NIHRDataInsights/HRCSData huggingface dataset:
Title: Cell signalling by inositol pyrophosphates
Funder: Medical Research Council

Abstract: Living cells are required to communicate and coordinate external inputs and internal needs in order to behave appropriately. Intracellular cell signalling networks coordinate cellular physiology by integrating and disseminating information. Understanding how this information is elaborated, stored and transduced represents one of the most fascinating aspects of biology. Inositol phosphates (IP), found as both lipid-bound and cytosolic isoforms, represent one of the most complex cell signalling systems. We are studying the inositol phosphate network with the aim of understanding the molecular logic of cellular signalling. Investigation into cellular regulation by IP has yielded surprising knowledge that reaches well beyond the established roles of IP3 (as calcium releasing factor) and PIP3 (as AKT activator). Indeed, I am interested in studying the numerous ‘non-classical’ aspects of the IP regulatory system. My primary interest is in the inositol pyrophosphates (PP-IPs), molecules which have not yet been fully characterised but are known to contain a high energetic pyrophosphate moiety, that are important controllers of cellular homeostasis and energetic metabolism. In comparison to the IP3/calcium or PIP3/AKT signalling paradigms, PP-IPs signalling is evolutionarily ancient, present in all eukaryotic organisms. The past ten years of research have positioned PP-IPs at the interface between metabolism and signalling, indicating that they are involved in the pathogenesis of important metabolic disorders like obesity and diabetes. Inositol pyrophosphates, by altering phosphate homeostasis, affect basic energetic metabolism and the synthesis of ATP and other phosphate-rich molecules such as inorganic polyphosphates (polyP). In spite of their clear relevance for a number of fundamental cellular functions, many aspects of the PP-IPs mode operandi remain poorly understood. Our research aims to fill this gap in knowledge by investigating how PP-IP levels are regulated, and elucidating the cross-talk between PP-IPs, polyP and ATP. To appreciate the importance of PP-IPs and of the complex IP signalling system in general, we should realise that the entire IP network of molecules is metabolically connected. Therefore, understanding how this network of molecules evolved and became one of the fundamental signalling systems of eukaryotic cells may also help us understand the evolutionary pressures that created us.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: ATP Synthase including Proteomics
Funder: Medical Research Council

Abstract: The F-ATP synthases in eubacteria and mitochondria are rotary machines with many common features. We will build on past achievements to extend fundamental knowledge about them and provide a basis for putting that knowledge to practical use. The mechanism of their catalytic domains is well understood, but how rotation is generated from the transmembrane proton-motive force is less clear. We will provide a molecular explanation of the generation of rotation. We intend to exploit mechanistic differences between human and bacterial enzymes to develop new drugs. One difference concerns their mechanisms of regulation. The mitochondrial enzyme is regulated by the inhibitor protein, IF1; in vitro, it inhibits ATP hydrolysis and not ATP synthesis, but its in vivo role is unclear, except that it inhibits the hydrolase activity of assembly intermediates. It may also inhibit in vivo ATP synthesis by a mechanism that we will investigate possible involving other unidentified proteins. Different regulatory mechanisms operate in eubacteria; for example in Mycobacteria, the enzyme can only make ATP and not hydrolyze it, but we do not yet know how hydrolysis is prevented. Eubacterial and mitochondrial enzymes differ also in their subunit compositions. They have a common core set to allow them to make ATP, but the mammalian mitochondrial enzymes have a "supernumerary" set of seven membrane proteins, each with a single predicted transmembrane a-helix. In mitochondria, these supernumerary subunits form an interface between monomeric complexes in the dimeric arrangements found in the inner membranes of the organelle. We are determining the structure of the dimeric complex to gain detailed information about how the membrane domain of the enzyme functions. As part of a wider collaboration we will study how the human ATP synthase is assembled.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Understanding genetic mechanisms modulating the clinical expression of mitochondrial disease.
Funder: Medical Research Council

