Babraham Institute - Research features 2016-2020

Babraham Institute Annual Research Report Features Collection

The essential element Oxygen makes up 21% of the Earth’s atmosphere and plays a pivotal role in biological systems. Despite this, huge gaps remain in our understanding of how this essential element regulates cell signalling pathways and affects our immune system – questions that Dr Sarah Ross aims to answer.

We all need oxygen. We breathe it in some 17,000 times a day. And although we might sometimes feel its lack – sprinting for a bus or travelling to altitude – oxygen levels in our tissues vary widely in health as well during disease.

We are still learning how cells sense and adapt to low oxygen, and how oxygen affects our immune system – knowledge that will be critical for developing new therapies for cancer and other diseases. In 2019, the Nobel Prize for physiology and medicine was won by a trio of scientists who uncovered how cells sense and adapt to low oxygen. At the Institute, Dr Sarah Ross wants to discover how low oxygen – or hypoxia – can prevent our immune system from working effectively.

Ross is studying killer T cells – a critical component of the adaptive immune system – whose job is to hunt down pathogens and protect against cancer by producing cytotoxic compounds. To do their job effectively, they must travel widely and work well in the myriad oxygen climates they encounter.

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“Our tissues have different oxygen concentrations and this has implications for immune cells,” says Ross. “T cells usually reside in lymph nodes and the spleen, but when they are called on to fight infection or disease they often find themselves in foreign oxygen environments.”

Many factors influence oxygen levels in our tissues: some are normal variations that reflect the oxygen needs of particular tissues, while others result from disease or ageing. Bacterial infections can drive up oxygen demand when bacteria and immune cells compete for oxygen. Areas around tumours can also become hypoxic due to uncontrolled cell division in cancer.

Ageing, too, affects the picture because diseases that affect the lungs or blood vessels reduce the supply of oxygen.

Teasing out how these low oxygen environments hamper T cells’ work is central to Ross’s research. Her work focuses on three key areas: the role oxygen plays during an immune response, how oxygen is linked to age-related declines in the immune

system and whether or not we can help T cells work better by targeting these oxygen-regulated pathways.

Answering such big physiological questions at a molecular level demands painstaking precision.

Ross works in vitro with T cell cultures grown in standard conditions and, while her methods sound simple, they pose huge technical challenges. “Putting cells in different oxygen environments is easy. What’s really difficult is controlling the amount of oxygen that each of those cells will sense,” she explains.

This is because of the many variables involved. Different culture media will affect oxygen availability, as will biological variation among the cells.

And variations in the density of cells in each culture also impact oxygen demand. “Some cultures use more oxygen than others, so we have to be very precise to avoid accidentally creating hypoxia,” says Ross.

It’s an observation that she believes has important implications for in vitro research well beyond her field.

“Even if you’re not studying oxygen,

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changes in cell density could be triggering hypoxia in cell cultures and causing variation in your data.

It’s across the board – in cancer cells, stem cells and immune cells – and while it’s rarely talked about it’s fundamental.”

Her first couple of years at the Institute have been busy ones: Ross’s group has been studying how duration of hypoxia affects T cells, how hypoxia alters the abundance of certain proteins and identifying which molecules are mediating these effects. Ongoing research is expanding this work to develop an understanding how the oxygen levels that a T cell experiences during an immune response defines their fate and function. The capability to do this research has been boosted by the acquisition of equipment to develop a hypoxia and physiological oxygen facility at Babraham, which was funded by the BBSRC.

Since joining the Institute in 2018 she’s also been identifying common themes with her colleagues across the Institute. “What we are discovering in immune cells has importance for other cell types too, and we are always finding new connections with the work going on in Signalling and Epigenetics.”

Understanding which proteins are being regulated in T cells and how these might be controlling T cell function has important implications, because by working out which molecules are involved, researchers will be able to identify new therapeutic targets against a range of diseases as well as using existing drugs in different ways.

“Hypoxia is relevant for multiple diseases. An obvious one is cancer, because we know it’s linked to hypoxia. But it might also play a role in how T cells function in inflammatory diseases like arthritis and Inflammatory Bowel Disease, which is something we need to investigate more,” Ross concludes.

‘Learning how oxygen affects our immune system is relevant for multiple diseases’

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Responding to the Covid crisis As well as exposing weaknesses in healthcare systems and supply chains, the coronavirus pandemic has underscored the importance of fundamental research and collective effort.

During 2020, scientists rose to the challenge of developing new vaccines and effective treatments for Covid-19. Institute immunologists Dr Michelle Linterman and Professor Adrian Liston describe how their labs responded and the lessons we must learn.

In the early days of the coronavirus pandemic, as lockdowns loomed, workplaces closed and travel slowed to a trickle, Dr Michelle Linterman was certain of one thing – she wanted to make her group’s expertise available to the global vaccines effort.

Among those working on a vaccine against SARS-CoV-2 (the coronavirus that causes Covid-19) was Dr Teresa Lambe at the Jenner Institute in Oxford. “I already knew Tess, so once it became clear they had a vaccine candidate, my first instinct was to ask her what we could do to help,” Linterman recalls.

As an immunologist, Linterman’s work focuses on how the immune system responds to vaccines. In particular, she wants to understand why older people respond less well to vaccines, something she studies using human vaccination studies and in aged mice. “I thought the most useful thing was for us to offer something that nobody else could contribute quickly – and that was our ability to use aged mice as a pre-clinical test of how this vaccine is

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likely to work in an ageing immune system,” she says.

in the midst of the pandemic,” she says.

When Lambe said yes, Linterman set up trials to compare immunological responses to the Oxford/AstraZeneca vaccine in young and aged mice, and discovered that although aged mice responded more poorly than young mice to a single dose, after two doses of the vaccine, the immune responses were very good in both groups.

Fellow immunologist Professor Adrian Liston also stepped up to the mark, using his research to help clinicians make the best treatment choices for Covid-19 patients and his communication skills to provide accurate information to journalists and the public.

The study helped both institutes.

For the Jenner, it showed two doses of the vaccine would give good protection against infection in all adults. For Babraham, it provided new insights into vaccine responses at a cellular and molecular level, expanded research into new vaccine platforms and led to new collaborations. Most importantly, it illustrated the value of publiclyfunded research.

“Because we’re funded by the BBSRC – in other words the tax payer – it was incredibly important to use our knowledge and expertise to contribute to vaccine development

“We need to develop good systems for treating emerging viruses before we know much about them, which is something my lab is working on,” explains Liston. “We are coming up with treatments that are vaccine agnostic, treatments that will work for most viruses with the potential to become pandemic, regardless of the actual virus.”

Liston’s group is also interested in systems immunology – exploring what makes people’s immune systems so different from each other.

This variation has been graphically illustrated during the pandemic, some people experiencing mild symptoms while others died.

“Diversity is intrinsically important

Immunology feature 2019/2020

LEARN MORE: Watch an animated description of the Linterman lab’s research work on the Oxford/ AstraZeneca vaccine.

It was incredibly important to use our knowledge and expertise to contribute to vaccine development in the midst of the pandemic – Michelle Linterman to the immune system. It’s the most genetically-diverse system in the human body, and there are other factors at play, such as age, gender and weight,” he explains.

Being so close to events has taught Liston and Linterman many lessons – lessons, they say, that are vital for political leaders to learn. First, zoonoses (diseases spread between animals and humans) with pandemic potential are far from rare events.

“They occur every couple of years,” says Liston. “We’ve had coronavirus outbreaks before, like SARS and MERS; they happen like clockwork. In the previous outbreaks we had better luck and better preparation. These are things we must prepare for.”

Secondly, we must guard against complacency. “If we pat each other on the back for a job well done, and then slash science budgets, the next outbreak will be as bad as this one,” he warns. “We must fund surveillance as well as immunology and virology research, because if you scale down this science it takes a decade or more to rebuild that intellectual capital.”

Confocal microscopy image of the spleen nine days after ChAdOx1 nCoV-19 immunisation in an aged mouse (22 months old). The image shows immunofluorescence staining to identify different classes of immune cell: IgD+ B cell follicle in green, CD3+ T cells in magenta, Ki67+ proliferating cells in blue and CD35+ follicular dendritic cells in white. Image: Sigrid Fra-Bido, Babraham Institute.

This preparation extends to supporting fundamental research in a broad range of areas. “We need to fund fundamental research because you’re never sure which bit of it will save you in the future,” says Linterman.

Third, a global approach to research, and funding to support this, is essential, because scientific discoveries are not bounded by borders, adds Linterman: “One of the reasons the Oxford vaccine was developed so fast was because of years of work on Ebola and MERS using the same adenoviral vaccine vector.”

As vaccines are rolled out, and countries emerge from lockdown, we might usefully reflect on what we would have done without a vaccine.

It’s a scenario that frightens Linterman.

“There wasn’t another exit strategy,” she says. “The vaccines are great, far better than we expected. But there are pathogens that we don’t have good vaccines for. For me, that’s the scary thing. We’re lucky the vaccines are so effective – but that doesn’t mean the same will be true for the next pandemic.”

We are coming up with treatments that are vaccine agnostic, treatments that will work for most viruses with the potential to become pandemic, regardless of the actual virus – Adrian Liston 23

New horizons for immunology New group leaders bring new skills, new expertise and new perspectives, and 2018 saw three new group leaders join the Institute’s Immunology programme. Professor Adrian Liston, Dr Claudia Ribeiro de Almeida and Dr Sarah Ross talk about their research, their ambitions and what makes the Institute such a special place to work.

They come from VIB in Belgium and the universities of Oxford and Dundee, they focus on different areas of immunology and bring new interests and expertise, but Professor Adrian Liston, Dr Claudia Ribeiro de Almeida and Dr Sarah Ross are all hugely excited to have recently joined the Institute.

Liston, already an established group leader, works on the specialist population of immune cells known as CD4 T cells. These cells effectively coordinate and ‘turbo charge’ our immune response. They are also the cells that are targeted by HIV, explaining why the disease causes immune system suppression and illustrating how crucial CD4 T cells are to our overall health.

At VIB, Liston specialised in translational immunology, understanding and then developing ways to treat children with rare immune diseases. “These diseases are incredibly severe, but once you understand them mechanistically you can work out ways to treat them,” he explains. “It was very rewarding because these kids that would otherwise often die can go on to lead long, healthy lives once 16

you’ve found out what’s wrong and how to fix it.”

At the Institute, Liston wants to answer three key questions: how the millions of CD4 T cells in our bodies communicate and cooperate; how they switch between a ramping up and damping down cell type; and what they do in our tissues.

Understanding how these cells modulate our immune system means that they can potentially be used as a tool to fine tune the immune system to help overcome age-related decline.

With its world-leading Immunology programme and cutting-edge facilities the Institute is a great fit for Liston’s ambitions. But what sets the Institute apart is how it nurtures scientific innovation and champions equality and inclusion.

“Great research requires fantastic people who think as differently as possible, which means having an environment that celebrates equality and inclusion. The Institute has a great reputation for this internationally – it’s setting the gold standard for equality and inclusion.

You can feel the difference here,”

says Liston. “The Institute provides an environment where you’re going to be stimulated and have the chance to explore the limits of your imagination.”

Ribeiro de Almeida and Ross both believe the Institute’s culture will help them build their first research groups. “It’s a very friendly, supportive environment.

Everyone is ready to help with time and feedback – they want you to succeed and that’s really special,” says Ross.

Ribeiro de Almeida’s work centres on B lymphocytes and the rare ability they have to rearrange antibody genes by cutting and pasting DNA in order to fight the plethora of pathogens to which we are exposed.

“I’m interested in understanding how this mechanism is regulated throughout cell development,” she explains. “It’s a fundamental question, because mistakes in this process can result in leukaemia and lymphoma. To understand these diseases and wider age-related immune dysfunction it’s important to understand how these molecular mechanisms are regulated.”

Immunology feature 2018

‘The Institute is setting the gold standard for equality and inclusion’ Dr Claudia Ribeiro de Almeida

Dr Sarah Ross

Professor Adrian Liston

As a postdoc in Oxford, she worked in a lab that studied gene expression rather than B cells, so she brings a more molecular approach to the programme. She also discovered an RNA-binding protein that plays an important part in B lymphocytes’ cut and paste process, something she’s keen to follow up: “The research I want to do next is to identify which proteins are implicated in this mechanism of gene rearrangement and how they modulate B cell responses.”

Ross specialises in T lymphocytes and the impact that hypoxia – or low levels of oxygen – has on the way they work. Because T cells commonly encounter hypoxic environments, they can adapt to low oxygen environments by changing the proteins they express. While this helps them survive, it can also make them less effective killers of disease cells.

“I want to understand how oxygen regulates T cells from a signalling and gene expression perspective,” she explains. “If we could identify factors

that we could target therapeutically to overcome the effects of low oxygen and boost the ability of T cells to perform their protective function, that would be amazing.”

We know that as we age, our immune system becomes less effective and poorer oxygenation is also connected with ageing, so what Ross discovers about hypoxia could have important implications, both for our understanding of the ageing immune system and in making immunotherapies more successful.

The arrival of all three is an exciting opportunity for the Institute, the Immunology programme and its three new group leaders. “It’s amazing – I’m still pinching myself,” Ross concludes. “It’s great to be able to make new plans and work out how to turn them into reality utilising the know-how and the facilities we have access to here. And it’s exciting to be here because my plans cover all three programmes – Immunology, Signalling and Epigenetics – adding my own to all the expertise here makes it hugely exciting.”

‘Great research requires fantastic people who think as differently as possible’ Image of Adrian Liston used courtesy of the Cambridge Independent.

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Vaccinations: a Global Challenge The Institute’s research is having a major impact on global public health. Although the first vaccines were developed more than two centuries ago, infectious diseases such as malaria and influenza still affect millions of people each year. By improving our understanding of the immune system and its response to modern vaccines, the Institute is paving the way for better vaccines that will protect more people from life-threatening diseases.

When it comes to human health, our immune system is our most important defence against illness and disease. Producing antibodies is one of the ways that the immune system counteracts pathogens – the causes of illness. Yet, this system is not perfect. Sometimes the body produces antibodies against the wrong things – resulting in allergies, autoimmune diseases and organ rejection – while at other times it fails to produce enough antibodies to fight infections including malaria and influenza. And as we age, our immune system becomes less adept at combatting infection and responding to vaccination.

As well as being extraordinarily powerful, our immune system is amazingly complex and continues to pose significant scientific challenges. Key among these is how to design ‘flu vaccines that are more effective in an ageing population, and how to boost the efficacy of vaccines to prevent malaria. Dr Michelle Linterman, a Group Leader 18

in the Institute’s Immunology research programme, is making important advances in both.

“One of our major goals is to improve vaccine efficacy as we age.

The seasonal ‘flu vaccine provides 80% protection against infection if you’re aged between 18 and 60.

Over the age of 60 vaccine efficacy decreases – and for people over 70 it’s only 25% effective,” she explains.

“This does not mean that older people shouldn’t get vaccinated, because complications associated with ‘flu can be very serious. But it does mean there’s an opportunity to improve the way these vaccines work for older persons.”

Part of the problem arises from how clinical trials have traditionally been run. Almost all immunology research – including vaccine trials – is done in young animals and people; what’s lacking is research in the populations that vaccines most need to protect. This is true not only of ‘flu but in malaria too.

Most malaria vaccine trials are run in European populations, and success here often fails to translate to those in most need – the people who live in malaria-endemic areas.

Most vaccines provide protection against infection via production of antibodies, the proteins our immune cells secrete. In ‘flu, for example, these antibodies bind to the virus and prevent it from infecting our cells. At the same time, antibodies signal to other immune cells to destroy the virus. Our immune systems are very diverse, which helps to protect us from pandemics, but complicates vaccination programmes as individual responses to vaccines are very variable.

What’s needed is more cleverlydesigned trials, which is exactly what Michelle and her team are doing in both Cambridge and East Africa. To design better ‘flu studies, she’s using the Cambridge Bioresource, a unique panel of 17,000 volunteers willing to

Immunology feature 2017

‘Our immune system is amazingly complex and continues to pose significant scientific challenges’ take part in research and who have already donated DNA. “The Cambridge Bioresource is a phenomenal research resource; it allows us to design much smarter studies because we can select people with particular genotypes and recruit people to studies much more quickly than before.”

These studies are revealing why older people produce fewer antibodies after ‘flu vaccination, opening up new ways of making vaccines more effective. “We’ve run two studies showing that the T cell response is impaired,” she says. “And now we know where the cellular defect lies, it should be possible to change the adjuvants – the ingredients in vaccines that stimulate the immune system – to boost these T cells.”

Thanks to support from the Global Challenges Research Fund, Michelle is working on large-scale collaborative vaccine trials in malaria-endemic Tanzania and Mozambique. Her aim is to understand – in immunological

terms – why people respond so differently to existing malaria vaccines, and discover whether new adjuvants could make malaria vaccines more effective. After analysing samples from children vaccinated with RTS,S (which is the best malaria vaccine on the market but one with plenty of room for improvement), the team uncovered important differences in the immune cells of children who respond well to the vaccine compared with those who do not. They also made new discoveries in the adjuvant trials.

“We’ve just finished a study in young Africans that clearly shows that a new adjuvant does a good job of boosting T cells,” she concludes. “Being involved in trials of new adjuvants is very exciting. Our research shows that these adjuvants could help boost the T cell response after vaccination in older people, and it illustrates that our fundamental science is crucial to delivering better vaccines across the world.”

‘Our fundamental science is crucial to delivering better vaccines across the world’

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Checks and balances in immune system development In 1796, a doctor in rural Gloucestershire took pus from a cowpox lesion on a milkmaid’s hand to inoculate an eight-year-old boy against smallpox. More than 230 years after Edward Jenner’s pioneering vaccination, we still don’t fully understand how our immune system works. Now, researchers in the Institute’s Immunology programme have uncovered a new layer of regulation in immune cells – a discovery that could have far-reaching implications for vaccines, cancer and healthier ageing.

Our immune system does a remarkable job of defending us against germs, repelling invaders and keeping us healthy. A key part of this system are our B cells – highly specialised cells capable of responding to myriad disease-causing pathogens. Not only are they hugely diverse in the pathogens they recognise, they can remember the pathogens we have been exposed to in the past, providing us with immunity against future attacks.

The vast repertoire of responses that these cells possess is due to their unique ability to cut up and rearrange their own DNA. “This variable-diversity-joining recombination only happens in these cells,” says Dr Martin Turner of the Immunology research programme, who wants to get to the bottom of when this takes place, and how the mechanism works.

B cells develop in a sequence.

During the process, there are 20

several discrete stages where DNA is broken and re-joined, allowing the cells to produce the many different antibodies we need to protect ourselves from many different infections. Rearranging DNA, however, is a risky process.

Breaking DNA at the wrong point in the sequence can cause cells to die, and making mistakes when re-joining DNA can lead to even more sinister consequences. When this happens, the mutated genes can create cancer-causing immune cells, resulting in diseases such as lymphoma and leukaemia.

“Immune cell cancers, such as lymphomas and leukaemias, are the payback we get for a functioning immune system,” he explains. “The good news is that knowing more about this DNA re-shuffling mechanism, including what happens when it goes wrong, means that in the future we’ll be able to treat these types of cancers better.”

During their development, B cells switch very rapidly between periods of quiescence (or rest) and proliferation. When they are resting, they cut up and rearrange their DNA, but as soon as this happens there is a rapid burst of cell proliferation. The problem is that DNA works too slowly to explain this switch. “DNA is very stable, it’s not a very dynamic on/ off switch, yet we know that cells do things very rapidly,” he says.

So what is switching cells between quiescence and proliferation – and back again? Received wisdom is that all the necessary information is encoded in the DNA and that you just need to look hard enough to find all the answers. Turner argues that there is another layer of regulation, and is now providing evidence that it exists, and that it has important consequences: “Many people argue that to regulate gene expression, all you need to do is regulate the tempo of what goes on at the DNA level.

Immunology feature 2016

‘Immune cell cancers are the payback you get for a functioning immune system’ What we’re working on is a bit left field, it challenges the orthodoxy about how things work.”

The Institute’s Immunology programme has discovered that the process involves a group of cell cycle proteins known as RNA binding proteins. These act as a switch by affecting the stability of RNA, a single-stranded nucleic acid, and silencing the cell signals promoting proliferation.

The same mechanism could also be important in other cell types. According to Turner: “It’s an interesting basic biological question, but there are good reasons why we need to understand the biology of these cells.”

B cells are what enable our immune system to remember past experiences, so knowing how they work is crucial for understanding vaccine responses and immunological memory. Turner’s latest work shows that RNA binding proteins help limit the intensity of the immune response, which ensures that the system isn’t activated inappropriately and that it shuts down as soon as it has fought off a pathogen such as influenza.

“When the ‘flu has been got rid of, you want the immune system to stop because it’s the immune response that makes you feel unwell,” he says. “The same is true of many diseases. In evolutionary terms, there’s been a trade-off between how actively the immune system attacks an infection and the damage that it causes the body. It’s about optimising that balance.”

Knowing that preventing cell proliferation is an active, rather than a passive, process is important in cancer research – and could also be crucial in understanding ageing. We are born with a limited supply of stem cells which we rely on to repair damage, so the body needs a mechanism to ensure these cells are used as sparingly as possible.

“The balance between quiescence and proliferation is important, because the pool of stem cells becomes depleted if it’s not kept quiescent,” he concludes.

“Maintaining quiescence is fundamental to the ability to rejuvenate. We know that the ability to rejuvenate deteriorates with age, so if we understand the process better, this could make for healthier ageing.”

‘Our work is a bit left field, it challenges orthodoxy’ 21

Back to basics Setting up a new group is exciting and daunting. Two group leaders who joined the Signalling programme in 2019 – Dr Hayley Sharpe and Dr Rahul Samant – talk about their research and the supportive, collaborative and open environment that they say marks out the Institute.

Lots of ingredients go into building a successful new research group.

Great ideas, a productive team and the right environment are all part of the mix.

A great illustration of the Institute’s ethos was a colleague’s reaction to news that Sharpe had been selected as an EMBO Young Investigator. “I was at my computer, saw the news and leapt up. One of the Principle Investigators happened to be passing and just walked in and gave me a big hug,” Sharpe remembers.

“Everyone is so supportive – and everyone’s made a real effort to make us feel very welcome.”

Sharpe’s group works on a family of enzymes that – for the past two decades – has been largely ignored but which Sharpe believes is ripe for a renaissance.

These Cinderella enzymes are receptor tyrosine phosphatases, which play a vital role in intercellular communication and in the 1990s were seen as promising therapeutic targets. “There was huge interest in them 20 years ago and lots of work was done,” Sharpe explains.

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“But they proved very hard to drug, so the pharmaceutical industry fell out of love with these enzymes and abandoned them,” Sharpe explains.

impressions as a new appointment at the Institute Samant says that what struck him most about the Institute was its openness.

Recent advances, however, have rekindled research interest. Big data, CRISPR and other new tools point to tyrosine phosphatases being important in many diseases – including some cancers and diabetes-related macular degeneration – as well as spinal cord injuries and skin ageing. “When you’re setting up a lab you want to go into an area where you can work for the next 30 years, hence the appeal of these enzymes,” she says.

“The environment here opens up broader scientific thinking; conversations are like relaxed brainstorming, and having people to bounce ideas off is important for me,” he says. “I do science because I want to know how things work. I want to be able to follow where the science leads me. And the Institute is one of the few research centres that has such a strong focus on fundamental, mechanistic biology.”

In a neglected field, developing new therapies means going back to basics, which is part of Sharpe’s approach. She is working at a molecular level to discover how these enzymes help build up the layers of our skin and other tissues.

She’s also using mouse models to understand their role in disease, aiming to translate new knowledge into future new therapies.

Basic biology is also what drives Dr Rahul Samant. Reflecting on his

As a cell biologist, Samant is fascinated by misfolded proteins and the way our cells prevent them from building up. Our cells are complex machines with many moving parts; to work smoothly, proteins must be the right size, shape, and in the right place. It only takes one misfolded protein to trigger a chain reaction that can lead to disease, so our cells invest heavily in sophisticated quality control systems to deal with misfolded proteins before they cause damage.

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‘The Institute is so supportive and everyone’s made us feel very welcome’ Hayley Sharpe This quality control machinery declines as we age. As a result, most age-related diseases, including Alzheimer’s disease, Parkinson’s and cancer, are related to misfolded proteins. “There is good evidence that these quality control machines get deregulated during many ageingrelated diseases,” he says. “So I’m trying to study these machines in great detail: how they work normally and how they get deregulated during these diseases.”

Despite being crucial for healthy ageing, this cellular clear-up process is shrouded in mystery. Text books tell us the major misfolded protein clearance route involves attachment of a ubiquitin tag, which serves as a fast-track protein disposal signal. But, says Samant, we have known for the past 15 years that this is too simple to be true.

“It’s very context dependent, and only now are we developing the tools to look at all the different type of ubiquitin tags in sufficient detail,” he explains. “I’m interested in using

this increased resolution to go back to these basic questions that we’ve assumed to be true, but which the data now shows to be vague and hand-wavy.”

To study the process, Samant combines tools he honed during his time as a research associate at Stanford University with the stateof-the-art proteomics facility at the Institute. He also collaborates with the Institute’s world-leading experts in autophagy – another crucial cellular process for clearing up misfolded proteins.

It’s work that could reshape our understanding healthy ageing and disease, identifying new therapeutic targets and allowing us to treat neurodegenerative diseases and cancer much earlier. But only, Samant concludes, if we go back to basics.

“We don’t yet understand how ageing affects the prevalence of misfolded proteins – and understanding these processes at a fundamental level is really important before we can start addressing the disease aspects.”

‘I want to follow where the science leads. The Institute is one of the few research centres with such a strong focus on fundamental biology’ Rahul Samant

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A remarkable partnership Great science depends on teamwork, yet genuine partnerships are rare, especially those which sustain success over decades. Dr Len Stephens and Dr Phill Hawkins, both group leaders in the Institute’s Signalling programme, have worked together for more than 30 years. Here, they reflect on their research, their relationship – and their distinctly different approaches to fishing.

In 1980, Fred Sanger and Walter Gilbert won the Nobel Prize in chemistry for work on nucleic acid sequences; Polish workers set up the trade union Solidarity; and the Rubik’s Cube made its debut. It’s also the year that Phill Hawkins and Len Stephens met for the first time, with Phill a PhD student and Len a final year undergraduate at Birmingham University.

Hawkins remembers their meeting clearly. “I was working late in the lab and Len came by looking for my supervisor, Bob Michell,” he recalls.

“When I told him it was late, and Bob had gone home, Len asked if he could come in and watch me do an experiment. We chatted, found out we both fished, and Len invited me to go fishing with him in Cannon Hill Park.”

After both worked as postdocs at SmithKline Beckman (now GSK) their paths diverged briefly, but in 1990 when an opportunity arose for Hawkins to join Stephens in Robin Irvine’s lab at the Institute of Animal Physiology at Babraham, they jumped at the chance.

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Irvine’s lab focused on cell signalling pathways involving a sugar-like molecule called inositol. Lew Cantley’s lab in Boston had just discovered a new enzyme called phosphoinositide 3OH-kinase, or PI3K for short, that made a new family of inositol-containing molecules in cells in response to growth factors. There was much to discover and while the science was challenging, there was a sense in the lab that they were hunting down something significant.

and division to cell survival and movement. When these signalling networks go wrong, they can lead to a range of diseases, including cancers, chronic inflammation and immunodeficiencies, so understanding the basic biology has opened up new treatments for these diseases.

“At the beginning it was about correctly identifying the molecules that were appearing in cells and working out how they were made,” Stephens explains. “Our instincts told us they’d turn out to be a key piece of biology that controlled how cells behave, and that spurred us on to try and understand what was going on.”

“We thought our research would be a fundamental bit of cell biology, but at the time we didn’t know where it would lead,” says Hawkins. “There wasn’t a single eureka moment, many small step changes along the way allowed us to piece together the basics of what was going on. Then other labs discovered that mutations in PI3Ks are often associated with cancer.

That’s when it became a much wider impact story, and attracted the attention of other researchers and pharmaceutical companies.”

We now know that cells monitor and respond to their environment by controlling the activity of a few key proteins, which in turn regulate a cascade of downstream events. Together, they orchestrate the complex behaviour that happens in cells, from cell growth

Since then, Stephens and Hawkins have worked closely with industry, collaborating with Onyx Pharmaceuticals, UCB, AstraZeneca, GSK and Pfizer. By 2013, the pharmaceutical industry had invested £350 million in PI3K research and had more than 20

Signalling feature 2019/2020

LEARN MORE: Watch ‘PI3K signalling: from basic biology to new cancer therapies’, an animated description of cell signalling and how a deeper understanging of this process is helping to improve human health.

Both of us wanted to find out something fundamental about how the world works, and how cells work – Phill Hawkins drugs targeting PI3Ks in clinical trials. In 2014 the first – Idelalisib – was licensed for treating chronic lymphocytic leukaemia.

Reflecting on their partnership, both agree that a natural friendship, shared values, and contrasting – but complementary – personalities have underpinned its longevity and success. Hawkins is more emotional, he says, his moods tracking the highs and lows in the lab, whereas Stephens is steadier and a battler, with a bold ambition for their science.

According to Stephens, having similar values is key. “The rest flows from there,” he says. “Are we similar in all respects? No, and that’s important.

We have different strengths and weaknesses. It’s about your motives, the things that inspire you, the things you respect in others, what you find joy in. And sometimes it’s about understanding – at a deep level – what can hack someone off.”

Both are eminent scientists and fellows of the Royal Society, but say that what matters most is a shared scientific curiosity, and a happy working environment. “Neither of us

wanted success for its own sake or accolades,” says Hawkins. “We wanted to find out something fundamental about how the world works, and how cells work.”

And then there’s the fishing, which seems to encapsulate what they share, as well as their differences. Like their research and friendship, their fishing goes back to Birmingham.

“When he invited me to Canon Hill Park, I saw fishing in a totally new light,” laughs Hawkins. “It’s a science for Len: what type of line to use, which home-made floats – he even made catapults with different types of elastic to deliver a certain number of maggots to a precise spot in the water! It’s fishing on a whole other level.”

Stephens agrees. “As far as I’m concerned it’s incredibly similar to doing experiments. I love trying to figure out what the fish are doing under the water, and doing experiments to work out how to catch them,” he concludes. “So yes, I can get very intense about going fishing.”

All our instincts told us PI3Ks would turn out to be a key piece of biology that controlled how cells behave, and that spurred us on to try and understand what was going on – Len Stephens 37

Welcome to the lipidome Once neglected as too dull to study and too sticky to work with, lipids are at last stepping out of the shadows. Institute Director Michael Wakelam and lipidomics facility manager Andrea Lopez-Clavijo explain the challenges of working with these cellular Cinderellas and share their excitement of research in a field that’s finally giving up its secrets.

For Professor Michael Wakelam, there’s never been a better time to be studying lipids. On becoming the Institute’s Director in 2007, he joined a thriving lipid research community. Things were very different, however, at the beginning of his career. “When I got my first lectureship in 1985 I worried that all the good stuff had been discovered,” he remembers. “Now, I wonder how I can cram it all in before I retire. I wish I was just starting out again, because the things we can do are awesome.”

Lipids are essential components of all our cells, but were for many years neglected by many scientists because they were difficult to study and seen as less exciting than genes or proteins. “They aren’t easy to work with,” Wakelam says. “They’re not water soluble and some lipids stick to plastic. It can be painstaking work and until recently they were incredibly difficult to analyse and quantify.”

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Today, all that has changed. The Institute has played a central role in lipid research since the 1950s, but it’s been the development of bioinformatics and massspectrometry over the past 20 years, together with the decision in 2016 that the Institute would co-host LIPID-MAPS, the world’s largest lipid database, which has opened up the field and fueled Wakelam’s excitement.

We now know that as well as making up membranes and storing energy, lipids play a vital role in cellular signalling pathways. “They don’t just hold things together and store energy. They’re actually incredibly dynamic and regulate almost every function of the cell,” he says. We have also discovered that the lipidome – which describes the total lipid landscape of our cells – is astonishingly complex and diverse.

Thanks to new mass-spectrometry techniques, many of which were pioneered at the Institute, some 20,000 different lipid species from

30 distinct classes have so far been identified.

Structurally, lipids are proving fascinating too. Small differences in lipid structure and saturation have major impacts on cell membranes: whether they are thick or thin, straight or curved, rigid or flexible all depend on membranes’ lipid makeup, with far-reaching implications for how immune cells work, how cancers spread and how viruses are able to infect our cells.

Lipidomics has exploded thanks to advances in mass-spectrometry.

“It’s allowed us to recognise an astonishing structural diversity in lipid molecules,” says senior research fellow and expert analytical chemist Dr Andrea Lopez-Clavijo.

“Without mass-spectrometry, we wouldn’t have been able to determine what lipids were there and in what quantities. And without the bioinformatics capability to understand this data, all this would be pointless.”

Signalling feature 2018

‘Lipidomics can change what we know about our own cells’ But gaining a clearer view of the lipidome is only the beginning, Lopez-Clavijo explains: “Lipidomics is about finding connections between the data and its biological relevance.

Making sense of our experiments is all about what the numbers tell us about the biology.”

Now that we can start asking more interesting questions, the data is revealing some remarkable things. In 2018 Institute researchers published an important paper using lipidomics to unpick the common cold. The cold virus hijacks the cellular machinery in order to replicate and release virus, so membranes must be modified for this to occur; the implications, however, had been largely ignored.

“How does catching a cold affect our lipid molecules during the first few hours of infection? It surprised me that no-one had asked this question,” says Wakelam.

By culturing human bronchial epithelial cells, infecting them with the cold virus and then using massspectrometry and bioinformatics

to examine changes in hundreds of lipids over the course of seven hours, they found that the infection caused changes in almost 500 lipids, a discovery that has allowed the team to identify pathways that could be new anti-viral drug targets.

More importantly, it shows that lipidomics has the potential to uncover new treatments for other previously hard to treat diseases from cancer to hepatitis. Recent studies with colleagues at Oxford, for example, revealed that the unsaturation of lipids affects the ability of hepatitis C virus to infect liver cells.

“Modifying the membranes modifies the viruses’ ability to get into cells.

Everywhere we look we find this – it’s a completely understudied area,” Wakelam concludes. “There are many more discoveries to be made with the help of lipidomics – and it has huge potential to change what we know about our own cells.” For a former cellular Cinderella, the future for lipid research looks bright.

‘Making sense of our experiments is all about what the numbers tell us about the biology’

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Making the Most of Signalling Research Bringing together the Institute’s researchers with scientists in the 60 companies on the Babraham Research Campus is helping turn innovative ideas into new benefits for human health – fast. Over the past two years, members of the Signalling research programme have transformed a conversation over coffee into a collaboration that could deliver new ways of treating some of the most intractable human cancers.

As Dr Simon Cook has discovered, caffeine can be a powerful catalyst.

In the past 18 months, what began as a conversation over coffee with scientists from PhoreMost – one of the 60 biotech companies that share the Babraham Research Campus – has developed into a collaboration that could yield new ways of treating some of the most intractable human cancers.

Simon, a group leader in the Institute’s Signalling research programme, works on protein kinases. By attaching phosphate groups to cellular proteins, these enzymes help to form our cells’ communication system, switching on and off their most basic functions – from surviving or dying to dividing and differentiating.

“We’ve been interested in one of these pathways, called ERK, for many years,” he says, “partly because we want to understand its basic biology – how it controls cell division, survival and differentiation 30

– but also because the gene that controls this pathway, KRAS, is one of the most common oncogenes in human cancer.”

In fact, KRAS mutations are responsible for almost 30% of all human cancers, including 25% of non-small cell lung cancer, 40% of colorectal cancer and up to 90% of pancreatic cancer, which remains one of the hardest of all cancers to treat. But although scientists have known for more than 30 years that mutations in KRAS cause cancer, they have struggled to develop drugs that inhibit KRAS. The biggest barrier is KRAS’s biochemistry. “It’s properties are unique. It binds to a co-factor called GTP, which in an ideal world would make a good drug target,” Simon explains. “But the affinity with which it binds is so tight – and it’s such a small protein – that it’s always been viewed as un-druggable.”

All that could be set to change thanks to the unique environment of the Babraham Research Campus.

Just metres away from Simon’s lab – which has over 25 years experience in KRAS biology – is the innovative drug discovery company PhoreMost.

Spun out of the University of Cambridge in 2014, PhoreMost has developed a completely new way of screening diseased cells to find hidden targets that can then be turned into drugs for previously untreatable diseases.

It’s hard to imagine a more promising pairing. “PhoreMost are literally next door to my lab – we often bump into them over coffee – so I knew about their technology.

They can interrogate novel druggable spaces in proteins that conventional drug discovery hasn’t been able to find – and we had the targets they needed,” Simon recalls.

“Using their SITESEEKER platform to find a new druggable space for the KRAS pathway we’re studying seemed like a perfect partnership.”

Signalling feature 2017

‘The fact we work alongside scientists from so many varied companies enables us to turn new ideas into new collaborations’ So after coffee and conversation, Simon took advantage of the Babraham Research Campus Collaboration Fund (BRCCF) – a scheme that encourages collaboration between Institute researchers and their neighbouring biotech companies – to set up a collaboration. And after successfully showing that they could build Simon’s knowledge of KRAS into PhoreMost’s screening technology, they were awarded £600,000 funding from Innovate UK in 2017 to get a new procedure up and running.

Nine months on and Simon’s team are close to perfecting a system with PhoreMost. The new cell line will be able to indicate whether or not a molecule has inhibited the KRAS pathway by living or dying. When KRAS is switched on, the cells die; conversely, anything that inhibits KRAS means the cells survive. These cells can then be studied to find out exactly what protected them.

“The first step is using PhoreMost’s technology to find these cryptic spaces on KRAS that have defied conventional drug discovery,” he explains.

‘It takes 17 years to translate basic innovation into a new drug or company… we can work much more cleverly’

“Our dream is that if we find things binding to KRAS, we can work with crystallographers to discover where it’s binding. And once we know the structure, we can design a drug-like molecule that does the same thing.”

If the collaboration ultimately leads to new drugs for diseases like pancreatic cancer, it will mark an extraordinary advance. But it’s the huge potential that this way of working represents that’s the real game changer, Simon believes.

“I’m a great believer in publiclyfunded research – the Institute does world-class research on a budget and because our funding comes from taxation we have a duty to squeeze every possible impact out of it. The fact we work alongside scientists from so many varied companies enables us to turn new ideas into new collaborations.”

Working this smartly radically speeds up the time it takes to turn new knowledge into impact. “On average it takes 17 years to translate basic innovation into a new drug or company. That’s too long and too random,” Simon concludes. “The Babraham Research Campus shows that we can work much more cleverly.

Here, we can facilitate and accelerate – funding basic bioscience and bringing people together who might otherwise never have talked.”

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The quiet pathway For many years regarded as merely a cell biological process, autophagy is now implicated in many diseases. Thanks to progress made in the Signalling research programme this year autophagy – the mechanism cells use to recycle unwanted or damaged components to create molecules they need – is now understood in greater detail than ever before. We find out how research at the Institute could harness autophagy to help us age more healthily.

The more we learn about autophagy, the more fascinating, important and complex it becomes. Literally the process of ‘self-eating’, autophagy is the cell’s way of recycling itself to survive short-term starvation, as well as cleaning itself of unwanted and potentially harmful material.

Although most of us know little about it, autophagy is vital from the moment we are born until we die.

“It’s a quiet pathway, but it’s super important,” says Dr Nicholas Ktistakis, group leader in the Signalling research programme.

“It is an ancient pathway – all cells have it – but normally it works in the background.”

Despite its usually unsung role, the better we understand autophagy, the more we discover about its links with health and disease.

As newborns, it is what tides us over the period immediately after birth when our cells are our only fuel. Boosting autophagy seems strongly linked with longevity.

There is evidence that by cleaning

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our cells of potentially damaging material, autophagy could be involved in protecting against neurodegenerative diseases such as Alzheimer’s and Parkinson’s.

We now know that cancer cells use autophagy to fuel their uncontrolled growth. And it is even linked to the health benefits of fasting, including the 5:2 diet.

First described in 1963, Ktistakis has found references to autophagy dating back to 1860. During the past 50 years we have learned that many steps, and more than 30 genes, are involved in autophagy, and that two protein complexes – mTOR and ULK – are pivotal to the process. We have also discovered that it can be turned on and off with remarkable rapidity, and that switching on autophagy by inactivating mTOR can increase lifespan in model organisms by an astonishing 30%.

Autophagy works by forming small membrane-bound sacs or autophagosomes to bag up material for clean up or for fuel.

It’s likely that these two types of

autophagy – the selective clean-up variety and the general nutrientgenerating type – share the same machinery but rely on different signals.

Understanding these early signals is a key focus for Ktistakis’ group and other researchers at the Institute. “A lot of our work is trying to figure out the signal the cell uses to start the process.

It happens very quickly – within 15 minutes of detecting a drop in nutrients – and must stop very fast when conditions improve, because you don’t want to be digesting yourself for any longer than necessary,” Ktistakis explains.

“We want to understand it at the molecular level – what happens when the signal arrives, how quickly mTOR is switched off and on, and what happens when ULK is activated and leads to formation of the autophagosome. I’m interested in this early part of the pathway – in identifying how dynamic it is and which are the important players controlling how it happens.”

Signalling feature 2016

‘When autophagy is more active, it makes cells healthier’ But studying such a complex, finely-tuned and rapidly reactive system is a huge technical challenge – one recently solved by the expertise in biological chemistry and imaging technologies in the Institute’s core facilities and collaborating teams.

With so many proteins involved, many of which are protein complexes rather than single proteins, developing ways to tag them with fluorescent markers in order to observe autophagy as it happens is a tall order.

And it’s not the only challenge.

Studying events so early in the pathway, before the autophagosome is visible, means Ktistakis had to develop new ways of seeing. By teaming up with scientists at the Francis Crick Institute in London and the Zeiss Microscopy Labs in Munich, the Babraham group has successfully combined live imaging with other forms of microscopy. These new techniques reveal how the first autophagy structure forms and the protein and membrane associations that lead to it developing into a fully-fledged autophagosome.

According to Ktistakis: “We now know more about where the autophagosomes form, and how the autophagy machinery uses the cell’s membranes to generate these tiny sacs. We still don’t know how these regions are selected, but we are keen to find out, because it will give us the final level of understanding.”

Understanding is important, but it’s the impact this knowledge could have on our lives that matters. Once we understand the process fully, it could enable us to find ways of harnessing autophagy to tackle neurodegenerative diseases and cancers, helping us age more healthily.

“When autophagy is more active, it is likely to make cells healthier, so knowing more about the process increases our ability to find ways to manipulate or boost it for future therapeutic benefit.

The idea ultimately is that if we understand autophagy enough we can change it in a way that benefits the cell and the organism,” Ktistakis concludes. “We think this is probably a very good idea.”

‘Autophagy is a quiet pathway, but it’s super important’

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How yeast is reshaping ideas on ageing Healthy ageing is one of society’s most pressing concerns, but basic questions like why we age remain a mystery. Dr Jon Houseley, a group leader in the Institute’s Epigenetics programme, studies the ways in which yeast cells adapt to new environments. As well as uncovering new connections between adaptation and ageing, his research is challenging our ideas about ageing itself.

Dr Jon Houseley is a heretic. Along with others in the field of ageing research, he is questioning longestablished orthodoxies of ageing.

For decades, ageing has been seen as inevitable, a paradigm that has so far failed to help us answer the most basic questions about the nature of ageing.

If you rewind to the 1920s, however, alternative theories of ageing existed. Rather than simply a slow, inexorable process akin to a once pristine car rusting and breaking down, some argued that ageing had evolved for some purpose. In the absence of evidence, they lost the argument. Today, Houseley and others think they may have been right.

“I’ve been in the field long enough to say that you should be wary of any theories about ageing – including mine,” says Houseley. “The problem is that 60 years on, it’s really hard to know what this conserved underlying mechanism that’s breaking down in ageing actually is.

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We need fresh ideas, even if they are heretical.”

Ageing is hard to study. So much happens in a slow and concerted way in myriad systems that coming up with cause and effect is mindbogglingly hard. Many genes and processes are involved, all of which are interconnected, so identifying the underlying ‘thing’ has so far proved impossible. It’s even possible that ageing is not, in fact, one single thing.

“Ageing is really difficult to get your hands on, which is why we’ve started to revisit these old debates.

But rather than argue about it intellectually, we have rolled up our sleeves and done experiments with yeast,” Houseley explains. “Using yeast, we are asking whether there are situations in which being old is an advantage – and it turns out that there are.”

One of Houseley’s central aims is understanding how organisms adapt to challenging – and changing – environments. “It sounds

like a weird fit with our focus on ageing,” he admits. “But a major angle we have on ageing is that it could be a process that exists in basic eukaryotes like yeast to help them cope with stress.”

His studies provide persuasive evidence to support this idea. One focused on CUP1, a gene in yeast that allows cells to survive in highcopper environments. Some yeast cells make extra copies of the CUP1 gene, allowing them to survive and outcompete cells with fewer copies of the gene.

Surprisingly, the study revealed that extra copies of CUP1 result from an active process rather than random mutations. “We think of genomes as long-term, stable repositories of information but they change – and not only over evolutionary timescales,” says Houseley. “We know genome changes are hallmarks of cancer, but we’re discovering them in healthy cells too. Some parts of the genome are very prone to change, suggesting that organisms

Epigenetics feature 2019/2020 have more control over their genomes than once thought.”

But this raises a problem: cancer aside, organisms care about the genomes they pass on to future generations and are careful to minimise mutation rates in their genes. This is where ageing can be useful, because genome changes can be restricted to old cells that only reproduce rarely, and to the strange non-chromosomal DNA elements that accumulate in old cells.

The Houseley lab examined how yeast forms circular nonchromosomal DNA elements in response to copper and how this differs between young and old yeast cells. The results revealed that older yeast cells hoard circular DNA containing extra copies of genes like CUP1. “It’s like a selfish insurance policy,” he says. “But while these extra genes might provide an evolutionary advantage, they might also come at the cost of ageing because these extra bits of DNA could hamper normal essential cell pathways.”

Understanding more about DNA circles, and how cells can change particular parts of their genomes in

Saccharomyces cerevisiae cultures growing on solid agar after inoculation by spotting.

Image by Conor Lawless, DropTest on Flickr.

Attribution 2.0 Generic (CC BY 2.0)

response to particular environments has important implications for both cancer and ageing. Cancers use DNA circles to carry cancer-causing oncogenes and to adapt in the face of chemotherapy, enabling them to develop resistance to anti-cancer drugs.

Houseley is at pains to stress that evidence for ageing being adaptive in yeast does not mean it’s also adaptive in higher eukaryotes. It does, however, explain how it evolved and may explain why ageing still occur in higher organisms despite bringing no benefit.

As well as setting us on a new path to better understanding ageing, his research is also relevant to efforts to stop cancers from becoming drug resistant and could pave the way to healthier ageing. “Ageing is the biggest risk factor in a vast number of human disorders, but to come up with ways of dealing with ageing, we first need to understand it,” he concludes. “At the moment, we don’t understand how ageing works in any organism, so knowing how it works in one – even yeast – would be a major advance.”

‘Some parts of the genome are very prone to change, suggesting that organisms have more control over their genomes than once thought.’

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Promoter Capture Hi-C: from academic tool to £1.5M startup Fundamental research is vital for science and society. Many medical and technological revolutions are rooted in basic research, yet those roots can be hard to trace. Today, spinouts are key to turning academic bioscience into healthcare treatments. Dr Stefan Schoenfelder, a group leader in the Institute’s Epigenetics programme and co-founder of Enhanc3D Genomics, discusses taking a tool developed for fundamental research and building a business around it.

Setting up a new biotech spinout is a demanding business, full of funding rounds, legal structures and recruitment decisions.

Doing so at the start of a global pandemic, however, adds a new set of challenges. Founded in January 2020, Enhanc3D Genomics secured its first round of funding the following month and by March 2021 had closed a second round of funding worth £1.5 million.

Being involved in a biotech spinout is somewhat surprising for Schoenfelder, who has worked at the Institute for 15 years, because it was never part of his career plan.

“If you’d asked me five years ago, I’d have said that I wanted to focus solely on academic research,” he explains. “I’ve always hoped my research would help patients, but never saw myself as part of the commercial world. Now, I believe that I can play a more active role in 50

making that transition from basic science to clinical application.”

The first fully sequenced human genome was published in 2003, with hope that this ‘operator’s manual’ for the human body would revolutionise our ability to treat, prevent and cure disease.

During the past two decades, however, research has revealed that our DNA contains intricacy and complexity unimagined in 2003.

Together with our genes, the noncoding sequences of DNA between the genes – once dismissed as ‘junk DNA’ – are just as important. And as well as its linear sequence, the 3D structure of DNA as it is folded within the nuclei of our cells is crucial, because it brings genes into close proximity to their regulatory elements – a key step in gene expression control.

According to Schoenfelder: “These regulatory elements function like molecular switches to control which genes are active, and thus produce proteins, in which cells. This process of gene expression control is vital to allow cells – which all contain the same genes – to specialise to carry out different tasks, and to help them respond to changes.” Identifying which regulatory elements act on which genes has been an epic challenge in genome biology, but thanks to an ingenious modification to the Hi-C technique called Promoter Capture Hi-C, developed

by Schoenfelder and his colleagues at the Institute, this can now be done for all human genes in a single experiment.

Crucially, studies deciphering the 3D folding of the genome at high resolution also reveal how small mistakes in regulatory elements interfere with normal control of

Epigenetics feature 2019/2020

LEARN MORE: Find out more about the 3D organisation of the genome and how regulatory elements control gene expression.

genes, leading to a greater chance of developing specific diseases.

into clinical applications was through a spinout.

The best example of how Promoter Capture Hi-C is helping researchers understand the genetic basis of important human diseases comes from so-called Genome Wide Association Studies (GWAS): hugely powerful studies sequencing the whole genome of people with and without particular diseases to spot the differences involved in causing the disease. By applying Promoter Capture Hi-C, research by the Institute linked the tiny changes in non-coding DNA to target candidate genes implicated in rheumatoid arthritis, type 1 diabetes and Crohn’s disease.

The company’s vision is ambitious.

“Our vision is to create 3D genome maps of all the cell types in the human body. If we succeed, it will be a unique database that will allow us to establish causal links between disease-associated regions and disease genes in almost every disease. Then, we will partner with experts in different disease areas to find new therapeutic targets,” Schoenfelder says.

“The vast majority of genetic variants associated with disease are located in non-coding parts of our genome,” says Schoenfelder. “That means if we want to understand how most diseases arise – and find new targets for therapy – we need to be looking in the non-coding genome.”

Having pioneered Promoter Capture Hi-C as a tool for doing fundamental research into gene regulation, Stefan and his colleagues soon realised it could be invaluable in understanding diseases and finding new ways to treat them, and that the best way to translate their fundamental research

Reflecting on a momentous year, he is enthusiastic about the spinout process and Enhanc3D Genomic’s potential: “The prospect of creating a legacy that uses fundamental research to create a business and help patients is hugely exciting.”

“Covid-19 has shown the world what small, agile biotech firms can achieve. The most amazing research stories have come out of companies like Moderna and BioNTech,” he concludes. “I hope more people now see there’s lots of interesting research going on in biotech. The Institute and the many companies on the Campus create the ideal environment to foster these interactions. We need to get out of our ivory towers a bit more!”

‘To understand how most diseases arise – and find new targets for therapy – we need to be looking in the non-coding genome’ 51

Riding the data wave Big data is revolutionising science. But as well as changing physics, chemistry and biology, it’s changing the nature of science itself. Institute researchers Wolf Reik and Stefan Schoenfelder and bioinformatics expert Simon Andrews reflect on how big data is re-shaping not only the way they work, but how they think. And we discover how bioinformatics – once considered a geeky corner of biology by some – has become central to scientific progress.

When Professor Wolf Reik, head of the Epigenetics programme, thinks about how big data has revolutionised his field he remembers the Swiss anatomist Karl Theiler. Theiler spent a lifetime creating ‘The House Mouse: Atlas of Embryonic Development’, painstakingly taking embryos at different stages of development and using staining and microscopy to identify each tissue type.

“Now, we take the same embryos and put them in a big machine which sequences up to 100,000 cells at a time. Through gene expression, it gives us an equally detailed atlas of development, but because we can now use multi-omics methods that link together different layers in a single cell – the epigenome and the transcriptome – we can ask much deeper questions about how these patterns arise mechanistically.

That’s what we really want to know,” says Reik.

Despite being a relic of an earlier scientific age, Theiler’s atlas remains on Reik’s bookshelves: an illustration of how big data has transformed the 40

scientific questions he can ask and an embodiment of how it’s reshaped the way his younger colleagues think.

Before big data, researchers thought and worked on single genes – how they were regulated and their role in development, health and ageing. Now, thanks to the recent developments in next-generation sequencing, the focus is firmly on the genome as a whole. “We can now look at 20,000 genes or 20,000 promoters and get huge amounts of information. The younger members of my group get excited about the whole genome and what it’s doing, whereas I was brought up in an era of asking what single genes do; it’s a fundamental difference in thinking,” says Reik.

Big data brings huge opportunities, but using techniques that generate massive amounts of increasingly complex data also presents huge computational challenges. So how do Reik and other researchers extract meaning from this deluge of data? The answer lies in bioinformatics, the science that

has emerged at the intersection of biology, computer science and statistics.

Dr Simon Andrews, head of Bioinformatics, belongs to this new breed of experts. Since joining the Institute in 2001, he’s seen the group expand from two to 10 staff, many of whom have their roots in biology.

“Lots of people in my group were once biologists who happened to play with computers for fun.

My mother was a primary school teacher. Sometimes she’d turn up with a computer that had been donated to the school, point me towards it and say ‘make this do something that I can take back into the classroom!’” Andrews recalls. “At university I built my own computers because we couldn’t afford to buy them, and when I started research we were beginning to get electronically-generated data.”

His PhD generated a respectable 1,000 bases of DNA sequence. Today, a single sample at the Institute yields 40 billion. “The fundamental change is that many experiments generate amounts of data that are

Epigenetics feature 2018

‘Big data changes how we think – and how we work’ impossible to understand without a computer. Before, computers were a nice add-on; now they are fundamental,” he says.

