Seed Awards in Science: people we've funded

This list includes current and past grantholders.


Dr John Apergis-Schoute

University of Leicester

Prefrontal control of hypothalamic feeding circuits: balancing executive control of eating

It is thought that diminished or excessive control over the drive to eat seen in people with eating disorders results from under- or over-activation of prefrontal cortical (PFC) brain regions where decision-making is controlled. We want to investigate the link between the underlying circuitry between the PFC and feeding-promoting circuits of the hypothalamus.

Novel circuit-mapping strategies will be used to determine the functional relation between the two structures. This will set the groundwork for relating PFC and hypothalamic activity in a rodent eating disorder model that promotes under- or overeating. There will be two phases, one where animals restrict their food intake, the other where they overeat. We will monitor and relate changes in PFC and hypothalamic activity across phases where animals exhibit distinct feeding patterns and then attempt to normalise eating by manipulating prefrontal inputs to the hypothalamus. This will show that this circuit has a causal role on the impulse to eat.

This project will link executive circuits with feeding circuits and provide insight into the neural mechanisms underlying maladaptive eating behaviour.

Dr Anat Arzi

University of Cambridge

Dynamic neural remapping across the sleep-wake cycle: A mechanistic link between sensory re-organisation and GABA

Across a single day, we undergo behavioural, physiological and neurochemical changes, from vigilant wakefulness to unconscious sleep. Sensory processing continues during sleep despite the loss of consciousness. Attempts to assess the differences between sensory processing in wakefulness and sleep have yielded contradictory results with studies showing greater, smaller and comparable responses to the same stimuli. It remains unclear precisely how sensory processing is modulated throughout the sleep-wake cycle. Most studies have focused on responses to specific stimuli, neglecting the relationship between different stimuli.

We want to find out how vigilance state dynamically shapes sensory processing, by combining electroencephalography (EEG), functional magnetic resonance imaging (fMRI), magnetic resonance spectroscopy (MRS) and computational tools, measuring neural distances between stimuli to quantify sensory remapping across the sleep-wake cycle. We hypothesise that gamma aminobutyric acid (GABA), an inhibitory neurotransmitter implicated in sleep regulation and correlated with sensory sensitivity, has a central role in sensory remapping. 

Our goals are to elucidate the temporal and spatial dynamics of sensory remapping throughout the sleep-wake cycle and investigate whether sensory remapping across the sleep-wake cycle is dependent on GABA.

Dr Angeliki Asimaki

St George's University of London

A dissection of the intercalated disk to stop sudden cardiac death

Every week in the UK, 12 people under the age of 35 die of sudden cardiac death (SCD). I believe that a key to preventing SCD is elucidating what happens at the intercalated disk (ID); the area of heart muscle that connects cells using mechanical and electrical coupling. We have shown that a few proteins are redistributed from and to the ID during SCD and this has significantly improved diagnosis and management of people who have a family history of SCD. The ID, however, was recently shown to contain more than 760 proteins.

I will employ a novel technology to isolate the IDs from formalin-fixed samples and use proteomics to resolve the full spectrum of protein remodelling in SCD-IDs due to arrhythmogenic cardiomyopathy and Brugada syndrome. I will evaluate the specificity of the novel diagnostic signatures using the world’s largest bank of SCD myocardial samples.

Decrypting the ID’s molecular remodelling will lay the foundations for mechanism-targeted therapies which could reduce the incidence of SCD.

Dr Maria Ávila-Arcos

Universidad Nacional Autonoma de Mexico

Real-time characterisation of pathogen evolution and the effect of post-contact epidemics on the native population of Mexico through ancient DNA

Understanding the molecular processes behind the initial contact between pathogens and immunologically-naive populations in major pandemics is crucial when developing strategies to face the potential devastating effects of reintroduction of a pathogen. Ancient DNA (aDNA) studies have revealed the causes of major historical epidemics and the genetic makeup of some ancient pathogens. aDNA can jointly characterise the genetic makeup of pathogens and hosts at the time of first contact. This is of particular interest in places such as Mexico, where a large fraction of the genetic variation in the native population was lost as a consequence of major outbreaks caused by pathogens introduced during colonisation by Europeans.

We will use aDNA to investigate the genetic interactions between host and pathogen in the native population and the pathogens zintroduced during the Spanish colonisation of Mexico. We will generate more than 20 ancient genomes from a pre-Hispanic skeleton collection in Mexico City and a collection of skeletons of people who died from the epidemic after Spanish colonisation. Pathogen DNA will also be retrieved and sequenced.

We will use the collections to identify variants that influence susceptibility to infection and the pathogenicity of ancient pathogens to determine the amount of genetic variation lost as a consequence of epidemics cause by pathogens introduced during colonisation.

Dr Emma Baple

University of Exeter

A community approach to accelerate the discovery of the molecular basis of neurodevelopmental disorders

The molecular causes of the majority of inherited neurodevelopmental disorders remain poorly understood. The cause of such disorders in rural Pakistan typically relates to founder mutations that have accumulated due to historical ancestral population bottlenecks, followed by population expansion. This provides an opportunity to study phenotypical, genetic and functional studies to discover the molecular causes of autosomal recessive, which will benefit medical science and help with disease diagnosis globally.

This study will cement new collaborative relationships and develop infrastructure in four Pakistani research centres enabling invaluable new opportunities to discover more about neurodevelopmental disease. We will unravel biomolecular developmental processes for future exploration using stem cell and animal models. The collaboration will also provide opportunities to improve local knowledge of the spectrum and causes of inherited neurodevelopmental disease, greatly facilitating development of diagnostic services in Pakistan.

These collaborative relationships will lay foundations for long-term future molecular studies to enhance scientific knowledge and define new therapeutic avenues for these disorders.

Dr Elena Bochukova

Queen Mary University of London

Modelling neurodevelopmental and molecular mechanisms of human genetic obesity

The principal goal of this proposal is to develop novel platforms to study neurodevelopmental and mechanistic causes of severe obesity. Body weight regulation is governed by the hypothalamus and this is established very early in human development. Genetic variants that disrupt hypothalamic function can lead to severe obesity. However, the manner in which these variants contribute to obesity by exerting neurodevelopmental and molecular changes have been difficult to study since human brain tissue is inaccessible. Rodent models have been used to improve our understanding of energy homeostasis, but they carry inherent limitations due to inter-species differences in brain structure and physiology, as well as gene sequences. 

The development of human study systems for disease modelling is an important complementary approach to animal and patient studies. We will use several novel methodologies – precise genome engineering with CRISPR/Cas9 in stem cells, 2D hypothalamic cultures, as well as 3D brain organoids – to generate physiologically relevant cellular and tissue models of human genetic obesity. We will investigate neurodevelopmental aspects of the disease and use the models to study molecular mechanisms that leads to obesity. 

Dr Luke G Boulter

University of Edinburgh

A forward genetics approach to define driver mutations in bile duct cancer

Cholangiocarcinoma is an aggressive malignancy of the bile ducts in the liver and has a poor prognosis, with 75% of patients dying in the first year after diagnosis and 5-10 per cent of patients surviving more than five years. Understanding the genetics of cholangiocarcinoma has been hampered by relatively small sample sizes, where whole exome sequencing (WES) has yielded a broad mutational profile that does not provide a standout mutational signature that can be targeted therapeutically.

We aim to use computational tools to conduct a combined analysis of 413 cholangiocarcinoma WES datasets. We will then define driver mutations using algorithms that predict the likelihood of a mutation being oncogenic. These computationally derived mutations will be used to conduct a forward genetic screen in bile duct organoids using Cas9/CRISPR. The expectation is that neutral mutations will be filtered out and we will be able to derive a list of functional oncogenic mutations. This combination of in silico and in vitro methodology will determine bona fide oncogenes from a highly-triaged list of candidate mutations.

This methodology will be important in identifying oncogenes in cholangiocarcinoma and other rare cancers or cancers which have diverse mutational spectra.

Dr Seth Coffelt

University of Glasgow

Understanding gamma delta T cell function in colorectal cancer metastasis

Metastatic disease and its complications are responsible for the vast majority of cancer-related deaths. In the metastatic process, immune cells function paradoxically: some cells prevent metastasis while other cells promote metastasis. We have shown how distinct immune cell subsets cooperate to support breast cancer metastasis by suppressing other anti-metastatic immune cells. This cooperation occurs between gamma delta T cells and neutrophils to inhibit cytotoxic T-lymphocytes. Gamma delta T cells are a rare population of cells that express a T cell receptor, function like innate immune cells and reside in mucosal tissues. Although we defined the role of gamma delta T cells in breast cancer metastasis, their function during metastasis in other cancer types is entirely unknown.

We will investigate the role of these cells during colorectal cancer metastasis. We will use a novel, spontaneous metastasis model of colorectal cancer metastasis.

The data generated from these experiments will improve our understanding of basic metastasis biology and gamma delta T cell biology and will uncover potential immunotherapeutic approaches for patients with metastatic disease.

Dr Samuel Cooke

King's College London

Translatable EEG biomarkers of intellectual disability in pre-clinical mouse models of fragile X syndrome and tuberous sclerosis complex

The neurodevelopmental psychiatric disorders fragile X syndrome and tuberous sclerosis complex both have known synaptic plasticity and excitatory/inhibitory balance phenotypes. Efficacious drug treatments have been developed but they are not ideal for human use.

This project will introduce new electroencephalogram biomarkers of known neuronal events, including synaptic plasticity, activity of two different GABAergic inhibitory neuronal subclasses and burst firing, which can be experimentally constrained in primary visual cortex by habituation to simple visual stimuli and presentation of novelty. The immediate goal of the project is to show that cortical dysfunction is severe enough to be evident in these biomarkers in pre-clinical mouse models of two highly penetrant, single gene causes of fragile X syndrome and tuberous sclerosis complex. We will also demonstrate that altered biomarkers can be remedied which could lead to new drug treatments for the disorders.

This seed study will lead to larger studies using genetic and invasive experimental tools to deeply understand processes of learning and memory in mice, and to understand their dysfunction in genetically defined neurodevelopmental psychiatric disorders. We also wish to translate the use of these biomarkers into human subjects for patient stratification and assessment of response to treatment.

Dr Vidya Chandran Darbari

Queen Mary University of London

Virulence strategies for mycobacterial persistence: investigating the role of the mammalian cell entry proteins

The global burden of mycobacterial infections, especially tuberculosis, is inconceivable with at least one new case of infection arising every second and about two million people dying annually. Persistence of mycobacteria arises from long durations of dormancy in host macrophages evading host defense mechanisms and using unusual nutrients. Mycobacterial mammalian cell entry (Mce) transport systems play an important role in facilitating cell entry and they also import nutrients such as cholesterol or lipid.

We will characterise the Mce4 proteins and their assembly in the Mce4 transport system. One of the key goals is to isolate a minimal hetero-complex of the Mce proteins forming the transport channel for structural and functional studies. Two possible models for organisation are proposed: a heterohexamer of six Mce proteins or a stack of six homo-hexamers of individual Mce proteins. Biochemical characterisation of individual Mce proteins and interaction studies between different Mce proteins will help establish the organisation model of Mce4 proteins. Structural studies using X-ray crystallography or other techniques and functional characterisation for cholesterol binding and cell invasion will shed light on the structure and function of Mce4 proteins within the transport assembly.

This study will improve our understanding of mycobacterial persistence.

Dr Rafael da Silva

University of St Andrews

Unravelling structure and mechanism of adenine(22)-tRNA methyltransferase: towards novel antibiotics against MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of hospital infections worldwide. This bacterium has been found to cause infections in otherwise healthy communities whereas it used to be restricted to healthcare facilities. MRSA isolates have emerged that are resistant to most antibiotics in clinical use. It is imperative that new drugs are developed to combat MRSA. It is easier to develop specific antibiotics when bacterial molecules are well understood. A drug could be developed that inhibits an enzyme essential for MRSA growth will stop infections.

The enzyme N1-adenine(22)-tRNA methyltransferase (TrmK) is essential in MRSA and absent in humans but we know little about its structure and function. In this project, we will elucidate the mechanism of action of TrmK using enzyme kinetics and crystallography.

Our results will pave the way for follow-up work to create specific inhibitors to be further developed into drugs that can treat MRSA infection.

Dr Guillaume De Bo

University of Manchester

Novel mechanochemical tension sensors for in vivo applications

Tensile forces influence cellular processes such as cell division, stem cell differentiation and gene expression. At the tissue level, these forces play a crucial role in morphogenesis, wound healing, the immune response and pathological processes such as cancer metastasis. However, our understanding of how force influences cell function in the context of whole tissues is limited due to a lack of techniques to measure force in live tissue. Genetically encoded tension sensors have been developed, but their use in whole tissues has been limited. One reason for this limited use is the low sensitivity of current in vivo tension sensors. At the molecular level, the unique ability of mechanical force to distort, bend and stretch chemical bonds has led to the development of mechanochromic molecules acting as spatially sensitive molecular probes or micro-crack sensors in synthetic materials. Chemical mechanosensors offer a potentially powerful solution to this problem but have yet to be translated into biological systems.

We will take a multidisciplinary approach to develop and test novel chemical force sensors suitable for measuring tensile forces in live tissues.

Dr Jonine Figueroa

University of Edinburgh

Temporal trends in incidence and mortality of molecular subtypes of breast cancer to inform public health, policy and prevention

Numerous molecular markers have been identified as having treatment and prognostic value for breast cancer, but their distribution and potential translation into cancer prevention or clinical interventions remains to be determined. Oestrogen receptor (ER) expression in tumours is a marker of aetiological and treatment differences, and preliminary data from more than 73,000 cases in Scotland show ER-positive breast cancers rising and ER-negative breast cancers declining from 1997-2014. The underlying reasons for these divergent trends are lacking and we do not know the differences in population trends, such as age, socioeconomic status and screening. Advances in ’omics technologies have changed breast cancer treatment regimens beyond ER, identifying subgroups of cases that might benefit from different chemotherapy, radiotherapy and hormonal treatment regimens.

We will use the electronic medical record datasets from cases of breast cancer in Scotland to develop a high-dimensional ‘omics dataset through a proof-of-principle study using 1,600 tissue samples from Lothian Bioresource from two five-year periods.

This proposal will quantify how many women might benefit from new ’omics-defined molecular subtypes of breast cancer, with the goal of defining the populations that might most benefit from prevention, screening or treatment interventions.

Dr Angela Flynn

King's College London

Prevention of gestational diabetes in obese pregnant women; a proof of principle study targeting early pregnancy intervention to women at risk

Obesity in pregnancy increases the risk of gestational diabetes (GDM) and its associated adverse outcomes. National Institute for Healthand Care Excellence (NICE) guidelines recommend that all obese women have an oral glucose tolerance test at 24-28 weeks gestation to detect GDM. However, excessive fetal growth in women with obesity is evident before diagnosis of GDM at 20 weeks gestation and is accompanied by an abnormal metabolome. Targeted intervention in early pregnancy is required to prevent GDM and improve outcomes for obese women in pregnancy.

We have developed a novel GDM prediction tool for early pregnancy. Our hypothesis is that giving the two first-line treatments for GDM – dietary advice and/or metformin – early in pregnancy will prevent gestational diabetes by improving glucose tolerance and metabolic function in at-risk obese pregnant women as identified by our prediction tool.

This study will identify obese women at higher risk of GDM and provide proof of principle of the efficacy of diet and/or metformin in high-risk women by the method of continuous glucose monitoring (CGM) and by evaluation of a targeted metabolome. Our study will determine feasibility of the intervention for obese pregnant women receiving antenatal care from the NHS.

Dr Firat Guder

Imperial College London

Integrated nucleic acid microsensor for on-site detection of infectious animal diseases

Despite the advancement of diagnostic technologies targeting nucleic acids (NA), there are no portable, disposable and integrated solutions for testing infectious diseases at the point of care (PoC). This is unfortunately the case for all infectious diseases affecting animals, humans and even plants.

We will develop a new class of NA microsensor called silicon-paper integrated diagnostics or SPiDx. This new technology will combine the versatility of paper-based microfluidics and performance of silicon microelectromechanical systems (MEMS) on the same platform for the first time. SPiDx will be capable of integrated thermal amplification and electrochemical detection of NA at the PoC, while supporting multiplexed analysis. The entire SPiDx platform will be produced outside the clean room which will dramatically reduce production costs.

We will focus on paratuberculosis, a fatal, chronic wasting disease affecting ruminant animals with significant economic consequences. Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent responsible for paratuberculosis may also be associated with Crohn’s disease in humans. We hope to develop a portable solution for testing these diseases at the point of care.

Dr Pia Hardelid

University College London

Exploring the epidemiology of respiratory syncytial virus in young children in the community using sparse serological survey data

Bronchiolitis caused by respiratory syncytial virus (RSV) leads to over 30,000 hospital admissions annually in infants in England. RSV infection only confers transient immunity and early RSV infection is associated with asthma in later childhood. Several vaccine candidates are currently in clinical trials. We currently know very little about how age at first infection is affected by, for example, the number and age of siblings, or what factors influence protection from maternal antibodies.

We will carry out the first community serosurvey of RSV in the UK using a unique collection of serial blood samples from babies linked to maternal, family and symptom data from the Born in Bradford study. We will develop novel statistical methods to estimate the age at first and subsequent RSV infection in the first two years of life, and validate our findings against parent questionnaires and routinely collected primary care data.

This study will provide important information about who to vaccinate, and when, to ensure babies are protected from early RSV infection. It will develop; novel methods to estimate age at infection from sparse serological data, and validated methods for a larger, pan-European study of the role of RSV infection in early life and respiratory health in later childhood.

Dr Alan Harper

Keele University

Platelet-targeted nanotechnology: a new approach to improve the efficacy of thrombolysis

Acute cardiovascular events such as heart attack and strokes are among the leading causes of premature death in the UK. Current treatment options include the use of thrombolysis to enzymatically breakdown the blood clot to re-establish blood flow through the blocked blood vessel. This treatment is limited by the short time window in which it is effective, and its potential to trigger intracranial haemorrhage.

We aim to create functionalised citrated magnetic nanoparticles (F-CA-MNPs) specifically targeted to activated platelets that can be used to both interfere with normal Ca2+ signalling pathways and to magnetically induce localised heating of the platelets to prevent clot retraction. By preventing clot retraction, we should be able to increase the porosity of the clot by preventing the compaction of the platelet aggregate.

We predict that our findings could facilitate the penetration of current thrombolytic reagents into the thrombi, enhancing the efficacy of this treatment and/or extending the time window over which this treatment could be used. These F-CA-MNPs could therefore be used to improve the safety and efficacy of current thrombolytic treatments.

Dr Leah Herrgen

University of Edinburgh

Cellular and molecular mechanisms of macrophage-mediated neuroprotection

Secondary cell death plays an important role in the pathophysiology of traumatic brain injury, spinal cord injury and stroke. Neuroinflammation was thought to contribute to secondary cell death, but clinical trials have shown that anti-inflammatory drugs can in fact be harmful. This suggests that inflammation can be neuroprotective, but the underlying mechanisms are not understood. Our preliminary results using an accessible larval zebrafish model of brain injury show that secondary cell death is strongly increased in a zebrafish mutant that lacks macrophages.

We will investigate the mechanisms underlying the neuroprotective effect of macrophages. We aim to determine the contribution of debris phagocytosis and identify macrophage-derived neuroprotective molecules. We will combine confocal live imaging of cell death indicators with pharmacological and genetic inhibition of phagocytosis to investigate the contribution of rapid debris clearance to macrophage-mediated neuroprotection. We will also use in situ hybridisation screening and RNA-seq expression profiling of macrophages that have been purified by fluorescence-activated cell sorting to identify macrophage-derived neuroprotective molecules.

This work will provide insight into the cellular and molecular mechanisms of inflammatory neuroprotection and will identify targets for manipulation of the mammalian immune system aimed at reducing secondary cell death after injury to the central nervous system.

Dr Louisa James

Queen Mary University of London

Understanding the functional heterogeneity between memory B cells expressing different immunoglobulin subclasses

The quality of the antibody response to different antigens in distinct microenvironments is determined by the functional properties of specific B cells. Evidence suggests that B cells expressing different antibody subclasses display functional heterogeneity that could influence their ability to expand, migrate and differentiate after activation.

This study will test the hypothesis that human memory B cells expressing different antibody subclasses are functionally distinct. Rates of clonal diversification – expansion, class-switching, somatic hypermutation and differentiation – by B cells expressing different antibody subclasses will be compared after antibody repertoire sequencing of B cell subsets from the human tonsil. In addition, the functional diversity of human class-switched B cells will be assessed by single-cell RNA sequencing. B-cell subtypes will be classified using gene-expression-based clustering and the distribution of B cells expressing different antibody subclasses across different clusters will be calculated.

Identification of genes and gene-related pathways that define functionally distinct B cell subtypes would lead to a more precise understanding of how B-cell memory is generated. This would inform approaches that aim to promote or suppress specific antibody responses and would provide a basis for examining mechanisms that drive dysregulation of B-cell memory in human disease.

Dr Isuru Jayasinghe

University of Leeds

Harnessing the molecular-scale resolution of DNA-PAINT to study the structural basis of electrical signals of the healthy and arrhythmic hearts

Single molecule localisation microscopy (SMLM) has revolutionised our understanding of signalling microdomains in many biological systems. Among such molecular systems are arrays of gap junction (GJ) channels paving the fundamental electrical signalling pathways of the heart. Conventional SMLMs are unable to visualise individual GJ channels within their native tissue environment because they are limited by resolution. One of the newest SMLM techniques, DNA-PAINT, promises a resolution of about 5nm which is sufficient to resolve single proteins in tightly packed arrays or clusters and to visually observe their interactions with other molecules. However, this technique is not suitable for imaging complex tissues such as the myocardium.

We will implement three possible modifications to the DNA-PAINT protocol to enable in situ optical mapping of GJ isoforms. DNA-PAINT will be further harnessed to quantify the changes in the phosphorylation states of GJ channels in ventricular cardiac tissue that exhibits pathological electrical disturbances known as arrhythmias.

The improved DNA-PAINT protocol and the pilot measurements on GJ remodelling will seed a larger investigation pioneering a direct, in situ, correlation of the GJ nanostructure and disturbed electrical patterns in hearts life-threatening arrhythmias.

Dr Daniel Jeffares

University of York

Understanding Leishmania parasite populations in Brazil

Leishmaniasis is a globally distributed disease that affects 700,000 people annually. It is caused by Leishmania parasites spread by sand flies. The most severe form, visceral leishmaniasis (VL), can be fatal if untreated. There is no effective vaccine against the disease and chemotherapy is the main method of reducing the disease burden. Leishmania infantum was introduced to Brazil during colonialism and is becoming more common as urbanisation increases, with 6,000 cases in Brazil each year. There are indications of resistance to miltefosine in Brazil, which can be an effective treatment in other continents.

We will establish an understanding of the dispersal and evolution of Leishmania infantum in Brazil and critical aspects of disease control. We will sequence the genomes of 200 strains of the parasite collected from two locations in Brazil 1,600km apart, including strains archived 20 years ago. By examining the movement of alleles between sites and over time, we will measure migration rates and recombination rates and screen for adaptive evolution. We will also analyse clinical data to examine whether parasite genes influence disease severity.

