NIHRDataInsights/HRCSData huggingface dataset:
Title: Single Molecule insights into Nuclear Mechanotransduction
Funder: Wellcome Trust

Abstract: Mechanical stimuli regulate a large number of cellular functions. However, how mechanical forces are channeled through the cytoplasm to eventually reach the nucleus and alter gene activity remains poorly understood. Here we propose to employ a combination of state-of-the-art nanomechanical techniques at different length-scales to uncover the molecular details underlying the main force propagation mechanisms of nuclear mechanotransduction. We will first study the dynamics under force of each individual protein of the LINC complex, which forms a long molecular tether between the cytoskeleton and the nuclear envelope. Secondly, we will investigate the emerging role of the nucleus as a mechanonsensor. In particular, we will test (i) the lipidome changes in the NE of cells exposed to mechanical stress; (ii) the mechanical effect of key post-translational modifications of cryptic sites in specific nuclear proteins after mechanical unfolding. Finally, we will use a combined mechanical-fluorescence approach to track the dynamics of nuclear shuttling of cytoplasmic transcription factors in order to directly test the hypothesis that mechanical unfolding of proteins accelerates their transport through the nuclear pore complex. Altogether, this multidisciplinary project will provide an integrated, mechanistic and quantitative view on how mechanical forces propagate to the cell nucleus, from a molecular perspective.

Lay abstract: Cells are continuously exposed to mechanical perturbations from the environment. While some of these mechanical inputs are sensed and remain at the cell surface, others can travel long distances inside the cell to reach the nucleus, where most of the cell fate ‘decisions’ are made. Mechanical forces determine many cell functions, for example in modulating adhesion, crawling or growth, and are also related to cardiovascular pathologies or cancer. However, the mechanisms by which mechanical forces travel across the cell and initiate biochemical changes inside the nucleus are poorly understood. Many of the scientific methods commonly used in molecular and cell biology cannot be used towards this goal because they cannot apply and monitor the effects of forces. My research will combine new techniques able to apply controlled forces to individual proteins and cells, and study how these forces are transmitted to the cell nucleus and impact on the cell behaviour.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Dissecting the molecular basis of eRNA function.
Funder: Wellcome Trust

Abstract: Enhancers are regulatory non-coding DNA sequences that control cell-lineage and stimulus-specific transcription. Enhancers are transcribed into enhancer RNAs (eRNAs). eRNAs are important for regulating gene expression, but the mechanistic basis for this function remains unclear. I recently demonstrated that eRNAs can stimulate the catalytic activity of the key transcription regulator CBP to promote transcription, interactions which were widespread at enhancers across the genome. In this study, I will ask what is the mechanistic basis for eRNA function? Using multidisciplinary approaches, I will address three related but independent aims: 1) I will use biochemical assays, together with complementary techniques to probe RNA structure. Together with a mutagenesis study of eRNAs using CRISPR-Cas9 in cells, this will highlight the sequence and structural determinants of eRNA function; 2) I will map how different components of CBP regulatory complexes bind to eRNAs across the genome. Combined with methods to highlight eRNA structures bound to the complexes, this will uncover how eRNAs organise CBP complexes across the genome; 3) I will use cryo-EM to study the structure of CBP complexes bound to eRNAs, including developing new methods to facilitate these studies. In combination, these techniques will provide new insights into how eRNAs regulate gene expression.

Lay abstract: Enhancers are regulatory DNA sequences that control when, and in what tissue, particular genes are turned on and off. Only a small amount of the genome contains genes, but much of the genome is transcribed into RNA; thus many RNAs do not code for proteins. I study one type, called enhancer RNAs (eRNAs) that come from enhancers. eRNAs are important for turning genes on and off, but it is unclear how they do this. I will use different techniques to look at how eRNAs work. I will look at how eRNAs fold up to form different shapes, and how this changes the activity of the proteins that turn genes on and off. I will do this in the test-tube and in cells, looking across the genome. I will also look at the atomic details of how folded eRNAs interact with regulatory proteins. This will uncover mechanisms describing how eRNAs work.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Carbohydrate Microarray Facility for the New Era of Glycomics
Funder: Wellcome Trust

Abstract: The Carbohydrate Microarray Facility at Imperial is an internationally leading operation providing collaborations for discoveries of glycan ligands to the biomedical community (http://www.imperial.ac.uk/glycosciences/). Data accrued are making significant contributions to understanding the involvement of specific glycans in health, infections, inflammation, immune responses and cancer. This unique collaborative way of serving the community, with follow-through of data from screening analyses, has enabled substantial advances to be made in glycobiology. Access to ample amounts of glycans that is often required to corroborate assignments from screening analyses has largely depended so far on external collaborations with chemists. New links that we are forging with the Department of Chemistry to provide desired glycans are of fundamental value for the future of the Facility. We are seeking 4 years support to further integrate the new era of glycomics into biology and medicine. We will 1. develop a unique human epithelial mucin/O-glycome resource for diverse recognition studies, in particular microbe-host interactions. 2. expand the ‘glycosaminoglycome’ and brain ‘gangliome’ library. 3. complement and diversify the library of glycan sequences with chemically and chemo-enzymatically synthesized glycans, guided from glycan array data. 4. introduce new software for integrated data management and data mining of glycome array analyses.

Lay abstract: Carbohydrate chains (glycans) are displayed on cell surfaces and surroundings. Innumerable processes in health and the majority of diseases critically involve specific glycan-protein interactions, for example the initial events in infection. Glycans are extremely diverse, can be isolated in minute amounts, and cannot be cloned. Their structural characterization and functional evaluation require specialist technologies. With support from Wellcome Trust we established a Microarray Facility with a highly skilled team equipped with state-of-the-art instruments and a unique technology for presenting hundreds of glycans on microarrays to study the interaction with proteins and microbes. We now request support to maximise diversity in our glycan library by isolating glycans from mucins and other glycan sources using our advanced Beam Search array technology and by synthetic strategies. We will continue to offer microarray analyses to researchers world-wide in a collaborative way as well as render the data more readily accessible to the biomedical community.

Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING);1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: Myosin structure and regulation
Funder: Wellcome Trust

Abstract: The human genome encodes 40 genes for myosin that can be grouped into 12 different classes based on their sequence similarities. Many are implicated in disease from cardio- and myo-pathies and blood clotting deficiencies (Class 2), to deaf-blindness (class 7) and neuronal and gut disorders (class 5). Each myosin is specifically adapted for its cellular role, with adaptations to the motor and lever domains dictating how the myosin interacts with actin filaments to generate motility and adaptations to the tail dictating its cellular cargos. However, we lack an understanding of how the activity of these motor proteins is regulated. Here I plan to focus on class 2, 5 and 7 myosins, to uncover how myosin-2 function is regulated by filament assembly and disassembly, how myosin-5 and 7 function is regulated by the formation of compact inhibited structures, how strain affects myosin structure, modulating its ATPase, a broad mechanism that regulates the behaviour of all myosins, and I plan to discover when and where myosin is switched off in in cells, a fundamental question in biology.

Lay abstract: Myosin is a motor protein found in every human cell. It is essential for the heart to beat, for muscles to contract, for platelets to form blood clots, in hearing, vision and many other functions. We know that there are over 40 different kinds of myosin, and that the individual properties of each myosin is exquisitely adapted for its cellular role. Mutations in the genes encoding these proteins lead to a wide range of diseases from heart disease to deafness and blindness. However, there are still many questions we have yet to find answers to about how the activity of these proteins is regulated. I plan to investigate three specific types of myosin, each associated with disease, to discover how these proteins are switched on and off, and when and where this happens in cells, to understand how mutations affect their normal cellular roles.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: InterPro and Pfam: Protein domains and families for biomedical research
Funder: Wellcome Trust

Abstract: InterPro is a core protein data resource that amalgamates 13 protein family databases (including Pfam) to provide the definitive description and classification of protein domains and families. Various scientific communities rely on the range of annotations provided by InterPro and its member databases to acquire novel insights into the vast amounts of new DNA sequence data, enabling scientists to interpret experiments and design new ones based on annotations spanning complete genomes down to single residues. The past five years have witnessed a major increase in the scale of sequences, concomitant with the emergence of AI/ML approaches for unlocking the biological signals encoded within the data. This project will exploit these innovative approaches to enhance protein annotations and refine classifications through the incorporation of additional data types, along with the application of ML methods and organisation of the protein family data. We will integrate KOfams and AMRFinder into InterPro, while continuing to scale the InterPro/Pfam/HMMER resources to tackle billions of proteins. Cumulatively, these developments will accelerate biomedical research by facilitating scientists to decipher the effect of human mutations, understand drug interactions, combat antimicrobial resistance, and tackle emerging pathogens.

Lay abstract: Molecular biology and by extension, the field of biomedical research have been revolutionised by our ability to read the genetic code. The string of ATGCs code for genes that in turn encode proteins, the essential molecular machines of life. Currently our ability to read the DNA of all species outstrips our capacity to understand the function of their encoded proteins considerably. Therefore, it is crucial to develop and apply existing and novel computational tools that facilitate transfer of functional information from characterised to uncharacterised proteins. InterPro, Pfam, and the HMMER web server are three resources that group similar protein sequences together, thereby allowing function to be attributed to previously uncharacterised proteins. In this project we will improve the scalability of these key resources and incorporate biomedically relevant data to enable Deep Learning artificial intelligence that will potentially revolutionise future developments.

Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE
Title: Stress signalling in intestinal maintenance and regeneration
Funder: Wellcome Trust

Abstract: Many adult epithelial tissues lose cells from constant environmental stress. Thus, an epithelium’s ability to sense stress, defend itself and stimulate repair (e.g. by stem cells) is vital to prevent tissue dysfunction, degeneration, inflammation and cancer. Despite its importance, this process is poorly understood. Using the adult Drosophila intestine and its unparalleled genetics, combined with proteomics, transcriptomics and fixed and live imaging, I will determine how stress signalling promotes epithelial resilience, maintenance and regeneration focussing on three main aims. 1) Reactive oxygen species (ROS) produced by damaged fly intestinal epithelial cells (IECs) promote intestinal stem cell (ISC)-mediated regeneration, partly via p38 signalling in IECs. I will determine how ROS promote intestinal regeneration by identifying ROS-controlled regulators of regeneration and determining molecular responses to ROS/stress signalling. 2) I have recently found that some stress pathways display rhythmic, circadian activation. I will investigate their role in intestinal maintenance. 3) I have shown that when new IEC production by ISCs is inhibited, IECs increase their lifespan to prolong epithelial maintenance. I will identify adaptive mechanisms that extend IEC lifespan when new cell production is blocked. Understanding these processes could provide novel therapeutic strategies for tissue regeneration, inflammatory diseases, cancer and age-related pathologies

Lay abstract: Many of our tissues, like our gut, lose cells from constant environmental insults, for example from pathogens or chemicals. Thus, a tissue’s ability to sense damage, defend itself and promote its repair is key for its proper function and preventing disease. Despite its importance, this process is still poorly understood. To better understand this, we are using the adult fruit fly intestine, which is remarkably similar to our own gut. Together with genetic, biochemical, molecular and imaging techniques, we aim to determine how oxidants and damage-sensing signals trigger cells to defend themselves and support tissue repair upon injury. We also aim to test whether biorhythmic cues received by tissues support their upkeep by fostering new cell production and to identify ways cells can survive longer to prolong tissue integrity when new cells can no longer be produced. Our work could provide novel therapeutic strategies for tissue repair, inflammation and cancer.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Mechanisms and roles of transmissible RNA
Funder: Wellcome Trust

Abstract: Protein coding and non-coding RNA can spread between cells and tissues of an organism. RNA mobility between organisms has been documented within and among different kingdoms of life including fungi, plants and animals. However, the underlying mechanisms and roles of such transmissible RNA are poorly understood. Our recent studies demonstrated that honeybees share biologically active RNA among members of the hive through secretion and ingestion of worker and royal jellies. The jellies harbor naturally occurring exogenous (e.g. viral) and endogenous RNA. These findings suggest that RNA transfer plays a role in social immunity and signaling between honeybees. Therefore, the key goals of this proposal are: to establish a metabolic RNA labeling system in honeybees; and to apply this system to study natural RNA transfer-mediated antiviral immunity and impacts on the physiology of recipient bees. To achieve these goals, I will combine RNA biology techniques and imaging with high-throughput sequencing to establish a functional transmissible RNA pathway in honeybees. This project will provide knowledge and tools that will enable studying the biology of RNA flow in other organisms, including humans, in diverse biological aspects; hence, will ultimately contribute to the development of RNA-based applications to promote health and disease control.

Lay abstract: Honeybees are eusocial insects, living in a colony that is often described as a superorganism. RNA mobility among cells of an organism has been documented in animals and plants. We recently showed that RNA spreads further in honeybees, and is horizontally transferred between individuals and across generations. Our understanding of the functions of such RNA flow has been limited to host-parasite interactions where the RNA negatively affects the recipient organism. Nevertheless, the question why any organism would uptake RNA from the environment has remained unanswered. To answer this question, I will adjust an established method that labels cellular RNA to tracking natural RNA transmission. This will enable study of the mechanisms and roles of transmissible RNA including social-immunity and genome regulation with impacts on physiology and fitness of recipient bees. This research will provide means and insights on beneficial RNA-based communication between organisms that could be applied to enhance health.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: KRAB-ZFPs and the establishment of lineage- and species-specific gene regulatory networks
Funder: Wellcome Trust

Abstract: KRAB-ZFPs constitute a large yet neglected family of proteins with around 350 members in human and mouse. Collectively, they target transposable elements and until recently were thought to be mostly involved in their transcriptional repression in embryonic stem cells. During my post-doctoral work, I unveiled the binding sites of most (222) human KRAB-ZFPs, but the role played by the majority of them could not be fully explained by current theorems. Instead, we found that many target ancient transposable elements which often contain regulatory platforms; we also obtained correlative evidence that these could affect the expression of nearby genes. We hypothesize that evolutionary conserved KRAB-ZFPs can use their heterochromatin-inducing capabilities to modify accessibility of these transposable element-derived regulatory elements. We propose to functionally demonstrate this potential by using large scale enhancer screens in multiple cell types. Furthermore, we want to follow-up on these findings by genetic manipulations aimed at characterizing the biological processes affected by a few KRAB-ZFPs, including the generation of mouse models. Finally, we want to better understand the evolution dynamics of KRAB-ZFP binding sites and verify if they can lead to lineage- and species-specific rewiring of gene regulatory networks.

Lay abstract: KRAB-ZFPs are a family of proteins so numerous that it was unreasonable to study them on a large scale until recently. Through indirect studies of a common cofactor, they were known for their role in ensuring that invaders of viral origin residing in our genome remain dormant. My post-doctoral work unveiled where each human KRAB-ZFP binds in the genome - however, the biological role of most of them remains nebulous. We found significant evidence indicating that that they could influence regulation of cellular genes at a distance. We propose to investigate this hypothesis using an approach that will directly test if they are functional in that regard. We also want to determine if they can help explain many of the differences that exist between species (for example, mouse and human). Finally, we want to improve our understanding of how they can generate these differences by comparing how the same sequences evolved in many related species. We will pay special attention to variability between human individuals, using genome sequencing data that is rapidly accumulating, as the targets they bind have in the past been largely ignored as 'junk DNA', but are now thought to play important roles in biology.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Pathfinder Commission for Planetary Health and Prosperity
Funder: Wellcome Trust

Abstract: We propose a global Commission to quantify evidence for national, regional and global actions that will be positive for health, the environment and the economy. It will draw on knowledge generated by other initiatives where relevant but will fill a major gap that is not currently addressed, namely the focus on human health as well as decarbonising economies. This will require identifying and assessing policies, technologies and interventions across a range of sectors including transport, food systems, cities, energy, industry and health systems. The Commission will fill a number of knowledge gaps that are impeding progress towards a healthy zero-carbon economy – namely which actions will have the largest multiple benefits for health, the environment and prosperity in particular contexts, and which implementation strategies should be employed for effective scale-up. In addition to synthesising and grading the evidence, the Commission will generate a framework for action in the form of practical guidelines targeted towards national and city governments, NGOs, civil society and the private sector. These guidelines will indicate how to assess which actions should be prioritised in particular contexts. It will also include a comprehensive influence strategy to be developed with partner organisations and a leading creative agency.


Research activity codes: 8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: GENERIC HEALTH RELEVANCE