NIHRDataInsights/HRCSData huggingface dataset:
Title: Biomolecular condensation of hairpin proteins coordinates cytoplasmic clients to spatially distinct microdomains of the ER membrane
Funder: Wellcome Trust

Abstract: The endoplasmic reticulum (ER), as a single continuous membrane network, coordinates a variety of biological processes across the entire cell, providing a platform for the spatiotemporal segregation of cytoplasmic biochemistry – a crucial feature for cell survival. Despite this, our understanding of how the ER corrals most cytoplasmic clients to specific sites on its membrane remains slim. ER structure is partially governed by a series of hairpin proteins known to stabilise specific membrane curvatures. The Reticulons (RTNs) and Receptor Expression-Enhancing Proteins (REEPs) are two such families of protein. We have shown that RTN/REEPs cluster into ER microdomains and contain cytosolic-facing intrinsically disordered regions which enable the formation of biomolecular condensates, potentially tethering specific cytosolic proteins to the ER membrane. Thus, we propose the novel and testable hypothesis that membrane curvature-stabilising RTN/REEPs drive regional functional specificities at ER microdomains. To test this, we will generate a comprehensive spatial map of RTN/REEP-microdomains using single-molecule localisation microscopy, with a custom optical-tweezer configuration used to quantify precise membrane curvature preferences for each hairpin. Using two orthogonal screens we aim to identify a complement of cytosolic proteins capable of co-condensing with each RTN/REEP, performing appropriate bioassays to assess the functional consequences of destabilising hairpin:cytoplasmic-partner interactions.

Lay abstract: The endoplasmic reticulum (ER) comprises a single continuous membrane network that extends across the entire cell, coordinating diverse cytosolic activities essential for cell survival. Despite this, our understanding of how the ER confines cytosolic proteins to specific regions of its membrane remains tenuous. We have demonstrated that several ER resident hairpin proteins cluster into unique spatial microdomains. Many of these hairpins contain large cytoplasmic-facing intrinsically disordered regions that we believe form biomolecular condensates with specific cytosolic partners. We aim to generate a comprehensive spatial map of ER-hairpin microdomains, subsequently using a series of screening approaches with targeted bioinformatics to identify cytosolic partners. Ultimately we will look to destabilise hairpin:partner interactions and observe the consequences on localisation and function for each partner. Our work will provide a novel molecular mechanism for ER-mediated cytoplasmic organisation, a fundamental cellular process, and set a basis for understanding misregulation of ER:cytoplasmic crosstalk in disease

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Determining the mechanisms regulating chromatin architecture in cell fate decisions.
Funder: Wellcome Trust

Abstract: During embryogenesis, signals control gene expression to ensure cells types are formed in the right time, place and proportion. Biological signals are integrated by Regulatory Elements (REs), making these vital elements in the information processing mechanism of the genome that controls gene expression. REs often lie long distances from a gene suggesting some long-range communication is necessary for their function. Recent technological advances have revealed long range interactions between REs and promoters, yet the mechanisms that control these interactions and how they influence gene expression are only superficially understood. To this end, we will take advantage of a model we have developed in which two long ranges REs associated with the motor neuron specifier Olig2 act in different combinations in hindbrain and spinal cord tissue. We will use chromatin contact assays to identify interactions between Olig2 and REs. To determine function, we will use gene editing and targeted perturbations to study how the REs effect gene expression. Finally, we will use cutting-edge techniques to force contacts between Olig2 and REs to identify how they act in tissue specification. This study will offer unique insight into the formation, control and effect of chromatin contacts in a developing mammalian tissue.

Lay abstract: During development, it is important to have the correct cell type in the correct place at the correct time. This is controlled by biological signals, that are interpreted by regions of non-coding DNA called regulatory elements, modulating gene expression. It is not clear how regulatory elements function to control gene expression. I will use a mouse embryonic stem-cell model of motor-neuron specification to study the control of Olig2, by two regulatory units. These regulatory units work in different combinations in motor-neurons in the hindbrain and spinal-cord. I will identify interactions between Olig2 and its regulatory units and use gene editing to alter where and when these interactions occur, assessing the effect on Olig2 expression during motor neuron formation. I will also force interactions to identify how regulatory elements control motor neuron-specification. This project will give new understanding of regulatory element function in development and disease in the brain and spinal-cord.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Enhancing electron microscopy facilities at the University of Sussex with High-Pressure Freezing technology
Funder: Wellcome Trust