Dr Yi Jin

Cardiff University

Targeting the allosteric control of alarmone synthetases to tackle bacteria persistence

The current crisis of antibiotic resistance has prompted the need to devise strategies to tackle the problem, with a strong focus on developing novel antibiotics. However, one major obstacle that is much overlooked is that persister bacterial cells are refractory to antibiotic treatment. A family of intracellular chemicals called alarmones are the master regulators for such persistence. Alarmones possess phosphate groups and enable pathogens to survive after prolonged exposure to antibiotics. Despite this key role, little is known about the enzymes which catalysethe manufacture of alarmones. There is a specific and significant need to study how these enzymes work and this information would help in the design of new antibiotics targeting the alarmone pathway.

We will apply combined techniques including F NMR spectroscopy and X-ray protein crystallography to reveal atom-level information about how phosphoryl groups are transferred and how alarmones are made. This work will advance knowledge of enzymes from the RelA/SpoT homologue (RSH) superfamily involved in alarmone regulation.

This data will form a sound basis for future drug design to combat antibiotic resistence.

Dr Vasily Kantsler

University of Warwick

Microfluidics tools for sperm selection and diagnostics

We will aim to improve male fertility assessment and assisted reproductive technology (ART) by developing novel microfluidic methods of selecting motile sperm. Research into spermatozoa boundary-following navigation by spermatozoa and migration against an external flow and along ratcheted boundaries will enable us to design efficient methods of sperm selection. We will also integrate additional stages of eliminating premature and apoptotic sperm, and develop microfluidic platforms and protocols to analyse motility of human sperm in correlation with the chromatin integrity in-situ via an on-chip integrated chromatin structure assay.

We will design methods that use the swimming behaviour of spermatozoa to sort them in accordance with chromatin integrity, which is associated with the probability of successful conception. The chromatin integrity assay based on a microfluidic chip will also serve as an easy-to-use tool to assess male fertility.

These results will form the basis of the next stage of our research on mechanisms and physiology of sperm visco- and thermotaxis.

Dr Robert Keers

Queen Mary University of London

Investigating a novel approach to gene-environment interaction in depression and anxiety

Psychosocial adversity increases the risk of depression and anxiety but only a minority of those affected will develop mental illness. It has been hypothesised that genetic factors make people more or less sensitive to environmental influences. Identifying these factors could provide insight into the biological mechanisms of risk and resilience and allow preventive interventions to be targeted at the most vulnerable. Nevertheless, capturing environmental sensitivity genes remains a significant challenge.

We aim to build on our pilot of a novel approach to this problem by establishing the Genetics of Sensitivity to the Environment Consortium which will bring together genetic data from twins from across the world. This will allow us to: replicate and refine our findings from the pilot study; investigate environmental sensitivity genes in different disorders and at different ages; and estimate the heritability of sensitivity to environmental influences.

This project will lead to a larger programme of research focusing on the mechanisms underlying genetic sensitivity to the environment in the development and treatment of mental illness. We will also establish a new resource for researchers by combining twin designs with genetic data.

Dr Helena Kilpinen

University College London

Genetic background effects in human iPSCs and iPSC-derived cell types

Human induced pluripotent stem cells (iPSC) have emerged as a key model system to study the function of genetic variants, as they provide access to relevant cell types and developmental lineages through cellular differentiation. However, while it has been shown that the genetic background of the donor individual has an effect on molecular phenotypes measured from iPSCs, it is currently not known how much the genetic background influences studies that use iPSCs to model rare disease mutations, making interpretation of results challenging.

I will use CRISPR-Cas9 technology to study specific rare disease mutations in different genetic backgrounds. Specifically, I will focus on loss-of-function mutations causing Kabuki syndrome, a disorder of the epigenetic machinery, and use patient-derived iPSCs together with engineered mutant and control lines to quantify the contribution of the genetic background on the transcriptome and epigenome of the iPSCs as well as neuronal precursor cells derived from them.

This project will establish the value of using patient-derived iPSCs over generic iPSC lines with engineered mutations. This information is critical for the design of subsequent studies in which iPSCs serve as the baseline, such as directed differentiation experiments and therapeutic targeting of the mutation.

Dr Garry Laverty

Queen's University Belfast

Novel peptoid hydrogels as long-acting injectable drug delivery systems

Long-acting injectable (LAI) nanosuspensions comprising water-insoluble drugs are already widely marketed for treatment of schizophrenia and are presently being evaluated in late-stage clinical studies as formulation strategies for pre-exposure prophylaxis (PrEP) against HIV infection. Alternative formulations are needed to overcome some of the disadvantages of nanosuspension injections, including the use of water-insoluble actives, the formation of amorphous drug during milling, and difficulties around large-scale manufacturing.

We will investigate the potential of novel peptoid hydrogels for long-acting subcutaneous drug administration. Peptoids are biocompatible molecules that mimic naturally occurring peptides. They form structured, tissue-like, hydrogel networks in aqueous environments and can offer sustained release of drugs. The formulations will comprise: a peptoid backbone capable of hydrogelation; a phosphate group to increase aqueous solubility and whose enzymatic removal triggers hydrogel formation in vivo; and a model antiretroviral molecule attached via a physiologically hydrolysable group. We will characterise antiretroviral-conjugated peptoids for their ability to form hydrogels, test the biocompatibility of peptoid hydrogels and evaluate sustained drug release properties.

Our findings could contribute to the development of alternative formulations for LAI drugs.

Dr Alpar Lazar

University of East Anglia

Early sleep and circadian markers of Alzheimer’s disease: the impact of APOE-e4 on circadian rhythm and sleep-wake homeostasis in humans

Sleep abnormalities are common in neurodegenerative disorders and can be present long before the clinical onset of disease. This is true for Alzheimer’s disease (AD) where the APOE ε4 allele, a genetic predisposing factor for AD, has been recently correlated with impaired sleep in healthy adults. These data suggest a mechanistic contribution of sleep to neurodegeneration supported by its essential role in energetic restoration, neural plasticity and beta-amyloid clearance from the brain. Less is known about how the circadian system and sleep-wake homeostasis are affected in people with AD and how it might interact in modulating or driving the onset and progression of disease, in particular in healthy people who have a genetic risk of AD.

We plan to investigate the impact of the APOE genotype on the circadian system and sleep-wake homeostasis and the way they interact in defining sleep and waking cognition in everyday life and in a sleep laboratory where we will experimentally modulate sleep pressure.

This study will improve our understanding of biological mechanisms linking cognitive deficits and sleep impairment in people with a high risk of neurodegeneration, which in turn will pave the way for future intervention studies to improve sleep function and potentially delay disease onset.

Dr Eylem Levelt

University of Leicester

Cardiac rest and stress metabolism in patients with type 2 diabetes

Patients with type 2 diabetes (T2D) are at significant risk of developing heart failure and related complications. Altered myocardial fuel selection may play a central role in cardiac disease risk in patients with T2D by affecting myocardial oxygen demand and metabolic flexibility. At any given level of cardiac work, an increased dependence on fatty acids (FA) relative to carbohydrates decreases cardiac efficiency, which may adversely affect cardiac function.

We aim to evaluate, in vivo, the effect of T2D on myocardial energy metabolism and metabolic flexibility. We will investigate whether patients with T2D have a metabolically inflexible myocardium with a fixed FA preference which is unable to increase the use of glucose even in response to acute increases in cardiac workload. We will also determine whether the fixed preference to use FA significantly contributes to abnormalities in contractile function. We will carry out a cross-sectional, case-control study among 22 patients with type 2 diabetes and 22 people without diabetes who have preserved cardiac function. Significant coronary artery disease will be excluded in all patients by coronary angiography. Myocardial metabolism will be determined at baseline and during dobutamine stress with measurement of transmyocardial arteriovenous differences of oxygen and metabolites. Participants will undergo a comprehensive evaluation of cardiac structure, function and perfusion using rest and dobutamine stress cardiovascular magnetic resonance tests.

Our findings will help us gain a greater understanding of why patients with type 2 diabetes are at significant risk of developing heart failure.

Dr Claudia Linker

King's College London

The genetic control of collective cell migration: insights from the neural crest

Collective cell migration refers to the movement of a cell population that acquires directionality through cell to cell interactions. All cells of the group may be capable of reading directional cues, or they may divide their labour with ‘leader’ cells indicating the path to rest of the group. The precise molecular signals that control cell identities and behaviour in the context of collective cell migration remain unclear. We have studied this process in neural crest (NC) cells, a highly migratory population that arise early during embryogenesis. Our recent work has demonstrated that zebrafish trunk NC (TNC) migrate collectively and present non-exchangeable leader and follower identities. The firm allocation of TNC identities strongly suggests these are transcriptionally regulated.

We will generate new NC zebrafish reporter lines that will allow the specific labelling of TNC populations by photo-conversion, identifying leader, follower or premigratory cells. Labelled cells will then be isolated and processed for RNA-Seq.

The datasets will allow us to characterise leader, follower and premigratory cells transcriptomic signatures which is an essential step towards the elucidation of the genetic networks controlling TNC identities and behaviour.

Dr Robert Lowe

Queen Mary University of London

Adenine methylation in Tetrahymena thermophila: a computational tool

Adenine methylation (6mA) is the main DNA modification in unicellular eukaryotes and despite being identified for some time, the biological functions of this modification are still poorly understood. As with many systems, computational modelling can provide important insights into molecular processes but efficacy is often restricted by the complex nature of multicellular organisms. Strikingly, organisms which have high levels of 6mA have low levels of 5-methylcytosine (5mC) while those with high levels of 5mC have low levels of 6mA. This suggests that there may be a common biological function for 6mA and 5mC and that understanding the biological function of 6mA may prove useful in understanding the biology of 5mC.

We will investigate the role of 6mA during growth in the single-cell eukaryote Tetrahymena thermophila. We will produce the first genome-wide maps of 6mA in a single-cell model eukaryote, determine the relationship between 6mA and transcription and investigate whether 6mA is dynamic during growth.

These studies will lay the foundation for Tetrahymena thermophila to be used as an effective computational model organism, exploiting its complexity, unicellularity and physiological responses to further explore the biological functions of 6mA.

Dr Eugenio Mancera Ramos

Centro de Investigación y de Estudios Avanzados del IPN

Analysing transcriptional circuits driving biofilm formation in Candida species to understand the evolution of pathogenic traits

Fungi from the genus Candida are important human pathogens. The ability of these species to form biofilms is essential for their colonisation of the human host. Recent characterisation of the transcriptional circuit that regulates biofilm formation in Candida albicans identified seven core transcription factors that regulate more than 1,000 genes.

We will characterise biofilm formation and the underlying transcriptional circuits in several related species of Candida to understand how such a complex transcriptional circuit developed. Our key goals are to understand how biofilm formation varies across different Candida species. Our preliminary experiments show that only species closely related to C.albicans are capable of forming structured biofilms. We will also assess the role of the seven core transcription factors in biofilm formation in related Candida species. We will reconstruct the biofilm transcriptional circuits in different Candida species by performing transcriptional profiling and by mapping genome-wide protein-DNA interactions. Comparison of these circuits will show how the biofilm circuit evolved. We will test the adaptive value of the observed changes by identifying their phenotypic implications.

This work will reveal how biofilm formation, an essential trait for colonising the human host, emerged in this group of human pathogens.

Dr Nikolas Maniatis

University College London

Investigation of the regulatory hot spots identified for type 2 diabetes

The complex causal chain between a gene and its effect on disease susceptibility cannot be unravelled until the casual changes have been localised in the DNA sequence. By exploiting high-resolution population-specific genetic maps, we have recently identified 111 additional locations of disease susceptibility, 93 of which are found in European and African-American people and 18 that are specific to Europe. We also refined previously identified type 2 diabetes signals and showed that many of these are also risk loci in African-Americans. We have obtained a precise location for the implicated functional variants and we were able to identify that the majority of the disease locations appear to confer risk of type 2 diabetes by acting as expression quantitative trail loci (eQTL) that regulate adipose expression levels of a large number of cis-regulated genes.

Our aim is to further characterise in detail all the 111 novel and previously found loci by effectively integrating all our causal location estimates together with cell-specific regulatory annotation and chromatin modifications. So far we have only used adipose tissue but we will also investigate all our disease and co-localised eQTL locations for tissue specificity by performing gene expression analyses in other tissues relevant to type 2 diabetes.

Professor Ciaran Morrison

National University of Ireland, Galway

Primary cilia and cellular senescence

Somatic cells undergo senescence after a finite number of divisions, indefinitely arresting their proliferation. The mechanisms of cellular senescence are not well understood, although DNA damage signalling is one major cause. We have found that senescent human fibroblasts have increased frequency and length of primary cilia, the antenna-like structures that sense and transduce extracellular signals.

We will test the hypothesis that primary ciliation contributes to cellular senescence. We will use genome editing in primary cells to ablate CEP164, which is required for primary ciliogenesis, and then follow the kinetics of cellular senescence in the knockout population. We also propose to examine cilium-controlled signalling pathways to determine how they are affected during the initiation of senescence programmes. We will perform competitive co-culture experiments between ciliated and non-ciliated populations to define how ciliation capacity directs senescence in mixed populations.

The proposed experiments will test a novel cellular mechanism of senescence, a process of great significance in human health and the normal ageing process.

Dr Jose Ortega-Roldan

University of Kent

In-cell structural biology: CLIC1 structure, function and drug binding inside tumour cells

Chloride intracellular channel (CLIC) proteins consist of a family of metamorphic proteins that exist in an equilibrium between a soluble and a membrane-bound state. The alteration of CLIC function has been involved in ischaemia-reperfusion and different forms of cancer. CLIC1 has been directly linked with the proliferation of glioblastoma tumours of the brain. It can be found as a chloride channel or as soluble reduced monomers or oxidised dimers with oxidoreductase activity. CLIC1 inhibitors block both its ion channel function and oxidoreductase activity. However, it is unknown what form or forms of the protein are relevant in the context of healthy cells and glioblastoma cells and how the equilibrium between them is affected in disease.

I will study the membrane-associated and free conformations of CLIC1 by solution nuclear magnetic resonance (NMR) both in vitro and in vivo using in-cell NMR in different cell lines in combination with traditional NMR methods and fluorescence microscopy. I will identify which CLIC1 conformer is involved in disease and drug binding to understand the factors governing the equilibrium between the different CLIC1 forms and to determine the mechanism regulating such equilibrium with atomic detail.

These findings will permit further studies to develop more specific therapeutic drugs for glioblastoma.

Dr Marcin Przewloka

University of Southampton

Novel role of a protein phosphatase in chromosome segregation

Kinases and their antagonistic phosphatases both provide a key regulatory mechanism that controls many cellular events. We do not fully understand the way phosphatases work at a molecular level but we have identified an interaction between protein phosphatase 4 (PP4) and Drosophila centromeres, which when disrupted affects the mitotic centromere integrity and activity at the spindle assembly checkpoint. This pathway remains to be elucidated along with its relation to PP4's deregulation in many cancers.

I will determine PP4’s mitotic functions in humans using CRISPR/Cas9 gene editing to generate cell lines expressing endogenous PP4 fused with the auxin-inducible degron (AID) tag allowing for inducible and rapid degradation of the phosphatase. This approach will facilitate PP4 removal specifically in mitotic cells, the effects of which will be characterised by cell imaging. Parallel studies, including proteomics, will deliver precise information on the human PP4 interaction network and behaviour during mitosis.

This study will reveal the affected processes and provide a ‘blueprint’ for subsequent detailed investigations that identify the involved pathways, PP4-specific substrates and their phospho-regulatory sites. The results of this study will be part of a larger investigation framework for chromosome segregation.

Dr Rocio Sancho

King's College London

Uncovering the molecular and cellular heterogeneity of pancreatic ductal cells

Data suggest that pancreatic ductal cells have a latent capacity for regeneration but the molecular regulation of this potential has been completely unexplored. I have recently optimised ex vivo pancreatic organoids as an efficient and tractable system to study the effect of perturbations on ductal cell fate.

I propose to use organoids to characterise the cell types coexisting in the ductal compartment that are permissive or non-permissive for changing cell fate and the molecular pathways involved. Differentiation will be induced by Ngn3/Pdx1/MafA overexpression or by a medium containing differentiation-inducing factors. I will use transcriptomics to delineate different cell types in ductal INS-GFP organoids to identify markers of reprogramming-competent cells. I will also compare RNASeq profiles of reprogrammed, intermediate and unchanged organoid cells to reveal genes required for cell fate change and perform a Crispr/Cas9-based loss of function screen to identify the crucial signaling pathways involved in the maintenance of duct cell fate, using CK19-cherry as a marker of ductal cell fate.

These results will elucidate the fundamental biology of pancreatic ductal cell plasticity and provide clues for how to unlock the regenerative capacity of pancreatic ductal cells in vivo for future therapies.

Dr Julie Seibt

University of Surrey

The role of sleep in brain plasticity: focus on the synaptic translatome

Brain plasticity consolidation involves stabilisation of changes at synapses. It can be supported by sleep but the molecular mechanisms underlying sleep’s contribution to synaptic consolidation remain largely unknown. Synaptic plasticity consolidation requires local protein synthesis, such as translation of mRNAs. These proteins are essential for the structural modification of synapses. The influence of sleep on the synaptic translatome – the pool of mRNAs actively being translated – has never been investigated.

We will demonstrate that synaptic translation is enhanced during sleep and more so in conditions of enhanced brain plasticity and we will identify the specific mRNAs that are translated during sleep. Translation at synapses will be quantified using puromycin labelling. Changes in the translatome at synapses will be quantified by exome sequencing of polysome-bound mRNAs. Cortical tissue will be harvested from rats after periods of sleep, sleep deprivation and/or exposure to an enriched environment and this will determine the role of sleep and plasticity in synaptic translation 

This research will produce data that can be used for a larger research application on the role of sleep in brain plasticity across the lifespan.

Dr Giovanni Stracquadanio

University of Essex

Network analysis of the effect of hypoxia and nutrient deprivation on motility and metabolic switching of cancer cells

A hallmark of cancer is the process of metabolic reprogramming, which supports the uncontrolled growth and proliferation of tumours. Metabolic changes support tumour growth under various conditions, including limited oxygen and nutrient supply. While the latter seems to increase motility and metastatic spread, the former induces angiogenesis, which can improve the delivery of metabolites. Unfortunately, anti-angiogenic therapies have limited success in targeting this metabolic adaptation. An alternative approach would be to induce tumour cell apoptosis by nutrient deprivation. However, since most cellular functions are the result of complex interactions between genes and proteins, we must first identify the pathways that mediate cancer progression under limited nutrient and oxygen supply. RNA sequencing and mass spectrometry can provide gene level information, but we need effective network discovery algorithms to analyse this data at the pathway level.

I will study the transcriptome and proteome of cancer cells under limited nutrient and oxygen conditions, and develop a new network discovery algorithm to integrate this data and identify pathways that promote cancer under these stresses.

Dr Emma Thomson

University of Sheffield

Molecular dissection of the pathways linking ribosome biogenesis, the nucleolar stress response and oncogenesis

Ribosome biogenesis is a fundamental cellular process that is inextricably linked to cell growth, proliferation and oncogenesis. Further, the site of ribosome assembly, the nucleolus, acts as a key stress sensor, where many cellular stresses converge and act to trigger p53 stabilisation. The molecular mechanisms linking and regulating these processes, however, remains largely uncharacterised.

I will investigate the links between these processes through the dissection of GLTSCR2, one of the few factors that has been directly implicated in each of these pathways. My first goal is to uncouple the functions of GLTSCR2 in each pathway. The dissection of GLTSCR2s function is possible as it interacts with key factors from each pathway. We aim to precisely map the nature of these interactions which will provide the foundation upon which to generate specific mutants of GLTSCR2. We will then establish an in vivo system where the mutant forms of GLTSCR2 can be analysed.

Our study will allow the multiple facets of GLTSCR2 biology to be explored and provide a base for understanding and analysing disease-linked mutations, shedding light on the overlapping nature of these fundamental processes.

Dr Yujiang Wang

Newcastle University

Identifying optimal neurostimulation for epilepsy using computational approaches (IONECA)

Epilepsy is a debilitating disease characterised by unpredictable recurrent seizures. Continuous electrical brain stimulation is a promising treatment option for patients who are resistant to drug treatments. However, we are unsure how the treatment works and its success rate varies. There is also no clear strategy on how it should be applied.

We will use network analysis and computational modelling to identify optimal stimulation settings on a patient-specific basis. In a retrospective study, we will compare the functional networks of patients with focal epilepsy during different stimulation settings and relate these changes to the effect on seizures. We will then use computational modelling and inference to simulate patient-specific functional networks that predict the stimulation effect for settings that have not been tested in the patient. We will combine our simulations with optimisation methods that will allow us to identify optimal stimulation parameters for individual patients.

We aim to develop a comprehensive network analysis and modelling framework that will help identify where and how continuous electrical brain stimulation can prevent focal epilepsies. This will result in an analysis software package which would help make neurostimulation a reliable treatment option for patients with epilepsy.

Dr Bonnie Webster

Natural History Museum, London

Snail molecular xenomonitoring of urogenital schistosomiasis transmission in Zanzibar

Schistosomiasis is a freshwater parasitic disease. Better tools for monitoring and surveillance of its transmission are required to help control the disease. We aim to provide and validate molecular xenomonitoring tools for the wide-scale surveillance and monitoring of urogenital schistosomiasis (UGS) transmission.

The study will take advantage of a five-year elimination programme – the Zanzibar Elimination of Schistosomiasis Transmission (ZEST) 2012-2017 – which has identified communities that have responded differently to control efforts. This provides a unique opportunity to evaluate the utility of the molecular xenomonitoring tools to detect the different levels of transmission or prevalence of human infection. We will develop a novel highly-sensitive high-throughput species-specific xenomonitoring methodology for UGS. We will then investigate the focal distribution and abundance of snail vectors in individual human water contact sites and how this correlates to transmission. This will clarify the role of the Bulinus snail in the transmission of UGS in Zanzibar. We will then provide a methodology to enable the detection of very low transmission levels and to certify the elimination and interruption of UGS transmission. We will also investigate why there are persisting hot spots for transmission that exist despite multiple intervention strategies.

The results of this study will assist with the monitoring and control of the transmission of UGS in Zanzibar.

Dr Tom Wingfield

University of Liverpool

Developing a locally-appropriate socioeconomic support package for TB-affected households in Nepal: a seed project to inform the END-TB trial

WHO’s End Tuberculosis (TB) Strategy advocates socioeconomic support for households affected by TB to improve control of the disease. My doctoral research trialled a socioeconomic intervention for TB in 32 towns in Peru. This included education, mutual support and cash for TB-affected households, and this reduced catastrophic TB-related costs and increased initiation of preventive therapy and treatment success. The next step is to replicate this research in diverse, low-income, countries.

Supported by researchers at the Birat Nepal Medical Trust and the infrastructure of the IMPACT TB study, I will evaluate the socioeconomic impact of TB with in-depth interviews during house visits to 200 TB-affected households in Nepal. I will also conduct a workshop with 30 stakeholders from different sectors in Nepal to create a shortlist of feasible and locally-appropriate socioeconomic interventions to mitigate the effects of TB.

