Ian Haydon, University of Washington

There’s a revolution happening in biology, and its name is CRISPR.

CRISPR (pronounced “crisper”) is a powerful technique for editing DNA. It has received an enormous amount of attention in the scientific and popular press, largely based on the promise of what this powerful gene editing technology will someday do.

CRISPR was Science magazine’s 2015 Breakthrough of the Year; it’s been featured prominently in the New Yorker more than once; and The Hollywood Reporter revealed that Jennifer Lopez will be the executive producer on an upcoming CRISPR-themed NBC bio-crime drama. Not bad for a molecular biology laboratory technique.

CRISPR is not the first molecular tool designed to edit DNA, but it gained its fame because it solves some longstanding problems in the field. First, it is highly specific. When properly set up, the molecular scissors that make up the CRISPR system will snip target DNA only where you want them to. It is also incredibly cheap. Unlike previous gene editing systems which could cost thousands of dollars, a relative novice can purchase a CRISPR toolkit for less than US$50.

Research labs around the world are in the process of turning the hype surrounding the CRISPR technique into real results. Addgene, a nonprofit supplier of scientific reagents, has shipped tens of thousands of CRISPR toolkits to researchers in more than 80 countries, and the scientific literature is now packed with thousands of CRISPR-related publications.

When you give scientists access to powerful tools, they can produce some pretty amazing results.

The CRISPR revolution in medicine

The most promising (and obvious) applications of gene editing are in medicine. As we learn more about the molecular underpinnings of various diseases, stunning progress has been made in correcting genetic diseases in the laboratory just over the past few years.

Take, for example, muscular dystrophy – a complex and devastating family of diseases characterized by the breakdown of a molecular component of muscle called dystrophin. For some types of muscular dystrophy, the cause of the breakdown is understood at the DNA level.

In 2014, researchers at the University of Texas showed that CRISPR could correct mutations associated with muscular dystrophy in isolated fertilized mouse eggs which, after being reimplanted, then grew into healthy mice. By February of this year, a team here at the University of Washington published results of a CRISPR-based gene replacement therapy which largely repaired the effects of Duchenne muscular dystrophy in adult mice. These mice showed significantly improved muscle strength – approaching normal levels – four months after receiving treatment.

Using CRISPR to correct disease-causing genetic mutations is certainly not a panacea. For starters, many diseases have causes outside the letters of our DNA. And even for diseases that are genetically encoded, making sense of the six billion DNA letters that comprise the human genome is no small task. But here CRISPR is again advancing science; by adding or removing new mutations – or even turning whole genes on or off – scientists are beginning to probe the basic code of life like never before.

CRISPR is already showing health applications beyond editing the DNA in our cells. A large team out of Harvard and MIT just debuted a CRISPR-based technology that enables precise detection of pathogens like Zika and dengue virus at extremely low cost – an estimated $0.61 per sample.

Using their system, the molecular components of CRISPR are dried up and smeared onto a strip of paper. Samples of bodily fluid (blood serum, urine or saliva) can be applied to these strips in the field and, because they linked CRISPR components to fluorescent particles, the amount of a specific virus in the sample can be quantified based on a visual readout. A sample that glows bright green could indicate a life-threatening dengue virus infection, for instance. The technology can also distinguish between bacterial species (useful for diagnosing infection) and could even determine mutations specific to an individual patient’s cancer (useful for personalized medicine).

Almost all of CRISPR’s advances in improving human health remain in an early, experimental phase. We may not have to wait long to see this technology make its way into actual, living people though; the CEO of the biotech company Editas has announced plans to file paperwork with the Food and Drug Administration for an investigational new drug (a necessary legal step before beginning clinical trials) later this year. The company intends to use CRISPR to correct mutations in a gene associated with the most common cause of inherited childhood blindness.

