NIHRDataInsights/HRCSData huggingface dataset:
Title: Uncovering new mechanisms of craniosynostosis associated with structural and copy number variation, using mouse modelling and human neural crest cells
Funder: Medical Research Council

Abstract: Despite adoption of whole genome sequencing in large clinical samples such as the 100,000 Genomes Project (100kGP), finding causative mutations outside the exome remains difficult. For the disorder craniosynostosis (CRS; premature fusion of cranial sutures), the diagnostic rate in 100kGP is only ~18%, despite careful case selection and intensive scrutiny for pathogenic single nucleotide variants (SNV). Structural and copy number variants (SV/CNV) are potent sources of genetic disease, for example SVs >20 kb are ~50-fold more likely than SNVs to alter gene expression. However, SV/CNV are difficult to identify in short read sequence such as in 100kGP, moreover the clinical pipeline in current use is suboptimal. We present several examples of SV/CNV segregating with CRS, and propose that the cranial suture acts as a sensor for aberrant gene expression caused by occult SV/CNV, with CRS providing an abnormal phenotypic readout. We will seek further SV/CNV in 100kGP data from cause-unknown CRS, by systematically seeking unique segregating/de novo rearrangements and intersecting the findings with clinical features suggesting a genetic cause. For the strongest candidate SV/CNV, we will construct mouse models and/or patient-derived neural crest cell (NCC) lines, phenotype mice for CRS, and measure functional parameters (RNA expression, including single cell transcriptomics in sutures; topologically-associating domain [TAD] structure; and chromatin landscape in NCC), providing evidence to assist pathogenic interpretation. Outcomes will include 1) Technology comparison of nanopore sequencing and optical mapping for identification of SV/CNV; 2) Single cell transcriptomic and TAD data will evaluate the cranial suture as a mis-expression sensor, and address how well disturbed TAD structure explains how SV/CNV cause CRS and other diseases; 3) Comparison of results in mouse models and NCC for the same SV/CNV, to determine feasibility of NCC to replace animal use.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: MUSCULOSKELETAL
Title: MICA: Development and Validation of a Transcriptomic-Based Model for Classifying and Predicting Treatment Response in Rheumatoid Arthritis (TRACT-RA)
Funder: Medical Research Council

Abstract: Rheumatoid Arthritis (RA) represents a huge public health problem. It is one of the most important chronic inflammatory disorders, leading to increased morbidity/mortality and a heavy health-economic burden. Although current medications have revolutionized the treatment of RA, they are not effective in ~40% of patients, the mechanisms of no-response remain unknown and there are no current predictors of treatment response. With MRC/Versus Arthritis support, by RNA-seq/NanoString analyses we have identified predictive signatures of prognosis and treatment response in the disease tissue (synovium) of early arthritis patients (PEAC) (Ref:6,7,8 in CfS) and delivered the first two biopsy-driven RCTs (STRAP and R4RA) worldwide. The aim of the proposed project is to develop and validate a transcriptomic-based model building on the PEAC signatures to be evaluated in STRAP & R4RA. The main hypothesis to be tested is that specific signatures in the synovium define disease and treatment-response subtypes (endotypes) that can predict prognosis and response to current targeted biologic therapies. We will test this hypothesis by applying robust analytical pipelines to our unique RNA-seq datasets developed by our team (Ref:6,14 in CfS). Given that RNA-seq is not practical or economical for translation into clinical practice, we will evaluate the portability of synovial RNA-seq signatures into NanoString panels also at blood level in collaboration with two of their most senior scientists. The development, validation and replication of our transcriptomic-based model using NanoString technologies, represent important steps toward future development of a clinical assay with potential major impact on patient care. This may enable a new molecular definition of RA and the definition of drug target modules in the disease tissue as predictors of response, which may transform current management of RA from "trial and error" drug-prescribing to rational therapy allocation.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: MUSCULOSKELETAL
Title: Allogeneic Chondroprogenitor Therapy (Phase II) (ACT2)
Funder: Medical Research Council

