CRISPR Update Could Make Gene Edits Easier, Discoverers Say

Xconomy Boston — 

The popular gene-editing system known as CRISPR/Cas9 has become an indispensable biological research tool, and it also holds profound therapeutic, environmental, ethical, and business implications. Now it has a cousin.

Researchers at several institutions, including CRISPR/Cas9 pioneer Feng Zhang at the Broad Institute, have published a paper in the journal Cell describing a CRISPR system that uses the enzyme Cpf1 instead of Cas9. They say it might help overcome some of the difficulties researchers have run into as they develop CRISPR-related treatments for human diseases.

That said, the Cpf1 work is still in its infancy. It’s well behind CRISPR/Cas9—which researchers have used to make changes in the cells of all types of organisms, including humans. Several companies are working with CRISPR/Cas9 to create therapeutics for genetic disease. None have reached clinical trials yet. Only Sangamo Biosciences (NASDAQ: SGMO), owner of a system called zinc finger proteins, has moved a gene editing therapy into human testing.

But work with CRISPR/Cas9 to modify the human germline—eggs, sperm, and embryos—is also coming faster than expected, sparking ethical concerns. An international summit on the topic is scheduled for December in Washington, DC.

Meanwhile, researchers around the world are working to find new versions of Cas9, or new enzymes entirely, like Cpf1, to make the whole enterprise easier. “There is little doubt that… there are additional systems with distinctive characteristics that await exploration and could further enhance genome editing and other areas of biotechnology as well as shed light on the evolution of these defense systems,” Zhang (pictured above speaking at a 2014 Xconomy event) and his coauthors write in the Cell paper.

In other words, Cpf1 is the tip of the iceberg. I’ll outline three differences between the Cpf1 and Cas9 enzymes that the paper’s authors have highlighted as potentially important for the field. It helps to provide a little background for those unfamiliar with CRISPR and gene editing. Think of these enzymes as molecular scissors. Bacteria use them in the wild to defend themselves against invading viruses, cutting up the viral RNA and storing the pieces in a kind of immune system memory bank.

It was only in recent years that the natural system has been modified and harnessed as a gene editing tool. The enzyme and its guide, which is made from RNA, need to do two difficult things: enter a cell’s nucleus and cut the cell’s DNA at the right spot.

Here’s why Zhang and his co-authors think Cpf1 could have advantages over Cas9:

—Cpf1 only uses one strand of RNA as a guide to reach its target gene. Cas9 uses two strands. A single-strand system might lead to simpler, cheaper designs and easier delivery of the enzyme-guide complex into cells.

—Once delivered into the cell’s nucleus, Cpf1 makes staggered double-stranded cuts in the target DNA, whereas Cas9 cuts both DNA strands in the same location. This could be important, Zhang and colleagues write, because the staggered ends make it easier to insert a new gene after the old one is removed. That could help get around one of the hurdles of Cas9: Scientists say using Cas9 to replace an old gene with a new one has proven far more difficult than simply cutting out a gene.

—When Cpf1 homes in on a gene, it actually makes the cut off to the side, relatively speaking—farther down the DNA strand. (Imagine your friend holding a string in the exact location that needs snipping. You don’t cut her finger; you cut off to the side.) Zhang and colleagues write that this could be a “potentially useful feature” because it preserves the target site for subsequent rounds of editing.

The ownership of CRISPR/Cas9 is in hot dispute, with Zhang and others in a patent dispute with Jennifer Doudna, of the University of California, Berkeley, and others. It’s not immediately clear how the discovery of Cpf1 as an Cas9 alternative might affect or affected by the IP skirmish.

I’ve put in requests for comment from Zhang and other scientists working on CRISPR and will update this story as I hear back from them.