Abstract: Mitochondrial disorders affect ~1 in 4300 of the population and cause progressive, incurable diseases that often result in premature death. The primary genetic defect affects either nuclear DNA or mitochondrial DNA (mtDNA), and ultimately leads to a biochemical defect of ATP synthesis. However, despite having the same basic biochemical basis, mitochondrial disorders have an enormously variable clinical presentation and disease course. My laboratory aims to determine the major nuclear and mitochondrial genetic factors which modulate the clinical expression of mitochondrial disorders, thus explaining the variable phenotype. Specific laboratory research themes include: (i) Defining the sub-cellular mechanism responsible for the mtDNA genetic bottleneck during female germ cell development in a germ-line model in vitro, and validating these findings in vivo in both mice and humans. Our aim is to use in vitro models to identify compounds that influence the transmission of heteroplasmic mtDNA mutations that could be used to prevent mtDNA diseases. (ii) Comprehensively characterising novel nuclear gene defects in patients with Mendelian mitochondrial disorders using exome and whole-genome sequencing. This will identify new mitochondrial disease genes that will undergo functional validation using tissue-specific cell lines differentiated from patient-derived induced pluripotent stem cells (iPSCs). This work is being carried out as part of the mitochondrial Genomics England Clinical Interpretation Partnership. (iii) Using state-of-the-art genomics and transcriptomics to define critical nuclear-mtDNA interactions through the investigation of homoplasmic mtDNA diseases with variable clinical penetrance. These three laboratory research themes dove tail into a clinical translational research programme studying the natural history of mitochondrial disease, and developing new treatments through investigator-led experimental medicine studies and clinical trials in partnership with the pharmaceutical industry.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Resource for innovation and application of genetic engineering strategies in embryonic stem cells
Funder: Medical Research Council

Abstract: This Resource aims to innovate genetic engineering strategies in mouse and human embryonic stem cells, and apply these strategies to address contemporary questions in molecular and developmental haematology. Application of these strategies includes: 1) monitoring and controlling stem cell self-renewal and commitment to differentiation by use of reporter transgenes and inducible expression systems; 2) facilitating functional analyses using both forward and reverse genetic approaches to understand the regulation of gene expression and the role and interaction of genes in haematopoietic development; 3) constructing new sophisticated models of human blood diseases for both in-vitro and in-vivo analysis, and for drug screening and development. In addition, this Resource is using its expert knowledge and newly developed technologies to assist other research groups in the MRC Molecular Haematology Unit in their individual Programmes.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Characterisation of ATRX, a chromatin remodelling protein
Funder: Medical Research Council

Abstract: In the next phase of our research we wish to build on the success of the last five years to understand the role of ATRX in the gene expression and in particular how mutations in ATRX lead to down regulation of  globin gene expression. The long term aim of this work is to see if this pathway is open to manipulation and whether it might be exploited therapeutically to modify the severity of  thalassaemia by reducing the pathological accumulation of  globin chains. It is apparent from our recent work that ATRX binds to tandem repeats throughout the genome. Many of these repeats are predicted to fold into non-B forms of DNA including G4 structures and we have shown that ATRX can bind G4 in vitro. When ATRX is mutated the expression of genes close to these ATRX targets is perturbed and the magnitude of the effect is related to the size of the repeat. It seems likely that ATRX modulates the effects of these repeats on gene expression. The current conundrum is how this might occur. Preliminary evidence suggests that ATRX plays a role in DNA replication and our working hypothesis is that these repeats and the structures they form inhibit the progress of the replication fork, a DNA damage response is triggered and as a consequence of this the expression of nearby genes is perturbed. A central focus of this programme will be to test this hypothesis and understand the mechanism underlying the abnormality in gene expression seen in individuals with ATR-X syndrome.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: The regulation of globin gene expression during haematopoiesis
Funder: Medical Research Council

Abstract: Now that DNA sequence is available for many mammalian genomes, recent studies have focused on genome-wide approaches to determine how the key elements are organized; how this relates to nuclear function (including DNA replication, recombination and repair, DNA transcription and RNA processing), and how these processes are influenced by interactions with epigenetic phenomena (nuclear position, timing of replication, chromatin modifications and DNA modifications by methylation and hydroxymethylation). In future we plan to use such approaches to analyse how genes are regulated during haematopoiesis and particularly in erythropoiesis. Valuable as this ‘big picture’ is, it is critical that the generalities it produces are assessed for their accuracy by examination of individual loci whose detailed structure and many natural variants have been determined, and whose function can be verified by experimental manipulation. The  globin locus and the surrounding region is one of the best characterised segments of the genome (in mouse and human) and therefore is ideal for testing predictions from the genome-wide studies. Equally, we will continue to test predictions made about nuclear processes from detailed analysis of this region by genome-wide studies. The ultimate goal of this work is to develop new ways to modify gene expression during erythropoiesis with the aim of manipulating globin gene expression and ameliorating the clinical phenotypes of patients with thalassaemia.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Haematopoietic stem cell ontogeny
Funder: Medical Research Council

Abstract: This programme is aimed at defining the core transcriptional networks that control the formation and behaviour of haematopoietic stem cells (HSCs), and the embryonic signals that establish and maintain them. We continue to exploit the technical advantages of zebrafish and Xenopus embryos in the knowledge that these core networks and their controlling signals will be conserved in humans. A major new departure will be to carry out cell tracking and molecular perturbations at the single cell level to clearly establish lineage relationships and to distinguish cell autonomous from non-cell autonomous effects. We will identify the locations of precursors in the embryo and explore the gene expression there with a view to predicting instructive signals not yet defined. These predictions will be tested using gain and loss of function assays, including at the single cell level. The regulatory relationships between transcription factors in the nucleus will be determined using similar gene function assays, and we will begin to extend to cell populations in the embryo, chromatin and protein complex affinity purification to identify direct targets and protein partners. Together, these approaches will enable the building of detailed networks of regulatory information which will enhance our understanding of HSC formation and behaviour. To gain insight into the mechanisms by which leukaemic fusion genes initiate leukaemia, we will also determine the impact of these genes on the networks built up in this programme, and screen for small molecules that exert control over fusion gene activity.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Transcriptional control of haematopoietic specification and differentiation
Funder: Medical Research Council

Abstract: Understanding how stem cells are specified during embryonic development and how lineages differentiate to produce mature and specialised cells are central questions in biology and are of crucial interest to elucidate pathways involved in diseases. The main aim of this programme is to characterise some of the molecular mechanisms engaged by key regulators of blood development (such as SCL/Tal1), with a particular focus on the early stages of mesoderm patterning and haematopoietic specification. Functional identification of protein complexes and their nuclear targets combined with molecular characterisation of their mechanisms of action and structural biology approaches will give insights into genetic interactions and transcriptional networks critical in decision pathways. Using in vitro differentiation of mouse ES cells, mouse haematopoiesis and Xenopus embryos as experimental models, we will start building networks of genetic interactions at the heart of haematopoietic development. These approaches are instrumental for our understanding of how a haematopoietic stem cell-specific protein complex might form and how, when this process is deregulated, this leads to leukaemia. Moreover, this might help characterise the pathways leading to definitive haematopoiesis and HSCs from hES and iPS cells that remain poorly characterised. This is important if one wants to be able to produce HSCs in vitro for regenerative medicine purposes.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Regulation of protein degradation and homeostasis by ubiquitylation
Funder: Medical Research Council

Abstract: Ubiquitylation is a versatile posttranslational modification that drives virtually every cellular process. An important role of ubiquitylation is in the quality control and degradation of misfolded and damaged proteins, a process central to maintaining a functional proteome or proteostasis. In addition, the ubiquitin proteasome system also mediates the degradation of signalling proteins that regulate cellular processes such as cytokine receptor signalling and the cell cycle. Failure to degrade proteins in a timely manner is the underlying cause of diseases such as cancer and neurodegenerative diseases that afflict millions of people worldwide. Hence, studying how ubiquitylation regulates protein degradation to maintain protein homeostasis is important to not only understand the molecular causes of disease but also for the development of effective therapeutic strategies, and forms the main research goal of my lab. Specifically, we want to understand the molecular mechanisms underlying the decoding of different ubiquitin signals that determine whether a ubiquitin signal results in protein degradation. We are particularly interested in how deubiquitylases (DUBs) act in quality control pathways that negatively regulate protein degradation. We also aim to explore how DUBs can be exploited in novel therapeutic strategies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Chromosome maintenance and repair in health and disease
Funder: Medical Research Council

Abstract: Genomic DNA is frequently subjected to insults that damage DNA, and if not rectified the resulting DNA lesions can cause mutations and human disease. Some forms of DNA damage block DNA replication, and cells have evolved protective mechanisms for preventing genome disintegration in the face of these and other obstructions. My laboratory focuses on the molecular mechanisms underlying the signalling and repair of DNA damage, especially those that perturb DNA replication, with emphasis on control of these mechanisms by phosphorylation and ubiquitylation. We are particularly keen to understand how derailment of DNA repair causes disease. In recent years, we have become interested in how cells repair DNA inter-strand crosslinks (ICLs), lesions that potently block DNA replication. ICL repair is important to study as defective ICL repair gives rise to Fanconi anemia (FA), a recessive disorder characterized by developmental defects, bone marrow failure and cancer predisposition. Furthermore, the anti-proliferative effects of some of the most commonly used anti-cancer drugs rely on induction of ICLs, and therefore understanding how ICLs are repaired may pave the way for sensitizing cancers to these drugs and overcoming resistance. In the current quinquennium, our work has provided new mechanistic insight into repair of ICLs and other DNA lesions. Much of our work has focussed on three DNA repair proteins, all of which are recruited to DNA damage sites by UBZ-type ubiquitin-binding domains to prevent genome instability: the structure-selective nuclease FAN1, the scaffold protein SLX4 which coordinates three separate structure-selective nucleases, and the DVC1/SPRTN protease. We have also uncovered new roles for the E3 ubiquitin ligase RFWD3 mutated in a new FA subtype.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: TGFβ and Wnt signalling during development and human disease
Funder: Medical Research Council

Abstract: Signal transduction pathways triggered by the transforming growth factor beta (TGFβ), bone morphogenetic protein (BMP) and Wnt ligands control a plethora of cellular processes throughout metazoan development and adult life. In humans, aberrations in these signalling cascades result in many diseases, including skin and bone disorders, fibrosis and cancer. My group studies the molecular mechanisms that underpin the regulation of TGFβ and Wnt signalling pathways. We identified the PAWS1 protein that is a member of the FAM83 family of previously uncharacterised proteins, and showed that it is not only a modulator of BMP signalling but also a critical anchor of casein kinase (CK) 1 that streamlines Wnt signalling. Excitingly, our work indicates that other FAM83 family members are also key anchors for different CK1 isoforms. These findings represent a significant advance in our understanding of how the CK1 family of constitutively active Ser/Thr protein kinases is regulated in cells, in order to control diverse cellular processes.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: The role of RNA in the response to cellular stress
Funder: Medical Research Council

Abstract: Modulation of gene expression via the delivery of nucleotide-based therapeutics has great potential for the treatment of a large range of human diseases. Major challenges still exist in the development of these next generation drugs due to limitations in our knowledge of RNA biology and delivery methodologies. In recent years, most attention with regard to gene-based therapies has focused on DNA and viral systems; however, their use is limited due to low efficacy, genetic transfer risk and poor control over dosage. More recently, the incorporation of modified nucleotides has meant that in vitro transcribed mRNA molecules have been successfully used for the delivery of genetic information without risk of genomic integration. These mRNAs are produced using modified nucleotides that mimic endogenous mRNA molecules and thus avoid activating the innate immune response. The relatively short half-life of RNA compared to DNA also allows precise control over final protein dosage. In terms of the safety of these synthetic molecules, there are major challenges that need to be addressed before the full potential of mRNA-based therapeutics can be realised. These issues mainly revolve around our current lack of understanding of how these RNA molecules are controlled. Our laboratory has been investigating how mRNAs are regulated and we have discovered that two RNA DEAD-box helicases associate with translationally repressed mRNAs. The association of mRNAs with these DEAD-box proteins has allowed us to identify multiple repressive mechanisms imposed by the major cellular mRNA silencing apparatus - the Ccr4-NOT complex. Until now, identification of mRNAs controlled by the variety of mechanisms that the Ccr4-NOT complex plays a role in would have been extremely labour-intensive, requiring a number of different techniques and would not have given sufficient resolution for mRNAs with low cellular abundance. In contrast, our methodology is a relatively straightforward approach, which allows for simultaneous identification of mRNAs repressed by the Ccr4-NOT1 complex in a given cell type or tissue. These repressive characteristics can be used to build a signature of the regulatory mechanisms operating within a particular cell type. We will determine the applicability of this approach to identify the repertoire of repressive mechanisms operating within a cell, in order to engineer therapeutic mRNAs for restricted on-target expression in particular tissues/cell types and disease states. This will facilitate the development of the next generation of mRNA-based therapeutics which will be specifically designed to minimise potential off-target adverse effects.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: GENERIC HEALTH RELEVANCE