such a complete story without that initiative, or without the willingness of researchers with different specialisms to work together. It is a good example of what becomes possible in a collaborative research environment.”

The research was supported by AstraZeneca, Pancreatic Cancer UK, Cancer Research UK, the Medical Research Council and the Biotechnology and Biological Sciences Research Council