NIHRDataInsights/HRCSData huggingface dataset:
Title: Computational modeling of retinal development
Funder: Medical Research Council

Abstract: The proposed research aims at a computational characterization of retinal development. I want to simulate the growth of the structural development of the retina, by incorporating results from different studies into a coherent framework. This detailed approach enables a mechanistic explanation for how retinal tissue develops from a few precursor cells, which has high relevance for stem cell-based treatments. This work will use genetic data obtained from retinal differentiation of human embryonic and induced pluripotent stem cells, from the collaboration with Prof. Lako. This is a unique dataset because the samples will be taken at different stages during retinal development. The fact that these are human cells renders these data highly relevant for medical purposes. Based on these data, gene regulatory dynamics will be inferred and related to the structural changes. This model will support the generation of tailored, multilayered neural retinas for drug discovery purposes, disease modeling and transplantation. Leveraging modern computer hardware and software, this Neuroinformatics project will incorporate very elaborate mechanisms. In contrast to existing approaches to model retinal development, physical forces will be taken into account to simulate cell interactions. The production, diffusion and detection of extracellular substances will enable the modeling of the guidance of neuronal growth processes. Also, the interaction between anatomical and electrophysiological development will be investigated. For example, dendritic growth can depend on electrical activity, as supported by experimental data. Importantly, the simulation is such that every cell behavior is based on information that is available at the location of the process in question. Overall, this detailed and mechanistic model of retinal development will generate experimentally testable hypotheses, and will account for findings such as the specificity of synaptic connections between neurons.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: EYE
Title: Development of a synthetic flowable dressing that prevents corneal scarring
Funder: Medical Research Council

Abstract: Corneal scarring occurs from a variety of aetiologies including infections, inflammatory conditions and ocular trauma leading to visual loss and is a WHO priority area programme for the prevention of worldwide blindness. Corneal infections are treated by a sterilisation phase with antimicrobial agents and a healing phase targeting inflammation control and promoting rapid wound closure to minimise scarring. There are few therapeutic options to modify, minimise or reverse scarring to maintain corneal transparency and visual function. We are developing a synthetic, optically-transparent, anti-scarring dressing suitable for the management of patients world-wide at risk of corneal scarring by promoting a microenvironment that enables anti-fibrotic and anti-inflammatory factors to promote scarless wound healing and improve clinician/patient-reported visual outcomes. To date we have: (1) engaged closely with clinicians to define the physico-chemical/phamacokinetic characteristics and technical specifications of the fluid biomembrane dressing according to a Target Product Profile to ensure suitability for clinical use, (2) investigated scaleable processes for manufacture, (3) performed pilot preclinical testing of a prototype using in vitro and in vivo models of corneal scarring, (4) prepared a GLP standard technical portfolio of data generated. We now seek further funding to allow progression of the project according to a defined translational and commercialisation strategy encompassed within a business plan that includes: (1) defining the pharmacokinetics/toxicology/efficacy of the released active compound, (2) reaching technical readiness for CE marking, (3) securing MHRA approval and a GMP manufacturing process for the ocular dressing and (4) executing a first-in-man clinical trial to assess safety and efficacy of our anti-scarring dressing to treat microbial keratitis. This will move the technology along the translational pathway towards commercial realisation.


Research activity codes: 6.3 MEDICAL DEVICES
Health categories: EYE
Title: 'Validating the application of iPSC-derived Müller glia in a glaucoma therapy'
Funder: Medical Research Council

Abstract: Glaucoma is a major cause of blindness characterized by retinal ganglion cell (RGC) loss and optic nerve damage. This study builds on our previous findings that a population of Müller glial with stem cell characteristics can be isolated from the human retina and can be induced to differentiate into the major types of retinal neurons in vitro. Upon transplantation onto the retina of RGC depleted animals, these cells induced a significant recovery of visual function. Sourcing Müller glia from donor eyes could limit therapy development due to limitations in obtaining tissue and compatibility issues. To develop a therapy that could benefit many patients, induced pluripotent stem cells (iPSC) may yield well characterized cells and may be potentially derived from cell banks to provide cells to a large number of individuals. On this basis, our objectives are to undertake a feasibility study and generate a proof of concept that iPSC-derived Müller glia may be used for development of therapy to treat advanced glaucoma. The main aims of the proposed research are: 1) To isolate and propagate Müller glia from retinal organoids derived from iPSC in vitro, and to examine their genetic and phenotypic characteristics as well as their ability to produce neurotrophins. 2) To transplant iPSC-derived Müller glia into the vitreous of the glaucomatous rat eye and to assess the thickness of the nerve fibre layer (NFL) in vivo, as well as the retinal function in transplanted animals using electrophysiological methods. 3) To examine the ability of transplanted cells to induce RGC/axon repair and RGC survival in the grafted eye using immuno-histochemical and electron-microscopy techniques, and to assess whether neurotrophins produced by MG may be present in the transplanted retina. We expect that the results will provide the basis for the future formulation of a pre-clinical development plan for the use of iPSC derived Müller glia as a therapy for end stage glaucoma.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: EYE
Title: Novel therapeutic approaches to rescue retinal dysfunction in patient-derived photoreceptors
Funder: Medical Research Council

Abstract: AIPL1 mutations cause LCA, the most severe inherited retinal dystrophy, for which there is no cure or treatment. We will combine our expertise in iPSC technology and optic cup differentiation with our understanding of AIPL1 function to model human AIPL1 LCA, to develop and test novel pharmacological and RNA-directed therapeutic strategies targeting the most common classes of AIPL1 mutations. iPSC will be derived from LCA patients homozygous for the c.834G>A(p.W278X) mutation by episomal reprogramming of renal epithelial cells. The c.834G>A mutation will be corrected by genome editing in the patient-derived iPSC using the CRISPR/Cas9 system followed by targeted homologous repair (HDR) with an AIPL1-specific piggyBac transposon. Patient-derived iPSC and control isogenic iPSC will be differentiated to retinal photoreceptor cells via the formation of 3D optic cups. Translational read-through inducing drugs (TRIDs) will be tested for their efficacy for recoding premature termination codons and rescuing the expression and function of full-length AIPL1 in vitro (p.R32X, p.W72X, p.W88X, p.Q163X and p.W278X) and in c.834G>A(p.W278X) patient-derived ocular cups. AIPL1 mutations disrupting a canonical splice donor dinucleotide (c.276+1G>A, c.276+2T>C) or consensus splice donor sequence (c.465G>T, c.642G>C, c.784G>A) will be targeted with modified complementary and exon-specific U1 snRNA. The rescue of transcription of the full-length gene, and expression and function of the AIPL1 protein, will be assessed in vitro and in optic cups derived from an LCA patient compound heterozygous for c.276+1G>A and a patient homozygous for c.624G>C(p.K214N). In situ splice site editing in optic cups will be achieved via direct delivery or viral transduction. Validation of these therapies in vitro and in patient-derived ocular cups will be critical for translation into the clinic, with broader application of our proof-of-concept findings to other inherited retinal dystrophies.


Research activity codes: 5.1 PHARMACEUTICALS;5.2 CELLULAR AND GENE THERAPIES
Health categories: EYE
Title: Investigating the influence of genetic variation associated with age-related macular degeneration on plasma levels of complement regulatory proteins
Funder: Medical Research Council

Abstract: Our objective is to measure plasma levels of Complement Factor H, Factor H-like Protein 1, and Factor H-Related proteins 1-5, encoded by a region of chromosome 1 where gene variants modulate risk of developing Age-related Macular Degeneration (AMD). It is hypothesised that these variants modulate protein levels leading to dysregulation of the alternative complement pathway and thereby driving AMD pathology. Immunoassays for these proteins are prone to interference from non-specific protein detection. We have developed a targeted liquid chromatography-selected reaction monitoring-mass spectrometry (LC-SRM-MS) method to measure all seven gene product from this region. In this project we will characterise this assay using guidelines laid down by the European Medicines Agency to assess its accuracy for analysis of large numbers of clinical samples, and subsequently deploy it in two related studies. The first will compare data generated using the SRM-MS assay to that generated by existing ELISAs on the same samples to determine the specificity and quantitative accuracy of the immunoassays. The second will measure the levels of these seven proteins in a cohort of 662 individuals from the MRC-funded Cambridge AMD Study for whom full genotyping data is available. Protein level and genotype will be correlated. Since we will be measuring all seven proteins simultaneously, we will be able to study the effects of stoichiometric ratios of these regulators on pathogenesis for the first time.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: EYE
Title: Development of AAV gene therapy for blindness caused by cone-rod dystrophy
Funder: Medical Research Council

Abstract: Cone-rod dystrophies (CRD) are an important genetic cause of irreversible, central visual loss. Gene therapy represents a logical therapeutic strategy to prevent or delay the onset of visual loss in patients with CRD. Next generation sequencing has identified CDHR1 mutations as a more common cause of CRD than previously considered (Charbel Issa, unpublished data). There are patients in the UK with CDHR1-associated CRD who may benefit from gene therapy. Proof of principle studies of gene therapy in other forms of inherited eye disease have demonstrated safety and efficacy in preserving the central vision in patients with other retinal degenerations. Gene therapy as a cure for CDHR1-related CRD has not been attempted, yet it is an ideal model to study gene therapy for CRDs in that: (1) the associated CRD has a relatively late onset with rapid decline and wide therapeutic window, (2) the relatively small size of CDHR1 (2,580 base pairs) allows AAV encoding of the transgene, (3) a CHDR1-/- mouse is available for the development of gene therapy. This has never been attempted; all experiments suggest here will be novel. I intend to phenotype the CHDR1-/- mouse using a variety of imaging, electrophysiological and histological techniques. I will then construct an adeno-associated viral vector (AAV-8) to restore visual function in CDRH1-/- mice using the identified outcome measures. In parallel, I intend to characterize the human phenotype in patients with CDHR1-associated CRDs identified from next generation sequencing databases. This will assist in identifying the optimal time in the course of the disease to undertake gene therapy in future clinical trials. The laboratory study and clinical phenotyping will be complementary in the targeted development of gene therapy for CDHR1-related CRD. This project will enable a greater understanding of human CDHR1-related CRD, and attempt to develop a gene therapy treatment to cure a currently blinding disease of the retina.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: EYE
Title: MICA: Antimicrobial bandage contact lenses
Funder: Medical Research Council

