It was Victoria Gray’s first time in London and, despite a sleepless plane ride across the Atlantic Ocean, she wasn’t about to skip sightseeing. While crossing Trafalgar Square, Gray paused briefly to reflect on her experience. “I would never have been able to walk this long before,” she told a NPR reporter. “I feel like I got a second chance.”
Four years earlier, in 2019, Gray had become the first patient with sickle cell anemia — a genetic disorder that causes red blood cells to become sticky and rigid — to receive an experimental treatment using CRISPR genome editing. The treatment, now known as Casgevy, became the first CRISPR-based therapy to gain FDA approval, in 2023. Gray, in London to discuss the significance of her recovery at the Third International Summit on Human Genome Editing, described Casgevy as “a new beginning for people with sickle cell disease.”
Despite its association with genome editing, CRISPR didn’t start out as a tool for fighting genetic disease. Instead, for billions of years, bacteria have used CRISPR systems to defend against invasion by viruses known as bacteriophages. Certain CRISPR components can add short DNA sequences from the genomes of defeated viruses into the bacterium’s own genome, creating a type of protective “memory.” These sequences, known as protospacers, can be found between short, repetitive DNA motifs — an observation that gave CRISPR, which stands for “clustered regularly interspaced short palindromic repeats,” its name.
Collectively, these repeat-protospacer regions are known as CRISPR arrays. The core of the CRISPR immune response is a guide RNA (gRNA) that binds to a CRISPR-associated (Cas) protein. Taken together, these components form what is known as a ribonucleoprotein (RNP) complex. If the same virus invades the cell a second time, the gRNA’s spacer sequence will bind to the matching viral DNA sequence, then be cut by the Cas protein. This allows bacteria to remember past viral infections and fight them off without mistakenly cutting their own genomes.
Since the early 2010s, biologists have been exploiting CRISPR’s ability to cut a diverse set of specific DNA sequences by altering gRNA sequences. Notably, this has led to the development of new medicines to treat genetic diseases — Casgevy was the first of these to gain FDA approval and is used to treat two blood disorders, called sickle cell disease and beta thalassemia. Dozens more clinical trials, based upon similar gene-editing technologies, are now underway. This article provides a summary of the major CRISPR systems, including the naturally occurring CRISPR-Cas9, -Cas12, and -Cas13 systems, as well as base editors, prime editors, and the recently uncovered bridge RNA system.
We made a digital poster that shows all the genome editing tools discussed in this piece in one large PDF. Visit our website to get a copy.
Cas9
Discovery
Cas9 became the first CRISPR effector (the protein that cuts or modifies DNA) engineered for genome editing in 2012, when Jennifer Doudna’s group at UC Berkeley and Emmanuelle Charpentier’s group at Umeå University showed that Cas9 could be guided to virtually any DNA sequence, not just natural targets from invading viruses, by tinkering with its gRNA sequence. Given the system’s bacterial origin, however, it was not guaranteed to work well in other organisms. Within a year, though, Feng Zhang’s lab at MIT showed that Cas9 worked in human cells, a result that other groups quickly confirmed in a flurry of papers.
The best-known Cas9 protein comes from a bacterium, Streptococcus pyogenes, that causes pharyngitis in young children. The protein is so good at cutting DNA that it still ranks among the most efficient Cas9 proteins and is almost certainly the most widely used genome editor today. Researchers have since discovered variants of the protein with additional useful qualities.
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