Revolutionary Gene-Editing Tool Delivers Unmatched Precision in Targeting Mutations

Key Facts:

• HACE creates mutations in specific genes while leaving the rest of the genome intact.
• It identifies mutations linked to cancer drug resistance and splicing defects.
• This tool may change therapeutic discovery and genomic research.

Gene mutations can have various effects, including resistance to diabetes and increased cancer risk. To study these mutations, scientists must directly introduce them into human cells, a task made challenging by the complexity of the human genome, which contains 3 billion DNA base pairs across many genes.

Harvard researchers have developed a tool called Helicase-Assisted Continuous Editing (HACE). This tool allows rapid mutations in specific genes without disrupting other parts of the genome. HACE can be applied to defined areas of the genome in living cells, as detailed in the journal Science.

“Tools like this significantly improve our ability to work with evolution directly inside human cells,” said Xi Dawn Chen, a lead researcher and student in synthetic biology. “HACE allows precise targeting in the genome, opening new avenues for creating enzymes and treatments that were previously difficult to achieve.”

HACE offers advantages over current mutagenesis methods, which typically alter multiple genes or insert additional gene copies. Instead, HACE targets specific locations like a direct address. Researchers combine a helicase—an enzyme that unwinds DNA—with a gene-editing enzyme. They use CRISPR-Cas9 technology to guide this combined protein to the desired gene. The helicase unwinds the DNA and introduces mutations at that specific site.

The researchers demonstrated HACE’s capabilities by identifying drug resistance mutations in the MEK1 gene. Cancer treatments often fail due to mutations in this gene. HACE enabled the team to sequence mutated MEK1 genes and identify several unique mutations linked to resistance against drugs like trametinib and selumetinib.

Additionally, the researchers explored mutations in the SF3B1 gene, which is relevant to RNA splicing. HACE helped clarify which mutations in this gene contribute to splicing defects, a common issue in blood cancers. In collaboration with other labs, they used HACE to study how changes in regulatory DNA regions affect protein production in immune cells, which are important targets for cancer therapies.

Bradley Bernstein noted that tools like HACE could enable extensive edits of gene regulatory sequences, combined with deep learning for analysis. This could lead to new therapeutic options by precisely editing these sequences to improve gene activity and reduce disease impact.

Funding: This research received support from the National Institutes of Health, the Broad Institute, and the Harvard Stem Cell Institute.