A new study suggests CRISPR gene editing therapies should be customized for each patient

You know a scientific advance is a big deal when it becomes the main premise and title of a Jennifer Lopez-produced TV drama. That’s the case for CRISPR, a revolutionary gene-editing technology that promises to yield treatments for a wide range of genetic diseases.

In fact, clinical trials using the CRISPR method are already underway with more on the horizon. And at CIRM, we’re funding several CRISPR projects including a candidate gene and stem cell therapy that applies CRISPR to repair a genetic mutation found in sickle cell anemia patients.

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Animation by Todd Dubnicoff/CIRM

While these projects are moving full steam ahead, a study published this week in PNAS suggests a note of caution. They report that the natural genetic variability that is found when comparing  the DNA sequences of individuals has the potential to negatively impact the effectiveness of a CRISPR-based treatment and in some cases, could lead to dangerous side effects. As a result, the research team – a collaboration between Boston Children’s Hospital and the University of Montreal – recommends that therapy products using CRISPR should be customized to take into account the genetic variation between patients.

CRISPR 101
While other gene-editing methods pre-date CRISPR, the gene-editing technique has taken the research community by storm because of its ease of use. Pretty much any lab can incorporate it into their studies. CRISPR protein can cut specific DNA sequence within a person’s cells with the help of an attached piece of RNA. It’s pretty straight-forward to customize this “guide” RNA molecule so that it recognizes a desired DNA sequence that is in need of repair or modification.

https://player.vimeo.com/video/112757040

Because CRISPR activity heavily relies on the guide RNA molecule’s binding to a specific DNA sequence, there have been on-going concerns that a patient’s genetic variability could hamper the effectiveness of a given CRISPR therapy if it didn’t bind well. Even worse, if the genetic variability caused the CRISPR product to bind and inactivate a different region of DNA, say a gene responsible for suppressing cancer growth, it could lead to dangerous, so-called off target effects.

Although, studies have been carried out to measure the frequency of these potential CRISPR mismatches, many of the analyses depend on a reference DNA sequence from one individual. But as senior author Stuart Orkin, of Dana-Farber Boston Children’s Cancer and Blood Disorders Center, points out in a press release, this is not an ideal way to gauge CRISPR effectiveness and safety:

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Stuart Orkin

“Humans vary in their DNA sequences, and what is taken as the ‘normal’ DNA sequence for reference cannot account for all these differences.”

 

 

One DNA sequence is not like the other
So, in this study, the research team analyzed previously published DNA sequence data from 7,444 people. And they focused on 30 disease genes that various researchers were targeting with CRISPR gene-editing. The team also generated 3,000 different guide RNAs with which to target those 30 disease genes.

The analysis showed that, in fact, about 50 percent of the guide RNAs could potentially have mismatches due to genetic variability found in these patients’ DNA sequences. These mismatches could lead to less effective binding of CRISPR to the disease gene target, which would reduce the effectiveness of the gene editing. And, though rare, the team also found cases in which an individual’s genetic variability could cause the CRISPR guide RNA to bind and cut in the wrong spot.

Matthew Canver, an MD-PhD student at Harvard Medical School who is also an author in the study, points out these less-than-ideal activities could also impact other gene editing techniques. Canver gives an overall recommendation how to best move forward with CRISPR-based therapy development:

canver, matthew

Matthew Canver

“The unifying theme is that all these technologies rely on identifying stretches of DNA bases very specifically. As these gene-editing therapies continue to develop and start to approach the clinic, it’s important to make sure each therapy is going to be tailored to the patient that’s going to be treated.”

 

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