NIHRDataInsights/HRCSData huggingface dataset:
Title: Genetics, Epigenetics & Bioinformatics
Funder: Medical Research Council

Abstract: The MRC Prion Unit Human Molecular Genetics of Prion and Related Dementias Programme investigates why some people, but not others, get prion diseases such as Creutzfeldt-Jakob disease (CJD). By comparing genetic differences between people who developed CJD and healthy people we hope to identify genes that influence why particular people are more susceptible to these diseases, and use this information to better estimate public health risks and to develop new tests and treatments. We also know that the fundamental processes involved in CJD, where one of the bodys own proteins becomes misshapen and then forms large clumps of material, are very relevant to other much commoner diseases such as Alzheimers Disease. ||Evidence in support of the involvement of non- PRNP genetic factors comes in part from work with laboratory inbred mouse strains, detailed in this groups section. A small number (~5) of quantitative trait loci (QTL) responsible for determining incubation time following intra-cerebral inoculation with prions have been mapped by the MRC Prion Unit and others using different crossing strategies and prion strains. The integration of unbiased genome-wide strategies in mouse and human prion disease will be an important in the success of both programs. Our discovery research utilises recently available genome-wide genotyping technologies. We have successfully conducted a pilot genome-wide association study with EA-Affymetrix 500K arrays (Mead et al. Lancet Neurology 2009). The necessary molecular genetic, bioinformatic, and statistical genetic expertise for genome-wide association study is either available in the Unit or through collaboration. Over the next few years we expect to develop our discovery genome-wide association research in larger patient cohorts using more advanced genotyping technologies, and focus on developing cellular and animal models to test the genes identified in our discovery research. It has become increasingly apparent that neurodegenerative diseases share fundamental mechanisms involving protein misfolding, including Alzheimers disease and Parkinsons disease. It is likely that genetic modifiers of prion pathogenesis may be of broader relevance to other protein misfolding diseases, and we intend to explore these possibilities.|One of the key goals of bioinfomatics in the Unit is to identity modifier genes, pathways and mechanisms controlling prion pathogenesis. The objective of this aspect of the programme is to use computational and statistical methods for the analysis and integration of these Unit based large-scale experiments (and also externally generated data sets) and their resulting data sets, which are large, inherently noisy and do not produce necessarily clear candidates.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Cellular Functions of the PrP
Funder: Medical Research Council

Abstract: According to the widely accepted protein-only hypothesis, prions comprise aggregated forms of misfolded host-encoded cellular prion protein (PrPC) generally referred to as PrPSc. PrPC is a glycosyl phosphatidylinositol (GPI)-anchored cell-surface glycoprotein, expressed in most cell types and tissues, but at the highest levels in the CNS and immune system. PrPC is highly conserved in mammals but a precise cellular function remains unclear although multiple functions have been proposed. However mice, in which the PrP gene has been knocked out, have no overt phenotype and a normal lifespan, but do not propagate prions and are completely resistant to prion disease, indicating that PrPC expression is absolutely required for prion propagation and prion-induced neurotoxicity. Like most GPI-anchored proteins, PrPC is predominantly found at the cell surface in lipid rafts which has led to the suggestion that it may be involved in signal transduction by acting as a cell-surface receptor. Since PrPC lacks a transmembrane domain for transmitting signals from the cell surface to the inside of the cell, much work has been done to identify binding partners that could transmit the signal from the cell surface to the cell interior. A number of putative binding partners have been identified but the biological significance of many of them is unclear since some are only present within the cytoplasm, whereas others are nuclear. Recent evidence has suggested that PrPC acts as a cell surface receptor for A-oligomers, the molecular species that mediate toxicity in Alzheimer’s disease. PrPC is also widely expressed in the immune system where it has been suggested to play a role in homeostasis as well as in the immune synapse and signalling. We have undertaken a reverse genetic approach, utilising alanine mutagenesis, to investigate the regions of PrPC that are required for efficient prion propagation in PK1 cells, a derivative of N2a neuroblastoma cells. This has identified three regions within the unstructured N-terminus as critical for prion propagation: residues 23-25 (KKR, Charge Cluster 1), glutamine 41 and residues 90-111 (Charge Cluster 2). Our aim is now to identify the proteins that interact with these regions. We also aim to develop cells that can efficiently propagate human sCJD and vCJD prions to set up an automated bioassay for human prions that can be used as a therapeutic biomarker. We will also develop a primary neuronal cell assay for prion neurotoxicity that will be applied to isolate and characterise the putative toxic PrP species.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Molecular and Phenotypic Analysis of Prion Strains
Funder: Medical Research Council

Abstract: Prion diseases are fatal neurodegenerative disorders that include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, Creutzfeldt-Jakob disease (CJD), Gerstmann-Straussler-Scheinker disease (GSS), fatal familial insomnia (FFI), kuru and most recently variant CJD (vCJD) in humans. Their central feature is the conversion of a normal host protein, the cellular prion protein (PrPC), to an abnormal isoform, designated PrPSc. This transition appears to involve only conformational change rather than covalent modification and confers PrPSc with resistance to proteolytic degradation and detergent insolubility. The marked clinical heterogeneity observed in human prion diseases has yet to be explained. However, it has been clear for many years that distinct isolates, or strains, of prions can be propagated in the same host and these are biologically recognised by distinctive clinical and pathological features. It is therefore likely that a proportion of clinicopathological heterogeneity seen human prion diseases relate to the propagation of distinct human prion strains. How this strain diversity is encoded by an apparently protein-only agent remains one of the most interesting and challenging questions in biology. Although distinct mammalian prion strains are associated with different prion protein conformations and glycoform assembly states their precise composition and the molecular determinants of strain remain unknown. Our integrated series of research projects aim to define the molecular composition and ultra-structure of infectious prions and elucidate the molecular basis of prion strain diversity. Knowledge generated by this research is expected to have direct translational benefit by facilitating improved methods of diagnosis and therapeutic treatments for human prion disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Prion Kinetics, Toxicity and Synthesis and its wider relevance
Funder: Medical Research Council

Abstract: Prions are lethal pathogens of mammals which occur in multiple biological strains, and yet appear devoid of nucleic acid and composed of aggregated conformational isomers of a host-encoded glycoprotein. Their unique biology, allied with the risks to public health posed by prion zoonoses such as BSE, has focused much attention on understanding the molecular basis of prion propagation and pathogenesis. However, it is clear that the underlying molecular mechanisms, involving aggregation of a misfolded host protein, are of much wider significance and, indeed, analogous protein-based inheritance mechanisms are recognised in yeast and fungi. The common neurodegenerative diseases also involve accumulation of misfolded host proteins and parallels, at multiple levels, in particular with Alzheimers disease, are becoming increasingly apparent. Recent advances suggest that prions themselves are not directly neurotoxic, but rather their propagation involves production of toxic species which may be uncoupled from infectivity. We have proposed a general model to encompass these phenomena, centring on the kinetics of prion propagation, and will test this model using various experimental systems. Our development of an automated, high-throughput, culture-based prion bioassay (ASCA) will be applied to study in vivo kinetics of prion propagation in multiple models and relate this to neurotoxicity and clinical onset. We aim to specifically characterise the determinants of chronic carrier states of prion infection. ASCA will also be used in large-scale studies to attempt high-titre prion synthesis from purified components, an approach completely impractical by conventional rodent bioassay, and determine the role of co-factors. The hypothesis that prion neurotoxicity is mediated by oligomeric species will also be directly investigated. We also aim to develop cell lines to efficiently propagate hamster and human prions to allow extension of these studies beyond mouse-adapted scrape strains and to provide rapid assay of vCJD prions. Interactions between prion and Alzheimer pathogenesis will be explored at several levels, and we will investigate the possible wider role of PrPC in neurotoxicity. Molecular reagents we have developed to target PrPC will be used to investigate possible wider therapeutic strategies in neurodegeneration. Our prion models also provide a test bed for investigating generic approaches to protein misfolding diseases.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Role of the Prion Protein and 'prion-like' mechanisms in Alzheimer's disease
Funder: Medical Research Council

Abstract: The programme has two main aims, the first of which is to better understand the role of the cellular form of the prion protein (PrPC) in Alzheimer’s disease (AD), particularly its importance relative to other potential cellular acceptors of the AD-associated amyloid beta peptides, by using cellular models of over-expression/gene silencing and to screen focussed libraries to identify tool compounds able to inhibit the interaction. We also plan use the well characterised interaction with PrPC to better biophysically define amyloid-beta species using asymmetric flow field flow fractionation and electron microscopy (in collaboration with Professor Helen Saibil at Birkbeck). Utilising our well-characterised PK1 cells which are capable of sustaining robust levels of prion infection, alongside mouse models of prion disease and human APP-expressing transgenic mice we also plan to better characterise what (if any) impact amyloid-beta and prions have on the each other in the development of prion disease and AD. These studies will utilise histopathological analysis to monitor the spread of both AD and prion pathogenesis, alongside the automated scrapie cell assay to measure the prion infectious titre. The other main objective utilises the Unit’s experience in studying prion disease to better understand the “prion-like” spread of AD. We have access to cadaveric preparations of human growth hormone which we have previously identified as being potentially responsible for the transmission of amyloid-beta pathology and cerebral amyloid angiopathy in clinical cases and to AD brain samples from typical, rapidly progressing and posterior cortical atrophy cases which we have already shown to give rise to structurally distinct amyloid fibres by solid state NMR. We propose to extensively characterise all these samples in: transmission studies using mouse models expressing human APP, biochemically using ultrasensitive immunoassays (in collaboration with Professor Dominic Walsh, Harvard), biophysically by fibre extension followed by NMR (in collaboration with Dr Robert Tycko, NIH), and in cellular models of neurodegeneration (with Professor Dominic Walsh). A better understanding of the potential transmissibility of AD has obvious public health implications especially for the decontamination of neurosurgical instruments, as well as permitting more informed risk assessment of the individuals who received preparations of the cadaveric human growth hormone.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: NEUROLOGICAL
Title: Neuronal model systems for examining toxicity
Funder: Medical Research Council

Abstract: Neurodegenerative diseases are caused by a combination of genetic and environmental factors selectively affecting vulnerable populations of neurons. In most cases the symptoms only occur when most of the neurons have already died and there is currently no cure. Therefore, it is important to understand early processes leading to disease onset and mechanisms of toxicity caused by exposure to environmental chemicals. Midbrain dopaminergic (mDA) neurons can be broadly subdivided into two major anatomically and functionally groups, which form the substantia nigra (SN) and ventral tegmental area (VTA). Despite commonalities in gene expression and developmental origin, only SN dopaminergic neurons degenerate in Parkinson’s disease. There are several indications that environmental compounds may cause neurodegeneration in Parkinson’s disease, but in many cases the cellular events leading to toxicity are not understood. In addition, it is unclear why SN neurons are in particular susceptible to toxic insults and the neighbouring VTA neurons are relatively spared. Progress in understanding the mechanisms of toxicity and disease onset has been hampered by the lack of human relevant neuronal model systems. Human pluripotent stem (PS) cells present new opportunities in this regard, however it is important that pure populations of the relevant neuronal cell types are generated. Our aim is to provide mechanistic insight into cellular events leading to the selective degeneration of SN dopaminergic neurons in Parkinson’s disease. We will explore mechanisms of toxicity for several classes of environmental chemicals in human ES cell derived SN dopaminergic neurons. Furthermore, we will identify cell intrinsic differences between these different populations of dopaminergic neurons that underlie their selective vulnerability. In this proposed study we will use a PS cell based model system for exploring toxicity and disease onset in highly vulnerable populations of SN dopaminergic neurons. Our human ES and iPS cell based platform can be used to examine mechanisms of toxicity of several environmental agents in highly vulnerable neuronal populations. The enriched cultures of human ES and iPS cell derived SN and VTA dopaminergic neurons enable system biological approaches to identify pathways and proteins that mediate the cellular response to the toxic insult. In addition, this approach will give insight in cellular response pathways that are contributing to disease onset. Altogether, we have developed an ex vivo model of healthy and diseased tissue that can be used to analyse mechanisms of toxicity.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Temporally patterned closed-loop stimulation for therapy of brain disorders
Funder: Medical Research Council

Abstract: Parkinson’s disease (PD) and Tremor can be treated using continuous high-frequency deep brain stimulation (DBS) of basal ganglia or thalamus. Both diseases are characterised by neuronal synchrony in the cortex, basal ganglia and thalamus that occurs concurrently with symptoms. In tremor, this neuronal synchronisation occurs at the same frequency as the tremulous limb. In PD, there is mounting evidence for elevated neural synchrony in the beta (~20 Hz) frequency band, and this correlates with severity of akinesia and rigidity. Our goal is to utilise this pathological activity to deliver a closed-loop brain stimulation framework that will significantly improve the treatment of these diseases. Although novel, these treatments will be tractable, based as they are on electrical stimulation that, even in its rawest forms, has already proven beneficial to tens of thousands of patients. To this end, we will develop three closed-loop strategies. Firstly, and most simply, we will limit stimulation to those periods during which pathological activity is elevated to give adaptive high frequency DBS (aHF DBS). We have shown that acute aHF DBS affords improved therapeutic benefit in PD patients as compared to continuous stimulation. We will continue to develop this strategy in both PD and tremor patients. Secondly, we will deliver stimulation locked to a particular point (phase) in the cycle of the underlying pathological activity to give adaptive phase locked DBS (aPL DBS). As oscillatory activity seems likely to be mechanistically important in driving symptomatology in PD and tremor, aPL DBS may be more specific and selective than conventional DBS by interacting directly with the pathological activity. We have demonstrated the potential efficacy of this strategy in tremor and will continue this work in patients. In PD, we will develop this methodology in the rat model and test the most successful protocols on patients. The pathological oscillatory activity in these conditions is likely an emergent property of altered functional connectivity, arising across specific circuit components as a consequence of chronic disturbances in neurotransmission. To this end, for our third strategy will use spike-triggered stimulation to progressively and selectively weaken or strengthen key connectivities over time to rebalance networks and ameliorate disease related impairment. These experiments will be carried out using animal models, to allow flexibility in stimulation protocols and the examination of structural changes in connectivity. Our approaches are intended to be generic and applicable to other brain targets and diseases, and eventually implementable by alternative, more selective forms of stimulation, when these become suitable for use in patients.


Research activity codes: 6.3 MEDICAL DEVICES
Health categories: NEUROLOGICAL
Title: Accessing and actuating specified neural circuits underlying motor function and dysfunction
Funder: Medical Research Council

Abstract: The design of new strategies for treating the symptoms of brain diseases must be tempered by a mature knowledge of how different nerve cell types fulfil their specialised roles to govern behaviour. The overarching goal of this Programme is to deliver high-resolution readouts and mechanistic explanations of brain motor circuit organization in the context of normal behaviours as well as impaired Parkinsonian behaviours. Focusing on the ‘motor domains’ of the neuronal circuits linking the basal ganglia, thalamus and cerebral cortex, we will harness cutting-edge technologies for identifying, accessing and manipulating neurons in vivo to provide fundamental new insights into the specific cellular substrates of the neuronal network dynamics therein. We will place special emphasis on defining how the interactions and activities of identified cell types in these motor circuits vary according to the temporal profile of dopamine release and movement. As a key corollary of this, we will define how a paucity of dopamine release, as occurs in Parkinson’s disease and its animal models, impacts on the neuronal encoding of behaviour in these motor circuits. To achieve our specific aims, we will couple novel and advanced analytical techniques with experimental interventions designed to probe causal interactions between specified circuit elements with high spatiotemporal precision. Our experiments will centre on the use of wild type and genetically-altered rodents with intact or comprised midbrain dopaminergic systems, the readouts from which will straddle multiple levels of function including molecular/genetic, structural, electrophysiological and behavioural. In capitalising on the new level of understanding of the dynamics of identified neurons that will be gained here, we will also exploit specified cell types and other circuit elements as novel points of entry for spatiotemporally-patterned interventions designed to correct circuit dysfunction and related behavioural deficits in advanced Parkinsonism.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: NEUROLOGICAL
Title: Using computer simulations for predicting interventions restoring healthy patterns of neural activity
Funder: Medical Research Council

Abstract: Many neurological disorders are characterized by abnormal patterns of oscillations in neural activity. However, due to the complexity of the circuits these oscillations originate from, it is often unclear how they are generated, and how to best control them. To understand dynamics of complex systems, mathematical and computational methods are routinely employed in more established areas of science and engineering, and they have been proved critical for developing effective mechanisms for control of oscillations. This programme will develop methodology for using computer simulations of neural circuits affected by neurological disorders to predict interventions optimally restoring healthy patterns of activity. It will initially focus on Parkinson’s disease, because the basal ganglia circuits producing abnormal activity in this disorder are relatively well understood. Computational models of the basal ganglia will be developed that will describe how it generates the pathological dynamics and how it responds to deep brain stimulation (DBS) and optogenetic stimulation. The unique aspect of these models is that they will be constrained by a wide range of the high quality experimental data directly available in the MRC Unit, and optimized to maximize their ability to predict responses to novel stimulation protocols. The models will be used to rapidly test candidate versions of closed-loop DBS in silico, and to identify how and when with respect to ongoing activity the stimulation should be provided to optimally restore neural activity normally present in healthy basal ganglia. The suggested closed-loop intervention protocols will be tested within the MRC Unit, and results will be iteratively used to further refine the procedure. Moreover, the programme will investigate how the developed methodology and theory can be generalized to other neurological disorders (e.g. essential tremor) and to other neural systems (e.g. hippocampus).


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL