THE wonders of the world tend to be quite conspicuous. You can hardly miss the Grand Canyon, say, or the Great Pyramid of Giza. You could, however, be forgiven for overlooking the great wonders of human biology. It is easy to take the brain or DNA for granted. And yet over the past year or so, living through the coronavirus pandemic, we have all come to better appreciate the marvel that is our immune system, a vast and diverse array of cells and molecules that defend us against viruses and other invaders.
One molecule in particular has taken centre stage: the antibody. These Y-shaped proteins, which we produce in response to infection, are a vital part of our defences. They are also the basis of many of the most important medicines. But we haven’t exhausted their potential yet – far from it.
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Typically, we have used antibodies in medicine pretty much as they come in nature, even if we select and mass-produce the versions we need. Now we can do much more. By manipulating genes in the cells that produce antibodies, or splicing together fragments of the proteins themselves, we can re-engineer their structures to create bespoke immune molecules.
In at the University of Manchester, UK, we use super-resolution microscopes to see how the immune system works on a molecular scale. We are just one of thousands of labs doing such work, which is fuelling a new age of antibody engineering. With researchers currently producing all kinds of tailor-made antibodies – from those that lure cancer cells to their doom to those that can actually infiltrate cells – we are on the cusp of a revolution in our capacity to fight disease.
Your immune system is intricate, to say the least. Your body’s familiar responses to a cut or an infection – redness, inflammation – belie a rich choreography beneath the skin, where swarms of cells move in to fight off germs, repair the damage and deal with the debris. Even for experts, the details are overwhelming. There is an incredible diversity of components to comprehend, all in delicate interplay with one another. Antibodies are just one element, but they are especially important.
We have been working to understand them for almost 140 years – a quest that could be said to have begun on the evening of 24 March 1882. That night, physician Robert Koch addressed the Physiological Society of Berlin to claim that tuberculosis, then considered an inherited illness, was caused by a minuscule bacterium. Another physician, Paul Ehrlich, rushed back to his lab and stained samples from tuberculosis patients. Early the following morning, under the microscope, he could immediately see clumps of bacteria, probably those that cause tuberculosis.
Ehrlich, Koch and others later found that some types of bacteria produce harmful toxins. Ehrlich then noticed something intriguing: if he increased the dose of a toxin in mice slowly, over many days, the mice could survive a level that would normally kill them. Whatever it was that the mice developed to bestow this resilience, Ehrlich named an antibody.
Today, we understand much more about what they are and how they work. For starters, we know that antibodies are made by specialist cells called B-cells in humans and other animals. We also know that every B-cell produces an antibody with a particular shape at the double-pronged end of the Y, called the variable region. This is the part of the antibody that sticks to its target, whether that is a toxin or a protein on the surface of a pathogen, known as an antigen.
In fact, the way that antibodies are made is a marvel in itself. As each B-cell is created in our bone marrow, the genes that code for antibodies are shuffled around so that the cell produces a specific antibody – one of billions made in the body overall. Every B-cell is then tested in the bone marrow to see if the antibody it produces would stick to anything naturally occurring in the body. If it does, that B-cell is killed off. That way, the only B-cells released into the body are those that make antibodies targeting things not normally found there, such as dangerous germs, rather than attacking the body’s own healthy cells. The billions of B-cells in you produce so many different antibodies that, in principle at least, there is at least one that latches on to any given invader.
The strategy isn’t always completely effective. Some viruses, like HIV, evolve rapidly such that proteins on their surface can change shape. This variation in the virus, even within a single infected person, makes it a hard target for antibodies. Another thing to bear in mind is that it takes some time for the body to produce extra antibodies against a threat. A B-cell that happens to make the right antibody has to multiply in number so that its antibody is available in bulk, and that doesn’t always occur quickly enough.
Creative surge
On the bright side, we don’t have to rely entirely on our body’s natural production of antibodies. For a while now, we have been able to harvest the B-cells of animals immunised with whatever pathogen we want to target, replicate them in bioreactors and mass-produce antibodies by design.
It is no exaggeration to say that monoclonal antibodies – antibodies made from a population of cloned B-cells – have become an essential part of modern medicine. They serve as treatments for any number of illnesses from psoriasis, arthritis, Crohn’s disease and multiple sclerosis to cancer. In 2019, seven of the world’s 10 best-selling drugs were antibodies.
But we can do better still. These days, it is possible to transform the basic structure of antibodies like never before. The truth is that we have been able to manipulate their structure for some years now – through genetic engineering or by separating and recombining parts of the protein. Even so, the tools have now reached a level of sophistication that has encouraged a surge of creativity.
One of the most promising strategies is to redesign antibodies so that they recognise and bind to three different molecular targets, known as antigens. This could be particularly useful when it comes to treating cancer by boosting our natural immune defences, known as immunotherapy.
Cancer immunotherapies are already in vogue. The 2018 Nobel prize for medicine was awarded for the development of antibodies called checkpoint inhibitors. These work by blocking proteins that act as brakes on immune activity: if someone’s cancer has managed to switch off an immune attack, checkpoint inhibitors can turn it back on.
This is great when it works well, but it doesn’t always. There can be side effects, sometimes serious, and boosting an immune response is unlikely to help if a person’s immune cells haven’t detected their cancer in the first place. The problem is that cancer is rarely caused by a pathogen, but instead by an abnormal expansion of a person’s own cells, which means there is nothing as obvious as a molecule from a virus, bacteria or fungus for the immune system to react against.
One way to overcome that problem is to find a way to bring together immune cells and cancer cells, which is where trispecific antibodies come in. In 2019, a team led by Eric Vivier, an immunologist at Aix-Marseille University and chief scientific officer at Innate Pharma, both in France, reported the development of an engineered antibody that : two receptors on immune cells called natural killer cells and an antigen on cancer cells. The idea is that this new molecule brings the body’s natural killer cells into contact with cancer cells and delivers a strong signal to attack.
Vivier and his colleagues made their trispecific antibodies by taking a fragment of one antibody that targets an immune cell receptor and stitching it together with another targeting a cancer antigen. They then used genetic engineering to ensure the stalk of the Y-shape is functional so that it targets a second immune cell receptor. This new antibody was then put to the test in mice with a B-cell lymphoma. It worked impressively well: doing better at inducing tumour cell killing than other treatments it was compared against. The potential for side effects was assessed by measuring the level of certain proteins known to cause problems in immunotherapies, and this seemed to be less with the new antibody. Further trials are under way.
Many other trispecific antibodies are in development. For example, , a receptor that activates immune cells called killer T-cells and a second receptor on killer T-cells that promotes long-lasting activity. By starting, rather than boosting, an immune attack against a person’s cancer, it is hoped that these trispecific antibodies could help those who haven’t responded to other immune therapies.
We must always be careful not to hype things while clinical trial results aren’t yet in hand. Even so, it is possible that these molecules could take immunotherapy to a new level, making it available to people whose immune systems haven’t mounted any kind of attack on their cancer.
It could work for viruses, too. French pharmaceutical company Sanofi has developed an antibody that . The thinking is that it would be harder for variants of the virus to evade being targeted by something that binds to three things at once. Results are striking. In a lab dish, one trispecific antibody could already neutralise 204 of 208 different versions of HIV.
Another approach to designer antibodies could let us infiltrate cells, by shrinking things down. This tactic was originally inspired by an unusual muse: the llama. Antibodies made by humans and most other mammals are quite large, as proteins go, which means they can’t easily access the inside of tumours or get inside cells. The antibodies made by llamas, camels and sharks are much smaller, so many researchers have turned to them for a blueprint to engineer so-called nanobodies.
The way they are produced is complicated and varied. One technique is to use what is known as a phage display library. For this, a large selection of different nanobodies are genetically encoded within bacteriophages, types of virus that infect bacteria. The phages are added to the wells of a plastic dish coated with the target pathogen protein. Those that don’t stick are washed off – only the remaining phages must be producing a nanobody of the right type to attach. Finally, the nanobody-encoding genes inside the leftover phages are isolated and used to scale-up production of a desired nanobody.
One synthetic nanobody called has already been approved for treating a rare blood disorder called acquired TTP, in which blood platelets form small clots where they shouldn’t. Elsewhere, nanobodies have been produced to target snake venom toxin, parasitic worms or the spike protein of SARS-CoV-2, the virus that causes covid-19. They have been designed to enter cells and . On account of their ability to penetrate deep into a tumour, nanobodies are also being developed as diagnostic tools that could help doctors determine the best treatment for a person’s specific situation. Most of this work remains experimental, but there is clearly a groundswell of activity around these smaller antibodies.
“These molecules could take cancer immunotherapy to a new level, and could work for HIV too”
In the meantime, there is fresh inspiration for antibody engineers. Just last month, a team largely at the Duke Human Vaccine Institute in North Carolina announced the discovery of produced by humans and macaque monkeys. The researchers were studying the immune response to HIV when they stumbled upon antibodies that are I-shaped rather than being the typical Y-shape. In fact, one antibody with this shape was isolated back in 1996. Now it is clear that this observation wasn’t just some unusual one-off. The Duke researchers and their collaborators have found that I-shaped antibodies could target the densely packed sugar molecules that cloak HIV, something that the immune system generally struggles with. Other I-shaped antibodies were found to target a pathogenic yeast called Candida albicans, as well as SARS-CoV-2.
The discovery came as a big surprise to most of us, and it shows just how much we still have to understand about antibodies – never mind the wider immune system. Now we have new questions to explore. Exactly how are these differently shaped antibodies produced in the body? And how can we harness their properties for medical purposes?
Speaking of how antibodies are produced, some people are beginning to explore a different approach. The idea, and it is just an idea at this stage, is that B-cells could be harvested from a person, engineered using CRISPR gene-editing technology to express a particular antibody, and then infused back into the bloodstream. Feasibly, this could give someone the ability to make an antibody against any specific pathogen – and it could do away with the need for multiple doses of antibody-based medicines. Maybe a library of B-cells could be infused with the capacity to produce a suite of bespoke antibodies to target different versions of any given virus.
Even if this sort of thing can be made to work, it is almost certainly going to be costly, which brings me to another point. Engineered antibodies are inherently difficult to manufacture, so they are all going to be expensive. What’s more, for antibodies, it is much harder to invoke the argument used for widespread vaccine deployment: that by saving ourselves, we are also saving others. Antibodies save lives by treating cancer or autoimmune diseases, but they can’t protect the whole of humanity in the same way a vaccine can. So another problem arises: how do we make sure the treatments we are trying to develop don’t become a new source of division in the world?
This is something many of us in the field worry about. We need a strong framework for fair and equitable access to all medicines across the globe, not only covid-19 vaccines. But that’s not to say we shouldn’t celebrate the scientific unravelling of the human body’s secrets and push forward with using our knowledge to create advanced new medicines – not least designer antibodies. For me, and I suspect for many others, we gain something else from fathoming the minutiae of what goes on inside our bodies. We understand ourselves that little bit better.
