- CRISPR gene-editing technology has been taking the medical world by storm, showing potential for treating diseases ranging from cancer to type 2 diabetes
- After sequencing the entire genome of CRISPR gene-edited mice, researchers found numerous unintended mutations, including more than 100 additional deletions and insertions and more than 1,500 single-nucleotide mutations
- While some of the mutations are likely benign, each mutation has the potential to lead to serious unintended and unexpected consequences
CRISPR gene-editing technology has been taking the medical world by storm, showing potential for treating diseases ranging from cancer to type 2 diabetes. The technology has been moving full-steam ahead, with a trial in humans already started, even as the repercussions of gene editing remain largely unknown.
A new study has highlighted the uncertainties, showing that unintended mutations may result when you dice and splice the human genome, but it’s too soon to say whether the mutations are a cause for alarm.
What Is CRISPR?
CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeat, is at the most basic level a very precise way of tinkering with genes. Whereas gene editing was once a very imprecise and expensive process, scientists can now go into your DNA and essentially cut and paste it at specified places. The technology can be traced back to bacteria, which protect themselves by cutting out invading viruses’ DNA and inserting it into their own, then replicating the new sequences to prevent future viral invasions.1
In 2012, researchers refined the system and revealed that any DNA (not just bacteria) has this ability — and the process works in humans. Wired reported:2
“In 2012, scientists turned CRISPR from a bacterial shield into a gene-editing tool. They replaced the bacterial CRISPR RNA system with a modified guide RNA. This RNA acts as a kind of ‘wanted poster’ — it tells a bounty hunter enzyme called CAS9 where to look.
The enzyme scans the cell’s genome to find a DNA match then slices for the DNA in the cell’s enzymes. To repair damage at that point, scientists can change or add DNA within the cell. By feeding CAS9 the right sequence or guide RNA, scientists can cut and paste parts of the DNA sequence, up to 20 bases long, into the genome at any point.”
Since its discovery, CRISPR has been used for a variety of impressive feats, from producing mushrooms that don’t turn brown to removing HIV from human cells. Progress is also being made in tackling genetic diseases such as sickle-cell anemia and certain forms of blindness and muscular dystrophy. A CRISPR clinical trial in humans is already underway in China, in which cancer patients’ T-cells are edited to remove a protein that halts immune responses.
The cells are then reinserted into the patients. The first CRISPR clinical trial in the U.S. has also been approved, which will involve three edits to T cells. According to Nature:3
“The researchers will remove T cells from 18 patients with several types of cancers and perform three CRISPR edits on them. One edit will insert a gene for a protein engineered to detect cancer cells and instruct the T cells to target them, and a second edit removes a natural T-cell protein that could interfere with this process.
The third is defensive: It will remove the gene for a protein that identifies the T cells as immune cells and prevent the cancer cells from disabling them. The researchers will then infuse the edited cells back into the patient.”
CRISPR Leads to Hundreds of Unexpected Mutations
A recent study published in the journal Nature Methods has raised concerns that testing CRISPR in humans may be premature, even with CRISPR-Cas9.4 By modifying an enzyme called Cas9, the gene-editing capabilities are significantly improved, in some cases reducing the error rate to “undetectable levels.” As precise as the technology is, however, it’s not perfect, and it may accidently hit other parts of the genome.
This flaw isn’t unheard of, and it’s been tested for before, typically using a computer algorithm to predict where such off-target mutations are likely to occur, then searching those areas to see if such mutations did, in fact, occur. The new study used a different method to search for unintended mutations, based on a separate study that used CRISPR-Cas9 to restore sight in blind mice by correcting a genetic mutation.
The researchers sequenced the entire genome of the CRISPR-edited mice to search for mutations. In addition to the intended genetic edit, they found more than 100 additional deletions and insertions along with more than 1,500 single-nucleotide mutations. Study co-author Dr. Stephen Tsang, of Columbia University Medical Center, told Scienmag:5
“We feel it’s critical that the scientific community consider the potential hazards of all off-target mutations caused by CRISPR, including single nucleotide mutations and mutations in non-coding regions of the genome … Researchers who aren’t using whole genome sequencing to find off-target effects may be missing potentially important mutations. Even a single nucleotide change can have a huge impact.”
That being said, many are still optimistic that the creation of unintended mutations is a solvable problem and believe the technology could be further improved to reduce off-target changes. Further, the clinical trials underway so far involve people with serious diseases who would likely want to continue with the experimental therapy even with the potential for risks.
Still, as Tsang told New Scientist, “This is going to clinical trials, and is being used in crops … Perhaps the USDA [U.S. Department of Agriculture] and FDA should require our method prior to approval of CRISPR guides in humans and food?”6
What Does This Mean for Gene-Edited Foods?
