NIHRDataInsights/HRCSData huggingface dataset:
Title: DNA damage-driven epigenetic DNA modifications lead to transcriptional alterations and play a crucial role in Dementia
Funder: Medical Research Council

Abstract: DNA damage is considered a relevant and characteristic process occurring during ageing and specifically, in age-related disorders such as Alzheimer’s disease (AD). Different epigenetic marks linked to DNA damage and dysfunctional DNA repair mechanisms have been reported in brains affected with AD, however, there is a lack of understanding of the effects of these changes in each cell type of the brain and how these alterations interact leading to pathogenesis. This study aims to evaluate how epigenetic modifications caused by the accumulation of DNA damage in coding and regulatory regions of key genes in AD are important mechanisms causing deterioration of cellular programmes in brain cells, leading to or contributing to dementia. Here, I will test this hypothesis using nanopore-based sequencing, an emerging sequencing approach which allows for native DNA and long-read sequencing analysis. A suite of methods will be further developed to comprehensively characterise DNA alterations in key disease-related genes in a cell type-specific manner. For this, I will customise a fluorescence activated nuclear sorting (FANS) approach based on probes targeting RNA molecules expressed in specific neuronal populations of the human brain, prior to analysis of their genetic material. By directly sequencing non-amplified human brain DNA extracted from specific cell populations, my aim is to identify functional chemical modifications such as 8-oxoGuanine, 5-methylcytosine and 5-hydroxymethylcytosine. In parallel, I will extract RNA to perform targeted transcriptome long-read sequencing in the isolated cell populations to fully resolve how DNA damage influences transcription rates and splicing, or whether DNA damage could result in pathogenic somatic mutations leading to disease. With the custom sequencing and bioinformatics analysis developed during this study, I will analyse a pilot cohort of neuronal samples from specific brain regions in AD and control donors to gather pilot data for larger studies including more samples or other cell types. By putting together epigenetics and transcriptomics information from cells largely involved in AD pathology and particularly vulnerable for DNA damage accumulation such as neurons, this study will start to illustrate the extent of the consequences of DNA damage in key associated genes involved in AD. This project will provide the groundwork to comprehensively characterise genome dynamics of the human brain during ageing and dementia, a promising but largely unexplored avenue to approach dementia treatment.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Protein aggregation as a host-pathogen relationship
Funder: Medical Research Council

Abstract: Protein aggregation underlies the development of neurodegenerative diseases. In Alzheimer’s disease, as well as numerous other neurodegenerative diseases, the cytoplasmic protein tau undergoes a change from soluble protein to aggregated, filamentous conformations. Although this change is closely associated with degeneration, the cellular control of aggregation is poorly understood. Our group takes a host-pathogen standpoint on this problem. We identify cellular co-factors that promote protein aggregation as well as those that can detect and destroy aggregates. We combine focussed and genome-level screens to identify such modifiers and seek to understand their activity at a mechanistic level. We exploit antiviral proteins, such as the intracellular antibody receptor TRIM21, to specifically identify and degrade protein aggregates. We investigate the role of TRIM21 in immunotherapy and as a potential route to new methods of targeted protein depletion. Throughout our work we make use of a range of molecular and cell-based experimental systems. This includes the use of reductionist in vitro reactions, cell lines, organotypic slice cultures and primary neural cultures. We further test our hypotheses in mouse models of neurodegenerative disease. Our ultimate aim is an understanding of protein aggregation in the host environment and the identification of novel therapeutic strategies for its prevention.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;5.1 PHARMACEUTICALS
Health categories: NEUROLOGICAL
Title: Unravelling the complex role of protein aggregation in Parkinson's disease using super resolution microscopy.
Funder: Medical Research Council

Abstract: The aggregation of misfolded proteins is a key pathology of Parkinson's disease and accounts for nearly 100% of known cases. Despite its central role in brain impairment, therapeutics targeting this pathway have failed in slowing disease progression in affected patients. Available drugs are designed to target single proteins, one-at-a-time, whilst neglecting the composition, structure and interaction patterns of each aggregate which render the disease highly complex for treatment using simple therapeutics as such. A quarter century of research in dementia and we still do not understand what are the main constituents of each aggregate, how does each aggregate interact with other protein machineries and when can aggregates induce neuronal death and brain disease. Without answers to these fundamental and complex questions, effective treatment is not foreseeable. We have previously developed super resolution microscopy, a cutting edge tool with a remarkable spatial resolution of less than 5 nanometers, and used it in imaging aggregates in the Cerebrospinal fluid and soaked post mortem brain samples of diseased and control patients. In this important pilot study, we will push the boundaries of this technology to image the structure and composition of millions of aggregates, one by one, in the synaptic terminals of human-derived stem cells. The discoveries made as part of this study will allow us, in the future, to answer the fundamental questions described above, decode the early molecular events underlying dementia, construct a comprehensive, moving atlas of interacting molecular partners and identify venues for therapeutic targeting.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Molecular architecture, function and dysfunction of the Blood Brain Barrier
Funder: Medical Research Council

Abstract: The UK Dementia Research Institute (UK DRI) is an initiative funded by the Medical Research Council, Alzheimer's Society and Alzheimer's Research UK. Funding details for UK DRI programmes will be added from 2020. Unlike other organs, the exchange of substances between the blood and the brain is tightly regulated by a multicellular functional entity called the Blood Brain Barrier (BBB). The BBB provides a cellular boundary that restricts the invasion of toxins and pathogens into the brain, controls the uptake of molecules from the blood, metabolizes nutrients and clears the brain of toxic by-products. Failure in BBB homeostasis leads to severe neurological disorders. Remarkably, BBB dysfunction is one of the earliest observations in neurodegenerative diseases and precedes neurodegeneration. In spite of the crucial function of the BBB and efforts made to understand the mechanisms that underlie its dysfunction, there are important aspects of BBB physiology that remain largely unexplored. How is the BBB maintained? How do the BBB cellular components interact? What are the molecular pathways leading to BBB dysfunction? The two most widespread components of the BBB are the brain endothelial cells (BECs) and the astrocytes. BECs form the first barrier between the blood and the brain parenchyma thanks to protein complexes called tight junctions (TJs) that keep BECs closely bound. Astrocytes have a unique strategic position in the brain by intimately contacting neurons and covering the vasculature of the brain through specialized structures called astrocyte end-feet. The understanding of the BBB cell interactions is necessary to better comprehend the BBB maintenance and pathology. We will use human samples, mouse and cell cultures and we will perform proteomics, RNA-seq, confocal and in vivo multiphoton imaging and behavioural assessment to reach our main research goals: 1. Comparative characterisation and functional exploration of astrocyte and BEC interactions during BBB maturation, and in neurological disease. 2. Functional mechanistic assessment, in vivo and in vitro, of new astrocyte-BEC interaction pathways unveiled by health and disease comparative studies. The studies undertaken in this UK DRI project will enable the development of new scientific tools and disease therapies by both identifying unknown BBB dysfunction mechanisms and providing target proteins to design treatments capable of crossing the BBB.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Defining and modulating myeloid cell function in neurodegenerative diseases
Funder: Medical Research Council

Abstract: The overall aim of this research programme is to better understand the dynamic complexity of myeloid cells in the central nervous system (CNS) and their interactions with neural and vascular cells in neurodegenerative diseases. We expect that this will help us to specifically target macrophages that reside within the brain parenchyma (microglia), choroid plexus, leptomeninges and cerebral vasculature in order to modify the course of neurodegenerative diseases. A first objective is to characterise the context-dependent compartmental responses of brain macrophages. To this end, we will isolate microglia and CNS-associated macrophages from post-mortem brain tissue derived from individuals with Alzheimer’s disease and Huntington’s disease. For comparison, we will study monocytes/macrophages from cerebrospinal fluid and peripheral blood. The cells will be analysed by high-dimensional single-cell techniques such as RNA-seq and/or CyTOF. We will also establish imaging mass cytometry in Edinburgh in order to obtain spatial information on immune cell activation in relationship to pathological processes involving neurons, macroglia and neurovascular cells. A second objective is to model myeloid cell functions in neurodegenerative diseases by using human induced pluripotent stem cells (iPSCs). We have established a novel protocol to generate macrophages and microglia-like cells from iPSCs which we will employ to test the consequences of the disease-causing mutations on gene expression, production of inflammatory mediators, phagocytic capacity and metabolism in human iPSC-derived myeloid cells. Non-cell autonomous effects will be explored using co-culture models and transplantation into animals. The results of these experiments will inform us about the changes that innate immune cells undergo in different tissue compartments during neurodegenerative diseases. The focus on human biosamples and iPSCs increases the translational relevance of our research programme. We will make our findings publicly available and where applicable we will protect intellectual property.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Determining how lysosomal dysfunction affects microglial function and lipid burden in neurodegeneration
Funder: Medical Research Council

Abstract: Microglial endolysosomal function/dysfunction, particularly in the context of lipid handling, has been strongly implicated in the pathogenesis of neurodegenerative disease. The ability to properly digest lysosomal cargo is believed to be regulated by glycoprotein NMB (GPNMB). GPNMB is upregulated in microglia in Alzheimer’s Disease (AD) and in mouse models of neurodegenerative disease and is linked with lipid overload. However, whether GPNMB plays a causal role in microglial lipid handling in neurodegeneration is unknown. In this project, I aim to build on preliminary data implicating GPNMB in neurodegeneration to produce a comprehensive package of pilot data investigating microglial endolysosomal dysfunction in vitro, in vivo and in human brain tissue. First, I will investigate how lysosomal dysfunction caused by GPNMB deficiency regulates the ability of microglia to engulf, digest and respond to phagocytic cargo such as myelin or apoptotic neurons. Next, I will determine for the first time the functional role of GPNMB in an AD model in vivo. This experiment will involve collaboration with lipidomics expert Prof Jules Griffin and will provide an atlas of the microglial lipidome and transcriptome in the APP knock-in mouse in the presence or absence of functional lysosomes. Finally, I will use a GPNMB antibody validated in our lab to investigate the spatial expression of GPNMB in human AD brains.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Simple questions about neurodegenerative diseases: where? When? How?
Funder: Medical Research Council

Abstract: The UK Dementia Research Institute (UK DRI) is an initiative funded by the Medical Research Council, Alzheimer's Society and Alzheimer's Research UK. Funding details for UK DRI programmes will be added from 2020. The overall aim of this project is to identify regulatory mechanisms which cause neurodegenerative disorders, along with the cell types in which they act, and distinguish those which are active during adulthood from those which are developmental. My approach is based on the usage of GWAS summary statistics to make inferences about causal mechanisms. Traditional interpretations of GWAS data have generally only acknowledged the role of rare genome wide significant loci; the approaches described here acknowledge that there are thousands of loci involved in disease processes. The hypothesis that will be explored here, is that these loci act via a finite number of distinct biological processes, and that these processes will act in distinct cell types and at different points in the lifespan (i.e. during development or adulthood). Methods and datasets will be developed such that the GWAS loci contributing to each process can be separated. The first step will be to define the cell types responsible for initiating or sustaining the disease. The second step will be to identify regulatory mechanisms (i.e. Transcription Factor, RNA binding protein or RNA-chromatin binding) acting within each cell. This work will be based on recent methodological developments which have shown that GWAS SNPs are directionally associated with genome wide changes in DNA binding10. The third step will be to determine the stages of the lifespan when these regulatory mechanisms act. This will be important for distinguishing regulatory mechanisms which act developmentally from those which act in adulthood. It will be vital for future drug development efforts that we target the processes which are active in adulthood, At the end of this project, the aim is to have candidate drug targets whose mechanism of activation is genetically interpretable, and for which effective drug efficacy could again be tested (or even screened for) using genetic heritability analyses.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Targeting FET proteins using synthetic RNA aptamers
Funder: Medical Research Council

Abstract: The FET family comprises the RNA-binding proteins FUS, EWS and TAF15 which have been linked to Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) where they mis-localise and aggregate in the cytoplasm of affected neurons and glia cells. Although it is emerging that the FET proteins cause neurodegeneration by a cytoplasmic toxic gain-of-function, there are currently no molecular tools to selectively target the FET proteins for therapeutic modulation. In my recent work, I uncovered how FUS achieves high-affinity binding to the U1 snRNA by simultaneously employing both of its RNA-binding domains. Given the extensive homology of the FET proteins, this knowledge allowed me to design synthetic RNA aptamers that are predicted to selectively interact with all FET proteins. In this project, I aim to assess if such aptamers can serve as a FET-targeting moiety for targeted protein degradation or co-import into the nucleus. In a first step, I will first carry out in vitro binding experiments with recombinant FET proteins and several RNA aptamer candidates to identify the strongest interactor. In parallel, pulldown experiments with biotinylated aptamers coupled to mass spectrometry will allow me to assess the specificity of these aptamers and identify potential off-target RNA-binding proteins. The most promising aptamers will then be coupled to thalidomide, a ligand of the E3 ubiquitin ligase cereblon, and transfected into HeLa cells to investigate if they can selectively degrade FET proteins. As a complementary approach, I will create a plasmid encoding an artificial snRNA containing the aptamer sequence, which upon transcription in the nucleus shuttles to the cytoplasm to assemble into a functionally inert snRNP that is then re-imported into the nucleus. To assess if an engineered snRNAs could co-import associated FET proteins into the nucleus, we will transfect the aptamer-snRNA expression plasmid into HEK cells that stably express cytoplasmic EGFP-FUS-P525L and evaluate the subcellular localisation of the tagged FUS by fluorescence microscopy. If successful, this proof-of-concept pilot study will support a follow up grant application with the aim to investigate the therapeutic potential of these aptamers in cellular and animal models of ALS and FTD. With the increasing number of RNA-binding proteins linked to neuron loss, such RNA-based targeting strategies may be widely applicable across neurodegenerative diseases.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: NEUROLOGICAL
Title: Point-of-care Diagnostics: Synthetic Biology
Funder: Medical Research Council

Abstract: The UK Dementia Research Institute (UK DRI) is an initiative funded by the Medical Research Council, Alzheimer's Society and Alzheimer's Research UK. Funding details for UK DRI programmes will be added from 2020. New tools are needed to monitor disease onset and progression in people living with dementia, to prevent accelerated cognitive decline and hospitalisations. This includes monitoring of significant co-morbidities such as infections. Urinary tract infections (UTIs) are one of the major contributors to clinical deterioration in dementia, and delayed diagnosis of infections can lead to episodes of delirium or aggression which increases the burden on carers. Thus, one branch of this research programme focuses on understanding the pattern of UTIs in a dementia cohort and aims to develop biological sensing systems (biosensors) to rapidly detect and monitor infections at the point of care. To do this, we are utilising CRISPR-Cas gene editing systems which allow detection of nucleic acid targets associated with UTI pathogens. This includes specific targets – such as antibiotic resistance genes – which could inform treatment or predict infection outcomes. Biosensor targets will be identified from longitudinal analysis of urine specimens from people with dementia who are enrolled into the UK DRI Care Research & Technology Centre (CRT) “Healthy Home” study. The CRISPR-Cas biosensor technology we develop will ultimately be implemented as paper-based assays and optimised for use in the home, in collaboration with UK DRI CRT colleagues in the Helix Centre for Healthcare Innovation. Biosensors will be evaluated alongside current “gold-standard” methods of UTI detection (dipstick, culture). This study will also involve in-depth evaluation of microbial diversity in the urine, to see how the urine microbiome changes over time during periods of clinical stability and infection and to guide biosensor design. Using synthetic biology approaches and CRISPR-Cas, sensing systems will also be developed for early neurodegenerative disease markers such as specific microRNAs (miRNAs) circulating in blood and/or other body fluids. CRISPR-Cas miRNA sensing systems will be evaluated both as a method of early detection of dementia but also to assess presence and quantity of different miRNAs in relation to disease progression in the “Healthy Home” dementia cohort. Biological measures of infection and neurodegeneration obtained in this research strand of the UK DRI CRT will be assessed against other clinical and behavioural measurements collected longitudinally for each participant in the “Healthy Home” cohort. Overall, this will be used to improve mapping of disease progression and guide management and treatment of dementia and co-morbid infections.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: NEUROLOGICAL
Title: Healthy Home, Care Research and Technology Centre, UK DRI
Funder: Medical Research Council

Abstract: The UK Dementia Research Institute (UK DRI) is an initiative funded by the Medical Research Council, Alzheimer's Society and Alzheimer's Research UK. Funding details for UK DRI programmes will be added from 2020. This programme focuses on developing safe, reliable and usable technologies for the collection of dementia relevant data. User compliance and acceptability is a key challenge and where possible we are developing passive monitoring using environmental sensors, reserving wearable technologies for when close proximity monitoring is necessary. We will develop adaptive and personalised AI/machine learning algorithms to predict clinically relevant information that adapt to seasonality, environmental and contextual changes. The Healthy Home will allow integration and fusion of existing and new forms of data and will provide flexible layers for developing and integrating continual and adaptive AI/machine learning algorithms and new observation generation and clinical pathways and response mechanisms.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY);4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: NEUROLOGICAL