Human Immunity to Cas9 Could Threaten CRISPR’s Future

New data shows that humans carry antibodies and even T-cells that target the Cas9 protein at the heart of CRISPR gene editing technology.

Westend61 via Getty Images
Westend61 via Getty Images

An early draft of a scientific paper about potential human immunity to the Cas9 protein caused the stock prices of companies developing CRISPR-based therapies to plummet last week as investors questioned whether the controversial genome-editing technology would ever be safe for humans.

Matthew Porteus, lead author of the paper and an associate professor of pediatrics in the divisions of hematology-oncology and human gene therapy at the Stanford School of Medicine, told Seeker that while his data certainly didn’t help stock prices in the CRISPR biotech sector, it was an “overreaction.”

“It was far better for the field to learn about this now, rather than later when something potentially more serious might have occurred,” said Porteus, who was a scientific founder and remains a scientific advisor for CRISPR Therapeutics, one of three companies racing to test CRISPR in human clinical trials.

The paper, which is still being peer-reviewed for a major scientific journal, revealed that most human immune systems carry existing antibodies and even some T-cells that target the two most common forms of Cas9 protein used in the CRISPR-Cas9 gene-editing system.

Cas9 proteins function as a genetic editor that can cut or introduce change in targeted strand of DNA. With CRISPR-based therapies, scientists hope to remove disease-causing mutations in a patient’s DNA and replace them with healthy code.

The US Food and Drug Administration has yet to approve human CRISPR trials, but 2018 is expected to be a banner year, with several companies and universities — including CRISPR Therapeutics and Stanford — set to apply for US trials to treat sickle-cell disease and beta thalassemia, an inherited blood disorder.

The new data on human immunity to Cas9 proteins could slow that progress.

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When Porteus and his colleagues screened human blood samples, they found that 79 percent carried antibodies for SaCas9, a common version of the Cas9 protein derived from the bacteria Staphylococcus aureus, and 65 percent carried antibodies for SpCas9, which comes from Streptococcus pyogenes. Digging deeper, they found that 46 percent of donors carried T-cells that specifically hunt down SaCas9, but none that target SpCas9.

Porteus says he was “mildly surprised” by the level of antibodies and T-cells detected, but that it wasn’t wholly unexpected. Both Staph and Strep bacteria are prevalent in the environment, and it’s only natural that our immune systems would develop defenses against these types of pathogens. What did surprise him was that no one else seemed to be worried about immunity issues with Cas9.

“I’d talk to people who do in vivo editing” — where CRISPR-Cas9 is used to makes DNA edits inside a living organism — “and ask them, ‘Aren’t you concerned about the potential for this bacterial protein to trigger an immune response?’ And people would nod their heads. Eventually I said, look, I keep bringing it up, at some point I have to put my money where my mouth is and look at it myself, so that’s what we did.”

To be clear, the paper did not prove that the existence of antigens and T-cells targeting Cas9 is necessarily a bad thing. The body may only react with mild, flu-like symptoms when Cas9 is present, or may not react at all. Also, many of the proposed CRISPR-based therapies are done ex vivo, where a patient’s cells are extracted, “fixed” with CRISPR, grown out in a lab, and then re-implanted back into the patient. In that case, little if no Cas9 will make it back into the body.

Still, there’s always the possibility of a worst-case scenario, in which the presence of Cas9 “causes a very serious inflammatory response and makes the patient very sick,” said Porteus. “And in the development of gene therapy, that has happened.”

Porteus was referring to the tragic death in 1999 of Jesse Gelsinger, who underwent an early gene therapy trial that used adenovirus as a vector to deliver a genetic fix to his cells. Researchers at the University of Pennsylvania had tested the adenovirus vector in mice, monkeys, and one other human patient with no serious side effects. When Gelsinger received the treatment, however, his immune system went into overdrive, triggering a chain reaction that quickly led to lung failure, kidney failure, and brain death.

Samarth Kulkarni, the CEO of CRISPR Therapeutics, was quick to downplay the significance of the immunity data. He told the Boston Globe that the antigen and T-cell numbers weren’t new. “What’s new is that someone in the press picked it up and sensationalized it, and all of a sudden everyone else picked it up.”

Porteus confirmed that CRISPR Therapeutics knew about his findings a few months ago, but that the company didn’t know he had decided to pre-print a paper based on the immunity data. Pre-printing is a growing trend among researchers to post drafts of paper for the scientific community to check out during the long and often laborious peer-review process.

“We really felt like it was important to let the community know that this exists,” said Porteus, “so while the paper was under review, people could start thinking about it, scientifically critiquing it, and building on it, so there wasn’t this scientific delay in getting this knowledge out there.”

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One reason is to speed the development of Cas9 alternatives that aren’t derived from pathogenic bacteria. Promising results have already been achieved with a protein called Cpf1, so even if Cas9 immunity proves a serious issue, it doesn’t mean the end for CRISPR-based therapies in humans.

What Porteus never expected was that his paper would get so much attention, or be the main reason why two rivals of CRISPR Therapeutics — Editas Medicine and Intellia Therapeutics — would see their stocks both drop by 10 percent on January 8, the Monday after the paper was posted. The stocks quickly rebounded, though, and all three companies’ fortunes are back on a steady upward climb.

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