Anti-CRISPR

By the time Doudna submitted her proposal to DARPA, other scientists had already uncovered significant insights into halting CRISPR's action. Phages, viruses that infect bacteria, have developed their own mechanisms to neutralize CRISPR. Recent discoveries have revealed the existence of "anti-CRISPRs," small proteins finely tuned by evolution to inhibit the gene-editing process.

The initial anti-CRISPRs were identified in 2013 by Joseph Bondy-Denomy, a student at the University of Toronto. He stumbled upon the phenomenon when he noted that certain phages could bypass CRISPR defenses in bacteria. “It was a serendipitous discovery,” recalls Bondy-Denomy, now a professor at UCSF. “We realized one of the phage's genes was responsible for this effect.”

While fewer laboratories focus on anti-CRISPR research compared to those working with CRISPR, this field is rapidly expanding. Over 40 anti-CRISPR proteins have been identified, many by Doudna's team. Other research groups are also exploring conventional chemicals that can inhibit CRISPR's activity. Recently, Amit Choudhary from Harvard Medical School announced two drugs capable of preventing gene editing in human cells. “Control is the hallmark of any powerful technology,” Choudhary asserts.

Researchers like Bondy-Denomy believe that anti-CRISPRs could enhance the precision of future gene-editing therapies. For instance, a German team demonstrated that combining CRISPR with anti-CRISPR could target DNA changes specifically in liver cells without affecting other cell types.

Another promising direction for anti-CRISPR research involves developing safeguards against "gene drives," which are engineered to propagate through populations. The Bill & Melinda Gates Foundation is funding a CRISPR project aimed at controlling mosquito populations to combat malaria, while other efforts target rodent eradication without using toxic substances.

However, the potential for unintended consequences remains. Researchers are investigating the possibility of creating organisms with anti-CRISPR integrated into their genomes, rendering them immune to gene drives. Initial experiments in Kansas successfully engineered yeast cells with anti-CRISPR properties to resist gene drives, illustrating the feasibility of this approach. “If a hostile entity attempts to deploy a gene drive to eliminate a vital crop, you could have a genetically modified crop that is resistant,” explains Erik Sontheimer from the University of Massachusetts Medical School.

A Biosurprise

The emergence of CRISPR in 2012 caught the scientific community off guard, as traditional genetic engineering methods quickly became obsolete. Experts tasked with predicting new threats "totally missed" the implications of CRISPR, according to Renee Wegrzyn, who oversees DARPA's program. The urgency to address this oversight has escalated into a significant national security concern.

The rapid advancements in CRISPR technology have led researchers, medical professionals, and startups to explore its applications across various domains, including plants, animals, and human subjects. As proficiency grows, the potential for new biothreats becomes more tangible.

By 2015, Doudna began to raise questions about the safety of CRISPR applications in laboratory settings. Some studies appeared risky—what if an accident occurred? “We are introducing these technologies into the world without the necessary safety protocols,” Wegrzyn remarked at a 2017 Long Now Foundation event in San Francisco. “There is a pressing need for action.”

Wegrzyn highlighted the dangers posed by gene editing, noting that researchers were already using CRISPR to induce illnesses in mice by disrupting crucial genes. “You don’t need to be a biosecurity expert to see the need for caution with a tool that can both heal and harm,” she emphasized. “If we need to halt a gene editor immediately, we currently lack the means to do so.”

The debate over the potential dangers of CRISPR remains unresolved. A series of "red team" exercises led by the CIA in summer 2016, where analysts envisioned worst-case scenarios, failed to reach a consensus. Subsequently, the National Academies of Sciences, Engineering, and Medicine assessed synthetic biology threats at the Department of Defense's request, placing CRISPR weapons in the middle of the risk spectrum. The military indicated that there was no immediate threat to personnel.

Doudna acknowledges that concerns surrounding CRISPR should not be exaggerated. “I frequently receive inquiries about the potential misuse of CRISPR, and I maintain that my apprehensions are no greater than for other technologies. After all, someone could synthesize the smallpox virus,” she states. While her research may eventually lead to an antidote, her work with anti-CRISPRs primarily addresses fundamental biological questions. “I’m still at the initial stage of understanding how these mechanisms function,” she adds.

Conversely, others contend that the risks are apparent and that the need for countermeasures is urgent. Some scientists have advocated for limiting public discourse on specific CRISPR studies or even erasing references to them online, likely to allow more time for developing safeguards. “The prevailing attitude is to avoid creating panic while we actively seek solutions. There’s always a fear of an early reaction,” notes Watters, a former collaborator of Doudna who explored the biosecurity implications of gene editing in a 2018 review.

CRISPR Defense

This year, as part of Doudna’s DARPA project, research teams are set to commence their first experiments on mice to assess the feasibility of shielding them from CRISPR. One participating lab at Sandia National Laboratories plans to use genetically modified mice that inherently express CRISPR's Cas9 protein in every cell.

Schoeniger, leading the Sandia initiative, intends to instruct the mice to perform self-editing while administering anti-CRISPR molecules to evaluate whether the process can be inhibited. “Anti-CRISPR functions effectively in natural settings, and we aim to determine its efficacy in living organisms,” he explains.

He believes there is a “significant risk of accidental exposure” to CRISPR agents. With a burgeoning industry centered around the editing tool, CRISPR is increasingly being incorporated into gene therapies, injections, and even food products, heightening the likelihood of laboratory mishaps. “In a secret bioweapons context, accidental release of a designer microorganism is more probable than a deliberate attack,” he warns. “As the usage of this technology escalates, the chances of inadvertent exposure increase.”

Developing an antidote could also serve as a crucial public relations measure. “Having a means to deactivate CRISPR might deter malicious intent,” Schoeniger suggests. “From a psychological perspective, it’s reassuring to have an ‘off’ switch, which could help position this technology more favorably in society.”

Schoeniger does not believe that a CRISPR antidote will eliminate risks entirely. In fact, as laboratories refine the tool and develop new iterations, the security challenges are likely to intensify. The rapid evolution of gene editing and synthetic biology, coupled with the dissemination of information online, presents formidable challenges for biosecurity experts.

“We must assess the overall risks posed by this technology, its continuous evolution, and the difficulty of keeping pace with emerging scenarios,” he remarks. In the interim, Schoeniger argues that focusing on strategies to inhibit CRISPR in its most fundamental form is a prudent starting point. “It’s clear that we should aim to regulate this technology while we navigate its complexities,” he concludes. “The pace of innovation is overwhelming.”

Antonio Regalado is the senior editor for biomedicine at MIT Technology Review, where he investigates the intersection of technology, medicine, and biomedical research. Prior to joining MIT Technology Review in July 2011, he reported on science, technology, and politics in Latin America from São Paulo, Brazil.