The CRISPR revolution

A gene-editing technique—which is not only of natural origin but also inexpensive, precise and versatile—could prompt revolutions both inside and outside the laboratory.

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May 10, 2016
By James Hataway
Illustration by Eleanor Davis

Scientists are buzzing over a recently developed gene-editing tool commonly known by the acronym CRISPR, which makes it possible to snip out and replace segments of DNA inside the cells of living organisms with extraordinary precision. The technology is only about three years old, but it’s both easier and cheaper than other gene editing techniques, and it is quickly taking the scientific world by storm.

So great is the promise of CRISPR (pronounced “crisper”) that the journal Science named it the “Breakthrough of the Year” for 2015, noting, among other things, its potential applications in medicine. “It’s only slightly hyperbolic to say that if scientists can dream of a genetic manipulation, CRISPR can now make that happen,” said John Travis, Science’s managing news editor.

Armed with this unprecedented command over the code of life, scientists could, with the requisite knowledge, improve the vitality of crops in the face of drought and pests; eliminate viruses such as HIV from the genomes of infected individuals; or “silence” the genes that predispose humans to a myriad of diseases, including cancer, diabetes, cardiovascular disorders and mental illnesses.

Microbial mechanism, human benefit 

CRISPR is a natural system that bacteria use to protect themselves from viruses. Researchers first uncovered the hallmarks of CRISPR in 2000, when a group of Spanish scientists noticed unusual sites in the genomes of bacteria, which contained multiple copies of a short repeated genetic sequence.

The sites were dubbed “clustered regularly interspaced short palindromic repeats” or CRISPRs, and scientists found that the repeated sequences separated snippets of DNA captured from bacteriophages—viruses that attack and kill bacteria.

“Essentially, CRISPR is a kind of bacterial immune system, and the pieces of viral DNA scientists found in the bacteria were a record of past infections,” said Michael Terns, a Distinguished Research Professor in UGA’s Franklin College of Arts and Sciences. He and his colleague Rebecca Terns were among the first to describe some of the fundamental mechanisms involved in CRISPR immunity.

When a virus invades a bacterium, the CRISPR system captures and stores a segment of the viral DNA in its own genome as a kind of microbial mug shot that allows the bacterium and its offspring to recognize the virus. The system then releases a team of two soldiers to seek and eradicate the alien attacker. One partner —a strand of RNA from the CRISPR— carries the captured viral sequence and acts as a guide for the other partner, a protein called Cas9.

The CRISPR RNA/Cas9 team works its way along the invading virus’s DNA until the RNA soldier finds the sequence matching the mugshot and signals the Cas9 soldier to permanently disable the virus by cleaving its DNA.

“This programmable ability to cut DNA so precisely is what intrigued many of us who were studying the system early on,” said Rebecca Terns. “Scientists began conducting experiments to see if the system could be harnessed to cut DNA in a variety of other organisms.”

Scientists found that they could design strands of CRISPR RNA to instruct the Cas9 protein to cut almost any organism’s DNA at precise locations. Researchers could also provide a template to direct replacement of a removed segment with a modified sequence, such as a “corrected” version of a gene with a disease-causing mutation.

CRISPR technology has made gene editing practical for a much broader group of scientists. “Almost anyone can do this,” said Michael Terns. “You don’t need a lab full of advanced equipment, and what used to cost thousands of dollars can now be done with just a few hundred.”

University of Georgia researchers in lab

Michael Terns, left, and Rebecca Terns, center, were among the first to study the bacterial immune system known as CRISPR. Along with postdoctoral scientist Yunzhou Wei, they are using CRISPR technology to improve foods, pharmaceuticals and biofuels.

 

What’s happening at UGA

The Terns laboratory is working to understand precisely how the CRISPR system works in the bacterium Streptococcus thermophilus, which the dairy industry commonly uses to make yogurt and cheese; and in the archaeon Pyrococcus furiosus, which aids in the production of numerous industrially important enzymes and chemicals.

In particular, “we’re trying to utilize this system in good bacteria that we exploit to make foods, pharmaceuticals, and biofuels,” said Michael Terns.

The Terns group is developing RNA as well as DNA targeting systems and have used customized CRISPR RNAs to successfully disrupt expression of a protein responsible for resistance to commonly prescribed antibiotics such as penicillin and amoxicillin. This discovery could help bolster treatments that, because of overuse and misuse, have become largely useless against infection-causing bacteria.

In another set of experiments, led by Rick Tarleton, UGA Athletic Association Distinguished Research Professor of Biological Sciences, scientists are using CRISPR technology to speed the development of vaccines, diagnostics and treatments against Trypanosoma cruzi, an insect-borne parasite that causes Chagas disease. Known to result in irreparable damage to tissues of the heart and digestive systems, Chagas disease is the world’s single most common cause of congestive heart failure and sudden death.

Tarleton and his colleagues are using CRISPR to edit the genome of T. cruzi so that they may better understand how it interacts with host cells. This could ultimately help them identify potential weak points in the parasite’s life cycle, which researchers would then aim to exploit.

“Development of CRISPR in T. cruzi has totally changed what we can do, and even think of doing,” said Tarleton, who is also a member of UGA’s Center for Tropical and Emerging Global Diseases. “Manipulations that used to take us months, we can now complete in days, and experiments we have dreamed of performing for over 15 years are now doable.”

Similarly, Boris Striepen, a Distinguished Research Professor of Cellular Biology, is using CRISPR to genetically modify cryptosporidium, a microscopic parasite that causes the gastrointestinal disease cryptosporidiosis.
Crypto, as researchers often call the microorganism, is most commonly spread through tainted drinking or recreational water. When a person ingests contaminated water, parasites emerge from spores and invade the lining of the small intestine, causing severe diarrhea.

“One of the biggest obstacles with crypto is that it is very difficult to study in the lab, and that has made scientists and funders shy away from studying the parasite,” said Striepen. As a result, there is currently no vaccine and only one crypto-fighting drug—nitazoxanide—approved by the U.S. Food and Drug Administration.

But Striepen and his colleagues are looking to devise a new weapon for that battle. By deploying CRISPR to knock out specific genes in the cryptosporidium parasite, they can test the genes’ importance for the parasite and assess their potential value as a drug target.

Proceed with enthusiasm—and caution

The speed with which CRISPR is developing, combined with its potentially wide range of applications, has spurred both excitement and concern: excitement that it may well signal a revolutionary technology that could change the world for the better; concern about the possibility it could also result in harm.

For example, some worry that the technology could be used to alter the DNA of commercially important plants and animals before the effects of these manipulations on ecosystems are fully understood. And others are troubled that CRISPR might trigger social havoc in a rush to create so-called “designer babies”—offspring whose genetic characteristics are customized prior to their birth.

“Society faces this challenge when any powerful new technology emerges,” said Rebecca Terns. But she is optimistic that the scientific community will proceed with an abundance of caution and that the world will see substantial improvements in quality of life as a result of CRISPR technology—as long as we keep the big picture in mind and proceed carefully.