NIHRDataInsights/HRCSData huggingface dataset:
Title: Mapping cell-type-specific regulatory genomic variation in Alzheimer's disease pathology.
Funder: Medical Research Council

Abstract: We propose the most comprehensive analysis of regulatory genomic variation associated with Alzheimer's disease (AD). The project builds on our previous work assessing the role of epigenomic variation in AD and success in developing methods for regulatory genomic profiling across distinct neural cell-types. First, we will profile multiple markers of genomic regulation (DNA methylation, DNA hydroxymethylation, lysine H3K27 acetylation (H3K27ac) and chromatin accessibility) in purified nuclei populations from the dorsolateral prefrontal cortex (DLPFC) from 200 donors with low and high AD neuropathology. We will use a fluorescence-activated nuclei sorting (FANS) protocol developed by our group to simultaneously purify nuclei from neurons, oligodendrocytes and microglia prior to genomic profiling. Second, we will validate regulatory regions associated with AD pathology in additional samples and datasets. We will use cell-type-specific epigenomic data to develop and validate cellular deconvolution algorithms, enabling us to leverage large existing AD genomic datasets generated by us and our collaborators for replication. We will also integrate our cell-type-specific epigenomic data with single nuclei transcriptomic data from the Multi-Omics Atlas Project (MAP) funded by the UK Dementia Research Institute (DRI). Finally, we will explore overlap with cortical genomic changes identified in our ongoing analyses of transgenic mouse models of tau and amyloid pathology. Finally, we will integrate cell-type-specific genomic annotations with AD genetic data, exploring the extent to which AD-associated variants are enriched for regulatory quantitative trait loci (QTLs). We will extend our use of co-localization approaches and Summary data-based Mendelian Randomization (SMR) analyses to identify variants that are pleiotropically associated with both AD and regulatory variation in specific cortical cell-types.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: The Glycine Cleavage System in Brain Development, Function and Disease
Funder: Medical Research Council

Abstract: This programme aims to understand how suppression of folate one-carbon metabolism (FOCM) leads to abnormal brain development and function. We focus on glycine decarboxylase (GLDC), a component of FOCM which has been implicated in neural tube defects (NTDs), hydrocephalus and Non-Ketotic Hyperglycinemia (NKH). Using genetic models in mouse and human iPSC models our main goals are: 1. To determine the effect of GLDC loss of function on metabolism, cellular phenotypes and patterning in embryonic neuroepithelium and neuronal precursor cells. We will use: (i) functional assays of energy metabolism, metabolic tracing and imaging of fluorescent reporters; (ii) assays of cell cycle and redox balance; (iii) evaluation of one-carbon donors and other metabolic intermediates for prevention/exacerbation of NTDs; (iv) gene expression analysis. 2. To test the requirement for GLDC in prevention of structural malformations that lead to hydrocephalus. Morphometric and gene expression analysis of diencephalon will determine where/when defects first arise, with conditional genetic rescue to localise the need for region-specific GLDC function. Potential causative metabolic and cellular defects will be examined by testing preventive methods. 3. To identify the role of GLDC in postnatal brain development. Cell cycle analysis in pre-natal progenitors and immunostaining in juvenile brain will reveal cortical layering anomalies. The requirement for GLDC in post-natal NPCs will be determined by lineage tracing, immunohistochemistry and single cell transcriptomics. Co-cultures will reveal whether GLDC loss in astrocytes has deleterious effects on metabolism or redox balance in adjacent neurons. Identification of pathogenic mechanisms underlying GLDC-related disorders will provide an opportunity for rational design of potential therapeutic approaches which will be evaluated for prevention of NTDs and hydrocephalus, and for amelioration of cellular and metabolic defects associated with NKH.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: Regulation of the time-sensitive period in neuronal circuit development by NTRK2/TrkB signalling.
Funder: Medical Research Council

Abstract: This project will examine the molecular mechanisms underlying time-sensitive periods in dentate granule cells (DGC) differentiation continuum leading to sequential maturation of intrinsic hippocampal circuits in normal and perturbed conditions. The guiding hypothesis is that early in postnatal development, BDNF-TrkB activation in immature DGCs provides an instructive signal that drives the sequential maturation of intrinsic hippocampal circuits via the depolarizing action of GABA. Disrupting this signal at a critical period leads to neurodevelopmental defects, followed by synaptic plasticity and cognitive impairments in adulthood. A key step to elucidate the mechanisms underlying the crucial transition of immature DGCs into the GCL is the coordinated analysis of these neurons' transcriptional and epigenetic properties at single-cell level revealing their cellular state and cellular capacity simultaneously. We have established platforms for genetic labelling and lineage tracing of developing DG neurons, single-cell RNA and ATAC sequencing, and in vivo viral transduction of the hippocampus. This project will carry out transcriptional and epigenetic profile analysis using scRNAseq and scATACseq, respectively, from wild type and Trkb mutant DGC populations at two critical time points of postnatal development. We will then perform a computational integrative analysis of epigenome vs transcriptome data obtained to select top candidate gene regulators of the DGC differentiation continuum. Finally, by functionally validating top candidates by rescuing the DGC differentiation block occurring in the absence of TrkB signalling, we will identify key molecular pathways that regulate the DGC differentiation continuum during time-sensitive periods of postnatal development.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;6.2 CELLULAR AND GENE THERAPIES
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: Loss of UNC13A: how it exacerbates amyotrophic lateral sclerosis, and how to correct it
Funder: Medical Research Council

Abstract: The RNA-binding protein TDP-43 is a central player in ALS and other neurodegenerative disorders. It accumulates in cytoplasmic inclusions and is depleted from the nucleus, where it normally resides to regulate fundamental processes including RNA splicing. As a consequence, widespread splicing changes occur in ALS, including the appearance of cryptic exons (CE): novel toxic intronic sequences incorrectly incorporated into mature RNA. Many CEs have been described and their role in pathology, if any, is largely obscure. However, we have identified a novel CE in the synaptic gene UNC13A that is incorporated due to TDP-43 depletion in neurons. Crucially, a genetic risk variant for ALS lies within this CE. We have shown this SNP enhances the CE inclusion. The CE causes a reduction of UNC13A RNA and protein; this event is specific for brain regions most affected in ALS. Thus, we hypothesise that UNC13A loss contributes to ALS pathogenesis and rescuing this may lead to amelioration of disease, potentially in ~97% of ALS with TDP-43 mislocalisation. We propose to investigate fundamental questions about UNC13A misprocessing in ALS, and how to correct it. We will further characterise WHERE the alterations occur in ALS brains, using single molecule RNA visualisation techniques and single neuronal nuclear sequencing to identify affected neuronal populations. We will use our established iPSC-derived cortical and lower motor neurons, in which we reliably recapitulate TDP-43 mediated loss of UNC13A, to understand WHAT the consequences are for neuronal biology-by analysing ALS phenotypes such as neuronal survival, neurite and axon growth, and with specific synaptic electrophysiology investigations. Lastly, we will determine HOW the UNC13A CE is regulated, and develop approaches to interfere with it, and rescue downstream consequences. These investigations will shed light on a crucial ALS pathogenesis step and set the basis for a novel therapeutic approach for ALS.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: DREADDs for clinical translation
Funder: Medical Research Council

Abstract: Abnormalities of neuronal circuit excitability account for a very large disease burden. Although much progress has been made in understanding the circuit basis of such disorders, treatment has lagged behind, mainly because of the very poor specificity of small molecules for defined neuronal circuits. Of the advanced therapies that have been proposed, gene therapy is closest to the clinic, because it allows the excitability of specific neuronal circuits to be modulated. Chemogenetics has the added advantage of allowing such modulation to be adjusted or used on demand. Our proposal aims to lower barriers to clinical translation of treatment using muscarinic Designer Receptors Exclusively Activated by Designer Drugs (DREADDs). We have extensively screened FDA/EMA-approved drugs that could be used as agonists of the inhibitory DREADD hM4D(Gi). Although we identified olanzapine as such a drug, its antagonism at H1, muscarinic dopaminergic and serotonergic receptors contributes to sedation, weight gain, and a lowering of seizure threshold in some people. However, by introducing additional point mutations to hM4D(Gi) we have made it highly sensitive to the over-the-counter antihistamine drug diphenhydramine, whilst preserving its coupling to intracellular signalling cascades, and without conferring constitutive activity. We refer to the modified receptor as a G-Protein-Coupled Receptor Activated by Non Prescription Agents (GRANPA). We will validate the use of the inhibitory GRANPA in a rodent model of epilepsy. In addition, we will introduce the same mutations to the excitatory DREADD derived from the human M3 muscarinic receptor (hM3Dq). This will broaden the application of GRANPAs to the treatment of neurological diseases where an increase in neuronal excitability is desired. Finally, we will design inhibitory and excitatory GRANPAs where intracellular sequences have been mutated to reduce internalization and desensitization, to optimise their long-term use.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: Mechanism of sex difference in severe brain malformations
Funder: Medical Research Council

Abstract: Sex differences in disease frequency and severity are common, and can arise before sex differentiation in the embryo. Anencephaly is a major congenital brain defect resulting from failed neural tube closure in the 3rd embryonic week. It affects 0.2-5 per 1000 births and is markedly more common in females than males. In mice, exencephaly - the forerunner of anencephaly - also shows a female bias, indicating a general mammalian phenomenon. The X chromosome inactivation (XCI) hypothesis views heavy usage of methyl groups in female cells as creating an 'epigenetic sink' that compromises other methylation events in the embryo. This proposal will: (i) test the XCI hypothesis, to determine why mouse exencephaly is predominant in females, and is hindbrain-specific, compared with males where it is forebrain-specific; (ii) determine the underlying molecular mechanisms by which methyl group availability impacts cranial neural tube closure. Brain closure will be studied in whole mouse embryo culture, which has already yielded pilot data consistent with the XCI hypothesis. Variations in sex chromosome constitution (XXY, XO) will provide a direct test of the XCI hypothesis while assessment of teratogens (e.g. valproic acid), and single NTD-causing genes, will reveal the generalisability of the XCI mechanism. Folates will be compared for preventive effects. The molecular analysis will involve assessment of downstream methylation targets in the embryo: DNA, where a methylation array will be used, and protein where methylation events involving cytoskeletal actin and tubulin will be studied. We will test whether methylation is critical for hindbrain neural crest emigration, that could underlie the female brain closure defect. Genes that 'escape' X inactivation will be evaluated for possible protection of females against forebrain defects. This project aims to resolve a long-standing knowledge gap in birth defects research, that has strong clinical implications.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: MICA: The role of excitatory synaptic scaling in epileptogenesis in rodent and human brain networks
Funder: Medical Research Council

Abstract: The processes underlying establishement of epileptic cuircuits in the brain remain difficult to pin down. Recently, it has been established that neuronal activity causes changes in both synaptic drive and intrinsic neuronal excitability - so called homeostatic scaling (HS). HS maintains a reciprocal relationship between excitatory synaptic drive and intrinsic neuronal excitability such that neuronal output is maintained within a window of stability. So far, HS has been little-investigated in the context of epilepsy, even though seizures represent the most extreme form of neuronal activity that might drive such a process. We have shown in rats that AMPAr expression in hippocampus collapses following initial induction of seizures. 80% loss of AMPAr in hippocampus progresses in subsequent weeks to loss of AMPAr in the wider temporal lobe. We have confirmed functional loss of neuronal network oscillations in affected regions (CA3 and CA1) in vitro. We now wish to explore the relationship between excitatory synaptic downscaling and intrinsic neuronal excitability, and between these changes and epilepsy severity. Using implanted EEG/depth recording in epileptic rats, we will calculate seizure burden (frequency, intensity, cumulative time spent in ictal activity) and disease stage (latent period, after development of SRS, treatment response) and test the hypothesis that the degree of AMPAr loss predicts seizure burden and intrinsic neuronal excitability. We will attempt to intervene in HS and thereby alter the epileptogenesis. This project offers a new way to treat epilepsy, through modification of unrelying mechanisms rather than focusing on seizure prevention. This project combines molecular biological investigations of AMPAr function with electrophysiological analyses of functional consequences at whole-brain, local network and cellular/synaptic levels with the ability of our industrial partner (GW Pharma) to provide genomic, proteomic and lipodomic analyses.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: Mechanistic studies of ALS-causative mutations and RNP-focussed drug discovery using in vitro reconstitution of RNP complexes
Funder: Medical Research Council

Abstract: Amyotrophic lateral sclerosis (ALS) is an incurable neuromuscular disease and a significant unmet medical need. A significant proportion of ALS cases is caused by mutations in RNA-binding proteins (RBPs) and/or involves their functional deregulation. In particular, it is well-established that dysregulation of RNA-RBP complexes (RNPs) triggers the downstream cascade of the pathology in many ALS subtypes. We demonstrated that the stress-induced isoform of the long non-coding RNA NEAT1, NEAT1_2, that nucleates RNP granules paraspeckles, is upregulated in the surviving motor neurons in the spinal cord in all major ALS subtypes. Moreover, many protein components of NEAT1_2/paraspeckle complexes are affected by ALS-causative mutations. Positive modulation of NEAT1_2 in ALS motor neurons is expected to exert a neuroprotective effect and hence provide a therapeutic benefit. However currently no specific NEAT1_2/paraspeckle targeted therapies are available. We have developed a scalable imaging-based platform for reconstitution of ALS-relevant RNP complexes in vitro and their quantitative analysis - "RNPs-on-beads". When functionalised with a structural motif of NEAT1_2 RNA, it can be successfully used for the reconstitution of paraspeckle-like complexes on beads ("PoBs"). We propose to validate this platform as a tool for rapid analysis of the effect of ALS-causative mutations on RNP complexes and for identification of small molecules - modulators of NEAT1_2/paraspeckles. In addition, we will test the principle suitability of our platform for RNA-focussed drug discovery aimed at other ALS-linked RNAs using C9ORF72 RNA with expanded hexanucleotide repeats and known mediators its neurotoxicity - SRSF1 and eIF4A proteins. In summary, results of this project will lead to a better understanding of the role NEAT1_2/paraspeckles in ALS, identify new tool molecules for ALS research, and create a framework for RNP-complex focussed small molecule drug discovery in ALS.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: L-Aspartate signalling in the brain
Funder: Medical Research Council

Abstract: By developing a biosensor selective for L-Asp over L-Glu, we have demonstrated electrically evoked, Ca2+ dependent release of L-Asp in the hippocampus. The L-Asp signal can be enhanced via blockade of either excitatory amino acid transporters or the intracellular enzyme asparagine synthetase (ASNS). Remarkably, inhibition of ASNS evokes seizure like activity, and we find that this enzyme is upregulated in tissue from human epilepsy patients. Our results suggest that L-Asp signalling, although subordinate to that of L-Glu, may be an important regulator of the excitability of hippocampal networks. We shall use a combination of electrochemical biosensing, electrophysiology, Ca2+ imaging, chemogenetics and targeted deletion of key genes to tackle the following aims: 1. To identify the cells that release L-Asp. Given that L-Asp colocalises with GABA at synaptic terminals, these are likely to be GABAergic interneurons and we shall identify which subtype is in involved. 2. To determine the postysynaptic targets of L-Asp. We shall screen, via imaging and whole cell patch clamp recordings, the cells that directly respond to release of endogenous L-Asp via NMDA receptor activation and document their patterns of activation. 3. To unequivocally link ASNS to the control of seizures. We shall identify precisely the cell types that express ASNS and whether this pattern changes in the epileptic brain. We shall test whether focal knockout of ASNS in hippocampus enhances seizure generation. We shall explore the functional consequences of the upregulation of ASNS in the epileptic brain. By using resected tissue from human epileptic patients, we shall demonstrate relevance to the human condition.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: Gut Imaging for Function and Transit in CF - The GIFT Study
Funder: Cystic Fibrosis Trust

Abstract: A study of 12 people with CF, compared to 12 controls who do not have CF to correlate the MRI measurements with a patient reported symptom score. Will also measure the effects of Orkambi™ (which corrects the basic defect of CF) on gut function. This will give pilot data to design studies which will test drugs to improve gut function in CF.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CONGENITAL DISORDERS;ORAL AND GASTROINTESTINAL
Title: Urofacial Syndrome a novel genetics model to understand human urinary tract malformations.
Funder: Wellcome Trust

Abstract: This project aims to learn about the cause of an inherited condition called Urofacial syndrome (UFS). People with UFS are born with an abnormal urinary tract (kidneys, bladder and the tubes between them). They also have an abnormal facial expression when attempting to smile and may have problems emptying their bowels. The genetic cause for some cases of UFS has recently been found. This project aims to find the genetic explanation for other cases of UFS. The project will also look at why peo ple with UFS develop the problems they have by trying to understand what jobs the gene(s) do in the body. The urinary tract problems seen in UFS are similar to those seen in other conditions affecting the bladder and causing vesicoureteric reflux (VUR), which is the abnormal flow of urine from the bladder back towards the kidneys. VUR is common affecting about 1% of children, it can be associated with damage to the kidneys and accounts for about 10% of the 40 000 people in the UK who need dialys is or kidney transplant. It is thought that understanding UFS will help explain why these more common urinary tract problems occur and help discover improved treatment.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;RENAL AND UROGENITAL
Title: Development of the World’s First Non-Invasive, Pre-Implantation Genetic Test (PGT-M) for Genetic Disorders in Embryos
Funder: Innovate UK

Abstract: Genetic disease results in significant morbidity and mortality in the population and early detection is key to improving outcomes and reducing suffering for affected individuals and their families. Couples at risk of transmitting serious genetic disorders to their children currently have the option of undergoing IVF and testing their embryos (using an invasive biopsy method) to prevent the birth of affected children. However, there is a significant lack of cost-effective, accessible and, specifically, an absence of non-invasive embryonic genetic disease detection methods. In addition, the COVID-19 pandemic has further impacted the existing challenges for current detection methods because of IVF clinic closures and redeployment of resources in the NHS. Igenomix, led in the UK by Professor Alan Thornhill (working alongside technical, scientific and entrepreneurial experts Seema Dhanjal, Darren Griffin, Alan Handyside and Roy Naja) aims to provide a non-invasive test to diagnose genetic disease in human embryos (ni-PGT-M). This test will provide an innovative, cost-effective and sustainable solution that will significantly improve the outcomes for couples at risk of transmitting genetic disease.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CONGENITAL DISORDERS;REPRODUCTIVE HEALTH AND CHILDBIRTH