Blog Post November 26, 2013

The power of CRISPR and genome engineering

“Clustered regularly interspaced short palindromic repeats."

Catchy phrase, right? Well, no, not really. Which is why, in the proud tradition of science and tech, it was given an acronym: CRISPR. Which provides no further clue regarding what the phrase actually means, but is at least memorable. Clumsy naming aside, however, CRISPR is a big deal. But why? What is it and why is it beginning to cause something of a ruckus in genomics circles? And why are three venture capital firms backing a new venture, called Editas, to the tune of $43 million up front, to develop CRISPR-based gene-editing drugs?

From humble origins

CRISPR is a new research tool that may end up representing the future of genomic editing and engineering, no more and no less. First discovered decades ago in bacteria, CRISPRs are DNA sequences that can be read the same forwards and backwards, hence “palindromic.” First thought to be an oddity of little interest, CRISPR came closer to the fore about six years ago when scientists realized that the sequences matched those in the genetic material of viruses that attack bacteria. This relationship merited further study.

It turns out that CRISPR is an immune system of sorts. When a virus attacks a bacterium, the CRISPR RNA transcripts guide enzymes to the virus’s invading DNA. The enzymes, called CRISPR-associated (or Cas, which is why the system is often spelled out as CRISPR/Cas), are powerful DNA cleavers, and they chop up the viral DNA to stop the virus in its tracks.

What does that have to do with genome editing? A scientist working on the bacterial system, Jennifer Doudna from UC Berkeley, teamed with Emmanuelle Charpentier from Umea University in Sweden to show that a particular Cas (CAS9) would provide defined DNA cuts at a site precisely specified by an RNA sequence. What’s more, the DNA sites weren’t specific to the native CRISPR system—they could manufacture an RNA sequence to recognize whatever DNA location they wished. So, on the surface, they had found something in bacteria that would work to recognize and cut DNA with high specificity and precision in other, more complicated genomes. And do so with relative ease. The next step, to employ it for genome editing, was an obvious one.

Rapid progress

The concept of genome editing is nothing new, and indeed functional systems were already being used before the CRISPR concept came along. The two most prominent used enzymes called nucleases (Zinc-finger nucleases (ZFNs) or transcription activator-like effector nucleases (TALENs)), which bind to and cleave DNA at specific sites. For both ZFN and TALEN to work, however, a different nuclease has to be developed and manufactured for each desired target DNA region, a costly process in terms of labor, time and expense. And the nucleases themselves don’t work with laser-like precision, leading to worrisome “off-target” DNA cuts.

As one might expect, researchers quickly jumped to work with CRISPR and see what it can do. What they’ve found is that CRISPR’s use of RNA to target the DNA sequence and deliver the cleaving enzyme has significant advantages over the ZFN and TALEN tools. Engineering custom RNA sequences is far easier and less expensive to do than creating nucleases. And CRISPR’s action is more precise, with less off-target cleaving action.

George Church’s lab at Harvard used CRISPR/Cas to cleave DNA in precise locations in the genomes of cultured human cells. Meanwhile, researchers led by Feng Zhang at the Broad Institute encoded multiple guide sequences into a single CRISPR system that allowed them to edit several different sites within the genome simultaneously. And Rudolf Jaenisch’s lab at the Whitehead Institute not only made targeted cuts in mouse genomes; they were able to develop mice with sophisticated genome edits—including the insertion of up to 3,000 base pairs of DNA—in one step. And they confirmed that non-specific DNA cleavages using the system are quite rare. For biomedical researchers, this means that mice useful for research into specific diseases can be engineered in weeks, not years, a huge potential boon to pre-clinical progress.

Editas

Not surprisingly, a buzz has been growing about CRISPR’s genome editing capabilities and how to move it from the lab to the pre-clinical space. The announcement about the new company, Editas, will greatly accelerate the conversation.

It looks like Editas is built upon a collaborative effort spearheaded by leading academic researchers, including Doudna, Church and Zhang, and three prominent venture capital firms, Third Rock, Flagship and Polaris. Polaris’s Kevin Bitterman, who is serving as Editas’s interim CEO, projects ambitious goals in the Xconomy article linked to above. “I would think of this as really the potential for a whole new class of therapeutics. We can go in and, without really any limitation since it’s a programmable system—we can target any gene in the genome and theoretically fix a mistake, remove a gene, or modulate expression in a very targeted way.”

It’s heady stuff, and not at all the same as the vector-based gene therapy that has caused so much excitement and unfulfilled promise in years past. That said, it’s also a relatively young field, with much work ahead. And even without the vectors and presumably without the worries of off-target DNA damage, finding safe ways to deliver gene edits in living human patients remains a formidable hurdle to overcome for Editas and any competitors that may arise.

A cautionary tale

Despite the known challenges ahead--no one is claiming it's ready for the clinic yet--CRISPR-based genome editing has such power that it has already sparked ethical concerns. After all, with great power comes great responsibility. And with statements like “Our results establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering” (Church 2013) appearing in scientific papers, which are not known for their dramatic prose, one can understand the reaction. Even the researchers themselves, who so often focus on progress and not consequences associated with basic research, have joined the discussion at this early stage.

The implications are profound. If we can engineer a gene with a disease-causing mutation so that it expresses a non-mutated protein—thereby curing the disease—what else can we do? As we learn more about how the genome itself is engineered, will we be able to influence other, non-disease traits like appearance and athletic ability? Or even intelligence? Will couples be able to choose in-vitro fertilization so that they can perform a form of quality control and repair on their future child before it’s even born? It’s a disturbing thought.

The ethical issues are so front and center that Bitterman addressed them in his Editas remarks. “There are ethical implications that we spend a tremendous amount of time thinking about. I would say the guiding light that holds this company together is a desire to impact patients. Where you’re going to see this technology used first is in the most grievous diseases where there is truly an unmet need and nothing to fix them today.” There promises to be an ongoing and lively discussion, with patient needs driving progress and ethical concerns promoting caution. One can only hope that, with the early attention and with the best minds in the field coming together in the first major commercial implementation of CRISPR, some important medical benefits can be developed without the emergence of a possible darker side of genomic engineering.