This animation depicts the CRISPR-Cas9 method for genome editing – a powerful new technology with many applications in biomedical research, including the potential to treat human genetic disease. (Feng Zhang/McGovern Institute for Brain Research/MIT)

Every human genome contains the blueprints for building a person, a library of roughly 20,000 genes that encode everything from eye color to cancer risk. Imagine if those genetic instructions could be tweaked at will — with a snip here and a cut there, a gene might be deleted, inserted or replaced by a different piece of DNA.

Tools that can do this already exist, but one in particular, called CRISPR/Cas 9, has leapt ahead of other genome-editing tools because it’s cost-effective and simple. Researchers say that human clinical trials to fix genetic diseases — for example, sickle cell anemia — are only a few years away.

Last month, a team of Chinese researchers reported that, in a first-of-its-kind event, they had edited the genomes of human embryos. (The embryos, obtained from local fertility clinics, would not have resulted in live births because they contained an extra set of chromosomes.) The scientists’ aim was to modify the gene responsible for a common blood disorder using CRISPR.

The majority of embryos developed unintended mutations, and only a small fraction of them had the blood-disorder gene correctly modified — not what you’d call a success.

Many experts believe it was too soon for such work to be carried out — both because the technology is not yet perfected and because the ethical, medical and legal implications of the research have not been hashed out. Soon after the results were published — by the open-access journal Protein & Cell — the National Institutes of Health reaffirmed its ban on gene editing of human embryos.

Gang Bao brings his expertise Rice’s Department of Bioengineering through a grant from the Cancer Prevention and Research Institute of Texas. (Jeff Fitlow/Rice University)

In a statement released April 29, NIH Director Francis S. Collins said that genome editing in human embryos is “a line that should not be crossed” due to safety and ethical issues “presented by altering the germline in a way that affects the next generation without their consent, and a current lack of compelling medical applications justifying the use of CRISPR/Cas9 in embryos.”

Genome editing of a human embryo would affect every cell in the embryo’s resulting fetus, as opposed to altering the DNA of a select type of cells — such as the stem cells that produce blood cells.

‘A molecular scalpel’

“You can think about it as a molecular scalpel,” said biochemist Jennifer Doudna of the University of California at Berkeley. “It’s a way for making a really precise change in an organism, such as changing a disease-causing mutation into one that is harmless.”

The CRISPR system is a collection of molecules that work together to edit an organism’s DNA. These molecules can be packed into an empty virus and then injected along with a molecule to jump-start the process once the virus encounters a cell. Another approach is to remove cells with undesirable mutations from the body, edit them in a petri dish and insert them back into the body.

Such an easy method of genome manipulation has prompted tremendous excitement in the biological sciences community, as a flood of academic labs and start-up companies scramble to take advantage of CRISPR’s capabilities. But with that buzz have come big ethical questions.

“No one should be doing anything right now until we figure out what the hell is going on with this technique in animals,” said bioethicist Arthur Caplan of New York University. “That’s how we perfected in vitro fertilization, and that’s how you establish safety — you do it in animals first.”

But amid the fears of mad scientists creating designer babies and real-life Jurassic Parks, experts agree on one thing: It is no longer a matter of if but rather of when CRISPR-based genomic surgery will come to a hospital near you. Genomic sequencing is readily and cheaply available, and genetic testing and disease screening have long been underway in clinics across the country.

An artist's rendering shows the CRISPR/Cas9 genome editing tool at work. (Stephen Dixon)

“As much as we worry about premature or ethical use, using these technologies to get rid of genetic disease would be amazing: Tay-Sachs, cystic fibrosis, sickle cell disease, hemophilia,” Caplan said. “We’ve never really wiped out a disease except for smallpox, and these technologies might actually add to the list.”

Rumors of the experiment by scientists based at Sun Yat-sen University in Guangdong spurred others, including Doudna, to meet in January to discuss the future of the technology and its responsible use in humans. A particular focus was germline editing, which refers to changing the DNA of fertilized eggs or embryos. Such editing affects all cells in the developing organism and passes those changes down to future generations.

The scientists, in a summary of their meeting published by the journal Science in April, strongly discourage their colleagues from attempting any germline editing in humans. However, they remain supportive of basic CRISPR research on animals and non-embryonic human cells to see if human germline gene therapy might be helpful in the future to fix genetic mutations.

Doudna is planning to convene a larger, international meeting later this year.

“We really need to be getting in front of this conversation,” she said. “The field has just taken off in an unbelievable way, with many hundreds of papers being published in the scientific literature now, not just in human health but other areas as well.”

While Doudna and French microbiologist Emmanuelle Charpentier are commonly cited as the inventors of CRISPR/Cas9, we can actually thank modest, single-celled bacteria for this revolutionary genome editing system.

“CRISPR” stands for “clustered regularly interspaced palindromic repeats,” first described in 1987 by Japanese researchers who found chunks of oddly repeating DNA sequences in the genome of E. coli.

It wasn’t until about 15 years later that scientists realized the purpose of CRISPRs: They are a key part of the bacterium’s immune system. Each CRISPR is followed by unique DNA segments of viruses that the bacterium previously encountered: If that type of virus tries to attack the cell again, a CRISPR can recognize and defend against it. CRISPRs have been found in 45 percent of sequenced bacteria genomes and in 84 percent of archaea, a type of single-cell microorganism.

Cas9, a scissors-like enzyme, uses the viral DNA segments as an identification system to check for foreign invaders. If the DNA of an incoming suspicious entity is a match, Cas9 proceeds to chop up the intruder’s genetic material by severing both strands of the double helix molecule.

In 2012, Doudna and Charpentier published a study in which they adapted parts of the bacterium’s immune system to create a simple two-part genome editing tool: The Cas9 enzyme and the guide sequence — a small piece of single-stranded RNA 20 nucleotides, or “letters,” long — could be used to target any spot in the genome for cutting.

From that point on, CRISPR/Cas9 technology exploded. The next year, it was used to edit the genomes of human and mouse cells, followed by frogs, monkeys and such crop plants as rice and wheat.

“The range of possible applications is really quite broad, but translating from this very experimental science into real therapeutics — there is a lot of work to be done,” said Katrine Bosley, chief executive of Editas Medicine, a start-up in Cambridge, Mass., that is trying to develop CRISPR/Cas9-based drugs to treat genetic mutations.

Perhaps the biggest issue left to solve involves off-target cuts, which occur when Cas9 gets a bit snip-happy and chops the genome in unintended places. These mistakes can cause big problems, including cell toxicity and cancer.

“Sometimes Cas9 can recognize sequences that are very similar but not identical to the target sequence,” said biological engineer Feng Zhang of the Massachusetts Institute of Technology, a co-founder of Editas and head of a lab at the Broad Institute, a Harvard-MIT biomedical research collaborative. “Depending on the specific sequence, the off-target effect may be more severe or less of a problem.”

Biomedical engineer Gang Bao of Rice University said that scientists cannot answer yet whether, even with some off-target effects, it can be used for humans.

In his lab, Bao is analyzing off-target effects for his treatment of the genetic mutation that causes sickle cell disease. The idea is to take blood-cell-producing stem cells from a patient, use CRISPR to correct the mutation and then reinsert the stem cells back into the bone marrow. Every step of the process requires precision, from minimizing off-target cuts to getting the modified stem cells to survive and transform into blood cells.

Stem cell trials

After having initial success using CRISPR therapy with mice, he has moved on to inserting human stem cells into monkeys for his experiments. He hopes to initiate the first human clinical trials in 2018.

Editas is taking a different approach, working to neatly package CRISPR/Cas9 into a virus for direct delivery into the patient’s body and letting the genome editing happen there. For certain diseases, such as cystic fibrosis, which affects the lungs and other organs, Editas researchers must figure out how to get the viruses into the right cells while avoiding others.

“From the patient’s perspective, [the therapeutic] would be an injection of some sort — maybe an IV, maybe a local injection,” Bosley said. “If you’re working on a genetic disease of the eye, you might do a direct injection into the eye.”

Bao and Bosley say they aren’t interested in germline editing and don’t believe that it is necessary for the medical applications they are working on. Their work, which involves modifying somatic, or non-germline, cells, might have unexpected consequences down the line as well. The technology is so new that no one really knows.

Kim is a freelance science journalist in Philadelphia.