NIHRDataInsights/HRCSData huggingface dataset:
Title: Identifying novel disease genes in patients with skeletal muscle channelopathies.
Funder: Medical Research Council

Abstract: Genetic defects in voltage-gated ion channel genes are known to be responsible for a wide variety of diseases including skeletal muscle channelopathies where the two main clinical groups are periodic paralysis and non-dystrophic myotonia. In these conditions mutations in recognised sodium, chloride, calcium and potassium channel genes often cause significant stiffness, weakness and neurological disability but these genes only account for around 80% of cases. The aim of this project is to improve our understanding of skeletal muscle channelopathies by: 1. Identifying novel disease-causing gene(s) in patients and families with undiagnosed muscle channelopathies. 2. Screening our cohort of undiagnosed channelopathy patients to establish range, frequency and ethnic variation of defects in these genes. 3. Investigating the pathogenicity of new mutations identified using an expression system. We have identified the sample population utilising probably the world‘s largest database of channelopathy patients at the MRC Centre for Neuromuscular Diseases (linked to the UK National Channelopathy clinical service funded by the UK National Commissioning Group). From this we have selected the group of genetically undetermined patients with clear clinical and electrophysiological signs of muscle channelopathies. This currently consists of 296 patients (23% of 1300). To identify novel disease-causing genes we have selected the 44 best probands from families that are negative for known genes. We will use targeted next-generation sequencing to analyse the coding and flanking intronic sequence of the 350 muscle channel genes. Four patients with known mutations in channel genes will be included as positive controls. Sequences will be aligned with the reference sequence and genetic variants cross-checked with public databases to identify true mutations and exclude normal polymorphisms The 1000 genomes project will also be important in allowing us to align control sequences from individuals with differing ethnicity. Probable mutations will be rechecked with Sanger sequencing and the entire cohort screened with the identified disease genes. Finally, to establish pathogenicity, we will use site-directed mutagenesis to develop mutated cDNA constructs to transfect HEK293 cells for expression studies. The expressed channels will be interrogated by patch clamping to identify the mutation‘s effect on its voltage-gating properties and help prove pathogenicity. This project will expand the pool of scientific knowledge in muscle channelopathies by identifying novel genes, targeting an MRC research priority area, Genes and Disease. It will have an impact on both the patients we diagnose and future diagnostic testing. It will also provide new targets for treatment in a group of diseases which lack substantial treatment options.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Selective targeting of synapses to specific dendritic locations and their modulation by voltage-gated channels
Funder: Medical Research Council

Abstract: Evidence for specificity in the properties of synaptic connections is growing, though few studies have examined this issue directly in the smaller dendritic branches of pyramidal cells. Fewer still have studied how the properties of postsynaptic dendritic compartments shape individual synaptic inputs and their summation with events from neighbouring synapses. Many different mechanisms contribute to dendritic properties; mechanisms that may be differentially expressed in different pyramidal cells, different dendrites and dendritic compartments. We will test the hypothesis that each class of synaptic input to a given class of postsynaptic cell is distributed over a highly specific region of dendritic space that is homogeneous in its active and passive properties, involves only certain types of dendrites and is at a given electrotonic distance from the soma. This project will compare the properties of two families of neocortical pyramidal cell dendrites, the apical oblique and the basal dendrites of layer 3 pyramidal cells and how their properties shape the synaptic inputs that impinge upon them. Inputs from layer 4 spiny cells selectively innervate the basal dendrites of layer 3 pyramids, while layer 3 inputs also innervate apical obliques. Calcium transients in the dendrite and voltage responses at the soma produced by the release of caged-glutamate onto different dendritic compartments will be recorded. These will be compared with responses to the glutamate released by the synaptic boutons of a single identified presynaptic neurone in paired recording experiments; the postsynaptic dendritic compartment(s) involved being identified by the close apposition of fluorescently labelled axon and dendrite and co-localised calcium signals. How voltage-gated K+ and cation-selective (HCN) ion channels modify glutamatergic inputs to different dendritic compartments will be explored with ion channel blockers and by comparison of wild type mice with mice lacking HCN or Kv4 channels. These data and 3D reconstructions of the layer 3 neurones will tune a detailed compartmental layer 3 pyramidal cell model and predictions eg. about summation tested experimentally. How both pre- and post-synaptic GABAergic inhibition in these same dendritic compartments interacts with excitatory inputs will also be directly assessed. In one block of paired recording experiments, the effect of uncaging GABA at different positions relative to a synapse(s) from a single presynaptic excitatory cell will be studied. In the other, responses to glutamate uncaged at different positions along a dendrite will be challenged with the input from a single inhibitory interneurone innervating the same dendritic branch.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: NEUROLOGICAL
Title: The Oxford Control Brain Collection
Funder: Medical Research Council

Abstract: A MRC UK review of brain banking has identified a severe shortage of well characterised normal brains suitable for next generation molecular neuroscience research. A need to provide researchers with tissue from disorders that are common but rarely undergo autopsy such as autism has also been highlighted. Here we propose that the Thomas Willis Oxford Brain Collection (TWOBC) is well positioned to provide a solution to this problem. The TWOBC is part of the emerging MRC UK Brain Banking network, founding member of the Brains for Dementia (Bdr) consortium, part of the MRC Cognitive Function and Aging Study (CFAS) and host of the newly formed Brain Bank for Autism. As part of the Bdr study we recruit healthy elderly individuals which are cognitively assessed and have pledged their brains for research. However, these numbers are low. Here we propose to retrieve control brain and cord donations matched with blood and relevant peripheral tissues via our Coronial service and in collaboration with our heart valve tissue transplant team. The potential donor cohort in Oxford includes over 800 Coronial autopsies. We have piloted a combined post mortem CT/MRI study on 110 Coronial autopsies with minimal post-mortem delay, 90% of which would be suitable for brain donation based on normal brain CT. We have also identified over 150 potential brain donors per year via our heart valve tissue bank. We have recently received support from the NIHR Oxford Biomedical Research Centre to establish routine DNA/mRNA/protein extraction and quality control protocols in neuropathology. We are actively collaborating with local basic scientists to establish sampling protocols for the application of next generation sequencing techniques to brain tissue. Infrastructure consists of newly built state-of-the art laboratories and tissue storage facilities with space for expansion. This is a single-site application based around a team of neuropathologists, general pathologists, and the directors of the Oxford heart valve bank and patient services (including bereavement). With the requested support we will fuse the heart valve and bereavement team services. Based on the above numbers we estimate that we will be able to collect 30 to 50 well-characterised control brains per annum and make them available for researchers. Some of these brains will have the added value of corresponding high-resolution post-mortem CT or MRI data which we would make freely available for researchers. We are fully HTA and CPA accredited and governance structures, consent and ethics protocols are established.


Research activity codes: 2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY)
Health categories: NEUROLOGICAL
Title: A survival factor for axons: roles in disease and downstream mechanism
Funder: Medical Research Council

Abstract: In neurodegenerative disorders axons typically degenerate before neuronal cell death. This sequence of events, and particularly the early loss of distal axons, is known as ?dying back? degeneration. The causes of axon degeneration include protein aggregation, inflammation, neurotoxicity and ischaemia, and many of these diverse stresses converge on a common degenerative pathway involving axonal transport impairment. Axonal transport is the bidirectional trafficking of molecules and organelles along axons for huge cellular distances. It is essential for axon survival but deficient in multiple sclerosis, glaucoma, motor neuron disease and many other disorders. Despite the prevalence of axonal transport impairment, the specific molecular changes leading to axon degeneration are poorly understood. Cutting axons, which causes Wallerian degeneration, is a useful experimental model that can help identify the key molecular events. A mutant protein named Wallerian degeneration slow (WldS) delays Wallerian degeneration by tenfold and alleviates some ?dying back? disorders, showing that the mechanisms are related. Thus, axons do not die by passive wasting when isolated from cell bodies but by a specific and regulatable process. WldS is an aberrant protein that occurs naturally in only one strain of mouse, so until now it has been largely unclear how we might use it to protect axons in human disease. Recently, we identified the NAD+ synthesising enzyme Nmnat2 as an endogenous regulator of the same pathway in primary neuronal cultures. Nmnat2 is an unstable protein, so if axonal transport fails to replenish it, continual protein turnover in axons takes Nmnat2 below a threshold level that triggers Wallerian degeneration. Nmnat2 is now the key to understanding the degenerative mechanism and thereby identifying suitable steps to target pharmacologically, but for the full picture it must also be studied in vivo. We hypothesise that depleting Nmnat2 is sufficient to initiate Wallerian-like degeneration in vivo and that failure to deliver it to distal axons in some axonopathies is the direct cause of ?dying back? axon loss. We also hypothesise that Nmnat2 and WldS control a common downstream pathway, which we can activate very specifically by removing Nmnat2. Thus, we can now factor out the many non-specific consequences of cutting axons or of blocking axonal transport, and focus specifically on events leading to axon degeneration. This is a unique opportunity to move towards translation for axonal transport disorders and for significant progress in understanding how axon survival and degeneration are controlled at the molecular level.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Integrins as a therapeutic tool for CNS repair
Funder: Medical Research Council

Abstract: The aims of the application are to use integrin engineering to promote axon regeneration after spinal cord injury. In order to regenerate in the damaged CNS axons must grow through the extracellular matrix, for which they need an integrin that recognises the CNS matrix glycoprotein tenascin However CNS axons lack a tenascin-binding integrin. By expressing an integrin that recognises tenascin we were able to promote exuberant growth on inhibitory environments. However this approach is only partially successful in vivo because the inhibitory molecules in the environment inactivate integrins and because integrin transport into mature CNS axons but not PNS axons is blocked at the axon initial segment. The programme will: 1) indentify the trafficking mechanism for integrins in PNS axons, 2) Investigate regulation of integrin trafficking by arf6, 3) find why transport of integrins and other molecles into axons is blocked at the axon initial segment of CNS axons and how to overcome it, 4)investigate the use of talins and kindlins to promote integrin activation in axons, 5)investigate the use of constitutively active integrins to promote axon regeneration in inhibitory environments, 6) investigate the use of integrin activating antibodies to promote regeneration. The successful strategies will be tested in a spinal injury model.


Research activity codes: 5.1 PHARMACEUTICALS;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Importance of long-range inhibitory connections in hippocampal network oscillations
Funder: Medical Research Council

Abstract: The spread of excitation in the hippocampus is controlled by inhibitory neurons. Various inhibitory cell types are responsible for shaping behaviorally dependent network activities such as theta and sharp-wave associated ripple oscillations. Based on the extent of axonal arborization interneurons are divided into local circuit and long-projection cells. Long-projection neurons exert a global effect on their target, but the function of these cells is unknown. The working hypotheses are: -Long-projection inhibitory neurons belong to a well-defined subpopulation of cells; -These interneurons play a crucial role in ripple oscillation; -Synchronization of ripple events between the two hippocampi is maintained by long-range inhibitory cells. Using a combination of in vivo cellular electrophysiology, multichannel recording, immunohistochemistry, electron microscopy and molecular biology, we investigate: 1) the proportion and the axonal arborization of long-projection neurons; 2) the synaptic targets of these neurons; 3) the axonal trajectory of the long-projection neurons to the contralateral side; 4) the firing pattern of these neurons in different network oscillations; 5) the effect of selective elimination of long-projection neurons in intra- and interhippocamapal synchronization. Thorough knowledge of inhibitory neuronal network is essential for understanding the involvement of the hippocampus in memory formation, ischemic damage, and temporal lobe epilepsy.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: NEUROLOGICAL
Title: Genetic Dissection of Neuromuscular Disorders
Funder: Medical Research Council

Abstract: Peripheral neuropathy is common, affecting approximately 2.5% of the UK population. Inherited neuropathy is usually called Charcot-Marie-Tooth disease (CMT) and is one of the commonest inherited neurological disorders affecting 1 in 2500 people. CMT usually starts in childhood or teenage years with progressive distal limb weakness, muscle wasting and glove and stocking sensory loss. Walking problems and foot deformities are common requiring orthoses, sticks and later wheelchair use. CMT is genetically heterogeneous with over 30 genes identified that have revealing important biological insights into the pathophysiology of the peripheral nervous system. The majority of genes have been identified in the demyelinating form of CMT (type 1), few genes in only a small proportion of cases have been found in the other types of CMT. After excluding the known genes, around 40% of CMT patients remain genetically undefined. Here we propose an unprecedented gene discovery effort to identify and characterise a large proportion of the unknown CMT genes. In the past we have been limited by the sequencing technology and the size of families, however, we can now perform whole exome sequencing of all protein encoding regions (exome) and flanking intron boundaries from enriched patient DNA samples. In our laboratory we have established next generation sequencing developing an effective exome sequencing pipeline that has so far, identified one novel disease gene. This method is perfectly suited to CMT gene identification, in small families or groups of patients with very similar phenotypes. Whole exome sequencing will be performed in 100 CMT families. Half the families will be dominant and half recessive, divided between CMT1, CMT2, distal HMN and HSAN. In dominant families two individuals will be sequenced and in the recessives one. After thorough filtering and bioinformatic analysis we expect to identify a number of disease genes, prove these defects in families and then examine our extensive CMT database of cases to assess frequency, mutation spectrum and phenotype correlations. Many genetic defects will require protein and/or RNA studies from patient material to prove the mutation mechanism. True functional analysis is beyond the scope of this proposal but we have established a number of fruitful collaborations that have allowed the successful investigation of CMT genes. We expect these genes to cluster into pathways that are important for peripheral nerve homeostasis and when defective lead to nerve degeneration. Through the identification of these processes the hope must be that treatment targets will become apparent.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: NEUROLOGICAL
Title: Basic science and preclinical development of cell transplantation for basal ganglia disorders
Funder: Medical Research Council

Abstract: The UK is taking an international lead in developing stem cells for cell-based therapy applicable to a broad range of diseases. The purpose of this programme application is to address the translational gap to deliver clinical-grade human neuronal cells from primary, expanded and pluripotent origins for transplantation in clinical trials of human neurodegenerative disease. We complement other stem cell programmes in establishing and maintaining the infrastructure for ethically-sourced, safe, quality-assured processing of cells of clinical grade under regulatory licence, alongside establishing relevant patient cohorts, assessment programmes and clinical trial expertise, without which advances in basic cell biology cannot progress to human use or clinical trial. A major component of this programme is to develop and refine the animal models to evaluate alternative sources of cells with predictive validity of likely functional efficacy in man. Immediate applications are set to commence using primary fetal cells in 2011-2012 in Huntingtons disease and Parkinsons disease, with subsequent applications in stoke, and using expanded fetal progenitors, pending the availability of clinical grade stem cells.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: NEUROLOGICAL
Title: From single units to local field potentials: Study of the timing of medial temporal lobe responses in humans
Funder: Medical Research Council

Abstract: The focus of this project is to study the temporal dynamics of the responses of Medial Temporal Lobe (MTL) neurons in humans. The neuronal responses are recorded by means of deep electrodes implanted in epileptic patients for clinical reasons. These electrodes can record the activity of single cells (spikes) or the average activity generated by a large number of neurons, leading to the so called Local Field Potentials (LFPs). It has been shown that neurons in MTL provide an abstract representation of the stimulus (e.g. picture presentations) since they respond to a given concept in disregarding the details of the particular picture shown. These responses consistently appear 300 ms after stimulus presentation, but how the brain manages to keep track for the post-stimulus timing and elicit such time-locked responses is still largely unknown and will be the main research question of this project. The initial hypothesis is that LFPs may act as a gating mechanism for the single cell responses to appear. I will first characterize LFP latencies and their relation to spikes (multi and single unit) in human MTL in response to picture presentations. In addition, I plan to analyse the contributions of spikes, LFPs, and the information carried by both together using the information theory formalism. I will also study the effect of stimulus recognition on the temporal dynamics of spiking and LFP activity. For this, the experimental paradigm will be modified to make recognition more difficult, i.e., delaying the onset of recognition by the subjects. The results of the analysis of these latencies will be compared with the ones from the first paradigm. The key question is whether a change in the behavioral response time will be correlated with a delay in the spikes and the ‘gating responses‘ of the LFPs. These results would be of large relevance because they can provide conclusive evidence about the roles of the LFPs for providing timing information in high order human brain areas.


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