NIHRDataInsights/HRCSData huggingface dataset:
Title: Regulation and function of RNF12 E3 ubiquitin ligase in Tonne-Kalscheuer Syndrome (TOKAS)
Funder: Wellcome Trust

Abstract: Background: Intellectual disability comprises a series of poorly understood neurodevelopmental disorders affecting around 1-2% of the general population. Tonne-Kalscheuer Syndrome (TOKAS) is an intellectual disability syndrome caused by mutations in the RNF12/RLIM gene, which encodes an E3 ubiquitin ligase that tags specific proteins for destruction in a process called ubiquitylation. In order to understand TOKAS disorder, the signals that control RNF12, the proteins it ubiquitylates and the cellular processes RNF12 governs must be identified. Approach: RNF12 is controlled by a chemical switch known as phosphorylation. My recent work uncovered a new function for a protein kinase called Aurora in phosphorylating RNF12. I will now use biochemistry and cell biology to study how Aurora phosphorylation of RNF12 controls protein ubiquitylation. I will then employ genome-editing technology and stem cell models to explore the impact of Aurora-RNF12 signalling on gene expression and development of the brain and genitals, which is disrupted in TOKAS patients. Finally, I will use proteomic technologies to search for new proteins that are ubiquitylated by RNF12, as these may be relevant to the development of TOKAS. Impact: These studies will provide new insight into regulation and functions of RNF12 protein ubiquitylation that are disrupted in TOKAS intellectual disability.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Structural and Functional Characterisation of the Very Large G protein-coupled receptor (VLGR1)
Funder: Wellcome Trust

Abstract: Very Large G protein-coupled receptor 1 (VLGR1) is an adhesion G Protein-Coupled Receptor (aGPCR/ADGR). ADGRs are cell-surface protein receptors which mediate signal transduction through coupling with G-proteins in the cell and with their characteristic large extracellular domains mediate cell-cell and cell-matrix interactions. VLGR1 is the largest cell-surface protein known and none endogenous ligand for its extracellular domain has been identified yet. It is highly expressed in the central nervous system and mutations in Vlgr1 gene lead to the Usher Syndrome Type 2C which is characterised by hearing loss and progressive retinitis pigmentosa. Mutations are also linked to audiogenic seizures in mice and humans. All these suggest VLGR1’s important role in the central nervous system and despite the importance and the recent research progress, the structure and functions of VLGR1 are not known. During my PhD I will use structural analyses, including X-ray Crystallography and cryo-EM, to characterise the structure of the extracellular domain of the VLGR1 receptor and I will aim to identify its biological binding partners using cellular assays. These studies will shed light on the biology of this poorly understood receptor and may suggest new ways of treating the associated diseases.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Limited Proteolysis Mass Spectrometry: A Pipeline for Investigating Loss of Proteostasis with Age
Funder: Wellcome Trust

Abstract: Cell populations are intrinsically changed by age, reaching a point of senescence (arrested division) that has been associated with misregulation of metabolism, circadian rhythm, the extracellular matrix and signalling to the immune system. Crucially, studies have demonstrated age-related abrogation of protein homeostasis – the maintenance of proteins in their functional, folded states. Given that the capacity of cells to maintain a correctly folded proteome, and thus functionality, is attenuated in ageing, understanding the biological mechanisms which underlie this loss of protein homeostasis is paramount. In this project, I will use proteomic and bioinformatical techniques to gain a fundamental understanding of the relationship between age and the loss of protein homeostasis. Limited proteolysis mass spectrometry (LiP-MS) is highly amenable to the study of protein folding, as it facilitates the characterisation of structural changes to the native proteome on both a global and local scale. I will apply LiP-MS to determine the extent of protein unfolding in primary human stem cells. Using replicative senescence as a model of cellular ageing, I will identify a candidate list of proteins whose folding/structure is not maintained at old age and use bioinformatic analyses to predict functional consequences of age-associated protein unfolding.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Investigating how ANCL-causing mutations lead to neurodegeneration
Funder: Wellcome Trust

Abstract: Human neurodegenerative diseases impose a great and increasing social, economic and health burden on society, due to our rapidly expanding ageing population. However, these debilitating and fatal disorders lack effective therapies as the underlying mechanisms remain unclear. A rare neurodegenerative disorder, termed adult onset neuronal ceroid lipofuscinosis (ANCL) is a devastating neurodegenerative condition, rendering sufferers with an average life expectancy of 45 years. This project will use a combined approach, utilising both roundworms and mice to elucidate the mechanisms behind the disease. The worm and mice genetic makeup will be manipulated to mimic the effects of the ANCL-causing mutations, to generate working models of the disease. Additionally, the cells of the brain, neuronal cells, will be extracted from mice to analyse the impact of the mutations on neuronal survival, connectivity and protein localisation. Furthermore, both the worm models and mice neuronal cells will be used to identify new protein interactions, and how these are impacted by ANCL mutations. Ultimately, this project aims to expand our knowledge on the mechanisms behind ANCL disease processes, to aid in the identification of potential therapies for ANCL, and potentially other neurodegenerative diseases.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Anomalous Transport of Organelles
Funder: Wellcome Trust

Abstract: From active transport by motor proteins to passive transport in the crowded cytoplasmic environment, the movement of organelles within cells is critical for cell function. This transport exhibits non-Brownian anomalous transport: sub-diffusion and super-diffusion. Abnormal transport can lead to disease, and understanding how this occurs requires systematic quantification of organelle movement combined with predictions based on biologically motivated random walk models with multiple states of motion. To simplify tracking and analysis we will study organelle motility in neurons that are one dimensional, due to the thinness of the axon, rather than the fibroblasts we studied previously. We will obtain and analyse organelle trajectories by live-cell imaging of cultured human neuronal-like cells, and individual neurons in the nematode C. elegans. Then we will determine how selected disease-causing mutations in dynein regulators affect motility. We will develop new mathematical models for non-Markovian stochastic transport and fractional Brownian motion with random Hurst exponents, validating and improving models using experimental data. Lastly, we will generate new neural network/machine learning algorithms to better segment and estimate different states of motion and use these to predict the effect of dynein disruption on motility in human motor neurons that can be 1m long.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Investigating Alzheimer’s Disease risk genes in Drosophila melanogaster
Funder: Wellcome Trust

Abstract: Alzheimer’s Disease (AD) is the most common form of dementia and over the last 10 years many genetic mutations have been identified that alter an individuals risk of developing the disease. In my research I will be using Drosophila melanogaster (fruit flies) to investigate genetic contributions to AD. I will manipulate levels of specific genes within the fly brain and investigate how this, in turn, effects levels of other genes throughout the brain using a technique called RNA sequencing. To complement this analysis, I will also be investigating the effects of such manipulations on behavioural traits associated with human AD, such as sleep and memory disturbances. Generating a greater understanding of these newly discovered risk genes will hopefully aid the pursuit for a successful therapeutic target.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Chromatin state transitions during quiescence and reactivation of neural stem cells in Drosophila melanogaster
Funder: Wellcome Trust

Abstract: In the adult brain, most cells that produce new neurons (neural stem cells) are found in an inactive state (quiescence). These cells can be awakened in response to various signals, including diet or injury. Importantly, active and inactive neural stem cells differ in the genes they express and the modifications present on histones, proteins that the DNA is wrapped around. Histone modifications play a crucial role in regulating gene expression. During my PhD project, I will examine these modifications in active and inactive neural stem cells in Drosophila, in which these cells are easy to identify and manipulate. Using Targeted DamID, a technique that makes it possible to identify protein-DNA interactions in vivo, I will profile the location of individual histone modifications neural stem cells and classify the chromatin in those cells into domains. I will use super-resolution microscopy to observe chromatin within the nuclei of neural stem cells. Finally, I will test the function of those genes that may be important for awakening neural stem cells or inducing them into the inactive state. Understanding the mechanisms that induce neural stem cell inactivity and reactivation can potentially give insights into new therapies for brain injury or neurodegenerative diseases.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Understanding the molecular basis for the ubiquitin-dependent activation of the TAK1/TAB complex
Funder: Wellcome Trust

Abstract: Cells respond and adapt to various stimuli through a variety of detectors, which receive the signal. To ensure that a signal is transmitted, key decision-making hubs that interpret the incoming signal and define the output are required.I am interested in one signalling hub the TAK1-TAB complex, which is vital for cells to respond to an infection or other external signals and decides cell death or survival. Correct interpretation of the signal by the TAK1-TAB complex is vital: human diseases ranging from inflammatory diseases, certain cancers and neurological disorders arise from defects within these hubs. I will use a toolkit of biochemical and biophysical techniques to understand how the TAK1-TAB complex is regulated and obtain molecular snapshots that will provide the three-dimensional structure of the complex before and after signal activation. Understanding the structure of this key signalling hub will, for the first time, provide a glimpse into its regulation. Furthermore, the structure will provide an explanation of how certain genetic mutations in the assembly and architecture of the TAK1-TAB complex leads to certain diseases, notably Crohn's disease and amyotrophic lateral sclerosis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Structure and function of membrane proteins important in synaptic signalling
Funder: Wellcome Trust

Abstract: Membrane proteins are integral to synaptic signalling, a process that enables the communication between a neuron and its target cell. Understanding the structure and function of such proteins is key to deciphering the biochemistry of our nervous system, which in turn will aid the development of new therapeutics. In this project, I aim to solve the 3D structure of membrane proteins using either cryo-electron microscopy or x-ray crystallography. The candidate proteins include: a) muscle-type acetylcholine receptor, an ion channel that is implicated in congenital myasthenic syndrome and myasthenia gravis, and b) the SLC1A family of membrane transporters which includes glutamate transporters and neutral amino acid exchangers – members of this family are associated with neurological disorders (Alzheimer’s disease, epilepsy and Huntington’s disease), cancer and other metabolic disorders. I will also test the effects of various compounds on purified proteins. These compounds could become useful tools for future studies or even evolve into therapeutics.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Cellular Dynamics and Tissue Mechanics during Junctional Neurulation in Avian Embryos
Funder: Wellcome Trust

Abstract: During early development, embryos begin to develop what will become the future brain and spinal cord in a process known as neurulation or neural tube formation. Errors in this process lead to common birth defects such as spina bifida and anencephaly, which can differ in type and severity based on location along the future spine. This process differs between the head and tail ends of an embryo, with the head rolling up from a flat sheet and the tail end forming a solid rod that hollows in humans and chick. Whilst much is known about these two disparate processes, the region where they join is poorly understood. We aim to generate a better understanding of this junctional region, and the cellular and mechanical changes that govern its formation, through studying the wider cell movements and then focusing on mechanics and hydrostatic pressure differences. Using advanced microscopy of live and fixed tissues, we will assess cellular and tissue movements and use the data gathered to create a computerised physical model to predict tissue mechanics. This work will provide new insights on the basic processes of neural tube formation and may also help understand the causes of some neural tube defects.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Molecular and cellular mechanisms directing neuronal microtubule rearrangements during vertebrate CNS development
Funder: Wellcome Trust

Abstract: Polarity, the asymmetric organisation of cellular components, is crucial for the function of many cell types. Newborn neurons in the developing spinal cord shed their tips to move to their final location, causing them to lose polarity and the ability to distinguish their front from their back. These neurons must then regain polarity to extend a long process, called an axon, which makes connections with other neurons. In the developing embryo, neurons polarise in response to external cues from the surrounding tissue, which determine the orientation in which the axon will form, and therefore the direction it will grow in, or if it forms at all. Thus, neuron polarisation is essential for the formation of neuronal circuitry; however, the mechanisms of vertebrate neuron polarisation within tissue are unclear. I will study the molecular and cellular mechanisms that direct this key cell-biological process using cutting-edge live imaging and super-resolution microscopy of developing neurons in the embryonic chick spinal cord. Not only will this work help us understand how the nervous system is built, but it will also enrich our understanding of the general cellular mechanisms of polarity transition in development and disease.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: The interplay of atypical protein kinase C and actomyosin regulation in tissue mechanics and cell fate
Funder: Wellcome Trust

Abstract: Many tissues of our bodies are made of sheets of polarised epithelial cells. During development, these features allow tissues to fulfil their physiological function and, during morphogenesis, to fold when individual groups of cells contract. How exactly does the machinery that polarises cells intersect with actomyosin and how does contractility impinge on tissue and cellular behaviour? In the nervous system of flies, cell polarity and actomyosin regulation intersect driving cell fate decisions. During human corticogenesis, forces and actomyosin control cell behaviour and fate. The signals regulating actomyosin and contractility in these contexts are unclear.aPKC, a key effector kinase of the polarisation machinery can negatively affect contractility by regulating Rho kinase. Our preliminary data suggest, however, that aPKC regulates actomyosin also through other pathways. We have developed a strategy to screen for genes regulating contractility in Drosophila epithelia, based on a contractility assay induced by acute and specific aPKC inhibition. We will further study the relationship between the cell polarity machinery and actomyosin regulation during human corticogenesis using iPS cell-derived neural rosettes. This work could help understand corticogenesis’ regulation by mechanochemical signalling which, in the long term, could help find strategies against developmental disorders or neuronal degenerative diseases.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Using Simulation to Understand Voltage-Gated Sodium Channels in Health and Disease
Funder: Wellcome Trust

Abstract: The electrical pulses our nervous system uses for signal transmission are generated by a controlled flow of metal ions into and out of neurons. One important class of proteins involved in the regulation of this flow are the voltage-gated sodium channels (Navs). Members of this class sit on neurons involved in important physiological processes, such as pain-sensing (Nav1.7) or heart muscle contraction (Nav1.5), but many questions regarding their mechanism of function remain. We don't know, for example, precisely what makes these different channels behave distinctly, or how interaction with auxiliary beta-subunits influences their opening behaviour. In this project, I will use state-of-the-art computational methods, including molecular dynamics simulations, to build on recent structural and electrophysiological data of these channels. My goal is to bridge the gap between these experimental results and arrive at a hypothesis for the full mechanism of function of these channels, including their regulation and the role of interactions with their associated beta-subunits. These results will provide a deeper understanding of neuronal signalling and regulation of a variety of physiological processes, and have the potential to be highly useful in drug-discovery projects.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Identifying novel drivers of OPC activation and remyelination
Funder: Wellcome Trust

Abstract: Oligodendrocyte progenitor cells (OPCs) must maintain myelin in the central nervous system (CNS), a lipid layer that supports neuronal function. Damaged or lost myelin therefore must be replaced by OPCs to preserve optimal CNS function through a complex process called remyelination. However, remyelination efficiency gradually declines with age until it fails completely, with recent work showing that aged OPCs are unable to activate and initiate remyelination. Intriguingly, if OPCs are pushed into an active state, the entire process of remyelination can be restored in aged animals. While this highlights the importance of OPC activation, its precise mechanisms are not well understood. In this project, I aim to characterise the changes in gene expression and chromatin accessibility in OPCs with activation and age through multi-omic analyses. This may identify novel genes that drive OPC activation and explain its impairment during ageing. I will then demonstrate the involvement of these candidate genes using in vitro assays with primary OPC cultures, and finally assess the ability of these candidates to bolster remyelination in aged mice. Such findings could reveal the key regulatory mechanisms of remyelination, and initiate the development of new therapeutic strategies for demyelinating diseases such as multiple sclerosis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Clinical and molecular delineation of neurodevelopmental disease within genetically isolated communities.
Funder: Wellcome Trust

Abstract: Inherited neurodevelopmental disorders affect brain development and function and occur as result of changes to the genetic code, which may be passed down through families. The causes of these disorders remain poorly understood, and they present an immense healthcare burden worldwide. This means that affected families may often undergo multiple investigations in search of a diagnosis. Some neurodevelopmental disorders, which are otherwise rare in the general population, may occur more commonly in certain communities such as the Amish and Palestinian populations. The unique genetic make-up of these communities makes it easier for scientists to identify the genetic causes of inherited neurodevelopmental disease, which in turn greatly aids scientific understanding of brain growth, development and function. This project aims to identify new genetic causes of human inherited neurodevelopmental disease within these community settings. Studying the biological function of these genes will help us understand more about human health and the medical problems which arise when the genes involved do not function properly. This knowledge is ultimately important to develop better treatments for these disorders. Crucially, this work will also provide diagnoses for patients and their families, not just in these communities, but also worldwide.


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