Abstract: Standard autologous chondrocyte implantation (ACI) is a 2-stage process: an initial knee arthroscopy and cartilage biopsy followed by a second surgical implantation of expanded chondrocytes. NICE approved ACI in Oct-17, but there has been poor adoption by NHS centres due to regulatory constraints and challenges surrounding an autologous product. We will manufacture and implant an allogeneic chondrocyte progenitor ATMP for cartilage repair in a phase II trial. This therapy could streamline NHS adoption, improve patient access & reduce morbidity in a cost-effective way compared to ACI. Key work package objectives: WP1: Validation of Osteochondral allograft supply chain from NHSBT in terms of cell viability and sterility. Optimised isolation, selection and tissue culture processes with future proofing by testing non-xenogeneic reagents. An initial 6-month shelf life will be confirmed via stability testing. Reference ranges for current potency markers will be set and future markers investigated by correlating levels with in-vitro chondrogenesis. The catapult will identify potential problem areas and cost savings in the manufacturing process, prior to GMP process validation WP2: SOPs developed in WP1 will be transferred to the ATF in Birmingham for expansion, storage and delivery of allogeneic CPs. Receipt of MHRA Manufacturer's Authorisation for Investigational Medicinal Products and CTA. WP3: A phase II, single-arm 20 patient trial to investigate allogeneic CPs for the treatment of isolated cartilage lesions in the knee. The primary outcome measure will be Serious Adverse Events and Lysholm score, at 3, 6, 9 & 12 months post-operatively. Secondary outcomes are repair tissue quantity and quality on MRI at 12 months and quality of life as measured by EQ-5D questionnaires. This innovative project will be an exemplar and allow development of an allogeneic ATMP for which a route to reimbursement is already established.


Research activity codes: 6.2 CELLULAR AND GENE THERAPIES
Health categories: MUSCULOSKELETAL
Title: Harnessing temporomandibular disc development to enhance regeneration
Funder: Medical Research Council

Abstract: Temporomandibular Joint discs have a very poor ability to repair. In order to repair holes a tissue bioengineering approach has been taken in a variety of animal models. The challenge is to create a tissue that does not undergo mineralisation and retains the discs unique properties. These problems are exacerbated by the fact that we know very little about the cells that form the disc, their lineage and genetic signature, how disc identity is regulated by molecular and mechanical signals, and whether the disc contains resident stem cells. This grant aims to address these key issues to ultimately enhance repair strategies. For this, we will take advantage of our knowledge of mouse craniofacial development, the availability of transgenic mouse lines to lineage trace and knockout specific genes, and the ability to culture disc tissue. We have three aims Aim 1: To assess the identity and developmental pathway of TMJ disc cells Aim 2: To assess how mechanical force impacts TMJ disc cell identity Aim 3: To investigate the impact of damage and the potential of adult discs to repair The first two aims focus on disc development. We will here use laser capture dissection to dissect out tissue of interest for comparison by RNASeq. The first aim will establish the lineage of the TMJ disc and how it relates to the condyle and the formation of sesamoids. In the second aim, we will compare disc development in mouse embryos with muscle defects, and in explant culture experiments, where we can follow disc development in the absence of mechanical force. Finally, in the third aim, we move to the adult disc and investigate whether a stem/progenitor cell population is resident in the disc. We will use lineage tracing of alpha-SMA and Gli1 mice and assess whether the disc contains any label-retaining cells. We will turn to culture to investigate how the disc is influenced by injury and whether the disc cells have potential for repair, using an explant model.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: MUSCULOSKELETAL
Title: Close regulation of peroxiredoxin oxidation is essential for maintenance of muscle mass and function in the elderly.
Funder: Medical Research Council

Abstract: Hydrogen peroxide (H2O2) is a key signalling molecule that is generated by contractions in skeletal muscle fibres and acts to stimulate beneficial adaptations of the muscle to exercise. The mechanisms by which H2O2 generated during contractions induces such adaptive changes have been unclear, but we have demonstrated that three 2-Cys peroxiredoxins (1, 2 and 3) in skeletal muscle fibres are oxidised following contractile activity, but we have not defined whether these oxidised proteins then mediate the adaptive responses to contractile activity. We will therefore follow an unbiased testing approach to identify the pathways involved including targeted RNAseq and proteomics. The project will determine the responses and adaptations to contractile activity in skeletal muscle which are mediated by specific peroxiredoxins and identify factors that control the extent of Prx oxidation and determine how they are modified by ageing. This will be achieved through 3 specific Aims: 1. To characterise the oxidation of peroxiredoxins and adaptive responses to H2O2 and contractile activity in immortalised human muscle myotubes in which specific peroxiredoxins are knocked out. 2. To determine functional responses to contractile activity in vivo in mice lacking specific peroxiredoxins (Prx1, 2 or 3 KO mice). 3. To identify key redox regulators of Prx oxidation in order to determine potential approaches that may be exploited to enhance the efficacy of the Prx signalling system.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: MUSCULOSKELETAL
Title: Muscle Activity and Growth: from Developmental Genetics to the Human Population
Funder: Medical Research Council

Abstract: Our aim is to understand the role of genetic and stem cell diversity, physical activity and the force it elicits, and environmental factors such as time-of-day and nutrition in skeletal muscle growth and the generation of muscle mass. We study somitic muscle growth in vivo in zebrafish larvae expressing genetic reporters by 3D time-lapse confocal microscopy using molecular genetics, physiological recordings and variety of molecular analytical approaches. We have developed time-resolved quantitative growth assays and shown that muscle contraction is necessary for normal larval muscle growth. We have identified distinct muscle precursor cells that reside in different somite regions, participate differently in muscle growth and repair and express different muscle stem cell markers. We have four Specific Aims: 1. To understand how a newly-discovered contraction-driven signalling pathway controls muscle growth. Using our rapid growth assay, genome editing and biochemistry, we will determine the time course, perdurance and molecular mechanism of the growth stimulus. 2. To define the succession of molecular and cellular events that drive muscle growth. By following in vivo the behaviour of individual muscle fibres and stem cells at min/hr time resolution after manipulations, we will determine how different growth modes in muscle are controlled. 3. To analyse how numerous signals are integrated to control muscle growth. By applying the above approaches, we will determine how exercise, nutrition and the circadian clock interact to control growth rate. 4. To apply our growing knowledge to the problem of sarcopenia in the human population using the UK Biobank. Using our past experience with a wide range of model organisms and human myogenesis, we are engaging with clinicians to refine our studies and explore the significance of our findings in the context of human health.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: MUSCULOSKELETAL
Title: Do systemic metabolites drive the chondroprotective effects of the IL18-/- gut microbiome in osteoarthritis?
Funder: Medical Research Council

Abstract: Osteoarthritis (OA) will affect around 50% of us over our lifetime and yet we still have no disease modifying drugs nor effective analgesics to reduce its societal burden. We have observed that deletion of IL18, and its down stream adaptor protein MyD88, strongly protects mice from developing experimental OA (induced by surgical destabilisation of the joint). We were unable to demonstrate a direct inflammatory role for IL18 in the joint. Rather, it radically changed the gut microbiome and we showed that this mediated the observed joint protection, as wild type mice co-housed with IL18-/- animals displayed reduced OA after joint destabilisation. Furthermore IL18-/- gut microbiome transferred to germ free mice (in our gnotobiotic unit) was able to suppress disease suggesting that the microbiome was releasing something systemically that could drive protection of the joint. Much of the published literature in recent years points to the role of gut microbes generating metabolites from dietary substances which drive systemic anti-inflammatory and protective responses. We propose that a similar mechanism exists in OA. This project will seek to confirm that metabolites are involved in IL18-/- joint protection by metabolomic screening of IL18-/- and WT mice, and careful dissection of the gut microbe species that confer this protection. We will recolonise mice with individual microbes and test the efficacy of candidate metabolites either by giving them directly (in the drinking water) or by optimising their release from specialised chow. Metabolites signal through specific G protein coupled receptors (GPRs), several of which are regulated in articular cartilage. These will be investigated through relevant knockout mice and available agonists/antagonists. Finally we will explore whether differences in metabolites are measurable in human OA and their role as prognostic biomarkers in OA risk following joint injury.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: MUSCULOSKELETAL
Title: Base edited T cell therapy against T-ALL (TvT)
Funder: Medical Research Council