I will publish two articles and make presentations to international policy makers including WHO Future studies. I will link the findings with data from partner countries in the Social Protection Action Research and Knowledge Sharing (SPARKS) network including Peru and Mozambique, to inform the design of my randomised controlled trial of socioeconomic support for vulnerable TB-affected households. 

Dr John Worthington

Lancaster University

Glucagon-like peptide-1; a gut hormone with the capacity to be pivotal in mammalian helminth infection

Intestinal helminth infection causes morbidity in millions of the world’s most deprived communities and often causes nutritional impairment. Helminth infection alters hormone-secreting enteroendocrine cells (EECs) of the intestinal epithelium, which respond to luminal nutrients by secreting peptide hormones to coordinate efficient digestion and nutrient absorption. As the intestinal epithelium must also act as a barrier against potential pathogens, it communicates with immune cells present in the intestine, which comprise the largest collection of immune cells in any tissue of the body. However, how EECs of the intestinal epithelium regulate the immune system during helminth infection is poorly understood.

This project will examine the novel hypothesis that EECs secrete the hormone glucagon-like peptide 1 (GLP-1) in response to sensing helminths. GLP-1 can then act as a cytokine to directly control the function of lymphocyte populations in the epithelium. I will then determine whether GLP-1 receptor agonist drugs, already in clinical use for diabetes, can be repurposed for use for during helminth infection.

My project will uncover key mechanisms by which the immunoendocrine axis regulates immunity in the intestine which can inform new therapies for inflammatory diseases and infections of the intestine.

Dr Matthew Yeo

London School of Hygiene and Tropical Medicine

A platform for the transgenic modification of sand flies (Lutzomyia longipalpis) and triatomine bugs (Rhodnius prolixus) towards deriving insect vectors refractory to disease agents mediated by CRISPR-Cas9 gene drive

Vector-borne pathogens Leishmania and Trypanosoma cruzi cause the devastating human diseases leishmaniasis and Chagas disease respectively. We will contribute to a new strategy to prevent these diseases by genetically modifying insect vectors, sand flies and triatomine bugs, leading eventually to transgenic insects that are resistant to disease agents.

We will use two different transgenic approaches, PiggyBac and CRISPR-Cas9. PiggyBac involves semi-random insertion of exogenous DNA into the genome. CRISPR-Cas9 is a highly targeted method to manipulate genes. Microinjecting insect embryos with PiggyBac plasmids will produce insects that express fluorescent markers for subsequent CRISPR-Cas9 knockout experiments. Knockout of fluorescent markers demonstrate that system components are functional and will allow us to precisely target genes of interest. We will create knockouts of endogenous genes that are either non-essential or important in sustaining infection in insect vectors. Insertion and expression of exogenous DNA will encourage inheritance to offspring at levels above Mendelian inheritance.

The findings of this study will help in the development of approaches that can interrupt the transmission of diseases by these vector-borne pathogens.

2016 Round 6

Dr Nizar Batada

University of Edinburgh

QMAT-seq: a novel CRISPR/Cas9 based assay for studying DNA-repair-associated mutations

Mutations are a root cause of cancer. In skin and lung cancers, they often result from exposure to environmental mutagens such as cigarette smoke or UV light. However, in other cancers, their causes remain unexplained. Restoration of DNA repair in mice with BRCA1 deficiency prevents tumour formation revealing that defective DNA repair contributes to cancer. The alternative non-homologous-end-joining (A-EJ) pathway has recently been discovered and has been shown to promote genome instability and therapy resistance in BRCA1-deficient cancers but only few components of the A-EJ pathway are known. In addition the causes of their activation remain elusive. Inhibition of A-EJ could be an effective therapy for cancers associated with DNA repair deficiency.

In pump-priming experiments that will establish proof of concept, I will develop a novel quantitative laboratory assay for A-EJ employing CRISPR/Cas9 genome editing, high-throughput sequencing and a machine learning algorithm. My long-term goal is to elucidate A-EJ regulation, to identify new members of the A-EJ pathway and to define its mutational footprints that will serve as a biomarker of DNA repair deficiency.

The outcomes of this seed funding will enable me to study A-EJ in cancer and its potential in cancer stratification and personalised therapy.

Dr Amaya Bustinduy

London School of Hygiene and Tropical Medicine

Validation of home-based cervical and vaginal self-sampling for the diagnosis of female genital schistosomiasis (FGS) in Zambian women with and without HIV seroconversion

Female genital schistosomiasis (FGS) affects more than 45 million women worldwide and in sub-Saharan Africa it is possibly the most underestimated gynaecological affliction caused by an infectious agent, the water-borne parasite S. haematobium (Sh). FGS is associated with infertility with compelling evidence of increased HIV prevalence in women infected with Sh. FGS diagnosis is extremely challenging as it relies on expensive equipment that is seldom available in areas with limited resources. The overall aim of this project is to test the performance and acceptability of home-based genital self-sampling procedures for the detection of Sh DNA, and to validate novel molecular diagnostic assays to diagnose FGS in Zambia, with and without HIV seroconversion. The project will also explore novel biomarkers of inflammation from vaginal fluid as potential markers of disease severity.

This study is a proof of principle study that can lead to future expansion of community-based diagnosis for FGS. The study has high feasibility as it will take advantage of resources nested in the largest HIV longitudinal cohort study ever conducted to date. Results can provide the groundwork for the design of large cluster randomised trials for the community diagnosis of FGS.

Dr Adam Byrne

Imperial College London

How does airway macrophage glycolytic reprogramming contribute to fibrotic lung disease?

Idiopathic pulmonary fibrosis (IPF) is the most common form of interstitial lung disease and is associated with high mortality. IPF therapies are limited and there is a significant need to understand the mechanisms involved. Airway macrophages (AMs) are the most abundant immune cell in patients with IPF. Recent work demonstrated that IPF-AMs are characterised by high expression of glucose transport molecules but it is unknown whether AM-glycolytic programming contributes to the pathogenesis of lung fibrosis.

My preliminary data indicates that IPF-AMs have a unique metabolic phenotype, characterised by reduced succinate and elevated Irg1 expression, a negative regulator of the citric acid cycle via itaconic acid. I hypothesise that AM glycolytic reprogramming contributes to the pathogenesis of lung fibrosis and manipulation of AM metabolism via itaconic acid, and can ameliorate the disease. I will determine AM metabolic signatures in the fibrotic lung using metabolic assays in IPF-AMs and murine models. Then I will assess Irg1 and itaconic acid levels in patients’ broncoalveolar lavage (BAL)/lung biopsies. I will use siRNA knockdown in IPF-AMs and Irg1-/- mice.

This work will provide proof of principle for development of therapies which correct AM-metabolic dysregulation during IPF. 

Dr Amanda Coutts

Nottingham Trent University

The role of autophagy in cancer cell motility

We will investigate the role of autophagy in cell motility taking advantage of novel prostate cancer cell lines that mimic stages of disease progression (including EMT and metastasis). In particular we will address the role of the actin nucleator JMY, a p53 co-factor that affects of autophagosome formation, cell motility and survival in autophagy-mediated effects on cell survival and the role of actin nucleation.

We will assess autophagy levels in cancer cell lines and correlate with cell motility and invasion also assessing cell survival and adhesion/motility events, using impedance measurements to distinguish between effects on proliferation vs motility. We will look at the impact of JMY on autophagy-mediated motility and the impact of modulating autophagy levels on cell motility during various stages in autophagosome formation.

Dr Abbas Dehghan

Imperial College London

Applying genome-wide association study to prioritise compounds in untargeted metabolomics for Mendelian randomisation studies

Untargeted metabolomics provides an unprecedented opportunity for epidemiological studies to identify novel chemical compounds that play a role in complex disorders. Studying the causal role of compounds, however, remains challenging. Use of Mendelian randomisation (MR), a well-established approach to address causality in observational studies, depends on strong genetic determinants of the metabolites of interest. The genome-wide association study (GWAS) has so far been unsuccessful in identifying genetic factors since the computational burden of studying millions of SNPs in relation to thousands of metabolites is huge.

I aim to adapt a novel method used primarily in brain imaging, to metabolomics data and perform GWAS on thousands of features identified by various assays of untargeted NMR and mass spectrometry (MS) metabolomics. I will use data from three large epidemiologic studies, MESA, The Rotterdam Study and Airwave (n=10,000). The analysis will highlight metabolic features that are strongly regulated by genetic variants and will identify genetic variants that could be used as instrumental variables in MR analysis.

The results of this project will allow me to perform MR studies on a selected set of metabolic features in relation to various complex disorders in my future research.

Dr Karel Dorey

University of Manchester

Molecular mechanisms regulating spinal cord regeneration

The transcriptome of spinal cord injuries (SCI) have been reported from different species such as mouse, rat, zebrafish and xenopus. These experiments led to a consensus that the immune response has a negative effect on the recovery following SCI and the characterisation of ‘regenerative-associated genes’ (RAGs). However, these experiments have yet to uncover the intrinsic mechanisms promoting spinal cord regeneration.

To uncover the genes and mechanisms upregulated during spinal cord regeneration, we will compare the transcriptome of the spinal cord three days after amputation when spinal cord re-growth begins in wild type xenopus tadpoles and those with Foxm1 genetic knock outs. Foxm1 is a transcription factor that we have identified as being specifically expressed in the regenerated spinal cord and is required for efficient regeneration. This is a novel approach as only a handful of transcriptomic experiments of neuronal regeneration using knock-out models have been reported.

This project will generate a dataset of new molecular players operating during spinal cord regeneration. This novel dataset will provide us with ample preliminary data for further exploration of the mechanisms of spinal cord regeneration, in particular its promotion in both amphibians and mammals.

Dr Annette Erhart

Medical Research Council Unit The Gambia

The hidden burden of rheumatic heart disease in the Gambia

Rheumatic heart disease (RHD) remains the leading cause of cardiac death and disability in children and young adults worldwide, with global estimates of 34 million people affected and 345,000 deaths, mainly in sub-Saharan Africa. RHD occurs after cardiac valvular damage caused by an exaggerated immune response to group A streptococcus infections, usually during childhood and adolescence. Complications include heart failure, atrial fibrillation, stroke, infective endocarditis and adverse pregnancy outcomes. Although RHD can be prevented using penicillin, there are numerous poorly understood barriers to effective control programs. In the Gambia, the RHD burden is probably high and yet there is no reliable data available and there is no control activity currently in place.

We will generate baseline information on RHD among children (aged 5 to 19 years) and pregnant women. This baseline study will include a population-based study with echocardiographic screening of children and pregnant women, and a hospital-based review of all RHD cases currently managed by the health services.

This study will be a first step towards a much larger multidisciplinary research proposal whose results may be used for the formulation of a nationwide RHD control program, and it will foster regional research collaborations on RHD control.

Dr Oliver Haworth

Queen Mary University of London

Aryl hydrocarbon receptor interacting protein (AIP) protection of Bcl-6

Aryl hydrocarbon receptor interacting protein (AIP) is a co-chaperone molecule that can bind to many proteins including heat shock protein-90 (Hsp90). We found that AIP conditionally deleted in B cells resulted in decreased germinal centre (GC) B cells and decreased expression of the proto-oncogene B cell lymphoma-6 (Bcl-6) that is over-expressed in many aggressive B cell lymphomas that are difficult to treat with conventional drugs. We found that AIP could bind to Bcl-6 and treatment of AIP-deficient B cells with a proteasome inhibitor increased Bcl-6 expression indicating that AIP protects Bcl-6 from being degraded, but it is not known how this occurs. AIP might function as a tumour promoter by protecting Bcl-6 from degradation.

We will study the molecular mechanisms by which AIP regulates Bcl-6 and test the effectiveness of inhibiting AIP on tumour growth in vivo. 

AIP would be a therapeutically attractive target, as it would lead to the loss of Bcl-6 and the treatment of aggressive B cell lymphomas.

Dr Noboru Komiyama

University of Edinburgh

Investigating novel therapeutic targets for the treatment of major depressive disorder

Major depressive disorder (MDD) affects about one in five people worldwide, and currently there are only limited pharmacological treatments available. Ketamine, a non-competitive NMDA receptor (NMDAR) antagonist, has been shown to have rapid-acting antidepressant effects in people with MDD, including those with treatment-resistant depression, but it can have psychotic side-effects It is important to understand the molecular mechanism underlying ketamine’s antidepressant effect so that better therapeutics can be developed. Evidence from in vitro studies suggests that ketamine is a partial channel blocker of NMDARs. However, our recent results using mouse lines containing mutations in the NMDAR cytoplasmic domain (CTD) show that in vivo the rapid ketamine behavioural effect is mediated by the NMDAR CTD, not channel blockade.

We want to investigate the long-lasting antidepressant effect of ketamine in these knock-in mice. With biochemical analysis of their ketamine-treated brains, we want to elucidate underlying molecular pathways and molecular targets among the proteins forming complexes with the NMDAR CTD. We plan to investigate the dose-dependent effect of ketamine (psychotomimetic vs. antidepressant) with a novel synaptic activity reporter (Arc-Venus mouse) combined with NMDAR CTD mutants.

Our goal is to generate solid preliminary data for future funding applications and our findings will help with the development of better therapies for MDD.

Dr Xinhui Ma

University of Hull

Three dimensional analysis of maxillofacial growth in patients with cleft lip and palate

Cleft lip and palate is the most common facial birth defect, affecting one in 700 babies with both functional problems – such as feeding, breathing, speech and hearing – and aesthetic problems that can lead to psychosocial and psychological problems. Poor maxillary growth affects nearly all patients with the condition and can result in substantial maxillary retrusion requiring orthognathic surgery and associated orthodontic treatment in early adulthood. Surprisingly, there is a lack of evidence supporting this strategy of late intervention. The absence of data characterising the precise anatomical location, vectors, velocity and magnitude of maxillary growth should be addressed as a priority to determine the optimum timing for surgical intervention.

We will develop, test and validate three-dimensional methodologies to quantify maxillofacial hard tissue growth and related soft-tissue changes. This pilot work will provide three-dimensional geometric morphometric algorithms and computational methods with corresponding benchmark software tools for a larger clinical study which will determine the full nature and extent of hard-tissue maxillary growth and related soft-tissue changes during late adolescence.

Our findings will identify if and when earlier maxillary advancement surgery could be carried out to expedite correction of dentofacial deformity and minimise the associated significant psychosocial problems.

Dr Fiona Murray

University of Aberdeen

Uncovering the pharmacology of GPR75: role in pulmonary arterial hypertension

Pulmonary arterial hypertension (PAH) is a devastating condition that if left untreated will leave the patient with an average life expectancy of less than three years from diagnosis. PAH is associated with proliferation of pulmonary artery smooth muscle cells (PASMC), which contributes to increased vascular resistance. The maintenance of the low vascular tone in the pulmonary circulation is dependent on the interaction of circulating and locally produced mediators, many of which act via G protein-coupled receptors (GPCRs). The accessibility of GPCRs on the plasma membrane, their tissue-selective distribution and role in regulating physiological functions make them excellent pharmacological targets.

We used an unbiased approach (GPCR real-time-PCR arrays) to profile GPCR expression in PASMC isolated from controls and patients with PAH. Our data revealed that PAH-PASMC uniquely express an orphan GPCR (whose endogenous ligand has not yet been identified) compared with control-PASMC, namely GPR75. We aim to validate GPR75 as a novel target for PAH by uncovering its pharmacology and the functional significance and expression of receptor variants in PAH and by elucidating its physiological role in vivo.

Our hypothesis is that GPR75 is a key regulator of PASMC proliferation that characterises PAH and this will be a new target or genetic risk factor for the disease.

Dr Filippo Prischi

University of Essex

Understanding how RSKs regulate transcription factors in triple negative breast cancer

There is a current gap in therapeutic approaches towards triple negative breast cancer (TNBC) and unlike other breast cancer subtypes, it lacks a recommended chemotherapy treatment. It is therefore essential to better characterise the signalling pathways that drive tumour growth to identify novel therapeutic methods.

I will characterise a novel drug target, the p90 ribosomal protein S6 kinase (RSKs) family. This family consists of four human isoforms (RSK1-4), which are multifunctional effectors of the ERK/MAPK signalling cascade. In cancer, RSK isoforms perform non-redundant functions and, more precisely, in TNBC RSK1/2 promote tumour metastasis, while RSK4 is a tumour suppressor protein. These opposite roles are linked to the ability of RSKs to differentially modulate gene expression by directly regulating transcription factors (TFs) activity. However, the mechanism that allows RSKs to recognise and modulate the activity of different TFs and initiate different signalling pathways, is still unclear. The aim of this project is to understand which RSK regulates which TF using a combination of biophysical, enzymatic and cellular studies.

The findings of this study will improve understanding of cell signalling and cell survival, which will form a foundation for the design of more specific inhibitors.

Dr Inga Prokopenko

Imperial College London

Identifying novel omics biomarkers for personalised type 2 diabetes patient profiling and disease prognosis tracking

Current treatment strategies for type 2 diabetes (T2D) are mostly uniform, contributing to inefficient long-term treatment and development of complications. T2D care could be improved using more personalised approaches by further classifying patients based on novel omics biomarkers, including those of disease progression, identified via longitudinal follow-up and genomic profiling. Missingness in phenotype data at one or more time points brings additional limitations for analyses of multiple traits simultaneously.

I will use a ‘reverse regression’ approach that allows analysis of multiple correlated phenotypes jointly to evaluate longitudinal effects, and I will implement an efficient imputation of phenotypes to deal with the missingness issue. I will develop an efficient approach and a software tool for longitudinal high-dimensional omics data analysis that will identify sets of omics biomarkers for personalised longitudinal T2D patient profiles for improved tracking of disease progression.

This project will lead to a large grant application tackling longitudinal multi-omics analyses in large-scale datasets for longitudinal disease prediction.

Dr Andrew Renault

University of Nottingham

Unexpected functionalities of a ribosomal protein in embryonic patterning

Ribosomes are cellular machines that synthesise proteins in all cells. We have isolated a drosophila line in which one of its ribosomal proteins, RpL39, is mutated. Mutant embryos have a specific axis-patterning defect which results from reduced levels of one particular Hox protein, AbdominalA (AbdA). This suggests that AbdA requires a currently unrecognised functionality of the ribosome for efficient translation.

We will identify this functionality by dissecting the AbdA coding sequence to determine the wider subset of affected proteins. We will also test if RpL39 is acting as a component of the ribosome and identify its precise role.

This seed work seeks to understand a ribosomal protein at a fundamental level and lays the foundation to explore the wider disease context by examining conservation of RpL39 function in humans. One hypothesis is that RpL39 is critical for co-translational protein folding, which is highly relevant to human proteopathies such as Alzheimer’s and prion diseases. AbdA contains a polyglutamine tract, a feature found in several human proteins implicated in disease, and we will examine if RpL39 is critical for expression of polyglutamine tract proteins.

Dr Daniel Rico

Newcastle University

Sex-dependent gene regulation in immune cells

Sex is a fundamental but frequently overlooked biological characteristic of humans and model organisms that affects immune responses.

I aim to develop integrative bioinformatics approaches to interrogate publicly-available transcriptomics and epigenomics datasets to delineate the sex-determined molecular mechanisms that modulate the immune system. My group will generate models of the sex- and cell-specific gene regulatory networks for the major blood cell types where data is available. We will study how these sex-specific networks derived from healthy cells are influenced by infections and other disease conditions. We will develop new bioinformatics tools to integrate the sex-specific transcriptional programs with diverse sources of epigenomics information to identify the distinct chromatin configurations that underlie the different immune responses in men and women.

These results will provide the necessary framework to understand the molecular differences in men and women in response to infections, autoimmune disease and in immunodeficiencies. This will provide new insights underlying disease pathogenesis and inform personalised therapy for men and women.

Dr Christopher Sibley

Imperial College London

Master regulators; from defining target networks to interpreting the impact of genomic variability on genome-wide activity

Transcription factors (TFs) are DNA-binding proteins which control the transcription – and hence expression – of their gene targets. The fate of a transcribed RNA as it proceeds from transcription to degradation is then largely determined by interactions with RNA-binding proteins (RBPs). TFs1s and RBPs3s each regulate hundreds to thousands of targets. TFs or RBPs are recruited to specific loci through recognition of specific features, such as sequence motifs, with these features widely dispersed across the genome/transcriptome. TFs and RBPs can collectively be considered master regulators (MRs). MR have fundamental roles in cell biology, and perturbed MR activity can contribute to disease aetiology. However, defining functional MR-target networks (interactomes) remains difficult.

I propose an innovative workflow to infer interactomes of all expressed MRs from large-scale transcriptomic datasets. My  key project goals will be to validate selected interactomes) exploit interactomes to interpret RNA signatures of selected disease and developmental paradigms, and explore how genomic variation affects MR activity at defined targets.

This project will seed numerous spin-off projects and generate substantial pilot data for future studies.

Dr Carole Torsney

University of Edinburgh

Accessing the allodynia circuitry for persistent pain

Chronic pain affects about 30% of the population and significantly reduces quality of life because treatments are ineffective. Allodynia or touch-evoked pain is a particularly debilitating chronic pain symptom. A significant challenge to improving pain management is that the spinal neural circuitry that mediates allodynia is poorly understood. Recent efforts to characterise this circuitry have focused on traditional inflammatory and neuropathic pre-clinical pain models. However, these models do not emulate the chronicity of clinical pain. More recently developed hyperalgesic priming models mimic the transition from acute to chronic pain and are therefore more suited to study the allodynia circuitry relevant for persistent pain. Moreover, the allodynia circuitry in hyperalgesic priming models may actually be different because the underlying pathological plasticity is distinct from that identified in classical pre-clinical pain models.

I will determine whether Fos-EGFP transgenic mice can be used to gain morphological, electrophysiological and genetic ‘access’ to allodynia circuitry, in the clinically relevant persistent pain model of hyperalgesic priming.

This approach will generate pilot data for a larger grant application to characterise and facilitate future therapeutic targeting of allodynia circuitry.

Dr David Tumbarello

University of Southampton

Investigating the mechanisms of Parkin-mediated mitophagy

Determining how cells maintain homeostasis in times of stress is vital to understanding a wide-range of disorders, from neurodegenerative diseases to cardiomyopathies. Autophagy is a catabolic cytosolic pathway that functions to degrade damaged organelles and misfolded proteins, while providing a protective mechanism under stress. Mitophagy, the selective autophagic pathway for mitochondria limits oxidative stress by degrading damaged mitochondria through a mechanism involving ubiquitylation and recruitment of autophagic machinery. One mechanism of mitophagy, which is dysregulated during Parkinson’s disease, is the PINK1-parkin pathway.

We will identify and characterise regulators of parkin which facilitate its recruitment to mitochondria. We will focus on an adaptor protein complex Tollip-Tom1, which has been suggested to be linked to this process and which functions to regulate trafficking along both the endolysosomal and autophagic pathways. We will use microscopic imaging and biochemical assays to dissect the spatiotemporal regulation of parkin-mediated mitophagy after targeted loss of function of Tom1 and Tollip. In addition, we will use CRISPR-Cas9 technology, coupled to cDNA reconstitution experiments, and primary patient-derived fibroblasts to understand mechanisms of parkin recruitment after mitochondrial damage.

The outcomes will provide crucial mechanisms that illustrate how cells regulate PINK1-parkin mediated mitophagy to maintain their health.

Dr Christian Wozny

University of Strathclyde

Unveiling the role of the subiculum in processing and routing hippocampal information

Hippocampal formation has a crucial role in learning and memory that is well recognised but the role of the subiculum (SUB) has received  little attention. The SUB occupies a pivotal role between the hippocampus and other cortical areas and it controls and routes most of the hippocampal information. The SUB has been implicated in many diseases, such as Alzheimer’s and epilepsy, however, still little is known about the cellular, molecular and synaptic features of subicular neurons.

We aim to investigate molecular marker genes of different types of subicular pyramidal neurons and to understand the flow of neuronal information from the hippocampus to the neocortex. We hypothesise that VGlut2-expressing subicular pyramidal neurons mediate the interaction between the hippocampus and the prefrontal cortex. By using powerful optogenetic tools we aim to label, identify and manipulate subicular pyramidal neurons.

Our results will be of interest to basic neuroscientists who wish to understand the role of the hippocampus in memory formation, and also to clinicians aiming to understand the cause of cognitive decline in patients suffering from neurodegenerative diseases.

2016 Round 5

Dr Darius Armstrong-James

Imperial College London

Clinical determinants of macrophage necrosis in pulmonary aspergillosis

Pulmonary aspergillosis is an opportunistic infection that affects 30% of adults with cystic fibrosis. Our studies show that calcineurin signalling regulates macrophage cell death during Aspergillus fumigatus infection and it is excessive in cystic fibrosis. Furthermore, cystic fibrosis isolates of Aspergillus fumigatus have enhanced pH and cell wall tolerance, suggesting macrophage adaptation. My goals are to determine if clinical Aspergillus fumigatus isolates induce higher rates of macrophage cell death, and if patients with cystic fibrosis have exaggerated macrophage cell death responses to infection.

We will define the necrotic potential of clinical strains of Aspergillus fumigatus. Patients with cystic fibrosis patients and environmental isolates will be compared for their ability to induce human macrophage necrosis in vitro. We will characterise Aspergillus-dependent macrophage necrosis in cystic fibrosis. Macrophages from patients with cystic fibrosis and control patients will be compared for their ability to induce programmed necrosis during Aspergillus infection. We will also define the role of macrophage cell death in vivo. Cystic fibrosis and environmental isolates will be compared for their ability to induce macrophage necrosis in vivo in murine pulmonary aspergillosis.

These studies will determine whether macrophage cell death responses to Aspergillus fumigatus are influenced by fungal strain phenotype and host immunity in cystic fibrosis.

Dr Stephen Butler

University of Loughborough

Real-time monitoring of kinase activity using luminescent chemical probes

Kinase enzymes represent one of the most promising targets for drug discovery in oncology. The search for new kinase inhibitors requires robust, sensitive, affordable assays for kinase activity. Most commercial kinase assays are restricted to end-point measurements, which give no kinetic or mechanistic information and require either expensive antibodies to recognise the phosphopeptide or chemically modified substrates. Crucially, there is no low-cost method available for continuous measurement of kinase activity, which limits our understanding of kinase kinetics.

We will create probes that provide a unique luminescent signal that precisely indicates the ratio of ATP/ADP in real time. We will develop luminescent probes that can distinguish between ADP and ATP at physiological pH, thereby allowing continuous measurement of the kinase-catalysed conversion of ATP to ADP. We will harness the long luminescence lifetime of europium probes to enable time-gated detection and removal of autofluorescence from peptides and proteins. We will also measure the activity of selected kinases by varying the amount of enzyme, substrate and co-factor systematically. This will require optimisation of probe sensitivity and calibration of luminescent response.

Once these parameters have been optimised, we will use our assay to examine selective inhibitors of kinase activity. Our findings could help with drug discovery in oncology.

Dr Stella Chan

University of Edinburgh

In search of vulnerability mechanisms for adolescent depression

Depression in adolescence can predict lifelong risk for mental and physical illness. Treatment outcomes are poor with a high relapse rate. We urgently need to develop more effective strategies for the detection of illness and early intervention to prevent depression from developing into a chronic and recurrent pattern.

This study aims to identify vulnerability markers for adolescent depression. The focus will be on potentially modifiable mechanisms; one strong candidate is neural-cognitive biases in emotional processing. This study will recruit 300 adolescents and their risk will be indexed by neuroticism, a robust heritable risk factor for depression. Neural-cognitive tasks will be used to assess the way they process emotional information across attention, interpretation and memory. Cortisol levels will be measured as a biological indicator of stress reactivity. This cross-sectional study will identify which emotional processing biases are most strongly associated with risk for adolescent depression.

Findings will establish a significant evidence base and feasibility for a future cohort study that will examine how these biases can be used to predict adolescent depression longitudinally. Identification of vulnerability markers before the onset of illness will potentially transform prevention and intervention by providing an objective screening tool and potential targets for new treatments.

Dr Joseph Cockburn

University of Leeds

Structural studies on CEP290, the ciliary gatekeeper

Cilia are the antennae of eukaryotic cells. They project from the apical surface of most eukaryotic cells and they are able to sense and transduce environmental signals from sources, such as light, molecules, proteins and fluid flow. The cilium possesses a distinct protein and lipid composition relative to the rest of the cell. This compartmentalisation is maintained by a structure at  the base of the cilium called the transition zone (TZ) which acts as a selectively permeable barrier to control the exchange of material between the cilium and the rest of the cell. The TZ comprises more than 20 polypeptide species. Mutations in TZ genes result in a number of inherited disorders characterised by retinal, renal and cerebral pathologies. However, the molecular mechanisms underlying these diseases are elusive because we lack a basic understanding of the structure and function of the TZ and most of its constituent proteins.

CEP290 is a major structural component of the TZ3 and is reported to bind to a number of other TZ components. For this proposal I will perform a structural and biochemical investigation into CEP290.

This research will give us a basic understanding of the structure and function of the TZ molecule.

Dr Michaela Dewar

Heriot-Watt University

When less is more – alleviating forgetting by reducing interference

During wakefulness our memory system encodes memories of sensory input and strengthens recently formed memories. For example, while reading this your memory system is encoding memories and attempting to consolidate memories formed earlier. Since encoding and consolidation have overlapping neural pathways, the memory system must minimise interference between encoding and consolidation. The mechanisms by which this is achieved are poorly understood. However, we need to identify them, both because of their fundamental importance in memory processing and because their malfunction could play a key role in amnesia.

We hypothesise that the healthy memory system minimises interference by switching between encoding and consolidation, and amnesia can be caused by defective switching, leading to heightened memory processing and interference. This deviates from the view that memory processing in amnesia is underactive. We will develop human neuroimaging protocols to test our hypothesis and conduct preliminary testing of our hypothesis in healthy people and establish the cognitive factors that determine the switch between encoding and consolidation.

This project will steer an interdisciplinary research programme that will shift our understanding of consolidation and reveal new avenues for memory therapeutics.

Dr Maria Dimitriadi

University of Hertfordshire

Spinal muscular atrophy: identification of pathways critical for SMN function

Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder primarily affecting children. It is caused by depletion of the ubiquitously expressed survival motor neuron (SMN) protein. Studies in people with SMA and murine SMA models have shown that increased SMN protein levels are associated with milder forms of the disease. Identifying the pathways and drug compounds that increase SMN levels would suggest a direct therapeutic strategy for treating SMA patients. However, another complementary approach could be considered: the identification of pathways that act independently of SMN function and can help correct levels of SMN.

Manipulation of these pathways can increase the effective activity of the SMN protein already present in patients with SMA. I have recently identified conserved genetic pathways that affect SMN neuromuscular function on a previously defined invertebrate Caenorhabditis elegans (C. elegans) model of SMA. In this study I will use the genetic tools of C. elegans to dissect the mechanism(s) by which the cross-species pathways control SMN synaptic function.

The ultimate goal is to identify novel therapeutic avenues that will attenuate SMA in mammalian models.

Dr Nicholas Hannan

University of Nottingham

Towards personalised therapies for Crohn's disease using primary intestinal enteroids

An estimated 620,000 people suffer from inflammatory bowel disease (IBD) in the UK. Poor access to primary tissue and a lack of animal models that faithfully reproduce the human condition has left us with an inadequate understanding of how to diagnose and treat IBD. Crohn’s disease (CD) is a debilitating IBD where chronic inflammation leads to intestinal perforation that requires surgical removal.

We propose to apply our recently published intestinal culture platform to model CD to generate an in-vitro intestinal enteroid model of CD. There are currently no reliable in-vitro models of CD. To create a new model of CD we will generate ‘mini-intestines’using intestinal biopsy from patients with CD to create a platform to study microbiota dysbiosis. Changes in the types of bacteria in the intestine is believed to be important in the initiation and progression of CD, however this has not been well studied.

This study will validate a bacterial injection platform into CD enteroids that can be used for future studies on microbiota dysbiosis.

Dr Neil Hardingham

Cardiff University

The effects of DISC1 disruption on the prefrontal cortex

Dysfunction of the prefrontal cortex is involved in schizophrenia and other psychiatric disorders. Therefore understanding the circuitry of the prefrontal cortex and how it is affected in psychiatric conditions is vital. One of the properties affected in psychiatric disorders is synaptic plasticity using a transgenic mouse with inducible disruption of DISC1 signalling. We have revealed a critical period for the establishment of mature properties, including synaptic plasticity. This coincides with a dynamic period of dendritic growth and spinogenesis. We want to establish whether there is a similar critical period in the prefrontal cortex.

Preliminary data suggest that a P7 DISC1 disruption has an effect on prefrontal cortex plasticity. Once this critical period is established in more detail we would like to examine effects of DISC1 disruption on the cellular properties and the cortical circuitry using imaging techniques. We have used RNAseq to identify downstream targets of P7 DISC1 disruption in barrel cortex and are keen to repeat this in the prefrontal cortex and attempt to rescue synaptic plasticity by agonising target molecules.

Our results will provide insight into the role of DISC1 in the prefrontal cortex and form a basis for subsequent studies

Dr Aidan Horner

University of York

Extracting patterns across memories to guide decisions

I will investigate how we use past experience to guide behaviour and how this process breaks down in specific patient populations.

I will do this by developing a novel experimental-computational tool to understand how people transform memories of previous events into generalised models of the world that allow them to behave appropriately in the future. For past experience to guide behaviour, we need to extract patterns across a set of events. These patterns allow us to predict what will happen in novel but related situations. I will use a new experimental technique in healthy humans (based on rodent research), where participants are required to extract patterns across a set of past events in order to make accurate predictions about future events. I will build computational models to predict and explain the participants’ behaviour. The models will assess what pattern has been extracted and how this differs from the pattern that would optimise future predictions. Critically, when a participant does not behave appropriately, the experimental-computational technique will reveal what is impaired and why.

This technique will be used to pinpoint impairments in memory-guided decision-making.

Dr Joanne Knight

Lancaster University

Multiple lines of evidence will improve power to identify genes involved in complex traits

Genetic variants associated with complex disorders have been identified using genome-wide association studies. However, the specific variant that has an impact on the trait often remains elusive. In-silico methods can help prioritise which variants should be used in functional studies.

I will use two novel methods to prioritise variant selection. I will explore published literature using Google’s SyntaxNet which overcomes limitations such as non-random selection of manually curated literature and unreliability of data in machine-curated literature. I will identify DNA sequence motifs that differ in frequency between regions with and without genetic risk variants and use such motifs to prioritise variants for follow up. I will publish power studies of both of these approaches using real data and create a tool that uses these two data sources to identify variants likely to be involved in complex disease.

This research will lead to the Integration of functional evidence based on previous work with text-based evidence and sequence motifs, the integration of pathway-based analysis and the application of the variant prioritisation technique to a large number of datasets.

Dr James McCullagh

University of Oxford

Metabolomics for therapeutic discovery: how do Isocitrate Dehydrogenase (IDH1) mutations impact on cellular metabolism?

The metabolic consequences of genetic and proteomic changes are widely implicated in cancer but remain poorly understood. D-2-hydroxyglutarate (D-2-HG) is the earliest known tumour-forming small-molecule reporter in glioma/glioblastoma, breast cancer, sarcoma and leukemia. The in vivo source of D-2-HG is a mutant form of the cytosolic enzyme isocitrate dehydrogenase (IDH, isoforms 1 and 2). However, it is unclear whether the IDH mutation, and subsequent D-2-HG production, is a consequence of the tumourigenic phenotype, or is directly driving the formation of tumours. Understanding the association of IDH mutations with changes in metabolism is important for understanding disease aetiology and development of early-intervention chemotherapy.

We will investigate the impact of IDH mutations and elevated levels of 2-HG on metabolism in IDH mutant cells using a mouse model and patient-derived tissues including bio-fluids using a novel metabolomics platform combined with stable isotope tracers to elucidate metabolic flux and pathway analysis. We will determine a robust molecular phenotype elucidating mutant-specific changes to metabolic pathways.
The aims of future work will be to use knowledge of aberrant metabolism to develop and test therapeutic interventions targeting IDH mutant-specific biochemistry.

Dr Joana Neves

King's College London

A novel system to study intestinal lymphocytes

The maintenance of intestinal homeostasis, which depends on a delicate balance between the immune system, the intestinal epithelium and the gut microbiota, has local and systemic implications for health, and gut inflammation contributes to multiple diseases, including inflammatory bowel disease (IBD).

I propose to validate a novel in vitro system that mimics the gut microenvironment and enables detailed mechanistic studies on the crosstalk between lymphocytes, the epithelium and the microbiota. Innate lymphoid cells (ILCs) have been shown to regulate intestinal homeostasis and inflammation and the epithelium and the microbiota interact closely with ILCs, controlling their differentiation and function. I will characterise the molecular interactions between ILCs, the epithelium and the microbiota. My pilot data show that three-dimensional cultures of intestinal epithelial cells (IECs), called intestinal organoids, support the development of ILCs. I propose to fully characterise the ILCs that develop in these co-cultures and to identify and validate key molecular pathways mediating the crosstalk between ILCs, IECs and the microbiota.

This will form the basis for larger studies and grant applications. Such studies are an essential foundation for future efforts aiming to manipulate interactions between these three compartments in order to promote intestinal homeostasis.

Dr Praveetha Patalay

University of Liverpool

Symptom networks in childhood: a new approach for understanding the structure and development of psychiatric disorders

Psychiatric disorders have been traditionally considered latent dimensions or factors that are represented by a set of symptoms. However, the adequacy of this approach is being questioned because it does not account for the inter-relationships between symptoms and their dynamic causal nature. Researchers have started visualising disorders as networks of symptoms, using analytic methods akin to mapping networks of people, leading to interesting insights for classification of psychiatric disorder in adults.

Given that precursors for psychiatric disorder are evident in childhood, we propose to investigate the network of symptoms that begin in early childhood and observe their evolution in childhood and adolescence. We will investigate symptom networks in disorders such as depression and hyperactivity, symptom networks across domains to identify comorbidities, and differences in the network based on gender, exposure to maternal depression in early childhood and between non-clinical and clinical samples.

This study will establish the suitability, feasibility and utility of analysing child symptom data and determine if the method offers new insights into the aetiology and development of psychiatric disorder.

Dr Frédéric Piel

Imperial College London

Public health surveillance of chronic diseases: suitability of spatio-temporal methods

Health surveillance is better established for infectious than non-communicable diseases (NCDs). The recent recognition of clusters of congenital anomalies (microcephaly) associated with Zika virus highlights the need and importance of a knowledge and understanding of disease occurrence in order to identify data signals in space and time and how less dramatic increases in incidence could be detected. The NHS has one of the most detailed database of health records worldwide, offering a unique opportunity to test and develop methods to detect spatio-temporal signals such as disease clusters or unusual trends. Early detection of such data signals is essential from a public health perspective to warrant further investigation of potential risk factors, including environmental pollutants and extreme climatic events, and to implement relevant prevention or protection measures.

Building on the unique expertise of the UK Small Area Health Statistics Unit, we will test the strengths and limitations, including accuracy and interpretability of results, of existing enhanced surveillance tools using data on known past signals; to assess their capacity to detect unidentified clusters and to define the optimal approach for prospective surveillance of NCDs.

The research findings could help improve monitoring and prevention of NCDs.

Dr Carla Robles-Espinoza

Universidad Nacional Autonoma de Mexico

Genomics of acral lentiginous melanoma

Melanoma is the most aggressive type of skin cancer, causing about 75% of deaths from dermatological cancer. Acral lentiginous melanoma is the most common subtype of melanoma in mixed Latin American populations, but very few genomes and exomes from people of European descent have been analysed across several studies. This means that the genomic landscape of acral lentiginous melanoma is currently unknown and genomic analyses on strong predictors of survival such as ulceration are lacking. Additionally, no genes are known to increase the risk to this melanoma subtype.

We propose to target-sequence and analyse 550 tumour/normal acral lentiginous melanoma pairs and, as a comparison set, 500 sun-induced disease samples that have been collected over 35 years at the National Cancer Institute of Mexico. We will define the somatic landscape of acral lentiginous melanoma, looking particularly at the site of presentation (acral versus non-acral)  and whether it influences driver genes and mutation spectra, what somatic mutations co-occur in tumours and which are mutually exclusive. We will also look at how somatic mutations influence patient outcome and determine where genomic aberrations exist that are predictive of ulceration in acral lentiginous melanoma and whether there are germline genetic factors influencing susceptibility to acral lentiginous melanoma.

Dr Amit Sachdeva

University of East Anglia

Modulating properties of antibodies using unnatural amino acids

Advances in molecular biology and genetics have greatly enhanced the production of proteins with unnatural amino acids having diverse chemical properties. Proteins from several classes are now being modified using unnatural amino acids that can add to or alter the natural properties of the protein. Antibodies, with their wide range of applications through molecular biology to medicine, present an attractive class of proteins whose properties may be modulated using unnatural amino acids.

We want to develop photoactive antibodies that can be controlled using light. Such antibodies could be used as research tools to study antibody-mediated processes, and also have the potential to be used in antibody-based photoactive therapeutics. We will also develop antibody-based optical switches – antibodies that become fluorescent upon binding to target antigens.

These switches would overcome a major limitation of current antibody-based detection methods, where immobilisation of antigen or antibody to a surface is required. Such optical switches are expected to have applications in cancer diagnosis and detection of viruses and bacteria.

Dr Helen Stagg

University College London

Epstein-Barr Virus: paving the way for a vaccine using epidemiological and mathematical modelling approaches

Epstein Barr virus (EBV), a lymphocryptovirus, permanently infects more than 90% of humans. EBV causes more than 90% of cases of glandular fever and is linked to 1% of global cancers. Why only a small fraction of infected people get cancer is poorly understood. No anti-EBV vaccines are currently licensed, although several candidates are in pre-clinical development. Lymphocryptoviruses have evolved with humans for many millennia. Our immune systems are likely to be well adapted to EBV and vice versa. The impact of EBV infection through the human life course is not known, nor is that of remaining permanently EBV-negative. As vaccines become available such questions will become increasingly important. Information derived from large cohorts and mathematical models of transmission will be critical before vaccines can be adopted. Before extensive investment in a vaccine for EBV, a feasibility and scoping exercise of currently available data and resources is required.

We will use pre-existing datasets, pilot assembly of a cohort of EBV-seronegative people for a life-course study and undertake systematic reviews to determine the strength of available evidence for different risk factors for EBV infection and EBV-associated cancers in different settings. We will also develop a preliminary transmission dynamic model for vaccination and identify knowledge gaps for a full model.

Our research can be used to inform the development of a vaccine for EBV.

Dr Sakthivel Vaiyapuri

University of Reading

The antimicrobial peptide LL37 underpins thrombotic complications in inflammatory diseases

LL37 is a powerful antimicrobial peptide present in human epithelial cells of airways, intestine, skin and innate immune cells such as neutrophils and monocytes. It exhibits direct antimicrobial activities against a range of bacterial species, fungi and viruses. Furthermore, LL37 induces innate immunity and inflammatory responses to accelerate the clearance of microbial infection. Its roles in the regulation of leukocyte-mediated inflammatory responses at various pathophysiological settings have been studied. However, the effects of LL37 in the modulation of platelet function have not yet been established. Although platelets play indispensable roles in the regulation of haemostasis, their inappropriate activation under pathological conditions leads to thrombosis and blockage of blood supply to vital organs. Platelets are also involved in the regulation of inflammatory responses.

In this study, we propose to determine the effects of LL37 in the modulation of platelet reactivity, thrombosis and platelets-mediated inflammatory responses and elucidate the molecular mechanisms through which LL37 controls platelet function.

Determining the effects of LL37 in the control of platelet function under pathological conditions will provide a new paradigm in platelet biology and help to improve therapeutic strategies for cardiovascular and inflammatory diseases.

Dr Giorgio Volpe

University College London

Towards controlling bacterial social behaviours in host-like habitats

The regulation of social behaviour in bacteria is key to several phenomena including biofilm formation and the virulence of pathogens. Quorum sensing is the chemical communication process bacteria use to coordinate changes in their collective behaviour in response to population density. A current challenge in the field is to understand how quorum sensing works in scenarios that mimic real host environments. I have previously demonstrated that patchiness makes an active matter system – a system of self-propelled elements, such as motile bacteria – switch between gathering and dispersal of individuals.

Using a novel combination of methods from microfabrication, advanced microscopy and molecular biology, the aim of this proof-of-principle project is to unambiguously demonstrate that bacterial quorum sensing can be triggered by similar dynamics of gathering and dispersal induced by spatial features in the environment.

The validation of such a hypothesis will inform a long-term research programme on the effects of the environment on different quorum-sensing related phenomena such asbiofilm formation and development, antimicrobial resistance, host pathogen interactions and the expression of virulence.

Dr Simon Waddell

University of Sussex

Bacterial RNA profiling to predict tuberculosis treatment failure

At present there is no way of accurately predicting tuberculosis (TB) treatment failure and relapse to active disease. This results in many patients who might safely stop the toxic six-month therapy earlier and their treatment is unnecessarily extended. It also extends the length and cost of clinical trials to assess new therapies, creating a bottleneck to progress.

This project will test whether the transcriptional response of TB isolated from patient sputa during the first few days of treatment can predict relapse months later. Building my study demonstrating that sputa TB mRNA signatures differ between patients and reflect clinical/microbiological measures of disease, this proof-of-concept prospective patient study will for the first time define markers of relapse. TB RNA from patient sputa will be assayed by targeted and genome-wide profiling techniques at diagnosis and at multiple time points during drug therapy. RNA yields and gene expression signatures will be analysed to determine key methodological parameters concerning the collection and detection of sputa TB RNA and to assess applicability in the UK and Cameroon. TB mRNA signatures from patients who have relapsed and those who have been successfully treated will be compared using this approach to identify biomarkers that predict relapse.

The findings of this study could transform the management of TB.

Dr Gabrielle Wheway

University of the West of England

Cellular mutation modelling of pre-mRNA splicing factors to elucidate their function at the primary cilium and their contribution to human disease

Primary cilia are crucial signalling organelles which, when defective, lead to ciliopathies, a range of developmental and degenerative diseases affecting multiple organs including the retina. Retinitis pigmentosa (RP), a retinal dystrophy, is the most common cause of hereditary blindness, some forms of which are caused by defects in the ciliated cells of the retina. Mutations in certain pre-mRNA splicing factors (PRPFs) lead to RP but the disease mechanism of this form of RP is poorly understood, with inconsistent evidence of splicing defects.

This project aims to elucidate the function of PRPFs beyond splicing, building on my work linking primary cilia to PRPFs in a whole genome siRNA screen. I will test the hypothesis that the role of these proteins at the base of the cilium is connected to the cell’s DNA damage response (DDR), based on published evidence independently linking both splicing and cilia to the DDR. The project studies the function of these proteins using disease-relevant cell systems, in which human disease mutations are modelled, employing two different mutation modelling strategies.

This study will establish molecular tools for the characterisation of other putative ciliopathy disease proteins identified from large-scale genomics screens in a larger study.

Dr Andrea White

University of Birmingham

cD1d-Restricted NKT-Cells: gate keepers of thymus function

The thymus plays an essential role in adaptive immunity by supporting the production of alpha and beta T-cells. By supporting the development of CD1d-restricted iNKT-cells, it also plays an important role in innate immunity. Although there is strong evidence for interplay between innate and adaptive immune cells in peripheral tissues, whether this exists in the thymus and the effect it may have on thymus function, is poorly understood. My recent research was the first to show that iNKT-cells influence the intrathymic stromal microenvironments that support alpha and beta T-cell development. Preliminary data suggests that the absence of iNKT-cells causes thymus abnormalities that lead to an intrathymic accumulation of newly-produced alpha and beta T-cells.

This work provides an opportunity to dissect innate/adaptive immune links in the thymus that may contribute to its specialised role in T-cell production. We will elucidate the cellular and molecular interactions taking place between iNKT-cells and thymic stroma, investigate how iNKT-cells influence the emigration alpha and beta T-cells from the thymus and determine whether intrathymic iNKT-cell activation represents a novel approach to manipulate thymus emigration.

Dr Arash Yavari

University of Oxford

Defining a role for AMP-activated protein kinase in the autonomic regulation of heart rate

The autonomic nervous system (ANS) is a fundamental regulator of heart rate (HR) and cardiovascular homeostasis. Dysregulation of cardiac autonomic balance – specifically excessive sympathetic drive and reduced vagal activity – contributes to the development and progression of many cardiovascular disorders, including hypertension, atrial fibrillation and heart failure. Therapies such as vagal nerve stimulation, are used that address this. Humans bearing activating mutations in the cell’s energy sensor, AMP-activated protein kinase (AMPK), express a phenotype (PRKAG2 cardiomyopathy) notable for high prevalence of symptomatically low HR (sinus bradycardia).

We have used gene-targeted mice to identify that AMPK both inhibits intrinsic sinoatrial pacemaker mechanisms, and may promotes a vagal contribution to the bradycardia, raising the possibility that AMPK regulates HR in physiology and disease through combined intrinsic sinoatrial and autonomic influences. This proposal will evaluate autonomic function in a unique cohort of patients with PRKAG2 cardiomyopathy and mouse models of altered AMPK function to determine the ANS contribution to AMPK-dependent bradycardia and investigate whether AMPK may physiologically effect neural HR control.

The findings will have therapeutic implications for PRKAG2 cardiomyopathy and common disease states of pathologically-altered cardiac autonomic tone.

2016 Round 4

Dr Stephane Baudouin

Cardiff University

The pathophysiology of Autism: developmental trajectories and neuronal networks underlying pathological behaviour in mouse models

The variations in the pathogenesis and symptoms of autism spectrum disorders (ASD) are two important factors limiting the development of new therapeutic strategies. Unravelling the molecular and cellular mechanisms underlying the different pathological behaviours is a way to better understand the complexity of the disorders and develop new treatments. Studies on mouse models for ASD have begun to reveal aspects of ASD neuropathology, but our knowledge on causal links between neuronal networks and behaviours remains limited.

We will look at several mouse models for ASD and identify general neuronal mechanisms underlying ASD-related behaviours. We will define the developmental trajectory of pathological behaviours and when interventions can be made to genetically rescue behaviour phenotypes. We will also identify causal relationships between neuronal circuits and pathological behaviours.

In the long term, we plan to use this knowledge to extend our approach to selected conditional mouse models carrying microdeletions frequently found in patients and this will inform new therapeutic strategies.

Dr Haider Butt

University of Birmingham

Nature-inspired contact lenses for continuous glucose monitoring in type 1 diabetic children

Over 3.9 million people have diabetes in the UK and living with it can be extremely difficult. People with diabetes need to regularly monitor their blood glucose levels and need to prick their fingers up to five times a day. This process is painful and it has low patient compliance, particularly among children. Researchers have tried creating ways to detect glucose concentrations in body fluids such as tears, saliva and urine.

We propose to develop contact lenses that change colour based on the variation in the concentrations of glucose in tears. This will allow continuous monitoring of glucose concentrations by observing eye colour using a phone app. The contact lenses will be developed using hydrogels which change colour due to the changes in glucose concentrations. The colour changes will be produced by surface texturing from arrays of nanostepped-pyramids inspired from the 3D structures that account for the bright blue colours displayed by morpho butterflies. This will provide a unique platform for producing contact lenses which reversibly sense analytes in tears.

The development of these contact lenses could make it easier for people with diabetes to monitor and manage their blood glucose levels.

Dr Alexandra Chittka

Queen Mary University of London

Protein arginine methylation in the control of neural stem cell ‘stemness’ and differentiation

During development, cortical neuroepithelial stem cells (NSCs) generate all the neurons and glia of the central nervous system in a precise spatiotemporal manner. Aberrations of this process are linked to neurological conditions, such as autism and schizophrenia. The molecular mechanisms controlling NSCs’ transition from ‘stemness’ to differentiation remain elusive. We recently identified a novel regulatory complex, comprised of PRDM4 protein and the protein arginine methyltransferase 5 (PRMT5), whose activity maintains NSC ‘stemness’ in vitro. 

We hypothesise that PRDM4/PRMT5-mediated protein arginine methylation (R-Me) is necessary to maintain NSC ‘stemness’. We have generated mice with the cortical NSC-specific deletion of PRDM4 and analysed changes in R-Me in these mice. We will investigate outcomes of the observed reduction in R-Me and validate the strongest candidate of the proteomic screen. We will characterise differentiation profiles of NSCs from the mutant mice and biochemically characterise PRDM4:PRMT5-mediated KSRP-R-Me in vivo and in vitro.

Our findings will validate a novel mechanism of NSC ‘stemness’ control, mediated by protein R-Me, providing the basis for further investigations into its role in NSC reprogramming and neurological diseases.

Dr Triona Ní Chonghaile

Royal College of Surgeons in Ireland

Determining the mechanism of action of a novel histone deacetylase 6 specific inhibitor that kills chemoresistant breast cancer

The majority of cytotoxic agents used to treat people with tumours kill cells via the mitochondrial pathway of cell death. Previously, I found that primary tumours that are chemoresistant in vivo usually contain mitochondria that are resistant to apoptotic signalling. We performed a small molecule screen to identify new therapeutic small molecules that can preferentially kill cancer cells independent of mitochondrial apoptosis and identified the first reported case of a specific novel histone deacetylase 6 (HDAC6) inhibitor. HDAC6 deacetylates tubulin along with other proteins involved in cell motility and traffics unfolded proteins for degradation through its ubiquitin-binding domain.

We aim to determine how the small molecule binds to HDAC6 using medicinal chemistry approaches and using a series of lead compounds with improved pharmacological properties, develop structure activity relationships. We aim to determine the molecular signalling events that occur after inhibition of HDAC6 to kill the chemoresistant cancer cells. We will also determine possible mechanisms of resistance to HDAC6 inhibition.

This drug discovery approach represents a paradigm shift to develop new therapeutics through pathways that are independent of mitochondrial apoptosis, ultimately addressing the lack of effective treatment options for refractory patients.

Dr Michael Clark

University of Oxford

Capture NanoporeSeq: a novel technique for targeted full-length transcript sequencing and gene expression analysis

The accurate characterisation and quantification of expressed gene isoforms is essential to understanding how genetic variation affects gene expression and ultimately the risk of disease. However, the expressed isoforms identified by standard RNA sequencing methods are often incorrect due to the near ubiquitous presence of alternative gene isoforms in the human transcriptome.

This project aims to address this problem by developing a novel technique (Capture NanoporeSeq) to perform full-length cDNA sequencing of target human genes and unambiguously identify which isoforms are expressed. Capture NanoporeSeq will provide high sensitivity for targeted gene isoforms. Once developed, Capture NanoporeSeq will be validated in post-mortem human brain tissue to identify the expression of gene isoforms from genomic regions linked to neuropsychiatric disorders.

These developments will improve our ability to accurately characterise and quantify gene expression. This can be used in neuropsychiatric disease genetics, helping to illuminate the impact that disease-associated genetic variation has on gene expression.

Dr Seamus Coyle

University of Liverpool

Biology of dying

We think there may be a physiological process to dying. Recognising when someone is in the last weeks or days of life is difficult. No diagnostic test is available and little is known about how people die from disease. This knowledge is crucial for providing the best care possible. We performed a small study to establish the feasibility of collecting urine samples from patients in the last weeks and days of life, protocol for gas chromatography-mass spectrometry analysis of volatile organic compounds (VOCs) from urine and the discovery of VOC biomarkers which may predict the dying process as well as preliminary evidence of potentially important changes in DNA repair/DNA damage signalling activity.

This pilot study will identify VOCs as potential prognosticators for dying patients with advanced cancer, create a model to predict the dying process and investigate biomarkers of a range of cellular phenotypes to include: DNA damage and stress responses, cell proliferation, cell cycle/sensesence, DNA repair and apoptosis. We will also plan and design a full study to validate our findings.

This work has the potential to have a profound impact on the understanding of human biology and on patient care.

Dr Maria Doitsidou

University of Edinburgh

In vivo dissection of neuroprotection using a novel c. elegans model of neurodegeneration

The discovery of neuroprotective genes and gene variants will open new therapeutic avenues for neurodegenerative diseases. Forward genetics in model organisms is an approach that dissects gene function. We will use high-throughput forward genetic approaches on the genetically tractable nematode C. elegans to discover neuroprotective genes. We have previously established a C. elegans model of neurodegeneration in which a mutation in a transient receptor potential (TRP) channel results in progressive loss of dopaminergic neurons.

Building on this model, we have engineered a novel strain suitable for automated phenotyping and mutagenesis-based screening. We performed a pilot screen and isolated 18 different mutants that are resistant to TRP-channel induced neuronal loss. We aim to identify the causal mutations for neuroprotection in the 18 isolated mutants, test whether the mutations that protect dopaminergic neurons in our model are also protective in other models of neurodegenerative disease, such as Parkinson’s, tauopathy and excitotoxicity C. elegans models, and perform preliminary characterisation of selected neuroprotective genes.

This research will provide insights into human neurodegenerative disease and set the groundwork for future in-depth mechanistic investigations of neuroprotection and collaborative translational research projects.

Dr Abdelkader Essafi

University of Bristol

Oncoenhancers: hubs for early embryonic reprogramming in cancer

Genome-wide studies have underscored a role for regulatory elements (REs) in driving tumour progression. This is partly because structural/epigenetic alterations to REs appear to reactivate dormant embryonic processes such as stemness leading to chemoresistance, metastasis and dormancy. However, the reactivated REs, or ‘oncoenhancers’, and the mechanisms regulating their early hijack remain unexplored. Therefore, I propose to build on my previous findings to delineate and characterise oncoenhancers reactivating the Wilms’ tumour protein (WT1) in epithelial cancers.

WT1 has topped a National Cancer Institute antigen prioritisation list because its well-documented expression in adult tissues is restricted to few non-epithelial cell types yet it is abnormally reactivated uniquely in epithelial cancer cells. We will use a human mammary epithelial cell model (HMLER), where WT1 is abnormally reactivated, to identify using sequencing-based approaches and functionally characterise the WT1-associated oncoenhancers as an example of RE reactivation in cancer.

This work will provide some understanding of dynamic embryonic enhancer malfunction in pathology. Future work will explore the functional relevance of oncoenhancers in maintaining the epithelial-mesenchymal balance upstream of WT1.

Dr Brian Ferguson

University of Cambridge

Regulation of HSV-1 infection by the non-homologous end joining machinery

DNA viruses, such as herpes simplex virus 1 (HSV-1), exploit specific host DNA repair mechanisms to assist their replication. More recently, the DNA repair machinery that senses damaged self-DNA was shown to function in the innate immune sensing of viral DNA during infection.

We aim to understand how a specific DNA repair pathway – non-homologous end joining (NHEJ) – affects HSV-1 infection and how this virus exploits or evades these host responses. Our preliminary data indicate that two NHEJ proteins act to restrict HSV-1 in different ways, via activation of innate immune responses or by directly affecting virus replication. This study will provide the mechanistic basis of these observations and compare these data with the other components of the NHEJ machinery and how they regulate HSV-1 infection.

This work will further our knowledge of cell-intrinsic immunity and DNA repair as well as leading to the rational design of improved vaccines and oncolytic viruses.

Dr Elizabeth Ford

University of Sussex

ASTRODEM: using astrophysics to close the ‘diagnosis gap’ for dementia in UK general practice

Dementia is one of the greatest public health challenges of our era. Timely diagnosis allows patients to benefit from current therapies, plan for the future and maximise their quality of life. However, there is a ‘diagnosis gap’ in UK general practice, with less than two-thirds of expected patients receiving a dementia diagnosis. Increasing diagnosis rates is a strategic aim of the UK government and NHS.

We aim to close this diagnosis gap in a novel collaboration between primary care epidemiology and astrophysics. We will use a very large set of electronic patient records (96,000 patients; 50% with dementia) spanning up to ten years per patient. We will use a probabilistic programming framework to apply statistical techniques to model dementia onset in this cohort, allowing for the inherent variability and duration of disease development. To achieve a clinically valuable model, these multi-dimensional data will require sophisticated analysis techniques that are not currently available in medical statistics and epidemiology, but which astrophysicists use daily. 

Our goal is to develop a statistical model to predict risk of dementia from patients’ GP records, which will help GPs and other NHS bodies better estimate and identify cases of dementia in the UK.

Dr Amanda Foust

Imperial College London

Holographic induction of neural circuit plasticity

Neocortical circuits modify both structure and function in order to learn, remember, refine task performance and recover from injury. Electrical patch-clamp methods have identified several plasticity mechanisms on the single-cell level. The number of cells that can be simultaneously patched is limited, hindering efforts to connect single-cell plasticity with circuit- and system-scale learning and memory. Computer-generated holography (CGH) combined with genetically encoded light-sensitive actuators (‘optogenetics’), holds immense promise to overcome this limitation by targeting light to rapidly activate one or several neurons without electrode penetration.

I will adapt two-photon CGH to rapidly map local inputs to a neuron in neocortical brain slices and manipulate the connection strengths between the neuron and its presynaptic inputs by holographically actuating spikes in the presynaptic neurons at short delays. CGH’s ability to rapidly map solicited spikes in hundreds of neurons will enable, for the first time, single-cell resolution plasticity interrogation in whole functioning microcircuits.

This research will enable these critical first steps toward connecting synaptic plasticity with neural circuit emergent properties, learning, memory, and injury recovery.

Dr Todor Gerdjikov

University of Leicester

Interaction between attentional signals and dopamine error prediction: focus on midbrain dopaminergic projections to prefrontal cortex

Mid-brain dopamine is implicated in motivation and attentional processes related to error prediction. However, the dominant model of dopamine error prediction advanced over the past two decades is at odds with key behavioural observations and recent theories of attention that suggest top-down cortical control over error prediction. This leaves open the question about how the dopamine signal interacts with these top-down mechanisms.

I will exploit recent advances in optical approaches to brain function to explore this question using behavioural tasks in rats. I will use fibre photometry to record from dopaminergic projections to the medial prefrontal cortex during a discrimination task. I will determine whether there is increased activity for both positive and negative prediction error. I will also carry out a causal experiment using optogenetic inhibition of prefrontal vs. dopaminergic projections received by the nucleus accumbens in a blocking behavioural paradigm. This experiment will determine whether these projections differ in their contributions to error prediction.

This work will uncover novel mechanisms of dopamine reward prediction with implications for our understanding of the fundamental nature of attention and motivation.

Dr Guillaume Hennequin

University of Cambridge

Control of limb movements by motor cortical circuit dynamics

The control of limb movements has been investigated but a unified theoretical understanding of how limbs are controlled by collective neuronal dynamics is lacking.

We will use an analysis-by-synthesis approach to relate the dynamics of the motor cortex to the computational objective of limb control. In this pilot project, we will make use of developments in the fields of stochastic optimal control and optimisation to build model cortical networks that control reaching movements in the presence of noise at all processing stages and under key physiological constraints inherent to brain circuits. We will then dissect the strategies used by the model networks to achieve robust control of limb trajectories, relate the model's activity to cortical electrophysiology, and use the models to guide future experiments.

In the long term, such models will provide unique insights into the dynamics of the motor cortex and suggest optimal ways to restore lost function via closed-loop neuroprosthetics.

Dr Bin Hu

University of Sheffield

The molecular mechanism of chromosome condensation mediated by cohesin and condensing

The condensation of chromosomes in the eukaryotic nucleus is essential for life and cells cannot faithfully segregate chromosomes without it. It is well known that the highly conserved condensin and cohesin protein complexes are the key factors for DNA condensation, but the mechanism for condensation remains unknown. One theory is that distant DNA segments in one molecule interact with each other mediated by cDNA bound condensin and/or cohesin. While methods, such as sister chromatid cohesion, have been established to study inter-DNA interaction no techniques have been established to investigate biochemical properties of proposed intra-DNA interactions, required for chromosome condensation. It is essential that new technologies are developed to understand how chromosomes are organised by condensation.

Condensation in Saccharomyces cerevisiae has been studied using repetitive rDNA sequences as a model for conserved DNA condensation. I have established a novel genetic system to isolate of condensed chromatin formed in vivo by intra-rDNA interactions. Using Cre recombinase condensed native rDNA, discrete chromatin circles can be liberated for biochemical characterisation.

These studies will help us formulate a hypothesis on how cohesin/condensin organises rDNA, to build up a solid foundation for further grant application.

Dr Elizabeth Liddle

University of Nottingham

RECOGNeyes: remediating cognitive control of gaze

Attention deficit hyperactivity disorder (ADHD) is typified by impairments in the control of attention and/or inhibitory motor control, both of which are related to gaze control. Visual attention requires control of gaze direction and gaze control is itself a motor control skill.

Our goal is to develop computer games that use eye-tracker technology where the player’s eyes become the game controller. To advance in the games, the player must gain control of gaze direction. The training games will be designed to improve fixation in the face of irrelevant distractors while monitoring the periphery. The games will also train the timing of saccadic responses in line with evidence that motor timing may be a related impairment in ADHD. Prototypes will be made in consultation with young people and adults with ADHD, and games will be programmed using a standard gaming platform with visual and auditory effects. We will produce a suite of training games that will be evaluated by students and teachers in local schools.

The games will help people with ADHD develop and improve gaze control and their control of attention.

Dr Louis Luk

Cardiff University

Dihydrofolate reductase interactome: an unrecognised network that can control DNA synthesis and cell replication

We aim to characterise and map the interactome of dihydrofolate reductase (DHFR), a well-validated anticancer drug target. DHFR is an enzyme that catalyses a key reaction in the biosynthesis of DNA building blocks. Although therapeutics targeting DHFR are available for cancer treatment, there is frequent resistance against them. To address this issue, it is essential to fully characterise DHFR from its catalytic behaviours to regulatory network and this information help future drug development. DHFR binds to a wide variety of biomolecules other than its substrates, including its parental mRNA and enzymes responsible for post-translational modifications (PTMs). It is crucial to investigate these non-substrate interactions, as their functional roles have not identified.

We hypothesise that DHFR is embedded in a molecular network of interactions that control the activity of DHFR. We will characterise the effect of PTMs on DHFR catalysis, isolate the effect of mRNA binding and map the interactome of DHFR.

This work will advance our knowledge of DHFR and help future development of cancer therapies. 

Dr Michelle Ma

King’s College London

Zirconium-89 cell labelling platforms for in vivo cell tracking with PET

We will develop cell-labelling platforms based on the PET isotope 89Zr, allowing cell tracking in vivo for several days post-administration. These platforms combine novel chelators for attaching to peptides/proteins, and will anchor the radiolabel to the cell membrane or deliver it into the cell. 89Zr uptake and retention will be screened in myeloma, macrophage, leukocyte and stem cells. We will determine the subcellular location of 89Zr, the metabolic fate of chelator-peptide/protein conjugates and the effects of ionising radiation on labelled cells. Selected platforms will be investigated in mice using PET scanning, ex vivo biodistribution, and fluorescence activated cell sorting of homogenised cells from harvested organs.

Outcomes will include proof of principle of a new cell tracking platform, with clinical applications in cell-based therapies. This will allow us to develop, apply and translate the technology further in a wider collaborative programme.

Dr David McEwan

University of Dundee

Determining the molecular mechanisms regulating lysosome damage and repair pathways

Lysosomes are ubiquitous membrane-bound organelles that release hydrolytic enzymes and hydrogen ions into the cytoplasm when ruptured. This can result in DNA damage, impeded degradation of lysosomal substrates, inflammation and neurodegenerative diseases. Understanding how cells respond to such stress and how the repair/removal pathways are regulated is paramount to controlling cellular and tissue homeostasis as well as developing future therapeutic strategies. A number of stimuli can induce lysosomal damage and rupture, including bacterial pathogens, viruses, silica crystals and lysosomotrophic agents (LLOMe). In addition, inducing lysosome damage in cancer cells with high levels of cathepsins is seen as a viable therapeutic option. However, there is a serious lack of knowledge regarding the mechanisms that sense damage, repair or remove lysosomes that are initiated when lysosomes are ruptured.

We will use a siRNA screen to identify key regulators of this process, with particular emphasis on potentially druggable targets. We will focus our efforts on kinases, phosphatases, de-ubiquitinases and membrane trafficking genes.

We hope to identify a number of genes that can be analysed in greater detail with particular focus on regulation of bacterial infection and lysosome-induced cancer cell death pathways.

Dr Claire McEvoy

Queen’s University Belfast

Mediterranean diet and cognitive decline: using epidemiologic and pilot study data to inform a large-scale intervention

Given the lack of effective treatments and projected increased prevalence of dementia, there is a need to identify strategies to prevent cognitive decline. The Mediterranean diet (MD) has anti-inflammatory and vascular benefits and may be neuroprotective. Meta-analyses have shown associations between MD adherence and protection against cognitive decline but evidence is limited. Further research is needed to investigate MD-associated neurological change from the earliest through to latest stages of cognitive decline. Intervention strategies require insight into mechanisms involved in diet-induced cognitive change and an understanding of how to support MD behaviour change, particularly in non-Mediterranean populations. 

We will integrate epidemiological and pilot behaviour change data to address identified gaps in existing knowledge and to inform the development of a large trial where the efficacy of an MD intervention to preserve cognitive function will be tested. We will comprehensively examine associations between MD adherence and cognitive function in non-Mediterranean populations, evaluate the feasibility of MD behaviour change in adults at high risk of cognitive decline and study mechanistic pathways by which an MD may act and identify cognitive outcomes most likely to respond to dietary change.

Our results will inform a large-scale intervention to protect against cognitive decline.

Dr Thomas Millard

University of Manchester

In vivo analysis of the impact of complex extracellular environments on cell migration

The extracellular environment through which cells migrate in vivo is extremely complicated and varies greatly in its chemical, spatial and mechanical properties. Understanding how the characteristics of the environment affect cell migration in vivo would be a major step towards the development of therapies to target specific migratory processes.

We aim to establish Drosophila embryonic haemocytes as a model for studying the impact of the extracellular environment on cell migration in vivo. We will use a combination of 4D light-sheet microscopy, automated tracking and genetic manipulation to determine how the spatial environment in a Drosophila embryo influences the migratory behaviour of haemocytes. We will also determine how haemocytes adapt their migratory mechanisms to move through extracellular spaces of different size and geometry.

The techniques established in this project will be used in a bigger study in which we will investigate chemical, spatial and mechanical aspects of the environment in parallel to achieve a comprehensive understanding of the impact of the extracellular environment on cell migration.

Dr Niamh O’Sullivan

University College Dublin

Uncovering the role of ER-shaping proteins in neurodegenerative disease

Hereditary spastic paraplegias (HSPs) are a group of neurodegenerative disorders characterised by degeneration of the longest motor neurons which leads to muscle weakness and spasticity in the lower limbs. There are currently no treatments to cure or even to slow the course of these diseases.

We aim to determine the molecular mechanisms by which disease-causing variants give rise to neurodegeneration in HSP. We will generate the world’s first in vivo models of HSP which endogenously express patient-specific gene variants via CRISPR-Cas9 gene editing in Drosophila. By integrating disparate genetic, proteomic and imaging analyses of these novel models, we will identify how HSP-causing variants alter protein expression, localisation and interaction. We will then establish the clinical relevance of identified mechanisms by studying disease-causing variants in human cellular models of HSP.

The findings from fly and human models of HSP will greatly enhance our understanding of the molecular mechanisms underpinning these neurodegenerative disorders. The models we generate will provide valuable investigative resources for studying the cellular events underlying neurodegenerative disease and a new method for screening therapeutic approaches for these degenerative disorders.

Dr Lisa Reimer

Liverpool School of Tropical Medicine

Dissecting the role of insecticide resistance in the spread of vector-borne disease

Insecticide resistance is the greatest challenge to vector-borne disease control. The vector population that persists after insecticide-based interventions will adapt to mitigate the effects of insecticide. Mechanisms of insecticide resistance, which may include increased detoxification or target site insensitivity, will affect vector behaviour and physiology in ways that aren’t fully understood. Resistance mechanisms may lead to either increased or decreased capacity through changes in fitness, immunity and behaviour. Research into the full spectrum of these effects is needed to inform the use of insecticides.

We will develop multiple strains of insecticide-resistant Aedes aegypti which will differ in their dominant resistance mechanism. A multiresistant strain from Recife will be differentially exposed to a combination of insecticides and synergists to select for one of three naturally occurring metabolic resistance mechanisms. A strain from Cayman with 80% knockdown resistant allele frequency will also be used. Transcriptional profiles will be evaluated to determine changes in the expression of resistance, detoxification, immunity and development genes. 

The validated set of strains will enable experimental work on vectorial capacity of resistant mosquitoes for multiple vector-borne diseases.

Dr Ellen Roche

National University of Ireland, Galway

Modelling of pharmacokinetics into ischemic heart tissue from an implantable, replenishable therapy reservoir

Precisely controlled delivery of drugs, bioagents and cells directly to the heart has the potential to dramatically improve regenerative cardiac therapy for ischaemic heart failure. Likewise, localised therapy delivery to ischaemic tissue can increase retention at the target site and reduce adverse systemic effects. 

We will use computational modelling to simulate drug release kinetics from a replenishable indwelling device (the therapeutic pericardiuim or ‘thericardium’) across a porous membrane to heart tissue to optimise the device’s design and provide insights into the functionality of the implantable drug delivery system. The key goals will be to experimentally characterise the drug transport and mechanical properties of this device for input into a computational model. We will create a multi-scale computational model that can predict therapy concentration in the tissue to allow the device to give accurate dosing and timing of therapy replenishments and the validation of the computational model compared with existing pre-clinical data.

Future work will include further pre-clinical studies to implement the enhanced design of the drug delivery device.

Dr Marco Saponaro

University of Birmingham

RNA Pol II subunits in the regulation of transcription and genome instability

The RNA Pol II complex transcribes the genes that codify the proteins in our body. This is tightly controlled through interactions with transcription-regulatory factors. Although there is much research characterising the roles of these factors, very little, if anything, is known about how the multiple subunits of the RNA Pol II are important for the regulation of transcription. So far the RNA Pol II has been characterised as a whole complex of 12 proteins. However, our analysis of cancer genomic databases shows that single subunits can be upregulated and this associates with aggressive tumours and poor survival.

We hypothesise that these single upregulations deplete transcription-regulatory factors from RNA Pol II. This would lead to a defective transcription process associated with increased genome instability. We will analyse how the overexpression of single subunits affects RNA Pol II transcription, identifying which transcription processes and stages are particularly affected. We will also analyse the genome instability, identifying the sites of DNA damage and correlating them with the transcription defects identified by our parallel analysis.

Dr Joanne Thompson

University of Edinburgh

Transfection technologies for investigating the role and antimalarial potential of GPCR-like proteins in Plasmodium

Malaria causes more than 650,000 deaths annually, and new antimalarial therapies are urgently needed. Signalling pathways acting through G-protein-coupled regulators (GPCRs) are the targets of the majority of drugs currently in therapeutic use, so they have high potential as antimalarial drug targets.

We will explore the function and therapeutic potential of Plasmodium members of an evolutionary-ancient family of proteins, GPR89, that are classified as divergent GPCRs and have been implicated in environmental sensing in a diverse range of eukaryotes. We will investigate the role of Plasmodium GPR89 in the regulation of parasite growth, differentiation, virulence and immunogenicity, and gain insights into signalling pathways operating through GPR89 by identifying binding partners in the infected erythrocyte. We will use transfection technologies for Plasmodium chabaudi, a particularly useful and relevant mouse model for studying acute and chronic malaria infection and for investigating host-parasite interactions that regulate cell-cycle progression, differentiation and immune evasion during blood-stage infection.

These studies will advance our understanding of GPCR-like proteins in Plasmodium and will bring technological advances to the P.chabaudi model, providing an experimental framework for the investigation and validation of a new class of therapeutic targets.

Dr Zahra Timsah

University of Leeds

Proteomic and structural profiling of PXXP-SH3 interactions as key regulators of membrane receptor activity

Membrane receptor signalling occurs upon growth factor stimulation. I have shown that fibroblast growth factor receptor 2 signalling can also be triggered without stimulation. This occurs when proteins with Src homology 3 (SH3) domain bind its C-terminal proline-rich-motif (PXXP) and modulate its activity to induce a homeostatic or oncogenic response. Whether this occurs in other receptors remains unclear.

I will test the hypothesis that these interactions are abundant and critical for functional regulation of receptors which dictates cellular response. I will use two model receptors to extract bound proteins from cell lysates and I will use mass-spectrometry to determine the identity of the SH3 domain-containing hits. I will run pilot biophysical experiments such as microscale thermophoresis to reduce confounding elements and evaluate functional modulation of receptors by running reverse-phase-protein-array and functional assays.

This project will set the foundation for characterising novel interactions to enhance our understanding of signalling mechanisms, particularly structural modelling of receptors. This may highlight new approaches for cancer therapy.

Dr Baojun Wang

University of Edinburgh

Low cost paper-based biosensors for point-of-care nucleic acid diagnostics of pathogens

We will develop ultra-low cost, paper-based biosensors that can provide point-of-care nucleic acid diagnostics of target pathogens in various specimens. We will design synthetic HPV viral DNA responsive genetic circuits and validate their diagnostic efficacy in a portable filter paper-based cell-free gene-expression system. This can be freeze-dried and rehydrated and can produce graduated colorimetric outputs to indicate HPV subtype and load in cervical cell samples lysed by inexpensive non-ionic detergents.

Our findings will contribute to a solution for a major global challenge – providing kits for self-diagnosis of infectious agents, such as HPV, at home which are sufficiently simple, cheap and robust to be used in the poorest countries in the world.

Dr Nicolae Radu Zabet

University of Essex

Investigating the effects of chromatin architecture on gene regulation

Transcription factors (TFs) are proteins that bind to specific sites on DNA, where they control the activity of genes. Despite the good success of current models to predict TF binding profiles, there are cases where all models fail. One frequent aspect of these models is that the DNA is linear, but this is clearly not the case and recent studies showed that the DNA in eukaryotes is highly compacted.

We plan to investigate whether the 3D structure of chromatin influences the binding of TFs and we will assess whether changes in the binding profiles of TF are specific to loci where the 3D structure of the DNA is changed. We will also look at whether DNA accessibility also changes at these loci (to evaluate whether DNA accessibility mediates this interaction). We will also investigate whether these changes in TF binding translate into changes in transcription levels. We will study Drosophila cells to generate binding profiles and expression data for the suppressor of hairless protein.

2015 Round 3

Dr Nasreen Akhtar

University of Sheffield

Force generated shaping of epithelial ducts

Hollow tubes and acini form the common units of most internal organs and they are essential for tissue function. However, virtually nothing is understood about the processes that engineer epithelia into these morphogenetic shapes. It is now recognised that mechanical forces originating both from within and outside cells contribute to tissue shaping. 

We will use the mammary gland system to determine how physical forces regulate tissue shape transformation. This tissue forms a network of collecting ducts connected to secretory alveoli, organised as a bi-layer of polarised luminal epithelia and myoepithelia. Basal myoepithelia are contractile in nature and form a dense coverage around ducts but sparsely subtend acini. We will determine whether a mechanical force generated by myoepithelial cells models the tubular shape of mammary ducts. Using primary 3D organoid cultures of breast epithelia that recapitulate polarised ducts and acini, combined with lentivirus gene knockdown and Cre-LoxP technology, we will perturb tension signalling from myoepithelia to determine their role. Live imaging and 3D-rendered data will be generated to build computational models that will be used in combination with experimental data to test future hypotheses.

This work will contribute significantly to solving key questions about mechanical control of branching morphogenesis.

Dr Joseph Bateman

King’s College London

Molecular basis of mTOR signalling in mammalian neurogenesis

Dr Vaughan Bell

University College London

A community of one: understanding the social core of psychosis

The delusions and hallucinations of psychosis are largely a social experience, typically involving the experience of illusory persecutors, conspirators and communicators. Evidence shows that current ‘static’ measures of social cognition, at best, only weakly predict their presence and poorly explain these significant sources of distress and disability.

This project aims to understand how illusory social agents come to form a central component of psychotic symptoms using the creation of the free, open-source SocialLab experimental design platform to allow researchers to build live, interactive, social experimental studies that can be run in the lab or over the internet for this project and a future research programme. We will use the software to run two studies in healthy controls and patients with psychosis that will validate the platform and will allow the testing of three hypotheses concerning the over-detection of social agents in psychosis, negative attributions of social agents in psychosis, and similar but attenuated effects in the general population that differ by levels of psychotic experience.

The project also includes dedicated time to transition to a future research programme with specific goals to widen the empirical investigations and examine their clinical relevance.

Dr Edwin Chen

University of Leeds

R-loop dysregulation in myeloid neoplasms

Dr Ruoli Chen

Keele University

Pharmacological accumulation of hypoxia inducible factors for neuroprotection in cerebral ischaemia

Dr Sonia Correa

University of Bradford

The MK2 cascade as a protective target in Alzheimer’s disease

Dr Timothy Craig

University of the West of England

Role of protein SUMOylation in glucose homeostasis and type 2 diabetes

Type 2 diabetes is a significant public health issue and its prevalence is rapidly increasing. It is thought to be caused by hepatic and peripheral insulin resistance, as well as deficiencies in beta-cell insulin secretion, but exactly how these processes become defective is still unclear. SUMOylation is a post-translational modification, analogous to ubiquitination. It has many nuclear roles, and it is also involved in neurotransmitter-receptor trafficking and neurotransmitter release. These processes have striking similarities with the intracellular pathways for insulin release and insulin responsiveness. Several studies have shown that insulin release is affected by SUMOylation, and that it might be defective in patients with advanced type 2 diabetes.

My hypothesis is that protein SUMOylation plays a key role in glucose homeostasis and the pathology of type 2 diabetes. The key goals of this project are to establish the mechanism for control of insulin release by SUMOylation and identify new SUMOylation substrates involved in diabetes and glucose homeostasis.

The findings of this study will open new avenues in research into type 2 diabetes and has the potential to identify novel therapeutic targets for the disease.

Dr Angela Donin

St George’s University of London

Developing a nutritional intervention to increase cereal fibre intakes in UK South Asian children

Dr Sara Goodacre

University of Nottingham

A new way to be deaf? Causes of congenital deafness in the world’s least diverse population

Dr Ian Goodhead

University of Salford

Experimental evolution of Sodalis glossinidius to reveal symbiotic mechanisms linked to trypanosomiasis vector competency

Dr Matthew Harper

University of Cambridge

The role of leukocyte, platelet and endothelial cell interactions in chemotherapy-induced venous thromboembolism

Dr Elizabeth Heron

Trinity College Dublin

Artificial neural networks, genomic data and case-control classification

Dr Susan Hodgson

Imperial College London

Childhood type 1 diabetes: an analysis of environmental and pre/perinatal risk factors across England

Dr Marko Kerac

London School of Hygiene and Tropical Medicine

Formative research towards a future RCT aiming to improve catch-up growth and reduce the risks of non-communicable disease (NCD) in stunted children: is there a ‘second window of opportunity’ in adolescence? (‘Stunting2Win’ study)

Dr Antonio Marco

University of Essex

Population dynamics of microRNA regulation: biomedical applications

Gene regulatory interactions form the backbone of any biological process. Indeed, it is well established that selection maintains regulatory sites. MicroRNAs are post-transcriptional gene regulators that target transcripts by pairwise complementarity at specific target sites. In a recent study I explored the evolutionary dynamics of microRNA target sites in the fruit fly. By developing a novel population genetics mutation model, I detected selection against maternal microRNA target sites in maternal transcripts. I suggested that this pattern of 'target avoidance' is a consequence of gene regulatory conflicts and that this may be a widespread evolutionary phenomenon. In a pilot study I observed that target avoidance also happens in human populations. I also showed that disease-associated regulatory interactions can be inferred by detecting target-avoidance events.

This proposal aims to develop a population genetics model of microRNA target site evolution based on my recent findings and to apply it to the analysis of human diseases. This project will also facilitate the establishment of collaborative links in the emerging field of evolutionary biomedical sciences.

Dr Pradeepa Marulasiddappa

University of Essex

Development of high throughput methods to decode the function of enhancers

Enhancers control development and cellular function by spatiotemporal regulation of gene expression. A large number of genomic regions identified by genome-wide association studies (GWAS) of human disease fall within enhancer regions, however the gene-specific regulatory mechanism for these enhancers is not known. Histone modifications, such as acetylation of histone H3 at lysine 27 (H3K27ac) and H3K4me1, have been widely used for identification of active enhancers. Using these marks alone for enhancer identification gives only an incomplete catalogue of active enhancer repertoire. We have discovered a novel class of putative enhancers in mouse embryonic stem cells (ESCs) marked by an H3 globular modification – H3K122ac but not H3K27ac. The importance of histone modifications is still not clear; moreover, functional characterisation of the full panel of these enhancers is challenging and requires efficient high throughput methods. 

By performing enhancer reporter assays and by deleting enhancers together by recruiting synthetic transcriptional repressors to enhancers, we have demonstrated the functionality candidate enhancers. We will perform high throughput screening of enhancer activity for putative enhancers in ES cells and screen for functionality of enhancers by recruiting synthetic transcriptional modulators at these enhancers.

Dr Amy Milton

University of Cambridge

A new approach to OCD: assessing the impact of environmental stimuli on functional and dysfunctional checking behaviour

Dr Augustine Odili

University of Abuja

Nigerian salt survey

Dr Patricija van Oosten-Hawle

University of Leeds

Are innate immune genes regulators of organismal proteostasis and transcellular chaperone signalling?

Dr Vladimir Teif

University of Essex

Nucleosome repositioning as a mechanism for cell memory in cancer transitions

Dr Andriy Temko

University College Cork

Sound-based observation of neonatal brain growth and status

Dr Yu-Hsuan Tsai

Cardiff University

Chemical biology tools for protein O-GIcNAc modification

Dr Timothy Weil

University of Cambridge

Elucidating the molecular mechanism of calcium in the activation of translation

Dr Helen Wright

University of Liverpool

Molecular properties of neutrophil extracellular traps (NETs) in rheumatoid arthritis

2015 Round 2

Dr Benjamin Almquist

Imperial College London

Bioinspired nanotechnologies for spatiotemporal tissue engineering

3D printing offers exciting possibilities for the fields of tissue engineering and regenerative medicine, enabling the ability to spatially pattern cells and materials in three dimensions. However, it currently lacks the ability to actively direct collections of various cell types to dynamically populate the engineered scaffolds in specific arrangements.

We will create an engineered mimic of the TGF-b large latent complex that will activate and release bound cytokines, peptides and small molecules upon direct application of integrin-mediated cell traction forces.
The overall goal of this proposal is to develop a bioinspired technology that will allow tissue scaffolds to harness spatiotemporal biological information as a means to direct cells to form hierarchical tissue structures.

After initial development, this new system will be used to dynamically coordinate the patterning of both neurons and vasculature in 3D printed tissue scaffolds.

Dr David Belin

University of Cambridge

Noradrenergic mechanisms in the nucleus accumbens shell as a gateway for the transition from impulsivity to compulsivity

Impulsivity represents an endophenotype of vulnerability to develop compulsive disorders such as drug addiction and obsessive compulsive disorder (OCD). However, the neural mechanisms that increase this vulnerability are unknown, thereby preventing the development of new effective therapeutic strategies.

We have demonstrated that the selective noradrenaline reuptake inhibitor atomoxetine prevents the transition from impulsivity to compulsivity in highly impulsive rats. The aim of this preliminary project is to provide proof of concept for a key contribution of the noradrenergic innervation of the nucleus accumbens shell (AbcS) from the nucleus tractus solitarius (NTS) to impulsivity and the associated increased vulnerability to develop OCD and other compulsive behaviours in rats.

We will demonstrate that noradrenergic mechanisms in the AcbS are involved in the well-established expression of compulsivity as measured using schedule-induced polydipsia (SIP), an established model of compulsivity. We will alsos identify noradrenergic correlates of impulsivity and compulsivity in the AcbS and demonstrate that specific optogenetic manipulation of the NTS-AcbS pathway influences impulsivity, compulsive adjunctive behaviour under SIP and compulsive relapse to seek cocaine in rats.

Dr Karl Emanuel Busch

University of Edinburgh

Electrical synapse plasticity in neural circuits in vivo

How plasticity of neural circuit function is governed is a fundamental question in neuroscience. Electrical synapses are formed by gap junctions and are widely present in nervous systems, including the human brain. Long viewed as a simple and static form of neural communication, recent in vitro data suggest that gap junctions can show highly dynamic properties. However, the regulation and plasticity of gap junctions in vivo is poorly understood.

This project aims to gain insight into the functional and structural dynamics of gap junction signalling in vivo, using the nematode C. elegans as a genetic model. We will establish tools in a sensory neural circuit formed by electrical synapses and identify environmental and sensory conditions that modulate a specific electrical coupling in this circuit to induce behavioural plasticity. We will examine short-term regulation by gating and long-term regulation by channel turnover. We will also characterise genetic and signalling factors underpinning gap-junction-mediated plasticity.

Electrical synapse plasticity is implicated in a number of neural disorders and our findings will offer a new perspective on treating these dysfunctions.

Dr Barry Denholm

University of Edinburgh

Piezo: a cardiac stretch-activated ion channel?

The heart senses and adapts to its own highly dynamic mechanical environment. This environment changes beat-by-beat, and over longer timescales due to physiological changes or disease. Failure to detect and adjust performance accordingly is associated with arrhythmias and sudden cardiac death. The molecular and cellular basis for this adaptation is not known, but mechanosensitive ion channels are thought to be key components. Preliminary data from our lab using the Drosophila heart model identify the stretch-activated Ca2+-permeable ion channels of the Piezo family as being central to this adaptive response. We propose that as the myocardium undergoes mechanical stretch when blood fills the heart, Piezo channels open, elevating intracellular Ca2+ leading to heightened cardiomyocyte contraction; thus aligning mechanical status with cardiac performance. This predicts that Piezo-/- hearts will be refractory to mechanical stretch, will have abnormal Ca2+ signalling, and will exhibit defects in contractility.

We will compare the parameters between wild-type and Piezo-/- hearts. Our data indicate that Piezo is a sarcoplasmic reticulum-resident channel. We will extend this observation to determine the precise subcellular focus of Piezo activity and use the power of Drosophila molecular genetics to identify further components of the Piezo pathway.

Dr Anne Fletcher

University of Birmingham

Identifying novel biologically relevant interactions between lymph node stroma and innate immune cells

Fibroblastic reticular cells (FRCs) are found in secondary lymphoid organs where they strongly shape adaptive immunity. However, interactions with immunologically important macrophage and neutrophil populations are completely undescribed. I recently found evidence that FRCs directly induce monocyte differentiation, and they attract macrophages and then arrest their migration. I also found that FRCs express a gene signature highly relevant to macrophage and neutrophil influx and function and that expression of key chemokines increases immediately after LPS exposure. As robust proof-of-principle, FRC depletion reduces macrophage numbers by 95% in lymph nodes. I hypothesise that FRCs fundamentally regulate macrophages and neutrophils in secondary lymphoid organs.

I will test FRC interactions with macrophages and neutrophils through co-culture and live cell imaging, developing relevant data, inhibit key factors produced by stroma, examining effects on macrophage and neutrophil migration, phenotype and function. I will also use a targeted in vivo model of FRC depletion (FAP-DTR) to dissect FRC-mediated control of macrophages and neutrophil function.

Dr Isabel Martinez Garay

Cardiff University

Protocadherin 19 in cortical development

Mutations in protocadherin-19 (Pcdh19), a delta-2 protocadherin encoded on the X chromosome, lead to epilepsy with cognitive impairment in heterozygous females. The early onset of disease suggests a neurodevelopmental basis for the disorder, but the function of this gene is entirely unknown.

We propose to use the developing mouse brain to analyse the role of Pcdh19 in neurogenesis, migration and circuit formation. Data from expression studies, anatomical analyses and the unusual inheritance mode of the disorder, where hemizygous males are unaffected, support the theory that Pcdh19 plays a role in these processes. We will first perform a comprehensive molecular and hodological characterisation of Pcdh19 expressing cells at different developmental stages. We will then analyse a Pcdh19 null mouse mutant and assess whether neurogenesis and/or migration are affected. We will directly interfere with Pcdh19 function using in utero electroporation, either by shRNA to cause an acute reduction of its levels or with mutant forms of the protein. Analysing synapses in embryonic stem cell-derived neurons and electrophysiological recordings in brain slices will complete the analysis.

Our results will provide insight into the roles of Pcdh19 during corticogenesis and form a useful basis for subsequent studies.

