A new genetic revolution

The take-away

  • The first two gene-editing systems were difficult to use and cost thousands of dollars. CRISPR can be bought off the shelf, and costs as little as $30.
  • The extent to which gene editing is used will depend on how well scientists can engage with the public. Poor communication from academics and companies alike has been a major cause of the public’s opposition to GMOs.

The announcement by Chinese scientists two years ago that they had altered the genetic material of a human embryo for the first time generated enormous controversy. They reported having attempted to modify a specific gene in several dozen unviable embryos from a fertility clinic – a procedure that could one day provide a cure for a blood disorder known as beta-thalassaemia. But the work had major shortcomings, producing the intended change in just four of the embryos while making numerous, potentially harmful, modifications to other genes.

Enabling the research was a genetic toolkit created in 2012 by French microbiologist Emmanuelle Charpentier and American molecular biologist Jennifer Doudna. Using a set of molecules known as CRISPR-Cas9, the kit allows scientists to make precise, targeted changes to the DNA inside living cells and is far cheaper, quicker and easier to use than previous gene-editing techniques. It is also extremely flexible, since it can be used to edit not just human DNA, but also that of a wide range of plants and animals. As such it has been rapidly embraced by biologists and medical scientists around the world, opening up the prospect of accelerated advances in crop science and livestock production, as well as in medicine.

Cellular playground

Rather than seeking to improve people’s health by modifying the human genome itself, Helene Faustrup Kildegaard (Technical University of Denmark) is using gene editing to bolster drug production.

The speed of CRISPR’s rise to prominence has left experts scrambling to make sense of the technology’s ethical implications, and is proving a headache for governments trying to work out how best to regulate it. While some scientists have urged restraint over its use in new applications, others seem happy to push the technique as fast as they can, according to François Hirsch, ethics committee head at the French National Institute for Health and Medical Research in Paris. “The technology is great but we need to sit down and think about its potential impact before pressing ahead”, he says.

The ability to engineer changes to an organism’s genome is not new – nor is controversy over its use. Scientists have been making genetically modified organisms (GMOs) since the 1970s, giving plants and animals certain desired traits by importing genes from a different species. The idea of tampering with nature has alarmed the public, raising concerns about the safety of food made using GMOs and about the effect that such technology can have on the environment.

Risky business

In principle, gene editing is less of a worry than earlier forms of genetic engineering because it is more precise. It involves modifications to just a handful of DNA base pairs, which is comparable to the change that can occur in a genome due to natural mutation. (A single gene can contain as many as a million base pairs.)

However, gene editing is not perfect. Often it doesn’t change the DNA in all cells, while sometimes it can alter parts of the genome it isn’t supposed to – making “off-target” changes that could potentially cause cancer. Plus, the very ease with which changes can now be implemented potentially opens up genetic engineering to abuse. Former US intelligence chief James Clapper categorised gene editing as a weapon of mass destruction.

Probably the most controversial application of the new technology is editing the human germ line. This involves modifying the genomes of egg cells, sperm cells or embryos, as the Chinese group claimed to have done in 2015. Germ line editing could have potentially huge benefits for treating heritable disease such as cystic fibrosis, sickle cell anaemia or Huntington’s disease.

It could also be used to enhance human attributes, such as food tolerance, longevity or mental capacities. But the genetic changes that occur will take place in all the cells of an organism’s offspring, ensuring that the modifications are passed on from one generation to the next and thereby transform the human gene pool.

Another potentially explosive application is known as gene drive, which involves editing an organism’s genome such that the genetic changes spread rapidly through a population. Normally a mutation in the genome of a particular individual will pass slowly through the members of a species because there is only a 50% chance that it will get passed to each successive generation. But gene drives would ensure that nearly 100% of offspring acquire the modification.

Hirsch says that the technique could have dramatic benefits, such as wiping out entire populations of malaria carrying mosquitos (if the modification were to impair reproduction, for example). But he warns that gene drives are irreversible and could have negative consequences, noting that mosquito larvae are eaten by some fish while female mosquitos transport pollen to plants.

Pressing ahead

Despite the risks, scientists are enthusiastic about gene-editing techniques, all of which follow the same basic principle. One set of molecules binds to a specific sequence of base pairs within a cell’s DNA in order to single out the gene that needs altering. A second set of molecules – an enzyme known as a nuclease – then acts like a pair of scissors to make a break in the genetic sequence. Finally, the cell’s own molecular machinery stitches the loose ends back together, and in the process either deletes DNA or inserts new DNA that the scientists want to add.

However, the first two gene-editing systems – known as Zinc Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs) – were difficult to use and the specialised kit could cost thousands of dollars. In contrast, CRISPR – short for Clustered, Regularly Interspaced Short Palindromic Repeats – can be largely bought off the shelf, and can cost as little as $30. Exploiting a mechanism used by some bacteria to defend themselves against viral attack, it consists of the Cas9 nuclease and a piece of “guide RNA”, and can be used to make multiple simultaneous edits.