Abstract: Corneal infection is a significant clinical problem. Following corneal surgery a bandage contact lens (BCL) is frequently used to protect the cornea and increase comfort for the patient. To reduce the risk of infection antibiotics are also normally administered. Current BCLs comprise silicone-hydrogel, hydrogel or less commonly, collagen-based materials. None have antimicrobial activity. Our BCLs will be produced from high water content, transparent poly-e-lysine gels. We can cast these gels using existing contact lens moulds. We have shown that poly-e-lysine can be covalently attached to the gel surfaces and these were shown to be non-cytotoxic to human corneal epithelial cells in culture and did not inhibit healing in an in vitro corneal epithelial scratch assay model. We have demonstrated that these gels can significantly reduce the growth of Gram +ve (S. aureus) and Gram -ve (E. coli) cultures. We will develop these as prophylactic BCLs to reduce the risk of infection post-surgery and determine their safety in a human trial. A second strand of this study will develop novel therapeutic BCLs. Treatment of corneal infection relies on frequent application of antibiotic drops; routinely every 5-15 minutes for the first 48 hours, then 2-6 hourly over 1-2 weeks. BCLs that deliver therapeutic doses of antimicrobial drugs in a sustained and controlled manner would provide a more effective treatment strategy and augment conventional treatments. We have demonstrated that Penicillin G (as a model antibiotic) and Amphotericin B (as a model antifungal) can be incorporated into the poly-e-lysine gels after synthesis through electrostatic attachment and have antimicrobial properties in vitro. We will optimise the properties of the poly-e-lysine gel lenses and their manufacture, incorporate clinically relevant antimicrobial agents to control major bacterial and fungal keratitis species using standard in vitro assays and an ex vivo corneal infection model.


Research activity codes: 6.3 MEDICAL DEVICES
Health categories: EYE
Title: Oral Levodopa treatment in Improving Visual development in Infants and young children with Albinism-the OLIVIA study
Funder: Medical Research Council

Abstract: There is a paucity of treatment options for albinism, a condition characterised by pigment deficiency and abnormal retinal development which results in a significant degree of visual disability. In this study, we aim to develop a treatment to improve vision in albinism. Our approach will be based on a similar concept to that of amblyopia treatment, where correcting the cause of the visual abnormality in early childhood results in improvements in vision due to neuroplasticity. We have previously demonstrated residual plasticity of the developing albino retina in young children, importantly suggesting a window, where we can modulate retinal development and improve visual function. L-3,4 dihydroxyphenylalanine (L-DOPA), a signalling molecule which is essential for normal retinal development, is known to be deficient in albinism. One potential treatment in albinism is L-DOPA replacement using an oral levodopa drug suspension - a drug that is currently being used safely to treat infants as young as 3 months of age with infantile dystonia. Pre-natal oral L-DOPA replacement appears to be effective in animal models of albinism. However, whether oral L-DOPA supplementation will also be effective in modulating post-natal retinal development and visual function is unknown. The aims of the proposed study is to: 1. Prove, for the first time, that post-natal retinal development, morphology and visual function in albinism can be modulated through oral L-DOPA supplementation in a murine model of albinism 2. Characterise the response of the developing albino retina to different doses and timing of postnatal L-DOPA supplementation 3. Test the feasibility of the intervention and trial procedures for a future randomised controlled clinical trial to test efficacy and safety of oral levodopa treatment in children with albinism If this study is successful, it will trigger a paradigm shift in how albinism and many other paediatric retinal developmental conditions are treated.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: EYE
Title: Understanding the mechanisms of cone opsin mediated disease to develop new therapies
Funder: Medical Research Council

Abstract: Mutations in the long-wavelength (LW) and middle-wavelength (MW) cone opsin genes are associated with a wide range of visual defects including red-green color vision deficiency, blue cone monochromacy and X-linked cone dystrophy. Advances in our understanding of the genetic basis of disease has revealed that different genetic mechanisms underlie the spectrum of cone photoreceptor defects, with different effects on cone photoreceptor viability and function. We have shown that interchange haplotypes are a common cause of disease, resulting in aberrant splicing and exon 3 skipping in vitro. The interchange haplotypes abolish Exonic Splice Enhancer (ESE) motifs and create Exonic Splice Silencer (ESS) motifs. Here, we will use the mini-gene constructs we have created for each disease associated interchange haplotype to test the potential of antisense oligonucleotides (AONs) to suppress exon 3 skipping and restore normal splicing of the cone opsin genes. We will create models of the human retina with LW and MW cone opsin mutations in genomic and cellular context by differentiating patient derived iPSC organoid optic cups. Using these models, we plan to define the number of cone opsin genes expressed in a human retina, investigate the effect of interchange haplotypes on the extent of mis-splicing and mutant opsin protein products, and test the most successful AONs from the mini-gene assay on human cone photoreceptors. We will correlate the context and consequence of mutations with the variable phenotypic spectrum of disease, to assess if cone photoreceptor survival, or the rate of photoreceptor loss and functional deterioration, correlates with cone opsin genotype. This knowledge is important for selecting the target cone opsin genes and context of mutations most likely to respond to a therapeutic intervention for potential restoration of visual function in patients with cone opsin mutations.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;5.2 CELLULAR AND GENE THERAPIES
Health categories: EYE
Title: iPSC modelling and multi-omics analysis to understand age-related macular degeneration
Funder: Medical Research Council

Abstract: The use of monogenic sub-forms to unravel the complexities of common disease is a recognised strategy that has been used to further understanding of diabetes, cancer and autoimmune disease. Age-related macular degeneration (AMD) is the leading cause of severe visual loss in the Western world. AMD exemplifies common disorders but is atypical in its genetic contribution. However, a major limitation in AMD research is a lack of comprehension of the functional impact of genetic contributors to disease outcome thus restricting the clinical usefulness of genetic information. Further, animal and cellular models do not replicate the genetic and metabolic complexities of the condition, thus impeding understanding and limiting the development of treatments. Recent research has implicated rare and common AMD-associated risk alleles in the Complement Factor H (CFH) gene as the underlying cause of monogenic, early-onset macular degeneration (EOMD); a condition that is pathologically similar to AMD. This study aims to investigate the role of CFH impacting variants using induced pluripotent stem cells (iPSCs) derived from genetically defined EOMD patients. The retinal pigment epithelium (RPE) is considered to be the primary site of disease in EOMD/AMD, therefore this project aims to develop an iPSC-RPE model of EOMD. By employing a multi-level, holistic, systems biology approach, this work aims to measure the genome-wide impact of impaired Factor H (FH) function with the aim of identifying novel gene regulatory networks and disease pathways that will inform understanding of monogenic and complex forms of macular degeneration. Increased understanding of the contribution of genetic variants to EOMD/AMD pathology will facilitate the development of stratified medicine approaches to patient care. Further, identification of the molecular mechanisms underpinning macular degeneration will expedite the development of novel therapeutic modalities.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: EYE
Title: Data driven public health approaches for diabetic retinopathy and age-related macular degeneration
Funder: Medical Research Council

Abstract: This fellowship will focus on the use of EHR and retinal imaging to improve population eye health. Developing novel outcome measures for chronic eye disease: Management of age-related macular degeneration (AMD) requires regular monitoring and rapid treatment if the wet form of the disease develops. Changes in either ocular structures or visual function can signal progression to wet AMD. 3D retinal imaging based on Optical Coherence Tomography can resolve ocular structures in unprecedented detail and QUB researchers have expertise using the latest modalities. However, analytical methods are sub-optimal, especially when attempting to link structural and functional changes. In this project, novel statistical methods will be developed to integrate a large retinal imaging dataset of AMD patients with EHRs of visual function. The aim is to develop meaningful outcome measures of AMD progression for use in clinical trials. Optimising diabetic retinopathy screening: Diabetic retinopathy (DR) is one of the most common causes of sight loss among working-age people in the UK. Those at risk of DR are screened; retinal photographs are taken at regular intervals and images are manually graded for specific pathologies. The aim of this project is to explore the potential of integrating automated image analysis into the Northern Ireland DR screening programme to both target treatment more effectively and reduce costs. A key challenge is predicting DR progression. There may be subtle patterns of retinal changes predicting DR progression that can be detected only by integrating data from many thousands of patients. Using screening images drawn from the NI diabetic eye screening programme (c. 87,000 patients), the fellow will apply the latest deep learning techniques (convolutional neural networks) to detect novel features predictive of DR progression. Performance of the automated methods will be assessed along with the potential for improvements to the screening programme.


Research activity codes: 4.5 RESOURCES AND INFRASTRUCTURE (DETECTION)
Health categories: EYE