One of the central questions in immunology is how adaptive immunity generates its diversity while maintaining tolerance. The key mediators of tolerance are T cells, which develop in the thymus, where thymocytes rearrange their T cell receptor genes and undergo positive and negative selection. This ensures their ability to recognise antigen in the context of MHC, whilst avoiding self-reactivity. We are still far from fully understanding the steps in these processes at the molecular level, especially in humans: What are the developmental trajectories of different T cell subtypes, and how do they relate to their journey through the organ during maturation? What is the functional role played by the macro- and micro-scale environments in regulating this? These questions have gained in importance since several T cell types are now therapeutics in cancer and transplantation, raising the question of how to engineer specific T cell subsets in vitro. In AIM 1, we propose to generate an organ-scale 3D thymic cell atlas at full genomic breadth through genomics and imaging technologies. By combining multi-modal single cell genomics with multi-scale spatial genomics and imaging technologies, we will generate a rich data set for deep and comprehensive reconstruction of tissue architectures in a thymic lobe. In AIM 2, we will carry out computational data integration with new methods for 3D multi-modal atlas assembly to predict lymphocyte developmental mechanisms at micro and macro scales. In AIM 3, we will use an artificial thymic organoid system to simultaneously validate our findings and enhance T cell engineering approaches. This powerful integrated approach combines genomics, imaging and tissue engineering together with computational analyses to dissect design principles of the thymus, a central organ of the immune system. This knowledge will guide the development of engineered T cells as research reagents, and ultimately as therapeutics.

The human immune system controls the efficiency to respond to infections and eliminate aberrant cells, such as cancer cells. Immune function depends on the balanced contribution of many genes, encoding for receptors, cytokines, cell signalling molecules and transcription factors and are modulated by a wide range of environmental and epigenetic factors. Monogenic mutations for immunerelated genes, also known as Inborn Errors of Immunity (IEI), provide unique examples for understanding immune fitness. IEI, individually considered as rare diseases, constitute a group of >400 immune disorders with a combined prevalence similar to leukemias (1/1,000-1/5,000). For a given mutated gene, IEI patients can display a wide range of phenotypic expressivity (from asymptomatic to severely impaired) and different responses to treatments. Therefore, there is an unmet need to address the wide underlying impact of IEI. Previous EU consortia have not addressed these questions in full. It is therefore needed a new generation of researchers, equipped with a complete set of scientific, technological and strategic skills; and a wide vision to face the outstanding challenges in the IEI field. To this end, the IMMERGE MSCA DN combines the talent of leaders from different clinical and basic research and biotech environments to train 11 doctoral candidates. Through our research activity and training activities, we will address key challenges in the field: 1) To assess the functional impact of IEI in different immune cell types through single cell and bulk multiomics. 2) To develop computational tools for dissecting the altered cellular pathways underlying specific IEI. 3) To genetically correct or model IEI and develop pre-clinical models. With our strategy, IMMERGE will generate an outstanding network of professionals able to develop impactful studies that will change the field, generate tools for personalised medicine and generate awareness in the society and influence policy makers

Colorectal cancer (CRC, or Bowel cancer) is the fourth most common cancer in UK, accounting for over 16 000 deaths annually (Cancer Research UK, 2016 statistics). It is also perhaps best understood of all cancer forms, in terms of how it forms, and which genes have a role in its formation. However, despite the large amount of work that has concentrated on understanding CRC, we still do not know all the genetic mutations that cause it. Furthermore, although more than 60 inherited genetic variants that increase risk for CRC are known, the mechanisms that generate the inherited disease risk are not well understood. This is in large part because the genetic variants that carry the largest fraction of population-level risk reside in the region of the genome that does not code for proteins. The variants are presumed to affect the amount of proteins made in particular cells, by affecting DNA binding of proteins called transcription factors. However, actual evidence for this mechanism is largely lacking, mostly because we do not understand exactly how the part of the genome where the variants are functions, and how changes in DNA sequence affect binding of the transcription factors and activity of genes. The proposed research project aims to understand how mutations or variations in DNA sequences that bind the transcription factors changes the activity of genes, and how the changed activity leads to tumour formation. This is basic research utilizing novel high throughput methods and computational data analysis of the experimental results. The project will first generate vast amounts of data in a laboratory, and then utilize and understand it using tailor-made computer programs. The work is very much a collaboration between biological and computational scientists, who will work closely together to understand basic mechanisms of how cells can tell when and where the genes written in their DNA should be active. The researchers will seek to understand 'the second genetic code'. The first genetic code that describes how DNA sequence is converted to protein sequence was decoded already more than 50 years ago, and the first draft of human genome, which describes the sequence of the chemical letters A, C, G and T found in all human cells was published in 2001. Determining the human genome sequence has had a very large impact in several fields of biology and medicine. However, knowing just the order of the letters is not enough to understand how they instruct cells to grow, and how this process goes wrong in cancer. Our project aims to understand how the network of proteins and genes talk and regulate each other when reading the second genetic code. To solve these issues is a short-term benefit to scientific community in terms of deeper understanding, novel methods and computational tools aiding to understand how cancer develops. In the longer term, our results are expected to lead to many applications that help to predict, prevent and treat disease. For example, the results and tools developed within the project can be used to improve predicting of who is at risk to develop cancer. In a wider context, the proposed project in part of a broader effort to use advanced genomic and computational tools to understand the basis of disease. Genetic variants that are located between genes, and are so common that most people have many of them have recently been found to be important in increasing risk to most common diseases. We therefore expect that the methods and tools developed within the project will be widely applicable to the study of the mechanisms that cause other common diseases. Hence, this project will not only impact research on colorectal cancer but will have broader implications for research, prevention and treatment of other common diseases.

Clostridium difficile caused or contributed to the deaths of 8700 hospitalized patients in the UK during 2007, making it the most significant hospital-acquired pathogen. C. difficile is estimated to cost the US health care system 3 Billion USD/year (no current estimates available for UK) representing a serious economic burden that impacts the overall performance and safety of our hospitals {Dubberke, 2009}. C. difficile persists in hospitals by exploiting an infection cycle that is dependent on humans shedding highly resistant and infectious spores. As a result, C. difficile is endemic in many hospitals and outbreaks are difficult to contain, highlighting the compelling need to understand the spore-mediated infection cycle and the factors that lead to C. difficile transmission between individuals. The proposed research will utilize cutting edge genomic and proteomic technologies in combination with in vitro and murine models to study the biology of C. difficile spores, specifically, the signals and molecular processes that lead to the formation of spores and the molecular interactions between spores and the host during colonization. This work has the potential to lead to novel infection control interventions that interfere with C. difficile spore formation and block host colonization by spores.

Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at https://www.ukri.org/apply-for-funding/how-we-fund-studentships/. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.