Abstract: We are requesting a high-pressure freezer (HPF) and freeze-substitution processor (FSP) at the University of Sussex to substantially enhance our transmission electron microscopy research and meet significant unmet demand. HPF/FSP is now the de facto standard for the highest-quality specimen fixation for ultrastructural work, offering key benefits for protein integrity, ultra-rapid controlled fixation, fluorescence preservation for correlative work and penetrative thick-sample fixation. The requested system includes modules for synchronizing optogenetic/electrical stimulation with freezing onset, offering revealing ‘snapshot’ views of rapid and dynamic events. Collectively, these advantages will open up major new directions for existing research programs within the School of Life Sciences, and wider afield. Planned research includes studies aimed at: defining synaptic vesicle recycling pathways in central and sensory terminals, revealing ultrastructural correlates of disease-related neuronal dysfunction, elucidating chromosomal breakage events during mitosis, investigating ultrastructural determinants of centrosome positioning, and characterizing protein organization in ionizing radiation-induced foci. The School has made major recent strategic investment in developing world-class electron microscopy facilities and the HPF/FSP will offer significant enhancements to this equipment for ultrastructural research. The system will be fully-integrated into the new purpose-built Life Sciences building (completion 2019-2020) ensuring its long-term sustainable use within a state-of-the-art dedicated Bio-Imaging centre.

Lay abstract: Electron microscopy enables the direct visualization of nanometer-level details of biological processes offering fundamental understanding about how structure influences and dictates function. For this, living samples first need to be preserved (fixed) but classically-used chemical methods are slow, often incomplete, and produce problematic structural artefacts. We are requesting a high-pressure freezer (HPF) system at Sussex that uses cryo-fixation for ultra-rapid and faithful preservation of biological samples down to molecular detail. HPF opens up significant new research directions and many local researchers will benefit from this technology. For example, cancer biologists will use HPF to investigate proteins damaged by radiation and characterize the chromosome damage occurring when cells divide. Neuroscientists will exploit the ultra-fast fixation to collect unique ‘snapshots’ of structural changes taking place when neurons transfer information. This exciting technology will significantly enhance our existing electron microscopy facilities and extend research possibilities across a broad range of Sussex research programs.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Light sheet microscope for 3D imaging of large samples and improved in vivo imaging
Funder: Wellcome Trust

Abstract: We are requesting funds to purchase a light sheet microscope that will be used as multi-user equipment by the applicants. The equipment is based on a technology that has two main advantages over other methods of fluorescence microscopy currently available to us. These advantages will enhance our research in a wide variety of different applications. First, light sheet microscopy can acquire optical images at very high speeds, and thus data collection of large samples becomes rapid and efficient. This will allow us to rapidly image very thick samples including small whole organisms (zebrafish and drosophila larvae, for example) and intact mouse brains. Second, light sheet microscopy substantially reduces photodamage to living samples compared to other imaging approaches because it only illuminates a small plane of the sample during image acquisition. This will allow us to image living samples for longer periods or increase our temporal resolution while imaging for shorter periods. The ten applicant groups, seven of which are currently funded by the Wellcome Trust, will be the primary users of this equipment. This number of researchers will maximise use of the equipment while guaranteeing sufficient hours for each group.

Lay abstract: To understand the mechanisms that regulate cell and organ development we need an efficient method to image the microscopic three-dimensional organisation of cells and tissues under normal and experimental conditions. In suitable model organisms this can done in whole living animals or explants of living tissue. In other cases we need to image large organs or tissue regions in samples that have been fixed, processed to reveal structure and made optically clear after removal from the organism. The purchase of a light-sheet microscope will transform our ability to carry out these analyses because light-sheet microscopy enables very fast acquisition of large images and also significantly reduces the effects of photodamage during imaging of living samples. These advances in imaging capabilities will benefit a large number studies aimed at understanding brain development in health and disease, together with studies aimed at understanding cell migration during development and diseases such as cancer.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Articulated Health CIC-Changing the face of public engagement in health
Funder: Wellcome Trust

Abstract: Patient Media CIC aims to break down barriers between health science and people with long term conditions by empowering them to play more active role in their own health and promote active collaboration between public and health scientists in driving healthcare innovation. This three year project will deliver the following impact: 1. Over 1 million people are engaged with health science and research and empowered and enabled to better manage their condition. 2. 9,000 health scientists better understand patients’ lived experience, unmet needs, and learn new ways of patient engagement using eHealth tools. 3. A new impact framework for public engagement in eHealth interventions developed and shared across communities of interest 4. 20 people recruited and trained to be closely involved in health sciences as a social or cultural activity. We are requesting a grant which will be used to: • Set up social enterprise to deliver our social impact and business model • Expand the MS Reporters core product into epilepsy and one other new condition • Develop at least two new public engagement products in MS and epilepsy • Achieve financial sustainability to be able to grow the social enterprise without further Wellcome funding


Research activity codes: 7.1 INDIVIDUAL CARE NEEDS
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Directly induced neural STEM cells from people with progressive multiple sclerosis for applications in REGenerative Neuroimmunology (STEM_REG)
Funder: Wellcome Trust

Abstract: Multiple sclerosis (MS), a disease of the central nervous system, afflicts 2-3 million people worldwide, most of whom will ultimately develop a progressive form of the disease with few therapeutic options. In this project we aim to develop the capability to generate clinical grade, patient-specific induced neural stem cells (iNSCs) from people with progressive MS (PMS). Upon transplantation, stem cells like iNSCs possess a powerful, multimodal therapeutic potential distinct from that of small molecules and biologics, making transplantation ideal not only for preventing the worsening of MS, but also addressing the unmet need for damage reversal. iNSCs are of particular interest as they will be generated from the patients themselves, avoiding a number of safety and ethical concerns intrinsic to other stem cells. The methods developed in STEM_REG will be applicable not only to the treatment of PMS but will pave the way for therapies for other chronic neurological illnesses.

Lay abstract: Multiple sclerosis (MS), an immune-mediated disease of the central nervous system, afflicts an estimated 2-3 million people worldwide, most of whom will ultimately develop a progressive form of the disease with few therapeutic options. In this project we aim to develop the capability to generate clinical grade, patient-specific induced neural stem cells (iNSCs) from people with progressive MS (PMS). Upon transplantation, stem cells like iNSCs possess a powerful therapeutic potential that is distinct from that of small molecules and biologics: they can sense diverse physiological signals, migrate to specific sites in the body, integrate into tissue, and execute complex responsive behaviours in response to their environment. These characteristics make stem cell transplantation ideal for not only preventing the worsening of MS, but also addressing the unmet needs of damage reversal and restoration of function. iNSCs are of particular interest in this regard as they will be generated from the patients themselves, avoiding a number of safety and ethical concerns intrinsic to allogeneic stem cells. The methods developed in STEM_REG will not only be applicable to the treatment of PMS, but will pave the way for therapies for other chronic neurological illnesses, such as stroke and brain/spinal cord injuries.

Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Full-Waveform Imaging of the Human Brain
Funder: Wellcome Trust

Abstract: Rapid brain imaging is central to the diagnosis and treatment of acute neurological conditions, but existing imaging methods require large, immobile, high-power instruments that are near-impossible to deploy outside specialized environments. We will create a device that can be simply and rapidly applied to any patient, any time, any place, exploiting advances that have already revolutionised imaging in geophysics. We will image the brain using sound waves, transmitted across the head, applying advanced computer modelling to remove the distorting effects of the skull, thereby enabling high-resolution high-contrast imaging of the brain unachievable by conventional ultrasound. Safe, fast, universally applicable, deployable continuously, and above all portable by paramedics, our device will revolutionise brain imaging, in health and disease. The technology has particular relevance to stroke – globally the second-commonest cause of premature death and a major, growing cause of adult disability – and to brain imaging in resource-limited and inaccessible environments.

Lay abstract: Rapid brain imaging is central to the diagnosis and treatment of acute neurological conditions, but existing imaging methods require large, immobile, high-power instruments that are near-impossible to deploy outside specialized environments. We will create a device that can be simply and rapidly applied to any patient, any time, any place, exploiting advances that have already revolutionised imaging in geophysics. We will image the brain using sound waves, transmitted across the head, applying advanced computer modelling to remove the distorting effects of the skull, thereby enabling high-resolution high-contrast imaging of the brain unachievable by conventional ultrasound. Safe, fast, universally applicable, deployable continuously, and above all portable by paramedics, our device will revolutionise brain imaging, in health and disease. The technology has particular relevance to stroke – globally the second-commonest cause of premature death and a major, growing cause of adult disability – and to brain imaging in resource-limited and inaccessible environments.

Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Sharing standardised experimental data and models of neural systems through the Open Source Brain repository
Funder: Wellcome Trust

Abstract: Biologically detailed computational models of neurons and circuits are powerful tools for understanding brain function in health and disease. Access to the experimental data used to build such models is necessary to understand them and adapt them for new scientific studies, but technical barriers have prevented these diverse datasets from being shared. To address this, we will radically expand Open Source Brain, an online resource of standardised models of different brain regions, to include the anatomical, electrophysiological, imaging and behavioural data used to build models. Unlike other model databases, the current version of OSB (version 1) allows collaborative model development, makes models accessible by visualising their properties in an intuitive format and enables simulations to be run without installing software or writing code. In this project we will build on this functionality by developing the infrastructure and standardised data formats to enable browser-based visualisation and analysis of experimental data. By extending model development to include data-constrained optimization, we will provide the necessary resources to update, adapt and reconfigure models. By closing the loop between data and models, OSB version 2 will provide accessible models of brain function that can be reused for new scientific questions, by the wider neuroscience community.

Lay abstract: Recent technological advances allow brain activity and structure to be mapped in unprecedented detail. Such data will enable us to build computational models that provide deeper insights into how brain function arises from neuronal circuits, and the effect of disease. Despite the value of such experimental data, relatively little is openly available and usable due to the technical difficulty of making it accessible. In this project we will substantially extend the functionality of Open Source Brain, an online resource we have created for sharing, exploring and running models of neurons and circuits, by developing the software infrastructure, standardised data formats and powerful analysis tools to make experimental data accessible through a web browser. By making models and the data upon which they are built and tested freely available, this resource will facilitate a new era of ‘open neuroscience’, enabling the development of more accurate and predictive models of brain function.

Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Spatiotemporally resolved proteomics of protein trafficking pathways
Funder: Wellcome Trust

Abstract: Defects in protein trafficking are a causal factor of neurodegenerative disorders such as Parkinson’s and Alzheimer’s diseases. Accordingly, there is interest in understanding the complexity of the protein sorting pathways. Despite the great efforts made in the last 20 years to study intracellular protein trafficking, there are still gaps in our understanding of these pathways. For example, the mechanistics of the secretory route from the Golgi apparatus to the plasma membrane remain poorly understood. Using ‘RUSH’ technology we reliably observe post-Golgi tubules that fuse to the plasma membrane. This unique insight gives us the opportunity to characterise this sorting route. To dissect the mechanistic details of this pathway we will perform a screen that combines RUSH technology with APEX2- a peroxidase that can be activated to conjugate biotin to proximal proteins. The APEX2 can be activated whilst the protein is in the tubules to label the proteins proximal to the post-Golgi tubules. These proteins can be enriched and characterised using mass spectroscopy. Positive hits will be analysed for their functional relationship with the tubules, and will concurrently be checked against unpublished GWAS/exome-sequencing datasets from studies into neurodegenerative disorders. Proteins functionally or physically associated with the tubules will be extensively characterised.

Lay abstract: Every human cell is characterised by a myriad of internal compartments. This system allows cellular components (such as proteins) with a shared role, to be collected in the same place. Transport between compartments ensure the balance of cellular components. Defects in transport pathways result in protein accumulation or mislocalisation and represent a key cause of neurodegenerative disorders such as Parkinson's and Alzheimer's diseases. Recent work has revealed a way to study an under-characterised transport pathway. In particular, we can directly observe tubules budding from one intracellular compartment (the Golgi) and fusing to the target intracellular membrane. To characterise the cellular machinery that forms these tubules and directs them, we will perform a screen that takes advantage of modern molecular technologies. These technologies allow components in a certain location in the cell to be labelled at the same time. In this way we will identify novel components of this transport machinery.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL