The Graham Lovitt story – an accidental turn and the road that followed.

November, 2018, the Frezza laboratory at the MRC Cancer Unit hosted a special person: Graham Lovitt, the Co-Chair of VHL UK/Ireland – a patient support group that supports cancer patients affected by VHL (von Hippel Lindau disease), HLRCC (Hereditary Leiomyomatosis and Renal Cell Cancer) , FD  (Fumarase Deficiency) and BHD (Birt-Hogg-Dubé Syndrome). Given the Frezza laboratories long-standing interest in HLRCC, it was a privilege for Christian Frezza and his team to host Graham, to find out about his experience with cancer patients, and more importantly, to get to know him as a person directly affected by HLRCC.

The story goes back awhile. Christian Frezza first met Graham Lovitt at the NCRI meeting in 2011, when Christian was a post doc at the Beatson Institute in Glasgow. This was the first session on cancer metabolism ever presented at the NCRI meeting and Graham attended this session to know more about the topic, especially because there was a talk on FH and cancer metabolism. The fact that Graham attended this conference perhaps already spoke for his unique approach to his disease. Graham eventually went on to start his own website on HLRCC and Christian joined it as a scientific member in 2017. Over the course of the year Graham and Christian had several digital exchanges till they finally decided to meet in the flesh in 2018.

That late autumn afternoon, when the quiet Graham Lovitt finally visited Christian and his lab at the Hutchison MRC Research Centre, his interest and enthusiasm for the science had not waned a bit.  He discussed the complexity of the disease, discovered tools to investigate how the loss of Fumarate Hydratase causes cancer, slowly but attentively trawled through the Mass Spectrometry room and peered down microscopes to see for himself how tissues devoid of FH looked. He interacted with post-docs in the lab during which he underlined the difficulties for patients with HLRCC in attaining a correct diagnosis before the development of aggressive renal cancer. He also highlighted how his support group could help patients with suspect clinical signs to overcome their fears and ask for genetic counselling. He was acutely aware of the current limitations in the development of pharmacological therapies for rare diseases and how much could and should perhaps be done to make research more translational.

In fact, the story about his diagnosis is emblematic and indicates the difficulty of diagnosis of rare cancers. Graham had retired in February 2009 from being a software quality assurance manager in software configuration management control. In January 2010 he was diagnosed with a Collecting Duct Carcinoma and possible metastasis to lungs as nodules. At this time, he also noticed a small surface skin lesion on the forehead and was seeing a dermatologist for its removal. About 30 years ago he had had an excision of what was diagnosed as a very rare benign ‘piloleiomyoma’ – a tumour of the muscle involving hair. He pondered as to whether it might be useful to tell the dermatologist about this benign condition from many years ago. Having forgotten how exactly to spell piloleiomyoma he “Googled” it. To his great shock the search revealed a connection between it and a rare sub-types of kidney cancer. He spent a day researching and found that skin lesion and renal cancer are part of a cancer syndrome – hereditary leiomyomatosis and renal cell carcinoma – HLRCC! He paused and reflected for long and in the end decided that there was a real possibility that there had been a misdiagnosis of his disease. Luckily, he was taken seriously and referred to an NHS geneticist…Graham was right!

The difficulty behind the diagnosis of a rare cancer syndrome inspired him to become a patient advocate and since then he has been the Vice Chair of the HLRCC Family Alliance, a project of the VHL Alliance. He has published an HLRCC Handbook and created a website for patients. He also started Support groups on Facebook and Smart Patients, which currently reach out to over 450 and 200 people worldwide. He is also the Chair of the VHL UK/Ireland Chair – a registered charity which was established to replace a previous VHL Support charity that had closed down. Till date, under Graham Lovitt, the new charity has raised about £100,000 for research and patient support.

Besides being a patient advocate, he is also actively involved with research. His removed kidney was used in research by the late Dr Patrick (Paddy) Pollard to confirm the presence of a novel post-translational modification triggered by fumarate, accumulated in tumours of HLRCC patients. His kidney (and his name in the authors’ list) features in the paper https://www.ncbi.nlm.nih.gov/pubmed/21630274Aberrant succination of proteins in fumarate hydratase-deficient mice and HLRCC patients is a robust biomarker of mutation status.

Back in the lab, the meeting with Graham was an inspiring and humbling experience for all in the Frezza laboratory. Here was a man who was a living testament to why research should not become an esoteric art confined within the laboratory environment or indeed a publicity gimmick, but must be translated into new therapeutic opportunities for patients, especially in the context of rare diseases where options are so limited or completely missing. It was a reminder as to how each unique patient story represents an additional impetus to making a difference not only in the field of research but in reality to someone’s life.

PS: Graham eventually found that 30-year-old piece of paper with the word “piloleiomyoma” …to think had he seen it before, he would never have Googled its spelling and stumbled upon HLRCC and the journey that it led to!

An Apprenticeship in Scientific Ethos

Ashley Ferguson (MPhil Student, 2017-18, Frezza Laboratory,  MRC Cancer Unit)

 

Thank you to Anasuya for giving me the space to reflect on my time here.

                                                                  ***

I arrived in Cambridge by taxi in a zombie-like state on a Tuesday morning at 2:00 am.  We don’t have porters at U.S. universities, so I was surprised when a friendly (and very awake!) young porter was waiting to show me to my room at Churchill College.  Despite jetlag and a nagging sense of Cambridge wanderlust, my research project was the first thing on my mind when I woke up the next morning.

Ashley Ferguson 2After working as a summer student in Christian’s lab in 2016, Christian agreed to support my application to come back for a master’s.  Before I left for the summer, he advised, “You should use this opportunity [of your master’s application] to begin to develop your own questions”.  What he meant was, in contrast to the summer I’d spent in his lab working on Isaac’s project, my master’s was my chance to explore my own scientific curiosities, within the context of the lab’s interest and expertise.  Though I had developed a strong interest in the intersection between mitochondrial morphology and cell metabolism, I didn’t have the technical expertise to translate this interest into a tangible project.  Christian’s goal, I believe, was to encourage me to start thinking about how to do this.

I took my first stab at formulating my own research project as a 16-year old at my science high school in Virginia, USA.  At the Loudoun Academy of Science, sophomores are asked to design their projects from scratch.  With generous funding from Howard Hughes Medical Institute, this can translate into teens doing tissue culture in a classroom.  Though unsurprisingly my high school cancer research project didn’t amount to any discoveries, I did get to experience the joy, and what I believe can only be called the addiction, of making observations based on my own questions.

In high school, research was set up to be entirely of the students, by the students, and for the students.  At university, I realized that concerns about funding, publications, and reputation are all part of the professional world of science.  Though I think it’s still possible to have a focus on student learning in a university lab, the pressures faced by a principal investigator are much different than those faced by teachers and directors at a science high school.

My love for science not only survived but also grew through the reality of university research as I realized I could do what I loved for a job.  I’m reminded of some advice one of my Biology professors once gave me about pursuing a career in research, “If you can think of anything else you might enjoy doing, you should do that instead”.  This wasn’t a cynical old professor trying to beat down an overly-eager young student: she loves her job.  Rather, she wants her students to be familiar with the degree of uncertainty, need to cope with relatively constant levels of failure and rejection, and likely poor pay that accompany each stage of training during the life of a scientist.

My fascination with the Warburg effect that developed during my high school research lead me to a mitochondrial biology lab at university.  When I realized that most scientific discoveries don’t translate into benefits for human health within a scientist’s lifetime, I learned to lean more on my desire to understand nature for motivation.  As my work became more mechanistic in its focus on mitochondrial dynamics, I found that I could be just as excited when science was stripped down to its bare essentials as when I could see its immediate application in a disease context.

My project proposal for my master’s involved breaking down the relationship betweenAshley Ferguson 1 mitochondrial morphology and respiratory capacity.  I wanted to interrogate whether elongated mitochondria better support oxidative phosphorylation, and if so, why. During our first meeting this year, Christian advised me that it would take years, not months, to address the connection between mitochondrial shape and ATP production.  Instead, he suggested I tackle the problem of altered mitochondrial morphology in FH deficient cells.  This shift in morphology had been observed but not quantified, and no work had been done to investigate the mechanisms or consequences.  The project appealed to me because it would give me a chance to dig deeper into the molecular biology of mitochondrial dynamics while maintaining a connection to cell metabolism.  The FH deficient system is unique in having a direct connection between mitochondrial dysfunction, altered metabolism, and a change in mitochondrial morphology.

In order to give me access to resources and expertise that would expedite a challenging interdisciplinary project, Christian brought on Julien Prudent from the Mitochondrial Biology Unit.  Julien’s knowledge of mitochondrial dynamics complements our strength in metabolism, allowing us to bridge the two fields.  Christian also asked Vinny to be my official point of technical support in the lab.

I felt that I stumbled for my first few months as I struggled to balance advice that I received from each of my mentors.  With time though, I realized that as a student it was my role to take in the differing opinions of these three experienced scientists and create a rationale for my experimental decisions based on the goals of my project.

Before I came here, I thought that training to become a scientist meant learning how to think: learning how to plan experiments and how to decide on the best questions to ask.  It might sound counterintuitive, as science is fundamentally empirical, but I didn’t realize how important it is to be strong technically to be a good scientist.  It’s taken me most of my master’s to realize how important it is to listen as an early scientist:  thinking independently necessarily follows mastery of technique.   When I move to my next stage of training, I’ll hold onto the increased self-awareness/humility I’ve gained here that has allowed me to understand that experience in a technique is not the same as mastery of it.

As the end of my year approaches, I remain grateful for the support I’ve received: that sense of treasuring the things I will come to miss in this place has already started to set in.

Ashley Ferguson 3

Comparing personal or academic challenges to climbing mountains or finishing races is usually cliché.  But at least once during my time in Cambridge, because I joined the Cambridge Hounds and Hares Cross Country team, I had to climb an actual mud hill (okay not a mountain) to finish a cross country race.

***

 

Memoirs of our week in the lab

Every year the MRC Cancer Unit hosts groups of high school students from across the region to give them an opportunity to experience first hand what life is like in a research laboratory! Here’s what one such batch of students  who visited us this summer had to say:

 

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Alicia, Ben, Carolyn, Charlotte, Leah, Shannon and Stephanie

 

We were given an excellent opportunity to experience what life is like as a scientist in Prof Ashok Venkitaraman’s laboratory at the MRC Cancer Unit for a week. The week entailed hands on laboratory work and talks from PhD students and Postdoctoral researchers. Below is a daily breakdown of our week. We thoroughly enjoyed being part of the Venkitaraman group albeit for a short time.

Monday 24th July 2017

On Monday, we first had an introductory talk and then on to the subject of bioinformatics, led by a PhD student. From him we learned how we could use google to make our own discoveries and what his field is about. It was a really interesting side of biology that we had not seen before and was a really good start to our week. After that, we went into the labs for the first time. With lab coats on, we prepared E.coli bacteria samples for a mini-prep we would be doing the next day. As well as a lot of pipetting with very fancy pipettes, this procedure involved using a lot of really specific equipment. For example, before we left for the day, we put our colonies of E.coli into a machine that would keep them at an optimum temperature and shake them all night to encourage their growth. The day overall was a great start to the week.

Tuesday 25th July 2017

On Tuesday, we continued with the DNA mini-prep we started the day before. In the morning, we collected the E.coli colonies we had selected on Monday and began to prepare them to be able to isolate their DNA. After isolating the DNA, we used restriction enzymes to break it up and expose the gene we were looking for. Then, we loaded the samples onto an agarose gel to undergo electrophoresis and separate the different genes. Unfortunately, this did not quite work out as we had planned (i.e. most of us did not get very good results or any real results at all). However, being able to complete a relatively complicated experiment in the lab was a really good experience and it did teach us a very important lesson: science does not always go right. This has just increased our admiration for the scientists in the lab for their perseverance for trying to find ways of beating cancer.

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Wednesday 26th July 2017

We began the third day in the labs by preparing some slides for confocal microscopy (and somehow none of us broke any), led by a PhD student, before going on to look at them under the microscope. We observed fixed cells under the microscope, and could see how different types of cancer cells (including the famous HeLa cells) expressed different amounts of protein for DNA repair which has implications for ways of treating different types of cancer. This research could one day lead to better therapies for those suffering from cancer and it was really amazing to see such experiments being carried out.

In the afternoon we were taught about protein gel electrophoresis and Western Blotting. Although there was not enough time to do the whole process of western blotting, we did get to do some protein gel electrophoresis and then see some results from already prepared Western blots in a dark room. An added bonus was that we got a little souvenir of the results to take home.Picture4

Thursday 27th July 2017

On the Thursday, we had an introduction to mammalian tissue culture followed by observation of live cells by microscopy and identification of phases of the cell cycle. This was a really good experience as we got to see what is taught to us in a text book in real life, in a real world setting – this was one of the best things about our time in the labs. After lunch we then got to observe a PhD student and her work using the DNA fibre assay. This was something that was new to us, so it was a privilege to see techniques and experiments which most Sixth Form students would not even have heard of. During the whole time, we have to thank the researchers for being so patient with us and answering all of our many, many (many) questions.

Friday 28th July 2017

On Friday, we watched a demonstration of a robotic arm moving cell plates to a confocal microscope. None of us had seen equipment like it being used before and it was definitely something to remember – in some ways it felt very improbable that a machine had been built with this sole purpose in mind. At the same time we also saw how automatic microscopy worked and how images were systematically captured to produce data. In the afternoon, we had the opportunity to take part in a Q & A session with a PhD student and a researcher at the lab. From this we were able to learn more about the different careers and paths within biomedicine. We are all thinking about pursuing careers in Medicine, Biochemistry, Biomedicine and other related fields so this was particularly useful for us – even if we did go off on a tangent at points. Either way, it was a great way to end a great week, and we would all like to say a big thank you to everyone in the Venkitaraman lab for being so welcoming and providing such a brilliant opportunity for us all.

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The long and winding road – never a dull moment!

Lorraine Smith, just retired from her post as Health and Safety manager for the Hutch, shares a very personal account of her journey through life in arriving at that destination.

 

His sister’s black but she is sho ’nuff pretty
Her skirt is short but Lord her legs are sturdy
To walk to school she’s got to get up early
Her clothes are old but never are they dirty
Living just enough, just enough for the city…um hum

                                      Living for the city, Stevie Wonder 1973

age 2 with sisterThis song conjures up strong emotions; we had to wash our hair in the sink and use the grill to warm the kitchen, but we were those sisters, growing up in the east end of London, grooving at Tottenham Royal; we were full of ‘soul’ and life was on the up!

Not really a typical teenager though, by chance my parents witnessed a drowning at Victoria Park Lido and so they were keen for us to be good swimmers. I turned out to be quite good at it and won the Middlesex Championships for the under 10s. I couldn’t get enough of it and by the age of 12 could map London by its swimming pools, from Havering to Hillingdon, there weren’t many that got past me! at 11 with medals

at 15 receiving trophy

So it wasn’t really surprising that the early part of my career was as a swimming pool and recreation manager. I loved being a trainee, I was involved in many varied activities including Hackney Council’s firework display (H&S was in its infancy…and it showed!), London Boroughs pensioners talent competition (the final was at the Guild Hall, Cambridge, my first visit) and the London Youth Games (our biggest achievement was finding a ski team in Hackney).  For 3 years, I attended day release at the South East London technical college (Lewisham), it was here that I first encountered the 1974 Health and Safety at Work act, but not all doom and gloom, I also discovered a liking for chemistry. After qualifying I became a recreation manager for the neighboring borough of Islington,  the main challenges were to optimise and promote the programme (including fitness and swimming lessons, school holiday timetable and other special events), report technical problems in order to avoid service disruption (sounds familiar!), staff management  and dealing with the public. The face of our industry had been changing, traditionally recreation departments would provide washing facilities (both self and laundry) in addition to swimming, mainly for children having fun. But in the mid 70s most people had more leisure time, they enjoyed their own bathrooms and washing machines, their jobs were becoming more sedentary and hence the evolution of, fitness swimming, gyms and sports centers.  The other revolution, technology was in its infancy, photo copiers could manage one copy at a time and these were normally, singed, but by the mid 80s I got my first computer at work, it was a portable word processor/printer, that saved about 40 pages of A4, I loved it.

So here I am aged about 30, my childish optimism coming true; I have a house, good job, married to Andy and have a toddler, Jacqui. I had it all then came prime minister Margaret Thatcher. In the 80s’ MT introduced ‘competitive tendering’ ; local councils had to invite private companies to tender for services; council departments could put in a bid themselves, but to be competitive redundancies were inevitable. After fully embracing my job for 16 years it was time to reassess, I volunteered for redundancy in order to become a full time student at Essex University studying Biochemisty. As a born socialist I found myself thanking Maggie, although I kept that to myself for years. To be honest, if I woke up and those 3 years had been a dream, I wouldn’t do it again, it was tough, more agonising than swimming training… childbirth, well nowhere near as painful, I’ll admit to that. But I’m really, really glad that I did the course, and have had the opportunity to work in science, in particular here at the Hutch.

When I told my family that I was to become a Health and Safety Manager, my daughter declared that I was an ‘unlikely suspect’, in fact the only job she felt I was less suited to was something that involved traveling, this is because I have a very bad sense of direction and am accident prone. I’ve tried to use the latter ‘quality’ to my advantage, hoping that I can give others the benefit of my experiences; if there is a hazard, I would have found it! For me life’s never boring, its always a surprise to me whose lab I will come out into when leaving an instrument room or which staircase I end up in, so although I wisely tell you all to use the quickest route if the fire alarm goes off, I do realize that this is often easier said than done!

The worst thing about being a Health and Safety manager is the bad publicity, even we make excuses for our being! If we are proactive, we can be seen as hindering business and if we are pragmatic we can be seen as timid and at worse lazy. I think the answer is to be true to yourself, research a problem, decide on the best (safe and practical) solution  and then give clear advice/recommendations. Once I had figured out this strategy, life as a Lab manager / H&S was just right, a nice mix of regular events, fire drills, lab inspections, committee meetings etc. And the unexpected, burnt popcorn (sorry), smelly drains, accidents, untimely floods and plant breakdowns.

So here I am now, retired and looking at the day; I have lovely granddaughters (thank you Jacqui), the sun is shining and my garden is looking good, Andy is in the garage making a noise, no, my mistake, he is in the kitchen making coffee, lovely, just got time then to wish you all well and hope to see you in the canteen from time to time.

with the grandkids

All the best, Lorraine

Of inspiring fresh minds & fresh new ways of looking at cancer

The MRC Cancer Unit has a longstanding tradition of engaging with young minds to encourage them into science and cancer research in particular. Towards this, every year we host visits from students to our research laboratories, be it in the form of summer placements (internships) or shorter, week-long visits from school students, with each stint encompassing both theoretical and practical aspects of the latest in cancer research. We believe this experience presents a unique opportunity to those who attend, to gain insight into the world of research, and explore future possibilities in science, in addition to providing us, as scientists, a chance to reach out and enthuse the next generation about how exciting and rewarding a career in science and research can be. This year was no different. We had three young visitors to the Fitzgerald laboratory over the summer and a bunch of curious sixth formers from the Hills Road Sixth Form College in Cambridge who spent a week at the Venkitaraman laboratory. Here is what they told us about what it all meant to them!

Our MRC Cancer Unit Experience!

Overall, the week spent at MRC Cancer Unit was amazing. We were exposed to very current and upcoming scientific topics and were also given the opportunity to use extremely advanced equipment and practice some techniques.

On the first day we learnt how to transform E. Coli bacteria using a technique called electroporation, which we were able to apply to practical work. Tuesday began with a talk by a former Hills Road Student, who has taken time from his medical studies to do a PhD at the MRC Cancer Unit. His talk gave us an insight on how different proteins work together to carry out actions in the cell. In the case of the particular protein that was the topic of the talk, we learnt that it must be degraded in order for the cell to survive, however, if it is allowed to accumulate inside the cells, the cell would be unable to grow and will die. Encouraging this signal may prove important in cancer therapy. Learning this theory helped me to understand how the MRC Cancer Unit lab are trying to better understand how cancer works and what type of research is possible to do in the future. In the afternoon, we completed our work from the day before and learnt that in research not all practicals go to plan, but learning from them is key to discovering new findings!

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Wednesday morning, we learnt about proteins; how to run polyacrylamide gels and how to interpret the results. We then moved onto Western blotting. The theory of the three-day process was explained, which involves applying the gel to a sticky membrane. This allows a print to be made of the gel, which can then be ‘probed’ using specific antibodies to show only the protein of interest. We then went into a darkroom and got to use the film processor to collect prints from our gel and analyse them; this was the highlight of my experience even if it was often too dark to see what you were doing!

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In the afternoon we were able to see the workings of a very new technique; CRISPR/Cas9. We were explained how this new technology allowed the researchers to make precise, targeted changes to the genome of living cells. Microbes have been using CRISPR/Cas9 for millions of years. It was fascinating to see how we have mastered one of nature’s techniques to turn it into our own advantage and for me, it was fascinating to see the potential that this technology could have, not only in the treatment of cancer but also other illnesses!

Thursday’s focus was microscopy. We watched the loading robot arm in action. It was used to move the plates with cells from the incubator to the microscope stage. Then we used the confocal microscope. Each member of the group located a separate field of view of the cancerous cells, which was then imaged every 2 minutes to show how the added solutions affected the cells. Next, we mounted a cell suspension onto slides, adding cover slips. The cells had been prepared with a dye so that, when we viewed them under the microscope, we could see the nuclei within each cell. It was fun to use such high tech equipment, despite some of the rooms having to be kept at a chilly 16oC so that the microscopes are able to function properly!

Friday was mostly an evaluation of the week. We had a careers session with another former Hills Road student, who is now working towards a PhD. He told us all about life as a student, as well as working within biomedicine which I found very interesting as well as useful for the future. In our feedback session with the scientists from Prof Venkitaraman’s group and Dr Harvey, the head of Biology from Hills Road, we discussed what we liked most about the week – for me it was getting involved in all the practical work, which we do not usually have the opportunity to do at school.

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(On behalf of: Alba Saenz de Villaverde Cortabarria, Diana Coroi, Elizabeth Ogilvie, Hannah Kilford, Lucy Wilkinson and Sabina Ray )


Cancer vs Computer Science – new ways of looking at an old disease!

Ben Hall spoke on his work using computer science techniques to understand cancer biology at the Microsoft Future Decoded Exposition, held at the ExCel in London, in November this year. In a programme of talks relating to how computing is transforming society in diverse areas including policing and health care, Ben highlighted how his lab uses concepts taken from the analysis of software and hardware to tackle the unique challenges in fathoming the early stages of cancer development. Here’s a bit more from what he had to say:

ben-hall-fd-talk

Cancer is a major problem in biomedicine. Whilst scientists have made great strides in some types of the disease, we have not been able to reduce adult mortality greatly over the past few decades. My laboratory at the Medical Research Council Cancer Unit at the University of Cambridge works at the interface between computer science and cancer biology, using our knowledge of the disease to build “models” of cancer- that is, mathematical representations that allow us to simulate and test our ideas, and to make new predictions. This work, carried out in collaboration with experimental and clinical collaborators, gives us an opportunity to find new ways of understanding and eventually treating this major illness. This is particularly valuable when considering the earliest stages of cancer, where the research could aid early detection and intervention leading to better clinical outcomes. It requires a new set of tools too, like the BioModelAnalyzer, which I will speak about at Future Decoded. The BioModelAnalyzer, developed by the Fisher group at Microsoft Research Cambridge, allows model creation and analysis through a bespoke user interface. Such tools empower experts in cancer biology to take advantage of the latest algorithms and approaches without requiring them to become computer scientists.

 The unique problems of cancer

 As a disease, cancer has been recognised for thousands of years. The earliest records of sufferers are from 3000 BC in ancient Egypt (1), where documents and mummified bodies show an acknowledgment, if not an understanding, of the disease. In the modern day, we have made substantial leaps forward in our ability to treat specific forms of the disease. There have been major successes in the treatment of chronic myelogenous leukaemia for example. The overall progress in treating adult cancers has been slow however, particularly when compared with the great successes in other areas such as cardiovascular disease (2).

 Two features of cancer present major challenges to our understanding and our ability to treat it. Despite one in two adults developing the disease in their lifetime, from a cell perspective cancer is an extremely rare failure. With 35 trillion cells in the human body at one time, only a handful will develop into cancer over a lifespan. The disease itself results from rare cancer progressing events, occurring in exactly the wrong order. Changing that order may prevent the cancer from growing, or reduce the disease’s aggressiveness (3). It’s hard to spot these rare events early, creating a barrier to understanding how cancers start.

 The second problem is biological complexity: within each cell is a large, complex network of proteins, genes, and metabolites that interact and exert different types of control on the behaviour of the cell. Whilst we may be able to draw out some of these networks, our view on the dynamics is clouded by the fact that our understanding is incomplete, with whole pathways and precise physical measurements missing.

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 A model of cancer metabolism in the BioModelAnalyzer.

 Novel solutions through CS

My group at the MRC cancer unit tackles these challenges by using techniques taken from computer science. The tools developed for the analysis of software and hardware systems allow us to address these problems by using abstract models to fight the issue of complexity. Alongside this we use “model checking” approaches that can draw out rare events from a network. They do this by providing guarantees of behaviour backed by rigorous mathematical proofs, ensuring that uncommon cancer progressing acts are found.

This creates a new type of problem; how to get these methods into the hands of the people who can take best advantage of them. One solution is bespoke user interfaces. The BioModelAnalyzer takes this idea forward; a web interface allows bioscientists to construct and analyse models, whilst abstracting the underlying CS research away. In addition to connecting the tools to a new audience, it also speeds up the work of experts in the field by simplifying the model construction process. My own laboratory has used this to understand the role of membrane proteins in determining the cells response to nearby tumours, as well as cellular metabolism and the cell cycle (see figure 1). These new models give us unique insights into the drivers of cancer, and help us explain why some drugs may fail. We can also identify new targets for drug development, and suggest treatment combinations that have not yet been explored. With these unique opportunities, these results show why bringing CS techniques to biology has a bright future!

  1. http://m.cancer.org/cancer/cancerbasics/thehistoryofcancer/the-history-of-cancer-what-is-cancer
  2. https://www.cdc.gov/mmwr/preview/mmwrhtml/mm6337a6.htm
  3. http://www.nejm.org/doi/full/10.1056/NEJMoa1412098

Inspiring the next generation of cancer researchers: the MRC Cancer Unit open day 2016

– The first annual MRC Festival of Medical Research took place from June 18-26 2016. The Festival was planned as a celebration of the medical research that is supported by the MRC and its benefit to society. MRC-funded research establishments showcased and discussed their work through events and activities at MRC-funded units, centres and institutes across the UK. Examples of some events include open days, public lectures/debates, activity days, workshops, interactive seminars and quizzes. As part of this Festival, the MRC Cancer Unit hosted an Open Day for Sixth form school students. Sixth-form students from a number of local schools came to visit the Unit on June 22nd.

Each tour began with a brief introduction to the Unit, followed by a health and safety briefing. Students (usually 8/school group) were then provided with lab coats and assigned to a chaperone (a Unit staff member), who took them on a tour around the labs. The students stopped in four different labs along this tour, where they met with research staff, who spoke to them about their research and then guided them through some hands-on activities. While the lab stops were short (20 minutes), every effort was made to ensure that all students were able to participate.

Carla Martins

Dr Carla Martins describes some ways in which lung tumours can develop

The first stop in the tour was in the labs of Dr Carla Martins and Dr Jacqui Shields. Here, the students were split into two groups, with each group completing an activity in one of the labs. The Martins group ran a computer-based demonstration looking at lung tumours and ways to determine their response to the investigational therapies that they are working with. They used microscopy to look at cancer cells under normal conditions (bright field) using fluorescence microscopy (examining glucose uptake into cancer cells). The students also had the opportunity to carry out some crystal violet staining to determine cell viability/health.

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The Shields group ran an activity based around their work on the tumour microenvironment

The Shields group work on the tumour microenvironment, with a particular focus on supporting (stromal) cells. They use antibody technology to investigate the stromal compartment. The students were given a brief overview of antibody technology and how antibodies can be used to stain the tumour stroma for research methods such as immunofluorescent microscopy and flow cytometry. The background to and differences between the two techniques was explained using a range of props, images and videos.

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The Fitzgerald group used DNA extraction experiments and Norman to demonstrate what they are doing to try to detect cancer before it develops.

The second stop on the tour took the students to the lab of the Fitzgerald group, where they were given a demonstration of the CytospongeTM (pill on a string) using Norman (a life-sized model of a human torso). The Cytosponge is a simple pill-on-a-string device for detection of the very early stages of oesophageal cancer development. The patient swallows the device, waits for 5 minutes (for the capsule to dissolve) and then the device is pulled back up the oesophagus (using the string), collecting cell samples from the length of the oesophagus along the way. The cells collected using this device can then be tested for the presence of TFF3 (trefoil factor 3), which is a known marker for Barrett’s oesophagus, a precursor for oesophageal cancer development. The students were invited to carry out some DNA extraction experiments (from strawberries!) and were given some background on the importance/uses of human DNA samples for the groups research efforts.

Computational modelling

Using computers to understand cancer metabolism with both the Frezza and Hall groups

Following this, the groups were then taken up to level 3 of the building, where they participated in a joint activity run by the Frezza and Hall groups. This activity demonstrated how the two groups are collaborating to use computational modelling methods (Hall group) to more clearly understand cancer metabolism (Frezza group). This involved looking at how the groups are using computers to simulate the effects of mutations to metabolism on the cells behaviour. A web-based tool (called the BioModelAnalyzer) was used to generate a model of cell behaviour (a schematic representation that describes how cellular proteins communicate with one another and change over time). Cells, genes, proteins and metabolites were drawn onto a blank canvas and each assigned a function (the model). Stability analysis (tells you how all simulations end) was then used to test the model and to see how it behaves.

 

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Students try their hand at multi-channel pipetting for the Venkitaraman group activity

The final activity of the tour took place in the Venkitaraman labs, where members of the
group gave the students a short talk on phenotypic screening for target-based drug discovery (explaining why phenotypic screening is more successful in this case). The robot that is used for screening was demonstrated to the students and they were then given a go at multi-channel pipetting (see image). Finally, fluorescence microscopy was used to demonstrate ways in which proteins are labelled (GFP) in order to track movement within a cell (a video of nuclear translocation was shown).

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Discussing the wide-range of science career paths with MRC Cancer Unit staff

The tour ended with a short careers session and some light refreshments on level 1. Students had the opportunity to meet with staff working in different roles/at different career stages from across the Unit to ask questions on topics ranging from their own research interests to their career path to date. A number of our staff have had unusual career paths to their current positions, so this was a great opportunity for the students to hear about their own personal experiences. This session was very well received by the students who will shortly be making decisions about their own futures.

The MRC-CU Open Day was a great success, which was enjoyed by both students and Unit staff alike. Its success is due in no small part to the commitment and enthusiasm of our staff to showcase the best of the Unit, to communicate the benefits of medical research to our visitors, and to inspire the next generation of cancer researchers! Hopefully we have managed to achieve these aims. The feedback we have received on this to date has been very positive, with one visitor remarking “I was so impressed by the amount of information and activities that you fitted into the time and how interesting it was to see such a variety of research groups and to hear from group leaders, postdocs and PhD students.” It was very rewarding to see such great enthusiasm and interaction from the students…..it definitely made our efforts worthwhile! We are looking forward to building on this experience for future outreach events!

 

The challenges of developing more effective treatments for cancer: An insight into therapeutic target discovery and validation efforts at the MRC Cancer Unit

– One of the aims of the MRC Cancer Unit is to create more effective treatments for cancer. Simon Stockwell is a postdoc working with the Venkitaraman group as part of the Therapeutic Target Discovery & Validation Programme. The team are focussed on devising new approaches for the discovery and validation of therapeutic targets, an essential early step in translating cancer biology findings of the lab into the new drugs in the clinic. In this post, Simon discusses his background, his role in this highly collaborative lead discovery effort and the many diverse processes and challenges involved in this process.-

I am a biologist working at the MRC Cancer Unit, previously having studied at the University of Manchester (UMIST), followed by positions at the Institute of Cancer Research and the UCL Cancer Institute. My training has focussed on cancer cell biology and the development of cell assays for chemical and genetic screens. The key techniques acquired in my earlier posts that I now use here are cell culture, assay development and high-content microscopy. My main role as a postdoctoral research associate in the Venkitaraman group is to support a lead discovery project through lab-work and coordination with a large project team from a broad range of research specialisations, including members of the Chemistry and Biochemistry departments of the University of Cambridge.

There are several lead discovery projects ongoing within the MRC Cancer Unit, all with the aim of finding new ways to target previously ‘undrugged’ proteins to identify new therapeutic leads that can be developed into drugs for cancer therapy. The nature of the work is highly collaborative and multi-disciplinary; In addition to the cancer biology expertise provided by the MRC Cancer Unit, lead discovery projects involve chemistry and biochemistry expertise. An exciting aspect of my work is to coordinate my lab-work with that of teams from these different disciplines in order to zero-in on the right kinds of molecules that show the best potential for development into drugs.

A key characteristic of the desired therapeutic molecule is that it will functionally interfere with, or inhibit, a specific part of the cell referred to as the drug target. The targets will vary between projects to suit particular cancers. From a biological perspective, lead discovery projects can be divided into two broad categories based on how the target for a particular therapy is determined; studies can be classed as being ‘target-based’ or ‘phenotypic’ (Figure 1). This distinction depends on whether the ideal biological target for a particular therapy is already known in advance, or alternatively, if a target needs to be identified after identifying a hit molecule producing the desired response, or phenotype, in the drugged tumour cells.

Target based and phenotypic screening

Figure 1 –Target-based and phenotypic screening strategies. Both strategies share similar steps using cell-assay screening of molecules, but they differ in the assumptions made about the therapeutic target, yielding different advantages. For target-based screens the strategy is focussed on a chosen target, which allows for direct implementation of structural and biophysical knowledge of the target to enhance empirical development of the target-relevant structure-activity-relationship (SAR). Greatly contrasting with this is the phenotypic screen, which is target-agnostic from the outset and allows for a broader variety of disease-relevant targets to be discovered. Target-based screens are highly dependent on choosing a relevant and tractable target; phenotypic screens may identify a diversity of promising hits, but establishing the target(s) of action can prove challenging.

Target-based and phenotypic lead discovery projects are both of interest to our team. Both types of project rely heavily on the reported findings of the entire cancer research community to identify the most promising targets or phenotypes in cancer that can be explored to reveal novel, more effective therapies. Understanding the underlying biology of the drug target is vital in allowing us to develop the cell biology tools needed to observe desired cancer cell phenotypes resulting from drugging these targets. Once a drug target is established for a project, the biochemists and chemists we work alongside provide the necessary skills to determine and use the molecular structure of the target to inform the design and synthesis of the molecules for testing (referred to in chemistry as compounds).

I am working on a target-based project, the goal of which is to identify new compounds that can therapeutically block the activity of a specific target protein known to be driving the proliferation of a range of tumours through roles in chromosome segregation. The Venkitaraman group have studied the biology and mechanism of this target for several years to suggest how it might be modulated for cancer therapy. Rather than block the active site of the target, this project aims to block the protein-protein interaction between the target and an activating partner protein. Since the drug target for the project has already been established, the team I work with has designed a series of cell biology assays to detect when tumour cells grown in the lab exhibit phenotypic behaviour characteristic of the successful blocking of that target.

The choice of phenotype with which to screen our series of compounds requires careful selection of an appropriate method of detection in the lab. In this case the depletion of a protein from the mitotic spindle in dividing cells is the primary phenotype. To monitor this behaviour we use a method called high-content microscopy to detect our desired drugging phenotype in fluorescently labelled images of cells treated with our compounds (Figure 2). High-content microscopy combines the information-rich data of microscopy with image analysis software to allow a wide range of cell phenotypes to be systematically detected on a cell-by-cell basis. In this case high-content microscopy allows us to exclusively observe specific subpopulations of cells for which the drugging phenotype is relevant (i.e. mitotic cells). The approach also enables us to isolate the mitotic spindle as the region in these cells that is employed for quantification of the target protein. We screen our compounds in this high-content assay by applying varying concentrations of each molecule to cancer cells grown in the lab. After a predetermined time the drugged cells are fixed, fluorescently stained with antibodies for the spindle and target, imaged and analysed to determine whether the desired phenotype can be detected. Image analysis software allows us to score the strength of the phenotype observed in the microscope images and determine how this varies with the concentration used for each compound.

High content assay for target depletion from the mitotic spindle

Figure 2 – High-content assay for target depletion from the mitotic spindle. Cells grown on 96-well plates are treated with titrations of test compounds to allow EC50 calculations of cell activity to be calculated per compound. The cells are fixed, fluorescently stained and imaged/analysed on a high-content microscope. Image analysis software is used to estimate the abundance of target protein (green) at the spindle (red). In the composite images above this spindle:target overlap is visualised as yellow. Hundreds of mitotic cells from each drugging condition are gated for the depletion phenotype using a spindle-localised target fluorescence intensity threshold established from the control cells on each assay plate (red line on histograms).

It is predicted that molecules inhibiting the target should reduce the viability of the drugged cancer cells. Those compounds that produce the correct responses in the high-content assay are subsequently assessed for how effective they are at killing cancer cells using a viability assay. The combined high-content assay and viability assay data are used to place the compounds in rank order of cell-biological effect. These results assist the project team in making an informed decision as to which structural characteristics of the tested compounds productively contribute to the desired cell activity, referred to as the structure-activity-relationship (SAR) between a compound and the target.

It is very rewarding to see new rounds of compound synthesis deliver advances in compound potency against the target in keeping with the predictions we make using the cell assay data and our ever-improving model of the SAR. The interaction between the different academic disciplines on the team is essential for identifying the key determinants that will govern the relative strengths of each compound. We are nearing the point when we will have a choice of several structurally distinct lead compounds to determine which has the best properties to be developed into a novel, clinically suitable therapy.