You may be surprised to learn that CRISPR and other gene-editing tools are also being used in the food industry. Gene-edited crops, in which DNA is tweaked or snipped out at a precise location, have already been created — and eaten. The New York Times reported on the first dinner on Earth with gene-edited foods, including soybeans and potatoes produced by a pharmaceutical company called Cellectis.
Unlike genetically engineered (GE) foods, which may have genes from other species inserted, “There is nothing taken out or added to the plant,” André Choulika, chief executive officer of Cellectis, told the Times. “It’s what nature would have produced.”7 It’s too soon to say what gene editing may do to food and the environment, for better or for worse, but the technology is already forging ahead, so we’ll inevitably find out, sooner or later.
Foods produced via gene-editing are not subject to regulation by the USDA or other regulatory agencies — although an advisory board advised that gene-edited foods could not be labeled organic. “They, at least for now, largely fall outside of current regulations,” the Times reported.8 To date, the technology has been used to produce soybeans with altered fatty acid profiles, potatoes that take longer to turn brown and potatoes that remain fresher longer and do not produce carcinogens when fried.
The latter could be sold as early as 2019. In an interview with GM Watch, Michael Antoniou, a London-based molecular geneticist, explained that significant changes could occur due to genetic editing, in both agricultural and medical contexts, necessitating long-term safety and toxicity studies. He explained:9
“Many of the genome editing-induced off-target mutations, as well as those induced by the tissue culture, will no doubt be benign in terms of effects on gene function. However, many will not be benign and their effects can carry through to the final marketed product, whether it be plant or animal …
Thus, not only is it necessary to conduct whole genome sequencing to identify all off-target mutations from CRISPR-based genome editing, but it is also essential to ascertain the effects of these unintended changes on global patterns of gene function.
… In addition, it is important to acknowledge that the targeted intended change in a given gene may also have unintended effects. For example, the total disruption or modification of an enzyme function can lead to unexpected or unpredictable biochemical side-reactions that can markedly alter the composition of an organism, such as a food crop.
The compositional alterations in food products produced with genome editing techniques will not be fully revealed by the molecular profiling methods due to the current inherent limitations of these techniques. So it is still necessary to conduct long-term toxicity studies in established animal model systems. In the absence of these analyses, to claim that genome editing is precise and predictable is based on faith rather than science.”
Are There Other Pitfalls of Genetic Editing?
With CRISPR gene-editing capabilities, three categories of DNA alterations become possible.10 Science and society will ultimately have to face and address the need and ethical requirements for all of them:
- Embryonic DNA is corrected to eliminate genetic defects associated with inheritable disease. (While this use has the greatest support, some scientists argue that using germ-line gene editing to eliminate genetic disease is unnecessary, since the technology to test and choose embryos free of genetic disease already exists, and is regularly used in IVF clinics)
- The alteration of genes to protect a person against future disease or diseases
- Genetic enhancement, in which genes are installed or modified to change a person’s appearance, or physical or mental potential
The latter brings up the potential of creating “designer babies” with a certain color hair or increased intelligence, which is one reason why about 40 countries have already banned the genetic engineering of human embryos and 15 of 22 European countries prohibit germ line modification.11 Time reported:12
“Using CRISPR on humans is still hugely controversial, in part because it’s so easy. The fact that it allows scientists to efficiently edit any gene — for some cancers, but also potentially for a predisposition for red hair, for being overweight, for being good at math — worries ethicists because of what could happen if it gets into the wrong hands.
… As CRISPR goes mainstream in medicine and agriculture, profound moral and ethical questions will arise. Few would argue against using CRISPR to treat terminal cancer patients, but what about treating chronic diseases? Or disabilities? If sickle-cell anemia can be corrected with CRISPR, should obesity, which drives so many life-threatening illnesses? Who decides where that line ought to be drawn?”
DIY Gene Editing
Such ethical and moral considerations are coming into play sooner rather than later, especially as gene editing has become so mainstream there are classes on the topic available at community colleges and even DIY kits you can order online. Even middle-school students may learn the basics of gene editing in science class, with some comparing the new technology to computer coding a few decades ago.
Everyone from professionals to individuals looking for a new hobby can learn the basics of genetic editing — no biology degree required. It’s a shift that’s both good and bad, with amateur scientists currently tinkering with a number of CRISPR-inspired projects, from creating a spicy tomato to rendering previously resistant bacteria vulnerable to antibiotics (the latter of which was accomplished by a 13-year-old).13 There can be both intended and unintended consequences of such experiments, of course.
Former Director of National Intelligence James Clapper even listed genome editing on the list of “weapons of mass destruction and proliferation,”14 so truly anything is possible. There’s no doubt that gene-editing technology is here to stay (unless something truly devastating cuts its popularity short). It certainly has the potential to do good, but it also has the potential to be misused and abused — especially since it’s far cheaper than it used to be and becoming increasingly accessible to anyone with an inkling of interest.