MRC Doctoral Training Partnership Programme in Translational Immunology, Inflammation and Cancer
Queen Mary University of London and the University of Southampton are proud to run a joint MRC-funded Doctoral Training Partnership. Starting in 2016 in collaboration with the Medical Research Council (MRC) we have established a successful programme that identifies excellent students and matches them with outstanding research projects. The MRC DTP programme began with a 4-year MRC-funded MRes/PhD programme in the areas of translational immunology, inflammation and cancer. Recently we also appointed additional MRC-funded students to study projects addressing skills of national shortage and iCASE studentships who study in association with a commercial partner. Together with university funding, the joint programmes have appointed over twenty students to our MRC DTP to date.
The MRes/PhD is undertaken at either the School of Medicine and Dentistry, Queen Mary or the Faculty of Medicine, University of Southampton. In the MRes year students study (at either Queen Mary or Southampton) three taught modules that include statistics, computational coding and quantitative biology skills. Additionally students undertake three 12-week rotation projects (usually two wet-lab studies and one of which must be predominantly mathematics, computational biology or bioinformatics) which are each assessed by a mini-thesis report. On successful completion and award of the MRes, students select one of the projects as the subject of their 3-year PhD. Thus students experience a variety of research environments and skills that arm them for their future career in the field of science. We are enormously proud of our students, many of whom offer commentary on their experiences to date.
Meet some of the Queen Mary MRes students...
About me: I received my BSc Biomedical Sciences degree from the University of Southampton where I first became interested in Cancer Immunology. This led me to complete an MRes in Cancer Biology at Imperial College London, where I worked in Ovarian Cancer Research and Glioblastoma Research labs. I then joined this MRC DTP at Barts and the London School of Medicine and Dentistry.
Current rotation: My first project combined Bioinformatic research, which I was completely new to, with Cell and Molecular Biology, which I was very familiar with. I undertook this project in Dr Miguel Branco’s lab at the Blizard Institute, where I have been investigating how metabolic changes in cancer affect transposable elements. I applied Bioinformatics techniques in the analysis of RNA-Seq data using R, a programming language. I also used R visually and statistically to analyse my qRT-PCR data.
We had the opportunity to learn Computational Biology, taught by Bioinformaticians at Southampton University, which ran parallel to our first project rotation. It was a very steep learning curve as I had very little prior knowledge on the subject, but the lecturers and demonstrators were really helpful and trained us in theory as well as the practice of Computational Biology. They also provided us with helpful resources on Blackboard, which is my go-to for any help. These sessions at Southampton really helped me get on my feet with my first project where I had to apply these skills in my research.
What skills have you learnt so far? I have already gained skills in bioinformatics and biostatistics. I will also gain biotechnology skills in my next project with Dr John Connelly’s lab, where I will get experience in organotypic culture, biomaterials and 3D bio-printing. I also hope to improve on my bioinformatics as I would like to use these techniques in my PhD and future research. In my final rotation, I hope to learn proteomic and mass spectrometry techniques.
What have you enjoyed the most and the least about your experience so far? I have mostly enjoyed learning a whole new area of research – bioinformatics. It has been very challenging, but it has been great to be able to use it in real research. It is hard to keep up with the work-load as it is a very fast-paced programme, but it has been a new challenge and an enjoyable experience.
Sheila Olendo Barasa
About me: My first degree was a BSc in Anatomical Sciences with Industrial Experience, which I completed at the University of Manchester. I went on to obtain an MSc in Cancer and Molecular and Cellular Biology at Queen Mary University of London.
Current rotation: My first rotation was a computational project, which I took in Dr Borbala Mifsud’s laboratory. Here, I looked at whether a correlation existed between differential gene expression and differential regulatory chromatin interactions in Acute Myeloid Leukaemia patient samples.
What skills have you learnt so far? For this project, I used a variety of bioinformatics techniques involving enrichment analyses, RNA-seq analysis, data integration, in order to analyse RNA-seq and promoter CHi-C data. I expect to become proficient in bioinformatics in my first year of the programme. I am also dedicated to having an in-depth understanding of bioinformatics; I have therefore chosen “bioinformatic-heavy” projects for all three of my rotations. Additionally, I expect to learn contemporary world-class wet-lab techniques, which I believe will be invaluable in a research career.
How did you find the mathematical/computational component of the DTP? Coming from a background with minimal bioinformatics knowledge and skills, the taught bioinformatics module offered at Southampton University as part of the MRC DTP programme provided me with a solid foundation and reinforced my understanding of bioinformatics techniques, which I used in my first rotation.
