Testing BRCA1 variants reveals differences in breast cancer risk

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Mutations in the BRCA1 gene, which normally helps to repair damaged DNA, can increase the risk of breast and ovarian cancer. Despite it being one of the most well-known and well-tested cancer risk genes, some mutations in BRCA1 lack clear evidence about their significance for cancer risk.

"People can be told they have a mutation in BRCA1, but that its significance is unknown," says Greg Findlay, who leads the Genome Function Laboratory at the Crick. "This leaves them in the dark about their risk of developing cancer."

Greg has developed a method called saturation genome editing, where variants in a gene are introduced one-by-one into cells in a dish, to work out how each variant affects the gene's function. His team have already used the method to unpick the effects of mutations in VHL, a kidney cancer risk gene, and RNU4-2, a non-coding gene behind a previously uncategorised neurodevelopmental disorder.

In research published today in Nature Genetics, Greg and team turned their attention to BRCA1. Though specific BRCA1 regions had been analysed with saturation genome editing before, a technical update to the method, developed by former PhD student in the lab, Phoebe Dace, gave the team several new insights.

Putting variants to the test

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Phoebe first edited over 4,000 BRCA1 variants into a widely used laboratory cell type, called HAP1 cells, to see which variants affected cell growth. In this first step, she identified 538 variants that impact gene function, through the BRCA1 protein's interactions with other key proteins to repair DNA, but also through how the gene is expressed to produce its protein product.

Because the effects of genetic variants can depend on the biological context, the team wanted to see whether the same patterns held true in cells more relevant to breast cancer, human mammary epithelial cells.

"This was the first time anyone had compared the effects of thousands of variants edited into a gene between cell types," says Phoebe. "We didn't expect to see so much difference between them."

Improving the interpretation

The team observed that some variants that had a damaging effect in HAP1 cells had much less of an effect in mammary cells, suggesting that the consequences of a BRCA1 variant can depend on the type of cell it's expressed in.

At first, the amount of difference led Greg and Phoebe to question whether the new method would add value for identifying disease-causing variants. But they then realised it was hugely informative for interpreting a variant's risk: the mutations that were harmful in the standard cell line, but not in the mammary cells, were associated with lower breast cancer risk than variants that had strong effects in both cell types.

"This suggests that mammary cells can buffer some functional impairment of the BRCA1 gene," explains Phoebe. "The mutations selectively impacting HAP1 cells therefore appear to be associated with an intermediate risk of cancer. Identifying such mutations hasn't been easy up until this point, as their effects aren't as striking as the ones that impact function across multiple cell types."

Conversely, the team showed that variants that are harmful in both cell types are associated with a higher risk of breast cancer. This is because they have a more severe impact on BRCA1's ability to repair DNA.

Improving diagnosis

Greg believes that one day, clinicians could go beyond a simple 'risk' versus 'no risk' diagnosis when people are told they have mutations in genes like BRCA1.

"Ideally, people could be given a precise risk estimate, that not only gives the individual a clearer idea about their actual risk, but helps doctors make decisions about which monitoring or interventions would be most appropriate to offer," he says.

The work also suggests that it's important to investigate how variants in a particular gene function in the cell types most relevant to a particular disease, allowing researchers to generate datasets that could ultimately help make genetic risk assessment more precise.

Phoebe and Greg worked with the Genomics and Cell Science teams on this work.