CRISPR Tool Eliminates Targeted Eukaryotic Cells

Cells reveal their type and function through patterns of gene activity, allowing distinction in diverse groups. This capability aids in purging harmful cells, such as those linked to disease or unsuccessful gene edits. Elimination strategies vary by situation, fueling need for flexible detection and removal methods in research, medicine, biotechnology, and agriculture. In bacteria, CRISPR-Cas systems already detect and destroy specific microbes. Guide RNA directs Cas proteins to slice matching DNA, inflicting lethal damage.

Eukaryotic cells, with nuclei housing DNA, resist such nucleases. Teams from Helmholtz Institute for RNA-based Infection Research, Braunschweig Helmholtz Centre for Infection Research, Julius-Maximilians-Universität Würzburg, Akribion Therapeutics, University of Utah, and Utah State University have now adapted CRISPR for targeted eukaryotic cell killing.

Earlier HIRI research showed Cas12a2 binds RNA targets, then rampantly cuts surrounding nucleic acids—RNA, single-stranded DNA, double-stranded DNA. “This activity leads to extensive DNA damage in bacteria, causing a halt in growth and thus preventing the spread of a recognized invader,” explains Chase Beisel, senior author on the new research published in Nature. “In contrast to activated Cas9, which makes a single precise cut in the bound DNA, RNA target-activated Cas12a2 shreds all DNA it encounters, effectively killing the cell,” states co-author Ryan Jackson. “Its goal is not to correct anything. Instead, it’s to destroy anything it sees,” notes Yang Liu, co-senior author.

Testing in yeast and human cells, the group found Cas12a2 inactivated only those harboring target transcripts, leaving others intact. “Cell death was sequence-specific, showed high sensitivity to mismatches, and occurred without any measurable unintended effects,” Beisel says.

“Our technology provides us with a powerful tool for sequence-specific depletion of pathogenic cells,” affirms first author Paul Scholz. Proofs included clearing virus-infected cells, point-mutation cancer cells, and boosting gene-edited cell purity. Programmable guides suit diverse RNA signatures.

In vitro hints suggested efficacy, but live eukaryotic effects were unproven—off-target concerns did not materialize.

From cancer and infections to gene editing, transcriptome-based killing expands options. “Because Cas12a2 can be programmed with a guide RNA to target any RNA sequence, and it shows little to no off-targeting, we believe we have discovered a way to selectively kill cells across all of biology,” Jackson asserts. “We show it can be used to enrich for gene editing, and to selectively kill cells harboring virus genes, and to kill cells with acquired mutations.” Beisel urges further community testing, as the team pursues clinical refinement.