What have you enjoyed the most and the least about your experience so far? I think that the MRC DTP programme could be improved by offering professional networking opportunities, for all students enrolled onto the programme, across the various institutions. I was however pleased to learn that the MRC DTP programme offered a selection of 27 projects to choose from, which boasted vast research topics and various wet-lab and dry-lab cutting-edge research techniques. This was of particular importance to me, as it enabled me to make an informed decision about my potential future direction in a research career.
About me: I am a pharmacist by trade who was lured by the bright lights of the laboratory, the excitement of research, and by a fascination with biology. Following a long-standing desire to pursue research, I completed an MSc in Cancer and Molecular and Cellular Biology at Barts Cancer Institute during the 2016/17 academic year, which not only built my base knowledge of molecular biology, the disease of cancer, and modern immunotherapies, but it also heightened my desire to pursue research at a higher level through a PhD. Having seen first-hand the brilliance of the scientists and expertise at Barts, it was a no-brainer to apply for their 4-year MRC-funded DTP. Additionally, having now completed my first rotation, I am determined more than ever to dedicate myself to these studies; the atmosphere in the medical school is contagious!
Current rotation: My first rotation has been based within the Breast Cancer Group at Barts Cancer Institute. We have been looking at how ductal carcinoma in situ, a form of pre-invasive breast cancer, progresses to invasive ductal carcinoma. In particular, we have been looking at the surrounding immune cell population and how these are implicated in the progression of the disease.
How did you find the mathematical/computational component of the DTP? The Quantitative Cell Biology module at Southampton was a fantastic introduction to bioinformatics, coding, and R Studio. Previously, I had never analysed large datasets or attempted any coding, and so this was a completely new skillset for me to develop. It is evident that this is a must-have skill for the modern biologist in the era of ‘Big Data’, where datasets of ever-increasing size and complexity are becoming commonplace in the laboratory. Therefore, exposure to this expertise at Southampton throughout the beginning of the DTP has been a privilege, gifting us a necessary vital edge.
What have you enjoyed the most and the least about your experience so far? The most enjoyable aspect so far has been to delve into new exciting areas of biology and research. The least enjoyable aspect has been the flipside; that the rotations are short and you have to move on, even when progress in an interesting area is being made.
Meet some of the Queen Mary PhD students...
What is your PhD project about? My PhD project is entitled “Application of circulating tumour cell (CTC) analysis to monitor and predict prostate cancer response to Docetaxel.” So far, the project involves isolating CTCs from patient samples and performing number counts before, during and after treatment, as well as RNA/protein analysis to determine differential expression of genes involved in resistance - with the view to develop a non-invasive liquid biopsy method of monitoring and predicting treatment response in a patient specific manner. The company ANGLE plc are involved in my PhD project.
How you think having a relationship with a company already at this stage of your PhD will help your career development? It’s a great opportunity to gain understanding of scientific research outside of academia, and to forge new professional relationships with people outside of the BCI. I will hopefully learn new, translation techniques that I can’t learn elsewhere that will aid my own research.
What have you enjoyed most and least about your experience so far? I have most enjoyed learning and improving my skills as a scientist, and meeting new and interesting people. I have least enjoyed that unavoidable circumstances that have led to a delay in getting started with my project.
About me: Before commencing the MRC-DTP course I obtained my undergraduate degree in Biomedical Science from Oxford Brookes, a Masters in Cancer Therapeutics here at Barts and spent two years working as a researcher in the Institute of Cancer Research, London.
What is your PhD project and how did you choose it? I chose to continue my final rotation in Molecular Oncology at BCI in the Martin lab as my PhD project. In this project, we aimed to establish the precise impact of DNA repair loss and DNA damage on PD-L1 expression and ultimately sensitivity to immune checkpoint inhibitors, and how this can be exploited therapeutically. I chose this particular project not only because I am fascinated by the research, but also because I felt like I would work well within the supportive and knowledgeable team and within a diverse and friendly large department.
What skills have you learnt so far? I have developed many skills throughout my MRes rotational year, which I would not have otherwise gained. New skills include InCell imaging, cloning, FACS and Flow Cytometry, Confocal Microscopy, tumour digestion and establishing primary cell cultures. I also have built upon existing skills and have had the opportunity to share these with members of my teams.
As my PhD unfolds I will gain more experience, namely in Mass Spectrometry. I also have had the privilege of gaining a sponsored CASE studentship from Astra Zeneca, who are interested in developing my project, providing me with the opportunity to work with them alongside the BCI.
What is your PhD project and how did you choose it? I continued with my 3rd rotation for my PhD. My 3rd rotation, entitled “Role of oncofetal glycosaminoglycans (OFGAG) for the immune privilege of pancreatic cancer,” looked at developing a new CAR-T cell for the treatment of pancreatic cancer. During the rotation I isolated primary human T cells from blood, performed PCR and lots of molecular biology to clone the constructs into a plasmid and performed cytotoxicity assays.
It was really hard for me to choose as I enjoyed all of my projects, but I chose this one because I am really interested in CAR-T cell therapy and liked the translational theme of the project.
How did you find the mathematic/computational component of the DTP? I think the bioinformatics part of the course was really valuable to me as it has allowed me to have a better understanding of what is possible to find from large data sets that already exist. Using the skill I have developed, I have been able to do some work independently and I hope to develop my skills further to incorporate more bioinformatics into my project in the future.
What have you enjoyed the most and the least about your experience so far? My experience of the DTP program has been really positive, I have met a lot of really great people and been allowed to develop a wide range of skills. I have really enjoyed the extra courses and teaching provided by the course, for example the media training day. One of the less enjoyable parts of the course was the first term when we had a lot of course work and teaching in combination with the lab project, which made planning your time difficult. Overall I’m really happy I chose the DTP program at Barts and I am loving my PhD.
What is your PhD project and how did you choose it? I chose to continue my third rotation- “Identification and interpretation of pathogenic noncoding mutations in pancreatic cancer”- as my PhD project. I am currently using bioinformatics to look at publicly available ChiP-seq and matching RNA-seq data to find hotspots of pathogenic non-coding mutations in active gene regulatory regions. Not only is this a subject area I am very interested in, the PhD also involves learning new bioinformatics and laboratory techniques that I have not used before and will be useful in the future.
What skills have you developed so far? So far I have learnt how to use R programming to analyse large data sets. I have also learnt to process and analyse ChIP-seq and RNA-seq data. Further into the PhD I hope to develop my laboratory skills, learning how to process samples for ChiP and RNA sequencing.
How did you find the mathematic/computational component of the DTP? The mathematic/computational component of the DTP programme and taking bioinformatics rotations has definitely helped me with the bioinformatics part of my PhD project.
What have you enjoyed the most and the least about your experience so far? Overall I’ve enjoyed the varied experience I have gained rotating through three different laboratories and meeting new people. I have least enjoyed presenting my work, however, this is necessary and good experience.
How did you choose your PhD project? I spent my third rotation in Sarah McClelland’s research group and have chosen to continue this project as my PhD, entitled “Development of a system to induce specific monosomies.” Our lab works on the underlying biology of the highly disrupted genomes of cancer, focussing on how huge alterations in chromosome structure and number are acquired and tolerated. When progressing from the MRes to the PhD, and choosing which lab to return to, I was looking for a group with a strong publishing record, expertise in techniques I was keen to learn, with projects spanning fundamental cell biology to translational work. For me, the McClelland group not only offered this, but also offered a project which I find interesting and am excited to work on, within a great team.
What skills have you developed so far? Through the rotations, I developed varied lab skills from western blotting, cell culture, immunohistochemistry, molecular biology, microscopy, and experience with CRISPR/Cas9 systems. To complement this, the course is structured such that the taught modules run in parallel to rotations to give a core foundation in the theory of research methods and also computational biology. For me, the content on bioinformatics has been invaluable.
Meet some of the Southampton students...
Jodie Ackland, Integrated PhD in Immunity and Infection
About me: I initially studied Biology at Aberystwyth University and really enjoyed the immunology and microbiology modules, realising that immunity and infection was the field that really captured my interest. Time spent in the lab for my dissertation project really showed me that I loved doing research, so I decided to pursue a PhD, which led me to the MRes PhD at Southampton University.
What is your PhD project and how did you choose it? My PhD project investigates host-pathogen interactions in asthmatic airways, investigating how macrophages respond to combinations of respiratory pathogens and viral infections in the asthmatic airway. This project was highly attractive to me as it encompasses the area of infection and immunity and combines lab techniques with bioinformatics. Together, this will provide me with the translational skills and training required to perform research in an interdisciplinary field such as immunity and infection.
What have you enjoyed the most and the least about your experience so far? I have really enjoyed working alongside other members of my lab group – we are a very translational team with access to clinical samples and pathogens, which is something that initially attracted me to the project. I have to combine lab projects alongside taught modules. Balancing time between lab work and bioinformatics is something that you definitely learn along the way!
How did you find the mathematic/computational component of the DTP? Initially I found the computational component quite challenging as most of it was brand new to me so a very steep learning curve! However, the opportunity to undertake a bioinformatics rotation project has allowed me to develop important employability skills in a more in-depth manner.
Cindy Jawahar, Integrated PhD DTP programme in Cancer Biology
About me: I did my undergraduate degree at Queen Mary in Medical Genetics. I decided to apply for the DTP as I thoroughly enjoyed the immunology and cancer biology modules offered on my course, and was intrigued by the field of cancer immunotherapy.
What is your PhD project and how did you choose it? My PhD project is entitled, "Vaccine Strategies to Target the Cancer Mutanome". It identifies tumour-specific mutations to develop more effective vaccine-based immunotherapeutic strategies. I chose to continue my first lab rotation for my PhD as I found the team supportive, the project fascinating and liked the balance between the dry and wet lab work involved.
What skills have you learnt so far? I have learnt a variety of skills so far - I have learnt how to use R coding algorithms to analyse data from microarray expression analysis to develop signalling petri-nets. I have also learnt how to mine WES data to predict neo-epitopes. I have also gained experience in molecular biology techniques, ELISpot assays and in vivo work with murine tumour models.
How did you find the mathematic/computational component of the DTP? The computational component on the DTP has been very valuable. It has given me a greater understanding of large data sets. I have also had the opportunity to familiarise myself with various packages on R, which I aim to use in my PhD.
Richard Stopforth, iPhD Case studentship
What is your PhD project and how did you choose it? My PhD project focussed on the development of cell-based assays to study Fc gamma receptors – the cellular receptors for antibody molecules. I was originally attracted to Southampton because of its impressive reputation for research in the field of immunotherapy. Moreover, the fact that the project had a company collaboration with Promega and therefore the opportunity to work in the USA was an advantage.
What skills have you learnt so far? During my PhD, I was able to build on my molecular biology skills and learn to perform a range of cell-based assays. I also had the opportunity to develop my presentation skills in countless meetings, journal clubs, and integrated PhD away days. Being part of a large group also provided me with skills in communication and teamwork.
How you think having a relationship with a company already at this stage of your PhD will help your career development? As well as being on the integrated PhD pathway, I was also lucky enough to have an industrial Collaborative Award in Science and Engineering (iCASE) studentship. This meant that the life sciences company, Promega, jointly funded my project. This gave me the opportunity to present my work to industrial collaborators regularly. Towards the end of my PhD, I also had the opportunity to complete an internship in the Research and Development department in the USA at Promega HQ. This allowed me to apply results that I had obtained in Southampton to the development of a new cell line, learn some new skills and gain interesting insights into how companies operate. Overall, having a company collaboration provided me with very useful experiences and contacts for the future.
James Dickie, Integrated PhD programme in Cancer Immunology
About me: After graduating from my BSc in Biomedical Science, I spent a couple of years working as a technician in the NHS to build up my confidence in the lab, before applying to Southampton. I knew I was interested in cancer immunology, but little more than that. Despite having no bioinformatic background, I also want to move into a career involving bioinformatics, so I have been learning by doing during my PhD. Now I have established myself as my group’s go-to Bioinformatician, constantly improving my skills through real-life problem solving.
What is your PhD project and how did you choose it? My project is to identify novel targets for oral cancer vaccines. I wasn’t sure what sort of project I’d work on when I started, but during the initial iPhD lab rotations I found a particular interest in cancer vaccines, and identified an approach I could take to employ bioinformatics to contribute to my ongoing project.
What skills have you learnt so far? Bioinformatics mostly, including all sorts of big data processing and analysis. I’ve also become a very confident presenter, happily speaking to groups and crowds about my work and my field. My science writing is markedly better than when I began, I can comprehend far more from fields both familiar and novel than before, and I’ve learned to work independently, forming my own ideas and acting upon them. A bit of everything really.
What have you enjoyed most and least about your experience so far? Academic freedom has been amazing for me. Being free to create my own questions, and find my own way of answering them, is incredibly satisfying. On the flip side of that though, my least favourite part is when you spend weeks working on an experiment only to find it does not work out. It’s frustrating, but then you learn to accept it as unavoidable.