Breast cancer: CRISPR supercharges BRCA1 research

Fifteen years later, Starita and his colleague Jay Shendure of the University of Washington and the Brotman Baty Institute for Precision Medicine have found a way to study BRCA1 at the Starita scale. In a study published in Nature, they evaluate the cancer risk of 3,893 BRCA1 mutations. This was made possible by CRISPR, a gene editing tool that allowed them to design the 3,883 mutations at one time.

"This work was truly a tour de force," says Susan Domcheck, an oncologist at the University of Pennsylvania, who was not involved in the study. It is still too early to base patients' decisions on the study alone, but it provides a roadmap for finding all unknown variants of BRCA1 and other cancer genes.

To introduce different variants in BRCA1, Starita and Shendure have ordered DNA extracts – scientists can simply do it online now – which corresponded to each possible single letter mutation on about 1,300 letters of the gene . (Since DNA has four different bases – A, T, C and G – there are three possible mutations at each location to give the 3,893 mutations reported in this study.) They then used CRISPR stick these segments in the DNA of human cells.

But they did not use any ordinary human cell. They specifically found a type of human cell that dies when its copy of BRCA1 does not work. It was smart because they just had to wait for the cells with different variants of BRCA1 to develop, noting which variants allowed the cells to grow (meaning that their BRCA1 was functional) and which made them die (non-functional ). Since BRCA1 normally removes cancer, a non-functional BRCA1 mutation is likely to put human breast tissue at high risk of cancer.

The team compared their results to a database of known variants of BRCA1 to test the accuracy of their results. Of the variants that they designed, 169 were found to be known pathogenic variants: 162 were nonfunctional, two functional, and five somewhere in between. Of the 22 known benign mutations, their test was considered functional 20, one non-functional and the other between. Not perfect, but close. In total, the work took about six months.

In contrast, says Couch, who did not participate in the study, his frequent research collaborator, Alvaro Monteiro of the Moffitt Cancer Center, analyzed mutations in BRCA1 one by one in cells growing a laboratory. In 15 years he has examined 300 to 350 variants. Her analysis has been validated more carefully than the actual patient data, so she has a little more weight.

In general, physicians are reluctant to base patient decisions solely on data from growing cells in a laboratory. "There is some caution," says Couch. But for some rare SUVs, it's perhaps what they have better. And large-scale methods like those described in this document Nature the paper could generate a lot more data quickly.

Starita and Shendure have not finished with BRCA1 yet. The complete coding sequence of the gene has a length of about 5,600 letters and this study only covered about 1,300 of them. "This is a first attempt in this regard," says Shendure. "With a new scaling, you can imagine much more ambitious efforts to create tens of thousands or hundreds of thousands of mutations in the genome." They are also looking to study other genes in the genome. such as BRCA2, PALB2 and BARD16.

Since BRCA1 is a particularly well-studied cancer gene, fewer than five in 100 patients will have variants of unknown significance when they are tested today. Many other cancer genes are even less well understood. And for those, this technique could quickly fill the gaps.