Professor Margarete Heck

University of Edinburgh

Function of the essential leishmanolysin-related protease invadolysin in flies and man

Invadolysin is a novel essential metalloprotease that is conserved among metazoans. We have demonstrated a localisation of the protein to lipid droplets, the dynamic fat storage organelle of the cell. We also showed that Drosophila that lacked invadolysin accumulated significantly lower levels of fat, and exhibited impaired insulin signalling while the level of invadolysin increased in in vitro adipogenesis models. We have very recently discovered that invadolysin is present in vertebrate serum and invertebrate hemolymph.

We will investigate what role this essential enzyme may play in common pathological states in humans, such as obesity and diabetes. We will ask whether invadolysin can be localised to a specific fraction of human serum, and if proteolytic activity can be detected therein. We also plan to characterise the catalytic motif(s) of invadolysin to discern their role in its function. Detailed phenotypic analysis will be performed on recently generated transgenic Drosophila expressing forms of invadolysin in which the conserved metalloprotease and a potential lipase motif have been mutated.

The combination of approaches in vertebrate and invertebrate systems will shed light on the role of invadolysin and generate crucial pilot data for future research grant applications.

Dr Sara Hillman

UCL Institute for Women’s Health

High altitude adaptation and pregnancy outcome study (HAPS): investigating the influence of hypoxia on birth weight

Intrauterine growth restriction (IUGR) results in babies being born with a low birth weight. Failure to adapt to a low-oxygen environment may impede placental growth and consequently, result in a low birth weight. LBW is especially common among newcomers to high altitude environments. People who have lived in high altitudes for a long time have some protection, potentially through evolutionary selection of advantageous hypoxia-related gene variants. If such variants could be identified, pathways that cause or protect from IUGR could be put in place. Researchers from the UK and India will collaborate to investigate this.

We will recruit 300 pregnant women from a hospital in Leh, India, which is in a high altitude area. Gene variants in babies associated with birth weight, will be identified. We will then seek evidence of how these gene variants might affect growth by measuring placental size and umbilical blood flow during pregnancy using ultrasound, and recording metabolic markers from the cord blood when the baby is born to see if they are associated with significant gene variants.

This work will inform further replication studies at high altitude and aid investigation of factors that play a role in causing IUGR/LBW at low altitude.

Dr Takanori Kitamura

University of Edinburgh

Role of macrophage chemokine signals in efficacy of therapeutic modalities for metastatic outgrowth of breast cancer cells

Metastatic breast cancer cannot be cured using current therapies including chemotherapy and immunotherapy. However, studies suggest that the efficacy of these therapies can be improved by depletion of macrophages as these cells protect breast cancer cells from the effects of cytotoxic drugs, such as doxorubicin, and immune cells, such as NK cells. We found that macrophages are recruited to the metastatic lung and interact with disseminating breast cancer cells via chemokine signals, which promotes metastatic tumour outgrowth. We will test whether macrophage blockade by chemokine receptor inhibition improves the efficacy of doxorubicin and NK-cell-based immunotherapy.

We have prepared bone marrow chimeric mice that lack chemokine receptors and mouse breast cancer cells that are killed by doxorubicin or NK cells in vitro but not in the tumour’s microenvironment. Using these tools and chemokine receptor antagonists, we will test whether chemokine receptor inhibition affects metastatic tumour growth in lungs under doxorubicin treatment or adoptive transfer of NK cells. We will also investigate number and status of cytotoxic immune cells, vascular status, and tumour cell apoptosis using flow cytometry and immunostaining to address possible mechanisms.

This study will test whether inhibition of macrophage-mediated chemokine signals can be a new strategy to improve therapeutic modalities for metastatic breast cancer.

Dr Michael Kohl

University of Oxford

Spatio-temporally multiplexed 2-photon imaging determining neural coding principles of sensory perception

How does the brain encode the contents of sensory perception and translate them into meaningful neuronal representations of our environment? We know approximately how sensory input is routed through different brain areas, each extracting distinct aspects of the percept, but the neuronal language used to represent sensory experiences remains elusive. We will unravel the coding strategies employed in the neuronal representation of tactile sensory input.

We will use two-photon microscopy and optogenetic tools to monitor and manipulate neural activity in the neocortex of mice. Combining cell type and circuit-specific optical recording and manipulation in studies of awake, behaving mice will permit significant conclusions about general coding principles and allow causal links between neural codes and behavioural output. We will record neural activity in at least two different depths in the cerebral cortex simultaneously.

Data generated with this technology will be key to understanding neural circuit function in different cortical layers and provide preliminary data for more substantial research

Dr Katherine Morley

King’s College London

ASTERISK: Addiction Services Treatment Evaluation of RISK

This proposal is the first stage of Addiction Services Treatment Evaluation of Risk (ASTERISK), an interdisciplinary project using the electronic health record (EHR) to predict risk and develop tools for stratified care in drug and alcohol addiction treatment. 

This initial project provides a foundation for further research by creating phenotype algorithms that can extract clinically meaningful data from the EHR for patients who have been treated for addiction. The algorithm will be used to identify liver disease risk factors in a cohort of patients with addiction issues using EHR data from a large UK mental healthcare provider. Liver disease will be used as an exemplar to establish the viability of ASTERISK, but the strategy will be applied to other clinical outcomes.

The research findings will form the basis of a grant to expand ASTERISK from identifying risk factors to developing clinical prediction tools. It will use EHR data to develop a prediction model, then investigate its clinical impact and test its validity. The outcome of this larger project will be novel tools for implementing stratified care, embedded in EHR systems.

Professor Richard Mott

University of London

The impact of epigenetics on DNA-DNA interactions

It has become clear that DNA-DNA interactions are an important component of gene regulation and of the genetics of complex traits. The impact of DNA variation of these interactions is less well understood. This project will characterise two important loci, the major histocompatibility locus (MHC) and the imprinted H19/Igf2 locus in mice. These loci play key roles in immunity and growth and serve as models for the rest of the genome.

We will use Capture-C sequencing to assay DNA-DNA interactions between sites within these two loci and the rest of the genome, and CTCF-binding genome-wide, in two divergent in-bred strains and in reciprocal crosses of these two strains. We will repeat these assays in knockout mice. The experiment will tell us which genome-wide loci  interact with these loci. In particular, we will be able to test a prediction from our previous work that physical interactions occur between the MHC and H19/Igf2, and that genetic perturbations at the loci disturb these interactions.

These experiments will provide important proofs of principle of links between imprinted loci and the MHC.

Dr Christopher Moxon

University of Liverpool

Transcriptomic profiling in an in vitro model and post-mortem tissue samples to investigate sequestration driven pathology in cerebral malaria

Cytoadherence of Plasmodium falciparum parasitised red blood cells (pRBC) to endothelium is a hallmark of human cerebral malaria (CM) but is absent in rodents. We have developed an in vitro model whereby pRBC are cultured with primary brain endothelial cells – pRBC cytoadhere – leading to endothelial and coagulation activation. A variety of manipulations are possible. We aim to validate the biological relevance of this in vitro model by comparing findings from archival post-mortem tissue from people with CM. Transcriptomics provides a means to profile and compare key cellular activities in the endothelium from post-mortem brain tissue and the in vitro model, providing an indication of the similarities and differences between these distinct but potentially complementary sources. We want to identify differentially regulated pathways induced specifically by pRBC in both post-mortem and in vitro samples.

If feasible this would enable mechanistic examination and screening of candidate drugs in vitro to targets identified to be relevant to disease in patients.

Dr Silvia Munoz-Descalzo

University of Bath

Wnt/b-catenin signalling facilitates cell face decision-making in the early mouse embryo

Wnt/b-catenin signalling is a widespread cell signalling pathway with multiple roles during vertebrate development and disease. In mouse embryos stem cells (mESCs), there is a dual role for b-catenin: it promotes differentiation when activated as part of the Wnt/b-catenin signalling pathway and promotes stable pluripotency independently of signalling. The first requirement for Wnt/b-catenin signalling during mouse development has been reported at implantation. The relationship between b-catenin and pluripotency and that of mESCs cells with EPI progenitors suggests b-catenin has a functional role during preimplantation development.

We predict that active Wnt/b-catenin signalling is involved in the decision between developing into epiblast or primitive endoderm (PrE). Our preliminary results support that Wnt/b-catenin signalling promotes PrE differentiation in the mouse embryo. Our hypothesis will be addressed using a single cell quantitative approach to define the role of Wnt/b-catenin during PrE differentiation from 1-18 months. We will also elucidate the cellular mechanism by which b-catenin (Wnt/b-catenin) facilitates PrE differentiation from 18-24 months.

This study will have important implications for assisted reproduction and stem cell biology.

Dr Pavel Novak

Queen Mary, University of London

Mapping mechanotransduction mediated by primary cilia at nanoscale

Mechanical stimulation is one of the key physiological stimuli. Abnormalities in mechanical load or in cellular mechano-sensitivity have been linked to diseases such as osteoporosis, osteoarthritis and polycystic kidney disease. No effective treatment exists for these conditions as our understanding of mechanotransduction is still incomplete. A unique membrane protrusion called primary cilium, and a number of membrane receptors sensitive to mechanical and chemical stimuli have been implicated in mechanotransduction, however the signalling pathways remain uncertain.

We hypothesise that the role of receptors involved in mechanosensing is affected by their precise location within the fine ultrastructure of the primary cilium. We will investigate this hypothesis using scanning nanopipette microscopy. We will establish recordings of channel activity in response to mechanical stimulation at precisely defined locations on primary cilium and develop a technique for mapping local sensitivity to chemical stimuli using highly localised dosing.

The established techniques will be used to gather preliminary data on the distribution of mechano-chemical receptors to support a research proposal aimed at understanding the reorganisation of mechanotransduction in ciliated cells during disease.

Dr Paul O’Reilly

King’s College London

Detecting inversion polymorphisms from SNP data

The overarching aim of this project is to determine the most powerful method for detecting and genotyping single-mutation inversion polymorphisms from data from single nucleotide polymorphisms. It is presently unclear which SNP-based inversion detection method is the best, and so before embarking on costly validation via sequencing in a larger study, we will perform a comprehensive comparison study to determine the most powerful method.

The development of the methodology, a comparison study and the associated software tool we produce will provide a perfect platform for a larger study and application to investigate the impact of inversions on disease, the genome and the evolution of our species.

Two methods will be developed to completion in the project and they will be extended to detect more complex inversions in the larger study.

Dr Smita Patel

University of Oxford

Abnormalities in V(D)J recombination in common variable immunodeficiency disorders

The common variable immunodeficiency disorders (CVIDs) comprise a group of heterogeneous primary antibody deficiencies and form the most clinically significant antibody failure in adults and children. For the majority of patients with CVIDs the condition is sporadic, heterogeneous and polygenic.

We have applied whole genome sequencing techniques to a small cohort of patients with sporadic CVID and preliminary findings reveal multiple variants in the DNA repair pathway, in particular the V(D)J recombination associated genes. We will use next generation sequencing techniques to identify V(D)J recombination defects on CVID patients and establish a causative link by mimicking identified defects in fibroblast cell lines using the CRISPR-Cas9 system. We will study the functional effect by analysing expression and radiosensitivity using the gH2AX assay. We will then link the genetic and functional defects back to the clinical phenotype.

We expect to identify a subgroup of patients with CVID with defects in V(D)J recombination that explains their complex phenotype. This will lead to better stratification, earlier diagnosis and potential new treatments targeting the DNA repair pathway.

Dr Davor Pavlovic

University of Birmingham

Examining the role of endogenous cardiotonic steroids in cardiovascular disease development

Cardiovascular disease is one of the leading causes of death in the UK and USA. Experimental evidence from animals suggests that chronic elevation of cardiotonic steroids (CTS) may play a pivotal role in development of cardiovascular disease. However, the chemical identity of CTS and their pathophysiological role in patients with cardiovascular disease remains unclear.

We will develop novel, sensitive, analytical liquid chromatography–mass spectrometry (LC-MS) techniques for detection and quantification of CTS in the serum. We will measure CTS serum concentrations in individual patients and the effects of serum on intracellular sodium and calcium concentrations in human-induced pluripotent stem-cell-derived cardiomyocytes. We will correlate the analytical and functional data we obtain with clinical cardiovascular parameters and functional outcomes in individual patients.

By generating fundamental tools that quantify individual CTS species in the serum and characterising their effects on sodium and calcium regulation in human cardiomyocytes, this study aims to provide crucial clinical information on the role of CTS in development of cardiovascular disease which will help with the development of management strategies for the disease.

Dr Argyris Politis

King’s College London

Determining the structure and dynamics of membrane transporters

Despite the realisation that lipids play a critical role for the structure and function of membrane proteins, the complexity of lipid-protein interactions makes them challenging to characterise by conventional tools and they remain poorly described at molecular level. Lactose permease (LacY) is a structurally well-characterised member of the major facilitator superfamily (MFS) of transporters; its dynamics however remain largely unknown.

We propose to advance knowledge regarding the conformational dynamics of LacY and its synergistic binding to lipids and other biomolecules. This will underlie efforts for drug discovery and human health.

We aim to provide an unprecedented level of molecular understanding of transmembrane transporters and their interactions with their surrounding environment. To achieve this, we will integrate a novel combination of mass spectrometry (MS)-based experiments with advanced modelling methods enabling investigation of previously intractable protein structures and molecular interactions. A key goal is to perform proof-of-principle studies on the structural dynamics of E. coli LacY and its interaction with lipids.

Dr Sovan Sarkar

University of Birmingham

Human cellular platforms for studying the regulation and therapeutic application of autophagy

Autophagy is an intracellular degradation pathway essential for cell survival. Stimulating this process is beneficial in diverse diseases, including certain neurodegenerative and liver disorders. However, therapeutic exploitation of autophagy in patients has not been achieved. Our studies indicate that not all autophagy inducers identified in non-human or immortalised human cells are effective when applied to people with disease, indicating cell-type specificity of drug action. This discrepancy cannot be resolved until the precise regulation of autophagy in the human system is elucidated.

In this proposal, we aim to establish the first physiological and disease-relevant human cellular platforms to study the autophagy landscape using human embryonic stem cells (hESCs) and hESC-derived disease-relevant cell-types. We have generated stable reporter and autophagy-deficient hESC lines using genome editing. We will investigate the autophagy-regulating kinome in hESCs, and establish hESC-derived neuronal and hepatic cultures with quantifiable autophagy readout to measure the kinetics.

We will extend this study to understand the regulation of autophagy in these human cellular platforms, and to identify human tissue-specific autophagy modulators for therapeutic applications.

Dr Stefania Spano

University of Aberdeen

Typhoid fever: novel cellular mechanisms driving host defence

Typhoid fever is caused by Salmonella enterica serovar Typhi (S. Typhi), a unique intracellular pathogen that only infects humans. The molecular mechanisms underlying this host specificity are still poorly understood. I have identified a novel trafficking pathway that blocks S. Typhi survival in macrophages from non-susceptible hosts, such as mice. This pathway, which depends on Rab32 GTPase, is emerging as a general antimicrobial pathway critical for killing intracellular pathogens. The differences in this pathway between mice and humans may underpin the successful infection of humans by S. Typhi. My preliminary data, backed by genome-wide association studies, suggest that this pathway is active in humans but there must be substantial differences to account for the different host susceptibilities.

The objectives of this project are to determine the role of the Rab32 antimicrobial pathway in controlling pathogen growth in humans and elucidate the mechanisms that kill S. Typhi in human macrophages.

These studies will empower a larger study to identify novel S. Typhi virulence factors and to suggest ways to boost innate immunity pathways to control bacterial diseases.

Dr Adam Tierney

Birkbeck, University of London

Speech perception in amusia

Amusia is a disorder characterised by impaired pitch discrimination, which interferes with the perception of music and speech in laboratory conditions. However, people with amusia do not report problems with speech perception in everyday life. We hypothesise that amusics compensate for their deficit by focusing on durational information in speech, which provides cues to structural elements marked by pitch changes.

We will develop a behavioural and functional magnetic resonance imaging battery designed to test this compensatory hypothesis. Lexical stress perception, prosody perception, and speech-in-noise perception will be tested in three different conditions: with unaltered stimuli; with only pitch cues; and with only durational cues. We predict that people with amusia will be impaired only on the conditions containing only pitch cues. We further predict that the pattern of activation elicited when both pitch and duration cues are present will closely resemble the pattern when only durational cues are present, while pitch- and duration-tracking networks will be equally represented in control subjects.

The development of this testing paradigm would enable evaluation of pitch and duration processing during speech perception in a variety of populations.

Dr Edze Westra

University of Exeter

Putative gene regulatory functions of Csy1, a component of the CRISPR-Cas adaptive immune system, in the opportunistic pathogen Pseudomonas aeruginosa

It is becoming increasingly clear that clustered regularly interspaced short palindromic repeats; CRISPR-associated (CRISPR-Cas) systems function beyond adaptive immunity. Preliminary data show that CRISPR-Cas deletion from Pseudomonas aeruginosa reduces both in vitro fitness and in vivo virulence. These phenotypes are caused by Csy1, a Cas protein thought to be involved in sequence-specific binding of the 5'-handle of crRNA. We hypothesise that Csy1 regulates expression of genes carrying sequence motifs similar to the 5'-handle. 

We will test this hypothesis using transcriptome analysis of WT and Csy1 deletion mutants, RIP-seq analysis of RNA co-purifying with Csy1 and EMSA to measure sequence specificity of Csy1-RNA interactions. This project will reveal whether Csy1 of the P. aeruginosa CRISPR-Cas system has a gene regulation function and will identify specific RNA motifs targeted by Csy1.

If successful, the data from this seed project will serve as a basis for a larger proposal aimed at validating the Csy1-motif interactions in vivo, generalising Csy1-mediated gene regulation across P. aeruginosa strains and testing the impact of Csy1 on P. aeruginosa virulence in other, more relevant, infection models, such as cell culture and thermally-injured mouse infection models.

2015 Round 1

Dr Emily Adams

Liverpool School of Tropical Medicine

Molecular diagnostic intervention in elimination campaigns for visceral leishmaniasis

The London Declaration set a target for elimination of visceral leishmaniasis (VL) in 2012, but data clearly show that elimination targets will not be reached by only diagnosing those who seek healthcare. Elimination is reliant on alternative diagnostic tests that are able to detect active leishmania. Much of the epidemiology of VL, including infection in asymptomatic patients, is unknown. A proven method of detection of active infection in asymptomatic patients would enable epidemiological research to better guide effective interventions. The simplified molecular diagnostic, LAMP, is capable of identifying people who are actively infected with leishmania regardless of disease status.

We aim to evaluate LAMP in a VL programmatic context, assess diagnostic accuracy for early diagnosis and test LAMP on near neighbours of index cases. These scoping studies will deliver evidence on the potential of LAMP to overcome existing deficiencies in VL diagnostics.

This study will seed future funding to redefine the epidemiology of VL, improve the design of effective interventions and monitor and evaluate programmatic end points.

Dr Paras Anand

Imperial College London

Molecular mechanism of NOD2-mediated anti-inflammatory signalling

The Nod-like receptor protein NOD2 participates in the recognition of conserved motifs in bacterial peptidoglycan and recruits adaptor RIPK2 to induce pro-inflammatory and antimicrobial responses through the activation of NF-kB signalling. Paradoxically, several studies have revealed that loss-of-function mutations in the Card15 gene encoding NOD2 predispose people to Crohn’s disease, a chronic inflammatory condition of the gut. Our preliminary data suggest that Nod2-deficient cells display deregulated NF-kB activation and that NOD2 interacts with family member NLRP6 in a RIPK2-independent manner. Studies suggest that both of these molecules are required to mediate anti-inflammatory signalling.

We propose to mechanistically characterise the NOD2-NLRP6 interaction in response to various ligands. We will also elucidate the localisation and kinetics of NOD2-NLRP6 assembly using immunofluorescence microscopy. Finally, we will measure the impact of this interaction on pathogen survival and inflammatory activity by studying NOD2-variants associated with Crohn’s disease.

These studies will allow us to identify potential therapeutic strategies for Crohn’s disease.

Dr Vassiliy Bavro

University of Birmingham

Elucidating the interaction of antibiotics with multi-drug efflux-pumps

Secondary transporters of the RND family, such as AcrB, are principal contributors to non-specific multidrug resistance (MDR). They do this by actively pumping antibiotics out of the periplasm of Gram-negative bacteria. Despite the progress in structural understanding of the RND-pump function, only a limited number of drug-bound complexes have been resolved. Finding out the binding mode of several important classes of antibiotics including fluoroquinolones and beta-lactams would inform the development of novel therapeutics. We have identified that the major cause for the lack of drug-transporter complex structures is that RND-transporters use detergents as their primary substrates.

We will target the problem by employing an alternative solubilisation-strategy of the transporter-antibiotic complexes, styrene-maleic acid co-polymer (SMA) which we recently successfully demonstrated in single-particle studies of AcrB. We will use this technology to solve structures of the wild-type and G288D mutant of Salmonella AcrB, creating a shift in the antibiotic selectivity of the pump.

These crystal structures will provide crucial information about the mode of fluoroquinolone binding and mechanisms of MDR, while the success of SMA-based crystallisation will allow effective antibiotic-soaking that will usher a new era of research into antibiotics and pump inhibitors.

Dr James Bowe

King's College London

Adaptation of pancreatic islets to pregnancy: a role for kisspeptin

In 2013, more than 60% of deaths and a massive burden of disease in children under the age of five years in sub-Saharan Africa were due to infections. However, individual responses to infection are highly variable and risk factors predisposing children to death and disease remain poorly understood. Potentially life-saving interventions that can reduce or remove risk factors may have been overlooked. A plausible risk factor is chronic infection with human schistosomes. Infection with these parasites causes schistosomiasis, the second most important parasitic disease in sub-Saharan Africa. In addition to direct local and systemic pathological effects, schistosome infection also exacerbates pathology and alters overall host immune phenotype and physiology. It is therefore surprising that the indirect, long-term effects of schistosome infection on host health remain un-investigated.

This project aims to optimise novel and innovative systems biology assays for assessing host health status including infection, clinical presentation of disease and response to vaccination. T
he project will act as a pilot for a larger study combining epidemiological investigations of schistosome infection in young children as a risk factor for subsequent death or disease due to other causes with investigations of altered progrOur preliminary data support a novel and important role for placental kisspeptin in beta-cell adaptations for the metabolic demands of pregnancy. This project will test the hypothesis that circulating kisspeptin in pregnancy acts as a placental signal to inform beta-cells of the pregnancy and to mediate adaptive responses to pregnancy in the cells. Failure of this system in pregnancy may reduce or prevent the pregnant woman’s adaptive responses to increased metabolic load and peripheral insulin resistance, leading to the development of gestational diabetes.

The hypothesis will be addressed through two main experimental objectives. We will define the role of placental kisspeptin in enhancing beta-cell insulin secretory responses to compensate for pregnancy-induced insulin resistance and investigate the role of kisspeptin in beta-cell proliferation leading to increased islet mass during pregnancy.

Dr Michael Bryant

University of Leeds

Exploring the links between metallic cardiovascular device degradation and local biological functionality

Stents are commonly used for the treatment of occlusive atherosclerotic diseases (OAD). In-stent restenosis (ISR) has been seen to occur at a very high rate six months after implantation. This can have devastating effects including death. Braided stents or stents in an overlapped configuration are commonly used to bridge atherosclerotic legions. However, this introduces interfaces that are susceptible to tribocorrosion (formation of metal ions and nano-particles). While it is hypothesised that metal-ion release affects local principal resident cells of the blood vessel walls resulting in adverse remodelling, the mechanisms for this are still unclear. The influence of nano-particles has never been considered.

This project aims to investigate the role of NiTi/CoCr alloy degradation on the adverse remodelling of vasculature. Through the use of novel fretting corrosion, organ culture and bio-reactor methodologies, the role of metallic debris on local biological reactions and subsequent toxicity of debris will be determined.

We will uncover the role of metal degradation and the mechanisms behind inflammation and in-stent restenosis using a combination of novel methodologies.

Dr Dermot Cox

Royal College of Surgeons in Ireland

Validation of FcgRlla as a potential drug target in sepsis

Dr Aude Echalier

University of Leicester

Regulation of the ubiquitinylation pathway by conformational inhibitors of the COP9 signalosome

The human deubiquitinylase (DUB) family that comprises five sub-families (four Cys-based and one Zn-dependent) play major roles in signalling pathways and are implicated in several cancers. Understanding the functions of Cys-based DUBs has been facilitated by tools selectively targeting these enzymes, whereas progress on Zn-dependent MPN/JAMMs has been hampered by the lack of selective probes.

Building on our recent work on MPN/JAMM CSN5, we are now directing our research towards the development of conformational probes that target MPN/JAMM DUB enzymes. This study will specifically target CSN5, the catalytic subunit of the COP9 signalosome (CSN), responsible for the regulation of Cullin-based E3 Ub ligases (CRLs). Outside of the CSN, CSN5 is kept inactive through a conformational auto-inhibitory lock and is void of deneddylase activity (hydrolytic activity on Nedd8-modified proteins). This project aims to: identify, characterise and functionalise Zn-binding groups selective f or the inactive form of CSN5; characterise the synthesised molecules and determine their inhibitory mechanism; and validate probes in vitro and in cell extracts.

We anticipate that these tools will be useful for several applications, including the study of CSN-dependent/independent functions of CSN5; the identification of CSN5 partners; and the development of CSN5 inhibitor lead molecules for bio-medical applications.

Dr Elian Fink

University of Cambridge

Baby talk and baby blues: harnessing technology to investigate mechanisms of influence of parental wellbeing on infants

Postnatal depression (PND) occurs in 10-20% of new mothers and is associated with adverse long-term consequences for children. Parents with PND are likely to be less responsive and sensitive during parent-infant interaction and this can have a negative impact on parental baby talk, a specialised form of speech used by adults when speaking to infants. Impairments in baby talk have long-term adverse effects on children’s social, emotional and cognitive development.

This project will investigate a cost-effective and efficient means to collect and code baby talk and parent-child interactions, which is currently extremely labour intensive. We propose to use LENA, a talk pedometer worn by babies to collect and code their linguistic environments, and EMOTIONSENSE, an application that tracks emotion over time. This information will then be used to examine differences in low, medium and high-risk PND groups in: baby-talk assessed via traditional gold standard methods and novel technologies; the links between pre- and postnatal parental wellbeing in parents; and the links between the quality of parent-infant interaction and emotional, cognitive and social development in early toddlerhood.

Professor Kevin G Hardwick

University of Edinburgh

Engineering a synthetic fission yeast chromosome

The spindle checkpoint is medically important, biologically fascinating, but mechanistically complex. All the major components have been known for decades, yet we still do not know how they work. Simple gene deletion/mutation approaches have reached their limitation as spindle checkpoint signals are transmitted by modulating protein-protein interactions and/or conformational changes, sometimes in response to post-translational modifications. We need a new approach to overcome these limitations.

I will use synthetic biology to artificially generate and transmit checkpoint signals from ectopic, non-centromere, locations. Signalling modules will be assembled de novo and assayed for activity. In the longer term we envisage analyses of multiple pathways to study cross-talk and inhibition. Our goals are: to definitively test models of spindle checkpoint signalling and find out how signalling scaffold is assembled and activated to generate a diffusible checkpoint signal. We will also construct synthetic arrays to provide a platform for functional dissection of this pathway in yeast. We will combine the array with chemical inducers of dimerisation (CIDs) and the SunTag. This will enable us to assemble and regulate a mitotic checkpoint complex (MCC) generator.

This research will help us to uncover the mechanisms that underlie the spindle checkpoint.

Dr Shobbir Hussain

University of Bath

Epitranscriptomics in neuronal circuit formation

Recent technological advances have allowed us to gain sequence-specific information regarding the occurrence of RNA modifications in transcriptome-wide settings and this has led to the emergence of a new field of study called epitranscriptomics. The field is progressing rapidly and has already yielded important biological insights. I previously developed a technique called methylation-iCLIP (miCLIP) that was used to determine methyl-5-cytosine (m5C) modifications in RNAs at nucleotide-resolution and in an RNA methylase-specific manner. Our evidence suggests a likely biological role in regulating axon guidance during neuronal circuit formation. This current proposal will strengthen and further establish these preliminary findings. 

We will use Xenopus as a model system to examine the molecular roles of RNA modifications in controlling cue-dependent localised mRNA translation in axonal compartments and determine the physiological roles in terms of regulating axonal navigation decisions and synapse formation.

Although epitranscriptomics is a new area of study, we aim to promote this field into mainstream molecular genetics research.

Dr Abderrahmane Kaidi

University of Bristol

Molecular mechanisms linking nuclear lamina and chromatin organisation

The nuclear lamina (NL), partly composed of lamin-A/C proteins, plays key roles in maintaining nuclear structural integrity and chromatin organisation with profound effects on genome transductions and cellular functions. Deregulation of lamin-A/C results in chromatin disorganisation and is associated with premature and physiological cellular ageing. However, mechanistic understanding of the reciprocal functional relationship between NL and chromatin organisation remain challenging.

After discovering that a key role for the lysine acetyltransferase KAT5 is sensing and transducing chromatin perturbation signals, we hypothesised that this pathway may mechanistically couple NL and chromatin organisation. Accordingly, we found that KAT5 is activated in lamin-A/C defective cells as well as in cells treated with lysine deacetylase (KDAC) inhibitors. We will use novel reagents and develop new experimental tools to determine: whether KAT5 mediates further chromatin disorganisation in lamin-A/C-defective cells and whether chromatin perturbations influence nuclear lamina in a manner that involves KAT5.

Achieving these goals will provide the basis for further investigations into the reciprocal crosstalk between nuclear lamina and chromatin organisation with the long-term vision of understanding the fundamental principals underlying genome organisation/regulation and their relevance to human ageing.

Dr Robert Knight

King's College London

Optogenetic dissection of NF-kB function in controlling macrophage behaviour during tissue regeneration

Transcription factor nuclear factor (NF)-kB is a critical regulator of macrophages and is implicated in several chronic diseases affecting muscle. Macrophages migrate into injured muscle during regeneration. This coincides with NF-kB activation in many cell types, but it is not understood how NF-kB controls macrophage behaviour in this context. Based on our characterisation of muscle regeneration in zebrafish, we propose that NF-kB activity directs macrophage migration and that this is important for effective regeneration. This proposal therefore aims to determine how NF-kB signalling regulates macrophage responses to muscle injury in vivo.

We will use a combination of genetic and optical techniques in the zebrafish to manipulate NF-kB activity and show how this affects macrophage cell behaviour in the context of tissue regeneration. We will build a novel optogenetic system for rapidly activating NF-kB in a highly localised manner. This will permit direct visualisation of macrophage cell responses to activation of NF-kB.

This project will allow us to show whether macrophage migration to wound sites requires NF-kB signalling and we will develop a light-controlled optogenetic system for control of NF-kB activity in individual cells. We will then be able to show whether macrophage behaviour is affected by optogenetic activation of NF-kB signalling.

Dr Andriy Kozlov

Imperial College London

Direct recording of mechano-electrical transduction currents and forces from individual stereocilia

Mechano-electrical transduction (MET) in the inner ear occurs when a sound's energy is transmitted to MET channels in the hair-cell stereocilia. The gating of channels and stereocilia motion are directly and reciprocally coupled. This mechanical coupling involves tip links which are molecular springs whose tension determines the channels’ open probability. Pulling on a tip link opens a channel and this relaxes the spring. This relaxation, called gating compliance, involves channel motions exceeding a dozen nanometres – astoundingly large for an ion channel. Classical models suggest there is one MET channel connected to a tip link's upper end.

Recent experiments reveal two channels at a tip link's lower end. No model today can explain the number and location of the MET channels, nor how the large gating compliance, necessary for sensitive hearing, occurs.
I propose that adjacent MET channels are energetically coupled through elastic deformations they create in the lipid bilayer, and that they open and close cooperatively. Large gating compliance arises naturally in my model, provided the channels are at the tip link's lower end. This collaborative project will quantify the MET-channel cooperativity and the associated gating compliance using two new methods – a single-stereocilia patch clamp and single-tip-link microrheology.

Dr Seung Seo Lee

University of Southampton

Novel strategy to tackle multidrug-resistant Staphylococcus aureus

Dr Andrew S Lowe

King's College London

Mapping the functional topography of vision in the zebrafish

Topographic organisation wherein neighbours in one space are neighbours in another space is a fundamental organisational feature of sensory processing. In the visual system, topography has been studied using non-specific techniques that average across cell types. These approaches cannot reveal unique biases in visual processing associated with individual cell types.

To understand biological vision we need to know how every type of retinal ganglion cell (RGC) in every part of the retina is mapped onto central targets. We will use a systems-based approach for revealing topographic maps for distinct functional types of RGCs innervating the optic tectum of the zebrafish. We aim to: derive topographic maps across the whole of visual space, for three distinct types of RGC inputs to the optic tectum and chart their developmental dynamics; provide an experimental, neuroimaging and informatics framework with which to map topography across all retino-recipient brain regions; and augment future studies designed to reveal and map all functional types of RGCs.

This work will introduce a conceptual advance in how visual processing can be studied.

Dr Vincenzo Marra

University of Leicester

Pre- and postsynaptic determinants of neurotransmitter release at individual release sites

Connections between neurons are made up of several individual release sites, each with a different probability of releasing a neurotransmitter upon arrival of an action potential. How pre- and postsynaptic neurons work in concert to regulate release probability (Pr) at different connection points is still unclear. A novel combination of techniques will be used to study Pr at individual active zones and to identify the mechanisms involved in its regulation.

We will test the hypothesis that Pr is regulated in concert by both pre- and postsynaptic compartments using electrophysiology, live fluorescence imaging and serial electron microscopy both at cortical boutons and at the Calyx of Held, a giant synapse in the auditory pathway. By labelling pre- or postsynaptic cortical neurons, we will ascertain whether the presynaptic origin as well as the target neuron play a key role in setting Pr at the cellular and network level. Using the Calyx of Held, where hundreds of active zones contact the same postsynaptic soma, will reduce confounding elements, such as compartmentalised postsynaptic activity.

This project will identify the mechanisms by which individual terminals embedded in a network set synaptic strength which will be useful for detection of synaptic changes and degeneration at an early stage.

Dr Clive McKimmie

University of Glasgow

Elucidating the mechanisms by which mosquito-borne viruses disseminate in vivo and cause disease

This project will determine the cellular basis by which arthropod-borne viruses (arboviruses) disseminate in vivo; a process that is essential for their transmission and pathogenesis. Arboviruses spread disease in humans and livestock. After infection by an arthropod bite, arboviruses disseminate to the blood (viraemia). Subsequently, arboviruses spread to distal sites where they can cause severe disease including encephalitis, arthritis or hemorrhagic fevers, the severity of which depends on the establishment of high viraemia. Importantly, little is known about which cell types fuel this viraemia and how arboviruses spread to distal sites.

This project will determine the origin of viraemia using an innovative technique based on inhibition of virus replication in specific cell types. By genetically engineering viruses to encode a microRNA target site in their genome, viral replication will be blocked specifically in cells expressing the corresponding microRNA. This will enable us to dissect the contribution of viral replication in defined cell compartments from the inoculation site to distal tissue, and so define the critical events that lead to systemic spread.

This will provide novel, fundamental insights that will aid the design of innovative treatment strategies.

Dr Francisca Mutapi

University of Edinburgh

Paediatric Schistosomiasis: indirect, long-term impacts on health

In 2013, more than 60% of deaths and a massive burden of disease in children under the age of five years in sub-Saharan Africa were due to infections. However, individual responses to infection are highly variable and risk factors predisposing children to death and disease remain poorly understood. Potentially life-saving interventions that can reduce or remove risk factors may have been overlooked. A plausible risk factor is chronic infection with human schistosomes. Infection with these parasites causes schistosomiasis, the second most important parasitic disease in sub-Saharan Africa. In addition to direct local and systemic pathological effects, schistosome infection also exacerbates pathology and alters overall host immune phenotype and physiology. It is therefore surprising that the indirect, long-term effects of schistosome infection on host health remain un-investigated.

This project aims to optimise novel and innovative systems biology assays for assessing host health status including infection, clinical presentation of disease and response to vaccination. The project will act as a pilot for a larger study combining epidemiological investigations of schistosome infection in young children as a risk factor for subsequent death or disease due to other causes with investigations of altered progression of a range of infectious and non-infectious diseases.

Dr Dervla O'Malley

University College Cork

Electrophysiological investigations on the molecular mechanisms underlying gut-to-brain signalling evoked by colonic microbiota

Studies have demonstrated how altering the intestinal microbiome with commensal probiotics has beneficial effects both on gut function but more intriguingly, on central nervous system (CNS) function. This has led to the concept of the 'microbiota-gut-brain' signalling axis. Although the vagus nerve has been implicated, little is understood of the cellular and molecular events that translate changes in external luminal bacteria to the enteric nervous or endocrine systems and on to the CNS. Neural, hormonal and immune factors are likely candidates. Indeed, we have previously demonstrated that activation of stress hormones in an environment of low-grade mucosal inflammation underlies the initiation, exacerbation and prolongation of bowel disorders.

We will use electrophysiology to record vagal nerve firing from intact ex vivo colon sections exposed to various probiotics (GABA-, conjugated poly-unsaturated fatty acid- and exopolysaccharide-producing Lactobacillus strains). Underlying molecular mechanisms will be investigated using pharmacological and immune inhibitors of likely molecular mediators, such as toll-like receptors, cytokines and gastrointestinal hormones.

This study will contribute significantly to our understanding of microbiota-gut-brain signalling and will support a larger grant application.

Dr Helen Price

Keele University

Nanoparticle-induced hyperthermia as a novel therapy for cutaneous leishmaniasis

Dr Subrayal Reddy

University of Surrey

Smart materials: development of molecularly-imprinted polymers as synthetic antibodies for the metaphylactic and therapeutic treatment of viral infection

Dr Tobias Reichenbach

Imperial College London

Multi-timescale processing of speech through cortical oscillations in health and in aphasic stroke

Aphasia is a communication and language disorder that affects a majority of stroke victims and that affects work, family life and everyday tasks. Rehabilitation from aphasic stroke is costly and yields mixed results. This project aims to develop a novel assessment of aphasia that can guide clinical treatment. This will use progress, including from my own group, on the multi-timescale neural oscillations in the cerebral cortex that track critical multi-timescale features of speech. I hypothesise that this neural mechanism for processing speech is impaired in aphasia.

I will investigate this hypothesis using EEG recordings of cortical responses to speech in health as well as in aphasic stroke. My goals are to investigate how cortical oscillations in response to speech differ in healthy people and in patients with aphasic stroke and how they recover during rehabilitation training from aphasic stroke. I will also examine how this can be used to stratify patients with aphasic stroke according to benefit from therapy.

This study will yield pilot data that will define scope and size of a larger systematic investigation.

Dr Marc De La Roche

University of Cambridge

SAR-guided engineering of stem cell probes

Stem cells orchestrate tissue development and homeostasis and hold vast therapeutic potential for tissue regeneration and repair. However, the ability to study basic stem cell biology in vitro is hampered by the lack of robust probes allowing their identification and isolation. R-spondins (RSPOs) are ligands for LGRs, receptors which have emerged as faithful stem cell markers in a number of tissues.

We have developed an expression system for the generation of RSPO fusion proteins that bind LGRs with high affinity. We will combine pairwise in vitro binding data between RSPO and LGR isoforms with functional assays of RSPO activity to predict optimal amino acid substitutions along the RSPO binding interface conferring specificity to each of the three LGR isoforms. We will refine these predictions based on structural analysis of RSPO and LGR pairs. Structure-activity relationships based on amino acid substitutions in the RSPO binding interface will instruct the engineering of RSPOs (engRSPOs) that selectively bind each LGR isoform.

EngRSPOs will be used for the isolation of individual stem cell compartments which we will exploit for future studies uncovering basic mechanisms that maintain stem cell pluripotency.

Dr Avinash R Shenoy

Imperial College London

Cell-intrinsic functions of inflammatory caspases in human diseases

Inflammatory caspases, which include caspase-1, caspase-4 and caspase-5, promote inflammation and antimicrobial immunity by regulating two key processes – the release of proinflammatory cytokines and danger signals and pyroptotic host cell death. Distinct cell-intrinsic substrates of caspases are likely to mediate cytokine release or pyroptosis but the precise mechanisms are unclear.

We want to test which caspase-1 substrates mediate cytokine release and/or pyroptosis. Deregulated cytokine release, seen in hereditary autoinflammatory syndromes, is a result of mutations in proteins, such as NLRP3, which lead to constitutive activation of Caspase-1. Data mining of exome sequences revealed several nonsynonymous single nucleotide polymorphisms (nsSNPs) in Caspase-1 substrates, which alter their susceptibility to proteolytic cleavage. We hypothesise that these missense mutations could also affect inflammation if they enhance cytokine release and/or pyroptosis. We will therefore test the phenotypic consequences of nsSNPs on caspase-1-dependent responses.

These mechanistic and phenotypic data will lay the foundation for a future project to study caspase-1 substrates in donor-derived myeloid cells differentiated from inducible pluripotent stem cells (iPSCs). We will examine the molecular links between cell-autonomous activities of caspases and human inflammatory diseases.

Dr Symeon Siniossoglou

University of Cambridge

Probing the unconventional functions of lipins in the nucleus

Lipins catalyse a key step in lipid metabolism that is essential for triacylglycerol production in the endoplasmic reticulum. Triacylglycerol is the major cellular energy storage molecule and disruption of its normal metabolism underpins type 2 diabetes and obesity. Surprisingly, lipins also have a distinct pool in the nucleus of many cell types. How their cytoplasmic lipid metabolic roles are coordinated with their largely uncharacterised nuclear functions is unknown.

We have generated lipin mutants that retain their activity as lipid metabolic enzymes but fail to enter the nucleus. Our aim is to use these mutants to define the functional and physical partners of the yeast lipin Pah1 in the nucleus. This is the first step of a longer-term plan to define the dual function of the lipin family of enzymes. The specific goals of the proposed work are to identify the complete set of genes that are transcriptionally regulated by the nuclear pool of Pah1 and determine whether this regulation is direct or indirect. We will also Identify the genome-wide map of chromatin-bound Pah1 genes and define which factors are required for the function of Pah1 in the nucleus.

Dr Sophie von Stumm

Goldsmiths College, London

Advancing data collection for the behavioural sciences: the practicability of LENA

In the behavioural sciences, conventional assessment methods, such as questionnaires and lab-based observations, produce data of limited reliability and validity, which can weaken studies on childhood development.

To overcome these limitations, I will use LENA, an audio-recording system that registers speech and sound environments of children and families for up to 16 hours. This unobtrusive method of observation could provide an unprecedented wealth of behavioural data on childhood development, including markers of language ability and other individual characteristics, such as temperament, family routines, patterns and environmental factors. My aims are to: test the practicability of LENA for collecting behavioural data from 100 children and their families; identify behavioural and environmental variables that can be reliably extracted from LENA recordings,and validate variables extracted from audio recordings against data obtained through traditional methods, such as questionnaires and testing booklets.

My findings will build the evidence base for a future grant bid for a longitudinal, genetically-sensitive cohort study on childhood development using audio recordings for repeated assessments.

Dr Meera Unnikrishnan

University of Warwick

Developing in vitro co-culture systems for investigating Clostridium difficile-host interactions

Clostridium difficile is a major cause of gastrointestinal infections in hospital settings. C. difficile colonises the human gut when there is an alteration in gut microbiota, usually after antibiotic therapy. The interactions of the bacterium with the host gut cells are of critical importance to infection, yet we know little about how the bacterium attaches, colonises and persists in the gut during infection. A major hurdle in studying host-bacterial interactions is the difficulty of in vitro investigation of this anaerobic bacterium with gut epithelial cells that require oxygen. 

We aim to establish in vitro diffusion chamber infection systems that will allow simultaneous culture of bacteria and intestinal cells under dual environmental conditions. These co-culture models will be valuable tools for studying multiple aspects of clostridial pathogenesis, including bacterial attachment, invasion, micro-colony formation, alongside the local host cell responses to C. difficile infection. We will use these tools to identify and investigate functions of novel C. difficile proteins and processes that mediate gut colonisation.

Robust in vitro systems that mimic the gut environment and allow examination of host-clostridial interactions will be an excellent technical resource for future research into C. difficile.

Dr Kerstin Voelz

University of Birmingham

Elucidating the role of early granuloma formation in dissemination during fungal infections in vivo

Over one billion fungal infections occur each year worldwide of which more than two million develop into life-threatening invasive mycoses. At the same time, our current anti-fungal therapies are ineffective, expensive and show substantial side-effects. As a result, up to 95% of patients with invasive fungal infections will die. Several major fungal pathogens are known to induce the formation of granuloma tissue, such as Aspergillus, Cryptococcus, Histoplasma.

I will initiate a new line of research investigating the role of early granuloma formation during fungal infections using an in vivo zebrafish model. I will determine whether granuloma formation during fungal infection protects the host by trapping fungi or damages it by allowing persistence. This approach will provide information on the spatio-temporal patterns of granuloma formation and immune activation and how these correlate with the spread of disease.

The data will be applied to explain the striking individual variability in susceptibility to and outcome of fungal infections.

Dr Hanieh Yaghootkar

University of Exeter

Monogenic diabetes in Iran

The prevalence of diabetes and obesity is high in Iran but family history and clinical criteria used in Europe may not be useful in diagnosis. Correct diagnosis is important because monogenic forms can often be treated with oral agents rather than insulin. The rate of consanguinity is high and identification of new recessive mutations/genes is easier in consanguineous families.

The aim of this seed project is to establish a collaboration with hospital-based researchers in Iran to understand monogenic diabetes in this Middle Eastern country. Identifying recessive mutations will inform us about the underlying mechanism and diagnostic tests for monogenic diabetes. This will be the first study of the genetics of monogenic diabetes in Iran using next generation sequencing and whole-exome sequencing. I will set up cohorts of monogenic diabetes and use advances in DNA sequencing to assess the role of known and novel genes in the pathogenesis of monogenic diabetes. I will use known genetic variants and non-genetic biomarkers to help classify young patients into type 1 diabetes or likely monogenic diabetes.

People we've funded

Many of our grantholders carry out research in Africa and Asia. See our directories: