NIHRDataInsights/HRCSData huggingface dataset:
Title: From Microcephaly to Genome Stability, Inflammation and Growth Regulation
Funder: Medical Research Council

Abstract: This program investigates the molecular mechanisms underlying Mendelian developmental disorders associated with neuroinflammation and microcephaly (microcephalic dwarfism). The autoinflammatory disorder Aicardi-Goutières syndrome (AGS) is a genetic mimic of congenital viral infections. We have established Ribonuclease H2, encoded by three of the AGS genes, as a key genome surveillance enzyme essential for development. We demonstrated its substrate, genome-embedded ribonucleotides (rNs), to be the most common aberrant nucleotides in the mammalian genome, occurring at over 1,000,000 sites in each replicating cell, greatly exceeding the sum total of base lesions removed by Nucleotide Excision Repair (NER), Base Excision Repair (BER) and Mis-Match Repair (MMR) pathways. We have since harnessed such genome-embedded rNs as a tool to track replicative polymerases, demonstrating that lagging-strand replication elevates mutation rates at protein binding sites in eukaryotic genomes. Furthermore, we have also established that the cytosolic dsDNA sensor cGAS is activated in RNase H2 deficient cells, linking genome instability with inflammation. We have discovered nine novel disease genes for microcephalic dwarfism in the last five years, identifying previously unrecognised genome stability proteins and the first condensinopathy genes. We have established systems to functionally characterise the encoded proteins using primary human cells, isogenic mES cell systems, zebrafish and mouse models and we have contributed to the development of cerebral organoids to model human brain development and microcephaly. Our work has provided new insights into the disease mechanisms of these disorders of extreme brain size and growth reduction, establishing them to be the consequence of impaired cellular proliferation during development.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;GENERIC HEALTH RELEVANCE
Title: Impact of missense mutations in recessive Mendelian disease: insight from ciliopathies
Funder: Wellcome Trust

Abstract: Background: Over 1,800 autosomal recessive (AR) Mendelian-disease genes have been identified. Missense mutations account for 59% of protein coding region mutations, yet their precise functional effects remain largely uncharacterized. Two important questions in human genetics aim to explain interindividual variation in phenotypic severity and assign pathogenic mechanisms to different disease phenotypes (including independent phenotypes within the same syndrome). For AR disorders, it is thought that many missense mutations cause protein instability. For these hypomorphic mutations, disease phenotypes are defined according to quantitative genetic threshold effects within a protein interaction network. Project: We will focus on a subset of AR ciliopathies which are strongly enriched for missense mutations, where complete gene knockout is thought to be lethal (see Rationale-below). We will use gene-editing and quantitative protein-protein interaction analyses to systematically compare the phenotypic effects of frameshift (likely knockout/null) and missense mutations. We will test our hypothesis that these missense mutations disrupt only a subset of gene functions/protein interactions, using phenomics algorithms we have developed and unbiased phenotyping in cell lines and mouse models, allowing us to assign pathogenic mechanisms to disease phenotypes. In future, this approach could be extended to the estimated 10-20% of >3,000 Mendelian-disorders enriched for missense mutations.

Lay abstract: More than half of the mutations that have been identified in human genetic disorders are single letter alterations that affect just one of typically hundreds of building blocks (amino acids) in a protein. This category of mutation are known as missense mutations. Unlike other types of mutation which, in general terms, completely destoy protein function, it is thought that many missense mutations only partially reduce protein function. This is particularly true for an estimated 600 genetic diseases where only missense mutations are ever observed. Most genes have many activites within the cell, but we propose that this particular category of missense mutation only affects a subset of these, and can therefore be used narrow down particular mechanisms of disease. The team have developed complimentary approaches to systematically analyse these mutations, which they will apply to 147 mutations causing one of the largest human disease categories, known as ciliopathies.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;GENERIC HEALTH RELEVANCE;MUSCULOSKELETAL
Title: Role of Glucose in Cystic Fibrosis Lung: Friend or Foe in Respiratory Infections
Funder: Medical Research Foundation

Abstract: Lung glucose concentrations rise in people with cystic fibrosis (CF) or elevated blood glucose and are highest in people with both CF and elevated blood glucose (CF-related diabetes; CFRD; ~4mM). CFRD develops in around half of adults with CF. Elevated lung glucose concentrations are associated with increased risk of infection with Staphylococcus aureus and multiple antibiotic-resistant strains of Pseudomonas aeruginosa in CF lungs. Glucose is a vital energy source for humans and bacteria alike. Glucose is important for the bacteria that cause lung infections and for the white blood cells (phagocytes) that try to kill them. Phagocytes in the lung provide a first line of defence against bacterial infection. The aim of this project is to determine exactly how lung cells control the right amount of glucose for phagocytes to kill bacteria without allowing so much glucose that bacteria can grow and how this goes wrong in CF. I will add bacteria (Staphylococcus aureus and Pseudomonas aeruginosa) and phagocytes to human lung cells in a range of glucose concentrations similar to those found in the lung and study how glucose affects the ability to kill the bacteria. Glucose-induced changes in bacterial killing/growth will be compared in experiments using lung cells from CF patients, in conditions mimicking those found in CF lung. This will determine specific alterations in CF lung cells that result in elevated lung glucose concentrations and favour bacterial growth. I shall then test drugs that improve the ability of lung cells to control glucose concentrations to see if this aids bacterial killing in my CF infection model. Overall, these experiments will help to determine the role of glucose in CF lung infections and establish exactly how much glucose is required in the lung to help the body fight infection rather than help the bacteria to grow. Given the link between glucose and the risk of respiratory infection in CF patients, modulation of lung glucose concentrations may represent a cheap, non-antibiotic therapy to suppress lung infections and exacerbations in CF patients. This work is important because there are few new, emerging antibiotics, at a time when “superbugs” resistant to antibiotics are increasing. Nonantibiotic strategies to prevent infection are urgently required and therapeutic manipulation of glucose levels is readily achieved. The first crucial step however is to establish the role of glucose in lung infection.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CONGENITAL DISORDERS;INFECTION
Title: Heparin mimetics: Novel non-anticoagulant compounds to promote CNS repair.
Funder: Medical Research Council

Abstract: Damage to the CNS (e.g. in MS) is complex and results in multifocal areas of demyelination walled off by astrogliosis and axonal damage. By initially focussing on astrogliosis we discovered that highly sulphated heparan sulphates (HS) attenuate reactivity. By screening a panel of HS mimetics (mHeps), with varying levels of sulphation, we showed that exogenously added low sulphated (LS)-HS can reduce astrogliosis. Moreover, using complex myelinating cultures that mimic CNS injury we demonstrated that these LS-mHeps promoted remyelination and neurite outgrowth. Using mass spectrometry and cytokine/chemokine arrays we found that the mHeps sequester heparin-binding inhibitory molecules released after damage, resulting in the promotion of repair. Thus, mHeps have multifactorial effects on promoting CNS repair. Preliminary data using both the EAE and cuprizone models showed promising repair potential of LS-mHep7. Interestingly, mHep7 treated animals showed significantly less weight loss than controls during EAE disease onset. We now aim to corroborate these results through more extensive animal studies as well as identifying mechanism-of-action (focussing on the immune response, weight modulation and the integrity of the BBB) as follows: i) Optimisation of the dose, concentration, mode of delivery and bioavailability of mHep7 by comparing the low MW form, expected to be more bioavailable. ii) Confirm efficacy of the optimised mHep7 in both EAE and cuprizone animal models. iii) Assess the mechanism-of-action in EAE mice by analysing the immune response (immunohistochemistry), multiplex assay, and FACS analysis, as well as correlating these findings with the prevention of weight loss by mHep7 treatment. These studies will provide proof-of-concept for a novel strategy to enhance CNS repair by manipulating the inhibitory environment induced after injury using non-anticoagulant druggable mHeps, and will provide the foundation for developing clinical translation studies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CONGENITAL DISORDERS;INJURIES AND ACCIDENTS;NEUROLOGICAL
Title: Pulsed Glucocorticoid Replacement Therapy
Funder: Medical Research Council

Abstract: Glucocorticoid hormones secreted by the adrenal cortex are critical for life, and before steroid therapy was available patients with Addison's disease, congenital adrenal hyperplasia (CAH) and pituitary deficiency did not survive. However, despite the fact we now have available oral preparations of glucocorticoids and we administer these in a twice or three times daily regimen to try and mimic the normal circadian rhythm, our patients still have double the normal age related mortality and have major morbidity - predominately a feeling of generalised fatigue and lack of energy. Underlying the classical circadian rhythm is a dynamic ultradian pulsatile pattern of cortisol secretion. This pattern is found in all mammalian species including man and is critical for normal gene regulation and for normal cognitive and metabolic function. It is now clear optimal regulation of glucocorticoid responsive genes absolutely requires pulsatile presentation of the ligand cortisol (in man) or corticosterone (in rodents). As we currently treat patients with constant as opposed to episodic receptor activation, we are inducing a very unphysiological regulation of both trans-activated and trans-repressed genes, which is likely to contribute both to the increased morbidity and mortality of our patients. We have developed a novel portable infusion pump that will deliver individually calculated pulsed subcutaneous hydrocortisone to more accurately mimic normal circadian and ultradian release. The aim of our proposed study is to validate this system in healthy volunteers and perform proof-of-concept studies in patients with Addison's and CAH. We shall examine the impact of our novel system upon biochemical parameters and assess the impact on psychological status using objective measurements of cognitive function, mood and tiredness as well as quality of life questionnaires.


Research activity codes: 6.3 MEDICAL DEVICES
Health categories: CONGENITAL DISORDERS;METABOLIC AND ENDOCRINE
Title: Cell mediated gene therapy for Duchenne muscular dystrophy: trans-correction of resident nuclei to amplify dystrophin expression
Funder: Medical Research Council

Abstract: In order to "cure" genetic diseases it is necessary to replace or repair the defective gene: this can be achieved with viral vectors, small molecules that correct the genetic defect, or stem/progenitor cells that are incorporated into the tissue. All these strategies are in pre-clinical or clinical experimentation for Duchenne Muscular Dystrophy, due to mutations in dystrophin gene. The absence of the protein leads to muscle damage during contraction and in time to wheelchair dependence, cardiac or respiratory failure and premature death. The innovative aspect of our experimental strategy is based upon intra-arterial delivery of mesoangioblasts (vessel-associated myogenic progenitors) that distribute uniformly throughout the body districts downstream of the injected artery. Some of these stem cells cross out of the blood vessel, move into the surrounding tissue of the body and eventually repair it. However, the process is not yet efficient enough and work is ongoing to implement these steps. Here we focus on enhancing genetic correction by using a lentivector that encodes a small nuclear RNA (U7) engineered to skip exon 51 of the dystrophin gene. As the snRNA assembles with proteins in the cytoplasm, it then enters all neighbouring nuclei thus, amplifying the therapeutic effect aim. This is tested by co-culturing in vitro one DMD genetically corrected cell with an excess (10, 30) of DMD cells and measuring the amount of dystrophin produced in these hybrid myotubes. After exploring the underlying molecular mechanisms in vivo experiments are conducted with human cells in immune deficient mice and with dystrophic, genetically corrected rat mesoangioblasts in newly developed DMD rat carrying a mutation in exon 52 of the dystrophin gene. Functional test on corrected rats will test the effect on motility. The successful completion of the research programme will rapidly lead to a new clinical trial, on young DMD patients with an implement protocol and "intent to cure".


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: CONGENITAL DISORDERS;MUSCULOSKELETAL
Title: Developing CDK12 inhibitors to treat Myotonic Dystrophy
Funder: Medical Research Council

Abstract: Myotonic Dystrophy type 1 (DM1), is a severe, progressive, debilitating condition which affects a range of systems including skeletal muscle heart and brain. Around 250,000 people in countries with developed healthcare systems suffer from DM1 and there is currently no treatment available. DM1 is an RNA-based disorder caused by a transcribed CTG-repeat expansion sequence located within the 3' untranslated region (UTR) of the DMPK (dystrophia myotonica protein kinase) gene. Mutant repeat expansion transcripts remain in the nuclei of patient's cells, forming distinct microscopically detectable foci that represent distinct hallmarks of disease pathophysiology. We have identified a set of small molecule inhibitors that remove nuclear foci and shown that their common target is cyclin-dependent kinase 12 (CDK12). CDK12 co-locates with repeat expansion foci in DM1 cells and its levels are elevated in DM1 patient muscle biopsies. CDK12 phosphorylates the C-terminal domain (CTD) of RNA polymerase II. It plays a role in the transcriptional stress response, and it is involved in the transcription of long genes. It may also play a role in RNA processing, the DNA damage response and chromatin regulation. Despite the multitude of proposed roles for CDK12, heterozygous Cdk12/- mice are viable and appear perfectly normal. We have undertaken a medicinal chemistry programme to develop novel and selective CDK12 inhibitors. We have shown that these compounds remove nuclear foci in patient-derived cell lines and our lead compound showed beneficial effects in an in vivo study using a mouse model of DM1. Thus our lead series of molecules are excellent candidates for further development for treatment of DM1 and this project is focussed on completing a Lead Optimisation study to progress our molecules towards pre-clinical studies.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CONGENITAL DISORDERS;MUSCULOSKELETAL
Title: Exploring the role of neuromuscular excitability in sudden infant death
Funder: Medical Research Council

Abstract: Five children in the UK die each week from Sudden Infant Death Syndrome (SIDS). The SCN4A gene codes for an ion channel Nav1.4 that is essential for muscle membrane excitability. Clinical disorders due to mutations in the SCN4A gene cause respiratory muscle impairment including life threatening apnoeas in infants. Based on these initial observations in infants I obtained new genetic and functional evidence that qualitatively similar SCN4A gene variants occur in some cases of SIDS. I hypothesise that ion channels and other proteins critical for skeletal muscle excitability may collectively account for a larger proportion of SIDS cases and that normal muscle development may contribute to the severity of these variants in early life. This proposal aims to: 1. Determine the frequency of rare gene variants encoding proteins that influence skeletal muscle excitability using WES data from c.700 SIDS cases and UKbiobank controls 2. Determine the frequency of SIDS amongst families with neuromuscular excitability diseases caused by variants in these genes 3. Characterise the developmental changes of muscle fibre types in human skeletal muscle 4. Develop an in silico programme to model the physiological consequences of the genetic variation identified and the effect of developmental and exogenous variables on muscle excitability A fully automated multi-coloured chromogenic IHC protocol capable of detecting myosin heavy chain isoforms I, IIA and IIX in a single skeletal muscle section will be employed on human control biopsies (age 0 to 16years) to determine the relative proportions of fast and slow fibre types at different ages. I hypothesise that excitability gene variants have a greater detriment to fast fibres and that infant muscle has more fast fibres than adults. A linear circuit model of mammalian muscle fibre will be used to ascertain the individual and combined effects of developmental variables on wild type and mutant muscle fibre function and performance.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;MUSCULOSKELETAL;NEUROLOGICAL
Title: Neurodevelopment from the fetus to childhood in individuals with congenital heart disease
Funder: Medical Research Council

Abstract: Congenital heart disease (CHD) is the most frequent congenital malformation. While most infants with CHD now survive, children and adults with CHD who required cardiopulmonary bypass surgery in infancy are at increased risk of adverse neurodevelopmental outcome. The underlying mechanisms leading to these impairments are likely to begin in utero when critical processes of brain development are taking place and may be related to impaired placental function. However, to date, the ability to assess placental function in vivo has been limited and little is known about the role of the placenta in brain development and subsequent neurodevelopmental outcome in children with CHD. In addition, while abnormal brain development has been observed in infants with CHD, information on how specific patterns of brain maturation, and how brain developmental trajectories relate to childhood outcome in this group is lacking. We will undertake placental MR imaging in CHD cases and controls to test the hypothesis, "placental function is abnormal in fetuses with transposition of the great arteries (TGA) and left ventricular outflow tract obstruction (LVOTO)". We will use state-of-the-art fetal, neonatal and childhood neuroimaging to detail patterns of structural and functional brain development from the fetus to childhood that are related to placental function and childhood outcome. We will also determine the relationship between potentially modifiable factors including parental mental health and parenting styles on neurodevelopment in children with CHD. These longitudinal studies will provide information about mechanisms underpinning impaired brain health in survivors of CHD which are essential to guide the development of new treatments; will improve our ability to identify at-risk fetuses and infants at an early stage, when intervention with appropriate therapies may be possible; and will provide imaging tools to test efficacy in future trials of neuroprotective therapies.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL
Title: Investigating the role of Leucine rich, glioma inactivated 1 (LGI1) in regulating pain sensitivity
Funder: Medical Research Council

Abstract: Enhanced neuronal excitability is fundamental to neuropathic pain conditions. Therefore, a better understanding of the factors which regulate neuronal activity is paramount to the development of improved pain therapies. Autoantibodies (-Abs) directed against Leucine-rich glioma inactivated 1 (LGI1) are associated with neuropathic pain in patients and these symptoms can be relieved with therapies that reduce antibody levels. LGI1 is a secreted protein which stabilises the expression of Kv1 channels in neuronal membranes and has been shown to regulate neuronal function. However, experimental studies have not yet directly investigated the role of LGI1 in pain. I aim to use my research to better understand the role of LGI1 in regulating neuronal excitability and pain sensitivity. Initially I will characterise the expression of LGI1 in pain signalling neurons and use transgenic mice to specifically ablate LGI1 in neuronal populations at the level of the DRG. The impact of specific LGI1 ablation on sensory function will be assessed using behavioural pain assays. I will test the ability of patient LGI1-Abs to cause neuropathic pain by developing a passive transfer model in mice and measure anatomical, biochemical and molecular outcomes. Electrophysiological approaches will assess the effect of disrupting LGI1 (genetic ablation or LGI1-Abs) on neuronal excitability and mechanistic understanding will be gained by looking at the function and expression of Kv1 channels. To investigate whether LGI1 is important in the more general context of neuropathic pain, I will use a preclinical model of nerve injury. I will generate recombinant LGI1 protein as a novel therapeutic approach for the treatment of pain. I will assess its impact on neuronal activity and apply it to preclinical models with the aim of reversing neuropathic pain behaviours in mice.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: CONGENITAL DISORDERS;NEUROLOGICAL