CRISPR will soon affect what we eat

Physicians and medical researchers are not the only ones interested in making precise changes to DNA. In 2013, agricultural biotechnologists demonstrated that genes in rice and other crops could be modified using CRISPR – for instance, to silence a gene associated with susceptibility to bacterial blight. Less than a year later, a different group showed that CRISPR also worked in pigs. In this case, researchers sought to modify a gene related to blood coagulation, as leftover blood can promote bacterial growth in meat.

You won’t find CRISPR-modified food in your local grocery store just yet. As with medical applications, agricultural gene editing breakthroughs achieved in the laboratory take time to mature into commercially viable products, which must then be determined to be safe. Here again, though, CRISPR is changing things.

A common perception of what it means to genetically modify a crop involves swapping genes from one organism to another – putting a fish gene into a tomato, for example. While this type of genetic modification – known as transfection – has actually been used, there are other ways to change DNA. CRISPR has the advantage of being much more programmable than previous gene editing technologies, meaning very specific changes can be made in just a few DNA letters.

This precision led Yinong Yang – a plant biologist at Penn State – to write a letter to the USDA in 2015 seeking clarification on a current research project. He was in the process of modifying an edible white mushroom so it would brown less on the shelf. This could be accomplished, he discovered, by turning down the volume of just one gene.

Yang was doing this work using CRISPR, and because his process did not introduce any foreign DNA into the mushrooms, he wanted to know if the product would be considered a “regulated article” by the Animal and Plant Health Inspection Service, a division of the U.S. Department of Agriculture tasked with regulating GMOs.

“APHIS does not consider CRISPR/Cas9-edited white button mushrooms as described in your October 30, 2015 letter to be regulated,” they replied.

Yang’s mushrooms were not the first genetically modified crop deemed exempt from current USDA regulation, but they were the first made using CRISPR. The heightened attention that CRISPR has brought to the gene editing field is forcing policymakers in the U.S. and abroad to update some of their thinking around what it means to genetically modify food.

New frontiers for CRISPR

One particularly controversial application of this powerful gene editing technology is the possibility of driving certain species to extinction – such as the most lethal animal on Earth, the malaria-causing Anopheles gambiae mosquito. This is, as far as scientists can tell, actually possible, and some serious players like the Bill and Melinda Gates Foundation are already investing in the project. (The BMGF funds The Conversation Africa.)

Most CRISPR applications are not nearly as ethically fraught. Here at the University of Washington, CRISPR is helping researchers understand how embryonic stem cells mature, how DNA can be spatially reorganized inside living cells and why some frogs can regrow their spinal cords (an ability we humans do not share).

It is safe to say CRISPR is more than just hype. Centuries ago we were writing on clay tablets – in this century we will write the stuff of life.

Ian Haydon, Doctoral Student in Biochemistry, University of Washington

Food intolerance is often dismissed as a modern invention and a “first-world problem”. However, a study analysing the genomes of 101 Bronze-Age Eurasians reveals that around 90% were lactose intolerant.

The research also sheds light on how modern Europeans came to look the way they do – and that these various traits may originate in different ancient populations. Blue eyes, it suggests, could come from hunter gatherers in Mesolithic Europe (10,000 to 5,000 BC), while other characteristics arrived later with newcomers from the East.

About 40,000 years ago, after modern humans spread from Africa, one group moved north and came to populate Europe as well as north, west and central Asia. Today their descendants are still there and are recognisable by some very distinctive characteristics. They have light skin, a range of eye and hair colours and nearly all can happily drink milk.

However, exactly when and where these characteristics came together has been anyone’s guess. Until now.

Clash of cultures

Throughout history, there has been a pattern of cultures rising, evolving and being superseded. Greek, Roman and Byzantine cultures each famously had their 15 minutes as top dog. And archaeologists have defined a succession of less familiar cultures that rose and fell before that, during the Bronze Age. So far it has been difficult to work out which of these cultures gave rise to which – and eventually to today’s populations.

The Bronze Age (around 3,000–1,000 BC) was a time of major advances, and whenever one culture developed a particularly advantageous set of technologies, they become able to support a larger population and to dominate their neighbours. The study found that the geographical distributions of genetic variations at the beginning of the Bronze Age looked very different to today’s, but by the end it looked pretty similar, suggesting a level of migration and replacement of peoples not seen in western Eurasia since.

One people that was particularly important in the spread of both early Bronze-Age technologies and genetics were the Yamnaya. With a package of technologies including the horse and the wheel, they exploded out of the Russian and Ukrainian Steppe into Europe, where they met the local Neolithic farmers.

By comparing DNA from various Bronze-Age European cultures to that of both Yamnaya and the Neolithic farmers, researchers found that most had a mixture of the two backgrounds. However the proportions varied, with the Corded Ware people of northern Europe having the highest proportion of Yamnaya ancestry.

And it appears that the Yamnaya also moved east. The Afanasievo culture of the Altai-Sayan region in central Asia seemed to be genetically indistinguishable from the Yamnaya, suggesting a colonisation with little or no interbreeding with pre-existing populations.

Mutations traced

So how have traits that were rare or non-existent in our African ancestors come to be so common in western Eurasia?

The DNA of several hunter gatherers living in Europe long before the Bronze Age was also tested. It showed that they probably had a combination of features quite striking to the modern eye: dark skin with blue eyes.

The blue eyes of these people – and of the many modern Europeans who have them – are thanks to a specific mutation near a gene called OCA2. As none of the Yamnaya samples have this mutation, it seems likely that modern Europeans owe this trait to their ancestry from these European hunter gatherers of the Mesolithic (10,000-5,000 BC).

Two mutations responsible for light skin, however, tell quite a different story. Both seem to have been rare in the Mesolithic, but present in a large majority by the Bronze Age (3,000 years later), both in Europe and the steppe. As both areas received a significant influx of Middle Eastern farmers during this time, one might speculate that the mutations arose in the Middle East. They were probably then driven to high levels by natural selection, as they allowed the production of sufficient vitamin D further north despite relatively little sunlight, and/or better suited people to the new diet associated with farming.

Another trait that is nearly universal in modern Europeans (but not around the world) is the ability to digest the lactose in milk into adulthood. As cattle and other livestock have been farmed in western Eurasia since long before, one might expect such a mutation to already be widespread by the Bronze Age. However the study revealed that the mutation was found in around 10% of their Bronze Age samples.

Interestingly, the cultures with the most individuals with this mutation were the Yamnaya and their descendents. These results suggest that the mutation may have originated on the steppe and entered Europe with the Yamnaya. A combination of natural selection working on this advantageous trait and the advantageous Yamnaya culture passed down alongside it could then have helped it spread, although this process still had far to go during the bronze age.

This significant study has left us with a much more detailed picture of Bronze Age Europeans: they had the light skin and range of eye colours we know today. And although most would have got terrible belly ache from drinking milk, the seeds for future lactose tolerance were sown and growing.

Daniel Zadik is Postdoctoral researcher in genetics at University of Leicester.

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It all started with a rumour. Then just six weeks ago, a warning rang out in the scientific journal Nature, expressing “grave concerns regarding the ethical and safety implications” of creating the world’s first genetically-modified human embryo.

Then last week, a Chinese group from Sun Yat-sen University, reported that they had, in fact, done it: they had created the first genetically-modified human embryo.

They reported that, in a world first, they had taken “human tripronuclear embryos”, and altered mutant DNA that causes the human disease β-thalassemia, which is life-threatening and affects 100,000 people worldwide.

But one person’s stern warning is another’s delight. The promise of technologies like this – to cure diseases like cystic fibrosis or Huntington’s, or even to remove the BRCA mutation, which dramatically increases a woman’s risk of dying from breast or ovarian cancer – have been exciting biologists for years.

Cut and paste

So what exactly did the Chinese researchers do? And why has it caused such an uproar?

First, the experiments were performed on human embryos. The researchers collected non-viable embryos from IVF clinics. Then they used this non-viability argument as the ethical justification for performing the work. Scientists know that the embryos were not capable of resulting in a human life, because they were tripronuclear. That means one egg had been fertilised by two sperm, a biological situation we know cannot result a live baby.

Into these embryos, the scientists injected “molecular scissors”, known as the CRISPR/Cas9 system, which can target a specific segment of DNA.

In this case, they targeted the HBB gene, which causes β-thalassemia. They then cut out the disease-causing region and replaced it, almost as simply as you may cut and paste in a word-processing document.

But it wasn’t quite that clean and simple. The researchers reported “off target effects” and “mosaicism”. This means the editing sometimes occurred at the wrong place in the DNA and that it wasn’t occurring in all embryos equally. There were many mistakes, which they could not have predicted.

Made to order?

This raises at least two issues. The first is the ethical issue surrounding the use of human embryos for scientific research, and associated concerns around creating designer babies. The second is the fact that this editing went so wrong in so many embryos.

Without total control of the DNA editing process, the outcome for a baby born from a technology like this one is completely unknown.

This unpredictability and uncertainty means the promise of eliminating certain diseases by editing the DNA of embryos is likely to be a very long way off. There is also the issue of testing whether the technology is safe.

The notion of testing the technology on a live human baby is problematic indeed. Should a scientific research ethics committee ever agree to let this research be performed?

Fortunately, in Australia, all research performed on human embryos is tightly regulated by the NHMRC, which prohibits human cloning as well as many other technologies, and enforces strong penalties for non-compliance. This means that, for the foreseeable future, this type of research is very unlikely in Australia.

While the scientific world is divided as to the possibilities for this technology in embryos, including the reality of preventing or curing disease, there is consensus that this research must proceed with extreme caution.

This article was originally published on The Conversation.
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Given the fact that there are seven billion people on Earth, one might conclude that human beings are pretty good at reproducing. But fewer than 30% of all fertilization events result in successful pregnancy, even for young, fertile couples.

The remaining 70% of conceptions result in pregnancy loss, with most of these losses occurring before the mother misses a menstrual period. This means that many pregnancies begin and end before the mother even notices. These early pregnancy losses are one reason why it generally takes several months for couples to achieve a successful pregnancy. But why is pregnancy loss so common?

Current evidence suggests that both the process of egg formation (this is called meiosis) in the mother’s ovaries and the initial embryonic cell divisions (called mitosis) just after fertilization are extremely error-prone, producing embryos with too many or too few chromosomes.

What happens after fertilization?

During fertilization, the sperm and egg fuse so that the resulting embryo will have 23 chromosomes inherited from the father and 23 chromosomes inherited from the mother. If all goes well, the subsequent cell divisions in the embryo (called mitotic divisions) simply replicate this 46-chromosome set as new cells are formed.

Chromosomes contain genes, the blueprints for human development. When processes go awry in meiosis or mitosis, chromosomes can go into the wrong cell or get lost completely, drastically altering this blueprint. The resulting cell will not possess the standard 46-chromosome set – an imbalance that is the defining feature of aneuploidy. This means that many genes will either be missing or present in extra copies, placing cells under stress.

Embryos with many aneuploid cells rarely survive. Trisomy 21, the genetic cause of Down syndrome, is one of the rare forms of aneuploidy in which the baby can survive to live birth. The vast majority of embryos affected with other aneuploidies perish in early development.

What causes aneuploidy?

Aneuploidy is associated with maternal age. Female meiotic errors (these are errors in the eggs themselves) increase from a frequency of less than 20% in mothers younger than 30 years old to greater than 60% in mothers older than 45. Errors in sperm, called paternal meiotic errors, are comparatively rare, affecting fewer than 5% of sperm cells.

But age isn’t the only factor influencing aneuploidy. Our recent work in collaboration with the genetic testing company Natera, published in Science, suggests that risk is also influenced by a common genetic variant in the mother’s genome.

Even when the egg and sperm are normal, aneuploidies often arise after fertilization, during the first three embryonic cell divisions. These initial cell divisions of the embryo are controlled by maternal machinery pre-loaded into the egg.

Unlike meiotic errors in the egg, mitotic errors do not increase with age, but affect all age groups.

A maternal genetic variant influences aneuploidy risk

Using data from in vitro fertilized (IVF) embryos screened by our collaborators at Natera, we found that mothers with a particular genetic variant on chromosome 4 tend to produce embryos with more mitotic aneuploidies – the aneuploidies that arise during post-fertilization cell division.

This effect was observed for mothers of all ages and from diverse ethnic backgrounds. This genetic variant is surprisingly common; approximately half of all people carry at least one copy of this risk variant.

The most likely suspect is a gene called Polo-like kinase 4 (PLK4), which is known to be a master regulator of the centrosome cycle. The centrosome is molecular machine that is responsible for proper cell division and distribution of chromosomes.

We estimated that each copy of the risk variant increases the rate of aneuploidy by about 3%, regardless of the mother’s age. Having two copies doubles this risk. This increased risk could be especially important for older mothers who are already more prone to aneuploidy. It is likely that there are other genetic variants that contribute to aneuploidy risk to a lesser degree, and further work will be required to determine if this is the case.

Because of the established link between aneuploidy and pregnancy loss, we hypothesized that the aneuploidy risk variant might also affect embryo survival. We found that mothers with the high-risk genotypes had fewer embryos available for testing, suggesting that their embryos are less likely to survive very early developmental stages due to aneuploidy.

Given these results, it seems like this genetic variant could influence the average time it takes to achieve successful pregnancy, an idea that we are hoping to investigate further.

A signature of natural selection: comparison to the Neanderthals

Normally, natural selection weeds out damaging variation, reducing it to very low frequency. But the aneuploidy risk variant is very common. Hoping to learn more about the evolutionary history of this variant, we compared human genomes to Neanderthals and Denisovans, our ancient hominin relatives.

Despite the fact that the harmful genetic variant is relatively common in humans, it was absent in these close relatives, meaning that it likely rose rapidly in frequency in an ancestral population of humans. If this is true, it means that this version of this gene was actually somehow beneficial (and maybe still is) while simultaneously being harmful in the context of early development.

So what could possibly have been the benefit?

We aren’t sure at this point, but we speculate that for ancient humans, there might have been a benefit to having a reduced probability of successful pregnancy per intercourse. Maybe the benefit had to do with infanticide – men may be less likely to kill a baby if there is a chance it is their child, and not that of a rival. Likewise, lower probability of pregnancy per intercourse might encourage repeated mating with the same female, fostering pair bonding and paternal investment. This hypothesis was first proposed by Alexander and Noonan in 1979 to help explain the human-specific trait of concealed ovulation and continuous sexual receptivity – women do not externally signal or limit intercourse to the fertile portion of their cycles as do some other primates.

Another idea is based on the fact that PLK4 is often mutated in human cancers. Could there be a beneficial effect of the risk variant in the context of cancer? PLK4 plays yet another role in testes development. Could the aneuploidy risk variant have a beneficial effect in this context?

We are hoping that additional data and future research can shed more light on this signal of human-specific adaptation. Is it real or simply an artifact of chance events in human evolution? Did our ancestors have lower rates of aneuploidy? What about Neanderthals, Denisovans, and living non-human primates? And perhaps the most basic question: why is human aneuploidy so common? Armed with modern genomic technologies, we can continue to chip away at these questions to understand not only the medical aspects of aneuploidy risk, but also the broader evolutionary basis of this intriguing trait.

This article was originally published on The Conversation.
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