A precise, inexpensive way of editing DNA could open up new paths to treating disease and improving our crops, but the technology is already proving controversial
Until very recently if you wanted to create, say, a drought-resistant corn plant, your options were extremely limited. You could opt for selective breeding, try bombarding seeds with radiation in the hope of inducing a favourable change, or else opt to insert a snippet of DNA from another organism entirely.
But these approaches were long-winded, imprecise or expensive – and sometimes all three at the same time. Enter CRISPR. Precise and inexpensive to produce, this small molecule can be programmed to edit the DNA of organisms right down to specific genes.
The development of cheap, relatively easy gene-editing has opened up a smorgasbord of new scientific possibilities. In the US, CRISPR-edited long-life mushrooms have already been approved by authorities while elsewhere researchers are toying with the idea creating spicy tomatoes and peach-flavoured strawberries.
But the game-changing technology could have the biggest impact when it comes to human health. If we could edit out the troublesome mutations that cause genetic diseases – such as haemophilia and sickle-cell anaemia – we could put an end to them altogether. The path for human gene-editing is littered with controversies and tough ethical dilemmas, however, as the news in late 2018 that – against all ethical guidance – a Chinese scientist had secretly created the first gene-edited babies.
Here’s everything you need to know about the complex and sometimes controversial technology driving the gene-editing revolution.
What is CRISPR?
CRISPR evolved as a way for some species of bacteria to defend themselves against viral invaders. Each time they faced a new virus, bacteria would capture snippets of DNA from that virus’ genome and create a copy to store in its own DNA. “They gather a set of sequences that they’ve been exposed to,” says Malcolm White, a biologist at the University of St Andrews, “these [bacteria] essentially carry a little library in their genome.”
To stick with the library analogy, these snippets of viral DNA were like little books – each one containing the data that allowed the bacterium to recognise and quickly kill off a virus next time it invaded. And in-between these chunks of useful DNA there are slightly less useful chunks of repetitive DNA keeping them separate – like a kind of molecular bookend.
These repeating segments of DNA are what gives CRISPR its name – Clustered Regularly Interspaced Short Palindromic Repeat – but it’s really the bits between these repeats that make CRISPR so useful. These useful bits are, somewhat unhelpfully, called spacers, and each one contains a reference to the DNA of a virus the bacteria (or its ancestors) had come across in the past. When a previously unseen virus attacks the bacterium, it adds another spacer to its library of previous attacks.
When a virus from that same species attacks again, the spacer corresponding to that virus’ genome swings into action. It’s a bit like the way that our own immune systems can recognise a flu virus if we’ve had that year’s flu vaccine. The spacer sequence is turned into RNA – a molecule that contains messages from DNA – and hunts down the corresponding piece of viral DNA. Once it finds it, an enzyme attached to the RNA string acts as a pair of biological scissors, cutting the target DNA and rendering the virus harmless.
You might have heard this system referred to as CRISPR-Cas9 as well as just plain CRISPR. In this case, the Cas9 bit refers to the enzyme used to cut the target DNA. “We can programme [Cas9] very easily to target one DNA sequence and to be very specific so it won’t cut anything that’s even similar in sequence,” says White. There can be other kinds of enzymes involved in gene-editing – Cas12 and Cpf1 for example – but all of them work in the same basic way.
How does it work?
Of course, all this is only useful if you’re a bacterium. So how do we turn an anti-virus defence mechanism into something that could let us edit human genomes at will?
Rather than relying on bacteria to create the molecules for them, scientists have worked out how to create their own versions of the CRISPR molecules in the lab. To start with, they need to work out the section of DNA that they want to target. For a condition sickle-cell anaemia, which is caused by a fault in a single gene, this is relatively easy, since we’ve already sequenced the gene that causes this disease and so know exactly the genetic code that we’re trying to target.The banana is dying. The race is on to reinvent it before it’s too late
Before we get down to the business of unzipping and chopping up DNA, it’s worth getting to grips with the basics of how DNA is structured. Holding together the familiar DNA double-helix are four different nitrogen bases: adenine (A), thymine (T), guanine (G) and cytosine (C). The ordering of these bases determines everything about us, genetically-speaking. Eye colour, how tall we’re likely to be, whether we’re susceptible to certain diseases, it’s all written out in base pairs in our genetic code.
Like teeth on a zipper, these bases always pair up with their complementary base. A always pairs with T while G always pairs with C, over and over again until you’ve got to the three billion base pairs that make up the human genome.
But DNA isn’t much use staying locked up in a double helix – it needs to get that information out there and into the cell where it can be used to create proteins, which are the building blocks of pretty much everything in our bodies. To do to this, DNA unzips itself, breaking apart those base pairs until they’re flapping about in the cell.
These flapping, momentarily unpaired base pairs match up with short segments of RNA which contain their own own bases. RNA shares three bases with DNA – G, C and A – but T is alway replaced by U (uracil). Similar base-pairing rules apply, so an exposed DNA G base will pair with an RNA C base while a DNA A base will pair with a U. If you have an exposed DNA sequence of GAC, for example, you’ll end up with an RNA sequence of CUG.
Scientists use these basic principles to create their own CRISPR molecules which, as we pointed out above, are short stretches of RNA. All you need to do is open up a stretch of interesting-looking DNA – like the bit that contains the mutation that leads to sickle-cell anaemia – and build the complementary RNA sequence, with DNA-chopping enzyme attached. It’s a bit like starting with one side of a zipper and using that to build the corresponding but opposite side of the zipper that neatly fits into it.
Once you’ve got your CRISPR molecules, you need them to get your target cell. Luckily, viruses love nothing more than injecting stuff into other cells, so popping CRISPR molecules into otherwise benign viruses is one particularly useful way of introducing CRISPR into cells that’s already been put to work with in numerous studies involving mice.
Now CRISPR-Cas9 can really get to work. The Cas9 enzyme starts by unzipping bits of the DNA double helix while the RNA molecule sniffs its way along the exposed base pairs looking for a perfect match. Once the perfect match is found, Cas9 cuts out the troublesome gene before repairing the remaining bits of DNA. Other enzymes can add in insert genes instead of deleting them, but the basic process of unzipping, recognising and editing remains the same across different CRISPR molecules.
What is CRISPR used for?
CRISPR is particularly attractive to the agricultural industry, which is always looking for a way to engineer disease- and weather-resistant crops which will increase yields and, subsequently, their profit margins. In October 2015, plant biologists at Pennsylvania State University in the US presented US Department of Agriculture (USDA) regulators with button mushrooms that had been edited so they go brown a lot more slowly than normal mushrooms.
A year later, the USDA confirmed that the same mushrooms would be cultivated and sold without having to pass through the agency’s regulatory process for genetically-modified foods. Now, non-browning mushrooms are hardly the most thrilling foodstuff, granted, but this USDA is a pretty big deal because it hints that CRISPR-edited crops might be able to sidestep some of the environmental backlash levelled at GMO crops.
And it’s not just mushrooms getting the CRISPR love. In Australia, one scientist has already used CRISPR to make bananas resistant to a deadly fungus threatening to decimate the world’s crop of the fruit, while others are working on using the technology to create naturally decaffeinated coffee or finally engineer the perfect tomato.
Timeline: When was CRISPR discovered?
2005After characterising CRISPR in 1993, Francisco Mojica at the University of Alicante in Spain became the first to hypothesise that the DNA sequences were part of bacteria’s adaptive immune system.2007Scientists at Danisco, a Danish food research firm, proved experimentally that CRISPR was part of a bacterial immune system and that Cas9 inactivates the invading virus.2011Emmanuelle Charpentier’s group at Umeå University in Sweden demonstrates the role of tracerRNA in guiding Cas9 to its cellular target.
Although the agricultural world provides some of the furthest-along examples of CRISPR in action, the stakes are much higher when it comes to human health. Animal studies are already underway to use CRISPR to tackle sickle-cell anaemia and haemophilia – two promising candidates for CRISPR-treatment because they’re determined by a relatively small number of mutations. In the case of sickle-cell anaemia, the condition is caused by just the mutation of a single base pair in one gene.
The more genes involved in a condition, the harder it becomes to use CRISPR as a potential solution. “There are not many human diseases where only one gene is mutated,” says White. Certain cancers, for instance, are linked to multiple mutations in different genes, and often the link between genetic mutations and cancer risk are poorly understood so there’s no guarantee that – even if we could use CRISPR to fix faulty genes – that’d it’d be any kind of panacea for cancer.
Why is CRISPR controversial?
Late last year, He Jiankui, a researcher the Southern University of Science and Technology in Shenzhen shocked the scientific world when he claimed responsibility for the world’s first CRISPR-edited human beings. He reportedly took embryos from couples where the father was HIV-positive and the mother HIV-negative and used CRISPR to edit the gene controlling a protein channel that HIV uses to enter cells.
The experiment – which was detailed in a YouTube video, not a peer-reviewed journal – was widely condemned by scientists. “It’s been widely acknowledged that the science is not yet ready for clinical application,” says Sarah Chan, a bioethicist and director of the Mason Institute for Medicine, Life Sciences and the Law at the University of Edinburgh said at the time. “More has to be done to resolve uncertainties, and to try and understand the risks.”
Although the He study does violate clear ethical boundaries, it does raise one of the big ethical conundrums when it comes to CRISPR. The problem is that it’s not that easy to use CRISPR to change your genome once you’re an adult – you’d need to find some way of introducing the molecules to every single target cell.
This is perhaps achievable for conditions like sickle-cell anaemia, where you only need to change the DNA in red blood cells. By using CRISPR to edit bone marrow – where red blood cells are produced – you might be able to target a relatively small percentage of cells and still fix the condition.
But if you want to change a person’s entire genome, you need to edit their DNA when they’re little more than a tiny cluster of cells. This leads to all kinds of ethical issues. Why stop at identifying and chopping out genetic diseases, for instance, if we could also tweak an embryo’s DNA so the resulting baby was more likely to be intelligent, or good-looking?
“What if we wanted to change future life span, or intelligence, or Alzheimer’s disease potential or whether they go bald when they get to middle age,” says White. “Societies going to have to come to terms with what we want – it’s not up to scientists.”
Although human gene-editing raises some of the biggest ethical questions, things aren’t an awful lot clearer when it comes to agriculture. In July 1018, the European Court of Justice threw the future of gene-edited crops into doubt when it confirmed that CRISPR-edited crops would not be exempt from existing regulations limiting the cultivation and sale of genetically-modified crops.
Crops that have been genetically-modified – usually by inserting a gene from one organism into another – have long been sidelined in Europe, despite their popularity in other parts of the world. Despite a scientific consensus that GM foods are safe to eat, headlines warning of ‘frankenfood’ and lobbying from environmental groups helped keep GM crops away from human consumption.
But agricultural advocates for CRISPR hoped that the new gene-editing technology would provide an opportunity to redress this balance. The ECJ ruling means that any CRISPR-edited food that is to be grown or sold in the EU must pass stringent safety tests that non-edited crops (or crops made using certain techniques like radiation mutation) do not have to face. For now, at least, one of the biggest barriers facing CRISPR isn’t science, but public relations.
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