Abstract: Novel strategies against T-ALL using chimeric antigen receptor (CAR) T cells are problematic because of issues such as fratricide of healthy T cells and the need to reconstitute protective T cell immunity. Suitable antigens for targeting T cell malignancies include CD3, TCR, CD5 and CD7. The latter has recently exhibited promise in trials where T cells were disrupted for CD7 to allow expression of anti-CD7 CAR (CAR7). Strategies for disruption include protein based inhibition of CD7, and genomic disruption using CRISPR/Cas9. We have developed a next generation base-editing approach which uses CRISPR guided cytidine deamination to create premature stop codons or splice site disruption through highly precise C>T base conversions. The technology has translated remarkably well to a GMP phase, and we are funded by Wellcome Trust (WT) to generate banks of 'universal' healthy donor T cells for Phase 1 trials in paediatric Acute Myeloid Leukaemia. Base-edited (BE) CAR T cells targeting either CD33, CD123 or CD7 are being generated, and the latter could have immediate impact against T-ALL. Our preclinical 'TvT' modelling has found BE-CAR7 cells are highly effective in vitro and in humanised models of T cell leukaemia. BE-CAR7 T cells express CAR7, but are devoid of CD7, endogenous TCRab (thus non-alloreactive) and CD52 (evade serotherapy). The application of base-editing rather than existing Cas9 which causes DNA breaks, has notable advantages in terms of eliminating translocations that otherwise arise during multiplexed genome editing.We propose an accelerated route to therapy for children with r/r T-ALL by drawing on BE-CAR7 cell banks with permission of WT. A TvT Phase 1 trial will aim to secure remission ahead of programmed allo-SCT and will generate important safety data. Children with r/r T-ALL will undergo lymphodepletion and receive a single dose of BE-CAR7 and if remission is secured within 28 days, will proceed to bone marrow transplantation and 12m follow-up.


Research activity codes: 6.2 CELLULAR AND GENE THERAPIES
Health categories: MUSCULOSKELETAL
Title: Preclinical Development of Peptide Oligonucleotides for Myotonic Dystrophy Type 1
Funder: Medical Research Council

Abstract: Myotonic Dystrophy 1 (DM1) is the leading cause of muscular dystrophy in adults (1:8000) globally. It is caused by a repeat expansion in the gene DMPK and results in severe muscle and heart disease, with significantly shortened life span. There are no disease-modifying therapies. We have developed a novel platform technology based on short cell penetrating peptides, which when attached to the antisense molecule provide highly effective penetration into cells and tissues such as heart. Difficulty in approaching such tissues is a major caveat for large drugs like antisense compounds. However, we have shown the ability of these antisense compounds to reverse the deterioration caused by DM1 in mice, and in cells from patients. Recent approval of the oligonucleotide drug Nusinersen by the FDA and EMA for treatment of spinal muscular atrophy marks the start of a major revolution in the treatment of genetic diseases. Nusinersen has major clinical impact and keeps patients alive who would otherwise have died. There is now urgent need to address similar diseases which are currently untreated like DM1. The major challenge in the field is to deliver the drug at an appropriate dose to the tissues in vivo which demonstrates therapeutic effect. Our solution does exactly that, and a unique distinction of our peptide-conjugated antisense compounds is that they can penetrate cardiac tissue which is critical for effective therapy since life span in patients is reduced primarily due to cardiac failure. For this reason, we would like to study in detail the effects of our lead compounds in the electrophysiology and transcriptome of cardiomyocytes derived from DM1 patient iPS cells, and in vivo in DM1 mice. The final goal of this 20-month programme is to identify a lead antisense compound suitable for testing in non-human primates and subsequent clinical development.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: MUSCULOSKELETAL
Title: Identifying New Disease Genes & Mechanisms for Musculoskeletal Disorders in 100K Genomes Project using Bioinformatics, Phenotyping & Machine Learning
Funder: Medical Research Council

Abstract: Whole genome sequencing (WGS) has the potential to revolutionise diagnosis of Rare Diseases. Recognising this, the UK has established a national programme to sequence 100,000 genomes (100KGP). To date, analysis in 100KGP has primarily focused on known disease genes for a given condition and on particular variant types - predominantly single nucleotide variants (SNVs) and a diagnostic yield of ~25% has been achieved. A more research-focused effort is now required to investigate novel disease genes and variant types, such as copy number, other structural variants (CNVs/SVs) and non-coding variants that are largely unexplored in the 100KGP to date. In order to address this requirement, we will focus on patients with musculoskeletal (MSK) disorders in the 100KGP which are a clinically and genetically heterogeneous group of conditions accounting for >1,000 cases in 100KGP. In preliminary studies, we have already identified a non-coding variant that contributes 1% to diagnostic yield of osteogenesis imperfecta and 2 complex SVs in known genes. We will use novel bioinformatics techniques to comprehensively analyse the WGS data, integrating the various variant types to identify putative novel disease genes. We will combine this with deep phenotyping as core MSK clinical data has not been collected by 100KGP and is required in the assessment of candidate genes. We will also evaluate whether machine learning can be used to identify clusters of genotypes or phenotypes from these complex high dimensionality datasets enabling novel genotype/phenotype correlations to be observed. Although this proposal focuses on MSK conditions, we anticipate that evaluation of the bioinformatics algorithms, platforms for deep phenotyping at scale and machine learning approaches will be informative for other disease domains in the 100KGP and can be leveraged to increase diagnostic yield across the dataset, as well as helping to maximise the research potential of this unique resource.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: MUSCULOSKELETAL
Title: Cellular and Molecular Pathogenesis of Osteoarthritis
Funder: Medical Research Council

Abstract: We will use tissue specific spatial transcriptomics of knee joints during the onset and progression of osteoarthritis to identify the cellular and molecular mechanisms of disease pathogenesis. Thus, we will undertake detailed phenotyping combining (i) back-scattered electron scanning-electron microscopy, (ii) iodine contrast-enhanced microCT, (iii) X-ray microradiography, and (iv) histological scoring together with 10x Genomics Visium spatial transcriptomic analysis in normal, aged and osteoarthritic knee joints. Subsequently, we will interrogate multi-omics and GWAS datasets to prioritise key genes that are expressed in disease relevant tissues. Finally, the credibility and tractability of candidate genes and downstream signalling pathways will be evaluated in a bespoke pipeline that integrates established informatics databases with our experimental datasets. Prioritised genes will be validated in vivo using our unique resource of disease models. In addition, we have recently identified a protective role for the homeobox transcription factor PITX1 in osteoarthritis pathogenesis and will investigate the cellular and molecular mechanisms responsible using inducible cell specific gene targeting in articular chondrocytes. These studies will define a cellular and molecular atlas of the knee joint and determine the sequential changes in gene expression that occur during the onset and progression of disease. Integration of multi-omic datasets will prioritise and validate the critical and tractable genes and pathways involved in the pathogenesis of osteoarthritis. Investigation of the role of PITX1 will define key target genes and downstream signalling pathways that are perturbed in articular cartilage following deletion of Pitx1, providing a new disease model to determine the therapeutic potential of targeting PITX1 signalling.


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