CRISPR has generated an ever-increasing number of scientific papers, patent applications and funding, while spawning several new biotech companies, including Crispr Therapeutics of Basel, which has raised nearly $90 million in venture-capital funding. “To say that CRISPR has revolutionised genomics is an understatement”, Hirsch says. Bruce Whitelaw, an animal biotechnologist at the Roslin Institute in Edinburgh, agrees. “The world is ignited by the word CRISPR”, he says. “But the excitement is justified. It is a revolutionary technology that will stretch into all of society in the years to come.”

Whitelaw and colleagues are using gene editing to make pigs that are resistant to certain viral diseases. They have employed ZFNs to so far create about a dozen pigs with the warthog version of an immune gene that should make them more resistant to African swine fever, a fatal disease that has spread throughout Eastern Europe. While hoping to test the pigs’ resilience to the disease later this year, Whitelaw’s group is meanwhile using CRISPR to engineer pigs that can resist a virus causing reproductive failure and respiratory illness. Rather than changing pigs’ immune response, the approach here is to prevent viruses from binding to cells in the first place.

When it comes to editing the genomes of human cells, scientists are making progress with modifications that are not passed on from one generation to the next – those of somatic cells, which make up blood, skin, bone, internal organs and much of the rest of the human body. In 2014, researchers in the US successfully carried out a clinical trial involving the use of ZFNs to edit the genome of a certain type of immune cell in blood from people with HIV such that the cells no longer had a receptor that the virus targets.

CRISPR, meanwhile, made its debut in clinical trials in October last year, when a group in China used the technology to disable a gene in a person’s immune cells in order to combat lung cancer. The extent to which gene editing is used commercially will depend on how well scientists can engage with the public, according to Hirsch. He believes that a lack of communication from academics and companies alike has been a major cause of the public’s opposition to GMOs. He also believes that researchers must find a new term for the organisms created using gene editing. “The name GMO is considered across the world to be a consequence of bad science and a threat for humankind”, he says.

The EU’s commissioner for health and food security, Vytenis Andriukaitis, is also mindful of getting the public on board. In a letter to European agriculture ministers last November, he said that informed public debate on the new technologies is needed to “reinforce public confidence on safe uses of modern biotechnologies”.

A call for ethics

Ultimately, the EU will have to decide whether gene-edited organisms should be subject to the same regulations as conventional GMOs. This question is complicated by the fact that gene edited modifications are at face value indistinguishable from natural mutations.

One option is simply to regard such edits as essentially natural. Indeed, the US Department of Agriculture has already decided not to regulate several gene-edited plants, including a CRISPR mushroom modified to resist browning that received the green light in April 2016 (although the outgoing Obama administration did draft new rules requiring the safety of all new gene-edited animals to be examined).Another option is to insist on an audit trail for each newly created organism, so that a plant or animal is known to have been genetically edited even though there are no tell-tale signs in its genome.

Whitelaw for one has little doubt that gene editing will prove safe when it comes to creating healthier animals. He claims that the problem of off-target changes is “a small and diminishing issue” which, like the intended modifications themselves, occur less frequently than natural mutations. He also contrasts the creation of new animals designed to be healthier than existing ones with those simply created to be bigger (in the case of cattle) or smaller (such as pigs sold as pets). “Those kinds of changes are not justified”, he says, “but if the modifications instead make animals immune to disease then that is worthwhile”.

However, it is one thing to make changes to an animal genome; another is modifying the genome in human cells, and particularly that in germ line cells. Indeed, many, if not most, scientists agree that germ line editing should not be used clinically, at least not yet. Where views diverge, however, is on basic research with germ line cells.

Disagreements on this point came to light at a meeting that several national academies organised in Washington, DC, in December 2015. Hille Haker of Loyola University Chicago called for a two-year research moratorium while seeking a ban on gene editing for reproductive purposes through the United Nations. But while the meeting’s organisers agreed that clinical applications of germ line editing must wait until the technology is safe and society broadly approves such applications, they nevertheless maintained that basic research should proceed. Hirsch hopes to raise researchers’ awareness, arguing that while scientists think more about ethical issues than they used to, some still remain too isolated within their labs. “The ethical discussion shouldn’t just be between ethicists, philosophers and social scientists”, he says. “We must also have geneticists on board.”

Cellular playground

Rather than seeking to improve people’s health by modifying the human genome itself, Helene Faustrup Kildegaard is using gene editing to bolster drug production. A molecular biologist at the Technical University of Denmark, she makes specific changes to the genome of Chinese hamster ovary cells so that the cells produce proteins used as pharmaceuticals. Among the products of these cellular “protein factories” are molecules used to treat anaemia as well as monoclonal antibodies, which are often used in cancer treatment.

Kildegaard points out that scientists have been using hamster cells as protein factories for more than 30 years. But she says that traditional approaches– such as simply dropping DNA mixed with a suitable reagent on to a cell suspension – do not allow researchers to control where the DNA ends up within a cell’s genome. Although the use of more and better-grown cells has improved the process, Kildegaard says the ability to make specific, targeted edits to genomes can improve protein quality and speed up the design of cell factories. “With CRISPR we can do a lot,it is really a playground for us”, she says.