One of the Institute’s core facilities, the Bioinformatics group provides computational power and data analysis plus expert advice and bespoke development work. “What fires me up are computational problems that spring from biology,” says Andrews, and what researchers often need most are ways of making their data more accessible. Over several years, Andrews’ group has developed packages capable of visualising sequencing data sets with billions of data points. “These are unfathomable on their own, but we can turn them into billions of positions in a genome, and visualise what they look like,” he explains.

‘Bioinformatics turns something unfathomable into something we can visualise’

Like Reik and Andrews, Dr Stefan Schoenfelder has lived through the revolution wrought by nextgeneration sequencing and big data.

“It changes the way you think and changes the way we work,” he says.

“When I did my PhD 15 years ago I spent all my time doing experiments in the lab. Now it’s the analysis that takes the time.”

Schoenfelder is interested in how gene function and gene expression are controlled by non-coding bits of DNA known as regulatory sequences.

In linear terms, genes and their regulatory elements may be some distance apart, so how the genome is organised in three dimensions is

one of his key questions. “Whereas we used to look at individual examples, now it’s possible to address those questions genome wide. We can get a complete picture of all the interacting sequences in a cell,” he says. “When I came here after my PhD, it was something I thought might happen at the end of my career. That it’s happened so quickly is incredible.”

It also means that researchers need to learn how to interpret data, so the Institute’s Bioinformatics group makes a major difference. “The skills I was equipped with in my PhD are not enough anymore. It’s normal to keep learning in science, but this is a quantum leap,” says Schoenfelder. “In a competitive field you need to work rapidly. I often work with dedicated bioinformaticians because it’s almost impossible to be an expert in both.”

The next scientific revolution is anyone’s guess, but Schoenfelder is sure it will only underscore how much more we need to understand.

“Sequencing and its impact on personalised medicine will continue to grow. High-resolution microscopy, observing live cells and even individual molecules, will be another game changer,” he concludes. “We make contributions all the time, but we know so little. That’s humbling – but it’s also very exciting to be a part of.”

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Informing Policy on Ageing Ensuring that the Institute’s world-leading research has a direct impact on people’s health means translating – and contextualising – our science for many audiences.

For parliamentarians and policy makers, healthy ageing is among the 21st century’s most pressing problems. So as well as pioneering research on healthy ageing, we’re ensuring science is accessible to decision makers through our knowledge exchange programme.

Across a handful of generations, average life expectancy in the UK has doubled. A baby girl born in 1841 could expect to live just beyond her 42nd birthday; one born in 2016 can expect to live until the age of 83. This extraordinary change is a triumph of public health; but it also presents major health and social challenges. Today, longer life expectancy is associated with increasing incidence of chronic diseases, from dementia and diabetes to arthritis and cancer, putting pressure on unpaid carers as well as health and social services.

Helping people remain healthier for longer is key to addressing these issues, and the Institute plays a pivotal role in advancing fundamental scientific knowledge and making it available to decision makers. Healthy ageing research spans and unites the Institute’s scientific themes. Our aim is to understand how our bodies change as we age and how this impacts our lives so that science can inform lifestyle changes, policies and treatments to help people stay healthier as they get older.

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For the past 30 years, the Institute has pioneered research into epigenetics – the mechanisms that control the way our genes function – revolutionising our concept of healthy ageing biology. In 2017, for example, Institute researchers identified a mouse epigenetic ageing clock and showed that lifestyle changes known to shorten lifespan, including a high fat diet, sped up the clock.

Doing ground-breaking science, however, is not enough. To maximise the impact of our research, we have to make it accessible to parliamentarians and policy makers, and last year Professor Wolf Reik and Dr Jon Houseley of the Epigenetics research programme contributed to a new POSTnote.

POST – the Parliamentary Office of Science and Technology – provides balanced, accessible overviews of scientific research. One of the tools it uses to put research into a policy context that can be used in Parliament is the POSTnote.

These concise peer-reviewed briefings distil literature reviews and

interviews with academic, industry, government and third sector stakeholders. In 2017, Sarah Worsley, a third-year PhD student at the University of East Anglia spent three months as a NERC-funded intern at POST, producing a POSTnote on the biological basis of ageing and how the ageing process can be manipulated to promote better health later in life.

“Collating 30 interviews into a four-page briefing and explaining complex science for an audience that has no knowledge of biology is challenging,” Sarah explains.

“Visiting scientists at the Babraham Institute, Newcastle University and the University of Southampton was vital to get the background to the biology of ageing. They told me about their work, and where they thought it fitted into policy and treatments for age-related diseases.”

The POSTnote introduces the idea of biological versus chronological age, the epigenetic clock, and considers potential therapies and public health policy interventions opening up through this research. “Scientists

Epigenetics feature 2017

‘Our research on healthy ageing has a direct impact on the nation’s heath’ are beginning to understand the processes that occur in our bodies that cause ageing – the damage that accumulates over time which causes ageing and age-related disease. The interest now is to look for ways to reduce this damage, either via new drugs or changes in lifestyle,” she says.

The POSTnote, published in February 2018, will be used by parliamentarians and policy makers who will be increasingly called on to regulate new drugs and set new directions in public health, ensuring that the Institute’s research has a direct impact on the nation’s heath.

“Nutrition and other environmental factors influence the epigenome and can have long lasting consequences, not only for our health but that of future generations,” says Wolf.

As well as public health and the development of new drugs, his research has other less obvious yet far-reaching implications, he adds: “Insurers might be very interested in people’s biological age, which raises many policy questions. And if it’s possible to influence the ageing process with drugs in the future, I think this has broader implications for population structure.”

Being involved in research that’s likely to have profound impacts on society as well as health makes him think about his science from new perspectives. “It makes us frame questions in a different way,” he says.

“It’s important to inform parliament and our policy makers about scientific thinking, because new science raises so many new ethical and legal questions.”

The POSTnote ‘The Ageing Process and Health’ is available online to download*

‘It’s important to inform parliament and our policy makers about scientific thinking, because new science raises so many new ethical and legal questions’ *https://researchbriefings.parliament.uk/ResearchBriefing/Summary/POST-PN-0571 41

Unlocking the secrets of early development Every cell type in our body results from a different reading of the same genome.

Over the past 30 years, scientists have learned that our genes are controlled by epigenetics – a combination of processes that switch genes on and off without altering the DNA sequence itself. But much of epigenetics remains a mystery.

The Institute’s Epigenetics programme is exploring the earliest stages of life and how understanding this could help reprogramme cells for regenerative medicine applications in the future.

From neurones and hepatocytes to lymphocytes and erythrocytes, our bodies contain more than 200 different types of cell. Thanks to them, we can perform the myriad functions necessary to survive, thrive and reproduce.

But how does this extraordinary diversity develop from one cell type – the zygote – when most of our cells contain the same genetic information?

It’s a puzzle Professor Wolf Reik, head of the Epigenetics research programme, has been working on for the past 30 years. “Every cell in the body contains the same DNA, so there must be something else that interprets it in a different way,” he explains. “This ‘something else’ is actually several things – transcription factors, proteins on the DNA that switch genes on and off – and it’s also epigenetics.”

Literally meaning ‘on top of our genes’, epigenetics refers to an extra layer of control achieved by annotating our DNA with a series of tags, such as the simple methyl group of one carbon and three 42

hydrogen atoms. It’s thought that each cell type has a different set of tags – a different epigenome.

Akin to highlighting recipes in a cookbook that together form a specific menu you want to create, each epigenome enables a specific cell type to develop by ensuring that only genes relevant to that cell type are switched on.

building new cell types and new organs. Without erasing the cells’ memory, the whole thing might become confused and lead to developmental problems and abnormalities,” he says.

As well as enabling cell differentiation, the system must also be heritable, so that as we grow and repair ourselves, our cells and organs retain their individual identities. “There is a memory in the system, and that’s important,” says Reik. “As a liver cell divides, it needs to remember that it’s a liver cell, and epigenetics helps with that.”

into any type of cell in the body, and which are present in early embryos. By studying these cells, they are discovering how epigenetic information affects the way that important organs – such as the placenta, heart and brain – function throughout our lives. “It’s a hugely exciting area for us now,” he says. “In early development, once you get away from all the cells looking the same, you have to make different cells to produce a body with all its constituent parts. How this happens is a huge, unresolved question.”

Equally importantly, the system must be able to forget, so that when we produce eggs and sperm, the newly developing embryo can start the development process afresh. “This is vital because after fertilisation, new embryos must undergo this process of diversification again,

Reik’s group is particularly interested in the epigenomes of stem cells, extraordinary cells with the capacity to develop

To answer that question, the researchers at the Institute have developed pioneering new single cell technologies able to read

Epigenetics feature 2016

‘It’s hugely exciting to see such progress in epigenetics’ the epigenome of an individual cell, without which it would be impossible to tease out how stem cells decide whether to become a blood cell or a brain cell, for example. They also want to answer two other key questions: how the global erasure process works, and how epigenetics affects ageing, both of which have major implications for maintaining health and managing disease.

For many years, regenerative medicine – using our own cells to repair or replace damaged or diseased cells – has offered a promising way of treating devastating diseases such as Parkinson’s and multiple sclerosis.

It’s becoming clearer that it is epigenetics that could be the key to unlocking the potential of regenerative medicine.

So-called embryonic stem cells and induced pluripotent stem cells are the holy grail for regenerative medicine, but many questions remain, including how to ensure that the memory of cells used in therapies have been wiped clean.

“For us, epigenetic memory is a problem that lurks in these cells,”

says Reik. “They are derived from skin and other cells but if they retain some epigenetic memory of where they come from, this could affect how well they perform in patients.”

As well as discovering how cells erase their epigenetic memories, the Institute’s researchers are also investigating links between ageing and epigenetics. It’s now thought that together with our chronological age, we have an epigenetic age influenced by our diet and environment. According to Reik: “We are interested in how the epigenetic clock ticks and how it affects the ageing process. We hope that by manipulating the ticking rate, we can have an effect on ageing.”

“As someone who has been in this field since before it was called epigenetics, it’s hugely exciting to see such progress. Instead of phenomena that couldn’t be explained, we now have molecules, mechanisms and the possibility of manipulating them in animal models and – potentially – in patients in the future.”

‘Epigenetics could be the key to unlocking the potential of regenerative medicine’ 43

The Sounds of the Genome The Institute does world-leading research, and using public engagement to enthuse, excite and inspire is a key part of our mission. This year, we teamed up with two innovative artists to transform our data into a virtual reality experience. The result, CHROMOS, is allowing new audiences to discover the DNA drama that goes on inside the nucleus of a single cell.

From Twitter to CGI, new technology is re-shaping how we work, play and communicate. But when Dr Mikhail Spivakov from the Institute’s Nuclear Dynamics research programme sent a tweet to music producer Max Cooper, neither thought that a 140-character message would evolve into a ground-breaking public engagement project.

Max – whose work spans dancefloor techno to fine art sound design – has more in common with Mikhail than meets the eye. With a PhD in computational biology but no formal music training, Max is fascinated by the rhythms of the natural world and the capacity of art and music for scientific storytelling.

“Mikhail tweeted Max inviting him to visit the Institute,” recalls public engagement manager Tacita Croucher. “He’d seen some work that Max was doing, thought it was really cool, and wondered whether they could collaborate.”

After meeting Mikhail and his team, Max decided that they should work together on a project inspired Dr Csilla Varnai’s research, whose

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computer modelling has revealed the 3D organisation of DNA in single nuclei for the first time.

understand how the activity of the genes encoded in DNA affect health, disease and ageing.

Our DNA is often represented as pairs of discrete X-shaped chromosomes, but the reality is altogether messier and more dynamic. With more than two metres of DNA packed into each cell’s nucleus, our chromosomes usually resemble a tangled ball of wool rather than neatly twisted skeins of yarn.

While for scientists the findings have important implications for human health, for Max they provide artistic inspiration. “This process of simulated folding to create our best guess of real chromosome structure is a beautiful process, so this beauty became the focus of the project,” he explains. And to bring out its full beauty, he decided to get CGI A-lister Andy Lomas – whose film credits include Hollywood hits from Avatar to the Matrix movies – on board.

This tangle of DNA is constantly moving, folding and refolding into different arrangements. When sections of DNA move from the centre to the periphery of the cell, meeting and parting company from others, they are effectively switched on and off in a way that enables the complex machinery of the cell to function correctly.

Because they can now study the relationship between DNA structure and function in single cells, researchers will be able to ask questions that would have been impossible to answer before – questions that should help them

Andy developed a way of transforming gigabytes of the Institute’s raw data into video sequences and a virtual reality experience while Max produced a musical score. “We wanted to express the data in this unadulterated form, so you can experience the real science in action,” Max explains. “It’s a glimpse into the complexity and form of one of the most important molecular structures in all of life.”

Nuclear Dynamics feature 2017

‘We wanted to express the data in this unadulterated form, so you can experience the real science in action’ The result is CHROMOS: shimmering strands of DNA dancing to complex, layered melodies played on a sansula, a magical thumb piano made from small metal tines. The video has been viewed thousands of times on YouTube and the VR experience enjoyed by audiences at London’s Science Museum, the Cambridge Science Festival and the Open Codes exhibition at ZKM Karlsruhe as well as in Berlin and Lisbon.

People’s responses, says Tacita, have been amazing: “Our aim was to spark conversation, make people think differently and engage audiences who would perhaps not usually engage in science research. And we’ve achieved that. It’s been a major success.”

The project has also attracted attention from the public engagement community. “CHROMOS was a significant investment for the Institute and very different from anything we’ve done before,” she says.

“Its success shows that by finding new ways to help our scientists tell their stories, the Institute can do ground-breaking public engagement as well as world-leading research.”

And for Institute researchers like Mikhail, it’s been hugely rewarding.

“As a biologist I’m passionate about finding ways to make our science more accessible, to help people understand what we do and why we do it,” he concludes. “It was amazing to see how the project took real data from the lab and turned it into a multidimensional experience which allows people to get more closely acquainted with our DNA, what it does and how it looks, making it almost palpable.”

To find out more about CHROMOS go to www.babraham.ac.uk/CHROMOS

‘By finding new ways to help our scientists tell their stories, we can do ground-breaking public engagement as well as world-leading research’ 51

Welcome to the 3D genome When the first draft of the human genome was published in 2001, it was described as a treasure trove of information. But using that information to understand disease demands going far beyond the DNA code. Now, researchers at the Institute are pioneering a new method of mapping our genome’s complex regulatory interactions that could open up new ways to treat genetic diseases and understand ageing.

If we think about our genome at all, it’s probably in a linear, two dimensional way: as a string of bead-like genes threaded along a necklace of DNA, a code to be cracked or a blueprint to be read. It turns out, however, that understanding what our genes do – and how tiny changes in our genome can cause genetic diseases – demands different ways of thinking.

The story begins, says Dr Peter Fraser, head of the Nuclear Dynamics research programme, by focusing less on genes – which occupy only 2% of our genome – and putting more thought into the remaining 98%. “This noncoding space between the genes, sequences of DNA that don’t encode for particular proteins, was once viewed as an evolutionary wasteland of junk DNA,” he says.

In fact, these regions are crucial because they regulate our genes by switching them on and off. “There are at least 1 million regulatory elements in the genome. Each of our 22,000 genes uses an average of five of them. But the problem has been understanding how a regulatory

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element so far away from the gene it controls actually exerts its influence,” Fraser explains.

To understand this, we must add new dimensions to our thinking.

“We need to think in 3D because that’s how it is inside the cell,” he says. “DNA is wrapped around proteins and how that bundle is folded in the nucleus is really important.”

Time matters too, because the folding is dynamic, not fixed, and as the folding patterns change, different genes make contact with regulatory elements in distant regions of DNA. But while this new way of thinking offers a better way of explaining how genes are regulated, how can we unravel such a complex web of changing connections?

For the past 15 years, Fraser and his team have been studying how DNA folds to bring genes and their regulatory elements together.

Now, they have developed a pioneering method of mapping these myriad connections, and produced the first ‘pages’ of an atlas they hope will eventually cover every cell type in the human body.

But why is this atlas so important in the quest to understand common genetic diseases – and find new ways to treat them?

The answer, he says, is because the atlas allows us to make sense of a vast database of hundreds of thousands of so-called SNPs (pronounced ‘snips’) – single nucleotide polymorphisms – the tiny errors in DNA that are related to genetic diseases such as Crohn’s disease and rheumatoid arthritis.

This database of SNPs has been built up over decades of research using genome-wide association studies – trials comparing the genomes of healthy volunteers with those suffering from a genetic disease.

Sometimes these variations occur in genes, making them malfunction and resulting in genetic diseases. More commonly, however, the error lies in non-coding DNA. Hundreds of thousands of these mistakes have been discovered, but until the atlas, it’s been impossible to explain how such a tiny change, so far from any known relevant gene, could affect a disease.

Nuclear Dynamics feature 2016

‘Our 3D maps can identify new potential diseasecausing genes’ According to Fraser: “What we’ve found is that these SNPs are in regulatory elements, so by being able to map these onto specific genes, we can identify new potential disease-causing genes.”

“The 25% of disease genes we already know about have been very hard fought – one at a time over decades of research. So what we’ve done has really burst the dam,” he says.

Precisely how powerful this mapping could be in combating genetic diseases can be seen from results that Fraser’s team published last year. By mapping the 750,000 connections between regulatory elements and the genes they control in 17 types of white blood cell they were able to identify 2,600 potential disease genes. Only 25% of these diseaseassociated genes had previously been identified – 75% were new, including genes involved in a range of autoimmune diseases from type 1 diabetes to celiac disease.

As well as white blood cells, the team has mapped the genetic connections in red blood cells and is moving on to map muscle and pancreatic cells. Fraser hopes that these findings will deliver candidate genes relevant to diseases such as certain types of anaemia, type 2 diabetes and muscular dystrophy.

As well as helping us understand the genetic basis of disease, the discovery of these potential disease genes also provides the pharmaceutical industry with new targets for novel drugs – or new ways to use (or repurpose) existing drugs.

With more than 200 different cell types in the human body, the atlas will be huge. And its impact on our understanding of disease and healthy ageing could be even more significant.

“It’s a big leap,” Fraser says. “There are SNPs in these databases associated with healthier ageing.

By mapping those, we may be able to identify more genes involved in ageing. There’s lots of work to be done and lots of genetic diseases we know nothing about. This could potentially crack quite a few.”

‘There are lots of genetic diseases we know nothing about; this could crack quite a few.’

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