Research Opportunities

Progression of arterial disease is critically determined by the response of smooth muscle cells (SMCs) within the medial layer. In their fully differentiated, contractile state, SMCs confer stability and regulate vascular tone. However, disease induces a ‘contractile-synthetic’ phenotypic switch which impairs function, leads to vascular stiffness and exacerbates inflammation, to promote atherosclerosis and susceptibility to abdominal aortic aneurysm (AAA) (1). In animal studies, we have identified candidate pathways, based on knowledge of embryonic SMC differentiation, with the potential to protect against AAA1 and atherosclerosis (2) by preserving contractile SMC phenotype. However, the low success rate in translation from animal studies to the clinic highlights the need to determine whether similar mechanisms serve to protect the human vasculature, and how they may be targeted to alleviate disease.

The aim of the project is to establish human-relevant SMC models in which to study phenotypic switching and disease: i) a monoculture of human coronary artery SMCs; the simple monoculture model will permit evaluation of factors that directly impact SMC modulation, without confounding influences of other cell types.  ii) a more physiologically relevant model of hcSMCs co-cultured with coronary arterial endothelial cells. EC-SMC interaction crucially maintains vascular tone and functionality and dysregulation of this crosstalk underpins pathological remodelling e.g. in intimal hyperplasia. These models will then be used for high genetic and pharmacological screening to reveal disease-modifying targets. The most promising will be explored in murine disease models.
 

1). Munshaw et al. (2021) J Clin Invest 131.(10):e127884.

2). Munshaw, Redpath, Pike & Smart. bioRxiv, 2021.2011.2030.470548 (2021).

Our group investigates embryonic mechanisms of cardiovascular development, to inform cardiac regenerative strategies, through reactivating of developmental processes in the adult heart1. The epicardium plays a crucial role in the embryo, to stimulate growth of the coronary vasculature and maturation of the myocardium (1). A key first step is epithelial to mesenchymal transition (EMT) to yield migratory cells which invade the myocardium and secrete potent paracrine factors. The adult mammalian epicardium is reactivated in response to myocardial infarction and contributes to repair (2), albeit sub-optimally, a major limitation being the extent of endogenous EMT. Based on our knowledge of ‘optimal’ embryonic mechanisms, we seek to enhance epicardial-based regeneration of the injured adult heart. Our preliminary data suggest a novel cell cycle-dependent mechanism controlling EMT and differentiation of epicardial cells, in line with the emerging paradigm of cell cycle control of stem cell fate (3). We will explore this exciting hypothesis by assessing how pharmacological and genetic perturbation of the cell cycle impacts EMT and fate, using functional assays, candidate and unbiased (e.g. RNA-Seq) approaches in cell culture, primary explant and genetic mouse models.

1). Redpath and Smart (2020). Stem Cells Transl Med. doi.org/10.1002/sctm.20-0352.

2). Smart et al. (2011) Nature. 474(7353):640-4.

3). Pauklin & Vallier (2013) Cell 155, 135.

All memories, including social memories, are encoded in neuronal ensembles. Neuronal ensembles are small populations of sparsely distributed neurons selected by specific stimuli. We recently developed and published a mouse model of volitional social learning using a custom-made apparatus. This model provides a unique opportunity to study the neurobiological substrates of volitional social learning and memory. Previous studies have shown that the hippocampus, in particular the CA2 region, is critical for encoding social memories. However, almost all prior studies on the neurobiological basis of mouse social interaction fail to account for the volitional aspect of social interaction. The project we propose entails a collaboration between our lab at University of Oxford and Dr. Hope’s lab at NIDA IRP to investigate the role of hippocampal neuronal ensembles in volitional social learning and memory. Dr. Hope and Dr. Ramsey have developed and implemented the volitional social learning task, and my lab regularly performs in vivo recordings in neuronal ensembles of the hippocampus.  Thus, we will co-mentor a graduate student through the NIH OxCam program to investigate activity in the hippocampus that encodes volitional social memories.

To date, neurodegenerative diseases have no cure and the clinical diagnosis is very challenging due to considerable overlap in the pathology and clinical symptoms. Thus, there is a strong unmet need for objective and sensitive diagnostic methods that can aid clinicians in early identification and differential diagnosis.

We have developed seed amplification assay (SAA) that detects alpha-synuclein (aSyn) aggregation in CSF of patients with synucleinopathies with much higher sensitivity and specificity than previously possible. Our findings also show that aSyn SAA is able to distinguish between Parkinson’s disease and multiple system atrophy and identify patients at high risk with REM sleep behaviour disorder prior to their conversion. Here, we suggest to build a “multiplex” SAA to detect multiple aggregating proteins (aSyn, tau and TDP-43) and test its ability to stratify between dementias of different aetiologies. We are in an exceptional position to deliver this goal because we have the necessary technical knowledge to build robust SAAs combined with access to unique clinico-pathological cohorts with longitudinal CSF and donated brain, where our assay can be tested and validated.

This proof-of-concept data will be used to further evaluate early and accurate diagnosis in larger longitudinal cohort of patients with mild cognitive impairment (MCI) and dementia. The proposed work aims to accelerate clinical trials by providing a “personal protein signature” that can be targeted by therapies tailor-made for individual patients aiming to lower the burden of these specific proteins (e.g. cocktail of vaccinations) and superior means to measure the efficacy of such treatments.

Parkinson’s disease is typically considered to impact motor functions. However, non-motor symptoms, such as visual hallucinations, increase disease burden. Developing therapies for hallucinations in Parkinson’s disease has been challenging, since we do not fully understand what causes them to occur. In the healthy brain, successfully interpreting what one sees involves different neurotransmitters like GABA and Acetylcholine; hence it is possible that pathological processes involving these brain chemicals relate to the generation of visual hallucinations.

The project will investigate the role of neurotransmitters GABA and Acetylcholine in sensory processing in the healthy and Parkinsonian human brain. It will combine pharmacological interventions with human neuroimaging (functional MRI, MR Spectroscopy) and non-invasive brain stimulation, to provide putative targets for therapeutic interventions to alleviate visual hallucinations in Parkinson’s disease.

Research in Oxford will take place at the Wellcome Centre for Integrative Neuroimaging (https://www.win.ox.ac.uk) and the MRC Brain Network Dynamics Unit (https://www.mrcbndu.ox.ac.uk), hosted by the Physiological Neuroimaging Group (https://www.ndcn.ox.ac.uk/research/physiological-neuroimaging-group).

It is becoming clear that the human microbiome extends beyond the gut with bacteria and fungi found in our cells and tissues. In a range of chronic diseases, evidence is emerging that combinations of pathogens are involved in disease.  Myalgic Encephalomyelitis/Chronic fatigue (ME/CFS), Chronic Lyme disease (CLD) and PANS/PANDAS have been linked to the presence of currently unknown pathogens. In CLD and PANS/PANDAS patients antibiotic treatments have been shown to improve symptoms. In ME/CFS raised levels of anti-microbial peptides, increased gut permeability and elevated levels of antibodies raised against specific bacteria have been found in blood. Data from our collaborator SoftCell biologicals indicates that high levels of wall less bacteria (L-Forms) can be cultured from blood, with high numbers of pathogens also detected by deep sequencing.

In this project we will examine blood samples of PANS/PANDAS, ME/CFS, CLD and healthy controls using metagenomic sequencing approaches. L-Form cultures will be established and subjected to anti-pathogen agents. Cell lines will be infected with L-Form organisms and thoroughly characterised using Raman microscopy and assays of mitochondrial function/dynamics. Oxford studies have shown that peripheral blood mononuclear cells from individuals with ME/CFS, multiple sclerosis and healthy controls are very different. Mitochondria also directly interact with parasites. Anti-pathogen agents and drugs which modulate mitophagy will be tested to determine if they can enhance the clearance of pathogens. The impact of Oxidative phosphorylation, glycolysis and different fuels on mitochondrial pathogen clearance will be investigated.

In contrast to patients after myocardial infarction, fish can fully regenerate their hearts. However, not all fish are able to regenerate to the same extent, allowing comparative inter- and intra-species analysis to identify novel mechanisms controlling successful heart regeneration. We have compared the response of seven different wild type zebrafish strains as well as Astyanax mexicanus surface and cavefish to cryo-injury. Preliminary data shows that there are large differences in regeneration within each species. Using RNAseq, we have identifed OXPHOS as a crucial regulator of this difference with increased OXPHOS being beneficial to long term regeneration. This finding indicates that the current stance in the field, that OXPHOS is damaging the ability for heart regeneration, needs to be re-evaluated.

In this project, we will investigate the mechanisms underlying the beneficial role of OXPHOS during regeneration and the techniques you will perform are targeted metabolomics, QTL analysis, RNAseq and Electron Microscopy. As the human heart relies on OXPHOS for energy, the findings from this project could help identify therapies that can direct OXPHOS to enhance cardiomyocyte proliferation and harness the potential of the human heart to regenerate.

The past decade has seen the emergence of population-level magnetic resonance imaging (MRI) studies like the UK Biobank, which is scanning an unprecedented 100,000 individuals. This imaging has enormous potential to inform about early pathology or susceptibility to disease. However, to translate insights from population-level health data resources into the clinic, we require approaches to translating, or ‘harmonising’, between datasets acquired under very different conditions.

A newly funded collaboration between Oxford and the NIH aims to deliver a novel harmonisation approach by linking relevant tissue biology to the physics of the imaging measurement. Core to this ‘biophysical’ approach is a framework for predicting imaging phenotypes from multi-dimensional spectral measurements of MRI-relevant tissue properties.

This DPhil project will deliver the multi-spectral measurements at the heart of this prediction framework. The student will work within our collaborative team to:

• Year 1: implement multi-spectral acquisition protocols and associated analysis pipelines for use in a large cohort;
• Years 2-3: develop novel biophysical modelling that enables us to characterise and restrict the number of modelled tissue compartments, enabling fewer measurements for clinical scanners;
• Year 4: demonstrate the ability to predict imaging phenotypes based on these measurements in order to harmonise measurements from multiple protocols.

This project would be jointly supervised by the neuroimaging experts in Oxford who are leading brain MRI in UK Biobank (Miller) and physics experts at NIH who have pioneered these multi-spectral measurements (Benjamini).

The brain is continuously bombarded with visual input but has limited processing capacity. Learning to selectively process visual features relevant for behaviour is therefore crucial for optimal decision-making and thought to rely on activity of GABAergic inhibitory interneurons. Altered inhibition is linked to perceptual and learning impairments and associated with neurodevelopmental disorders including schizophrenia and autism.

The aim of this project is to understand the precise role of different types of GABAergic inhibitory interneurons during visually-guided learning and decision-making. Mice have a similarly organized visual cortex and show complex decision-making behaviours. Mouse brain circuits can be measured and manipulated during behaviour in ways not possible in humans.

Our approach is to train mice, including pharmacological and genetic mouse models of neurodevelopmental disorders and healthy controls, in visual decision-making tasks. We measure activity in visual cortex in specific cell types using 2-photon imaging and electrophysiology and use optogenetics to activate or inactivate activity of specific interneuron cell types. We will also apply two new innovative methods to optically measure the inhibitory neurotransmitter GABA (developed in the Looger lab, UCSD) and to locally pharmacologically manipulate GABA levels in the brain (collaboration with Malliaras and Proctor labs, Dept of Engineering, Cambridge) during visual learning and decision-making.

The PhD project is associated with a Wellcome Trust funded Collaborative programme with a cross-disciplinary international research team to investigate the role of GABAergic inhibition in both mice and humans at different scales, from local circuits to global brain networks.

Lab website: https://www.pdn.cam.ac.uk/svl
Contact: Jasper Poort jp816@cam.ac.uk

One of the major obstacles to effectively treating central nervous system (CNS) tumors is the integrity of the blood-brain barrier (BBB). The BBB prevents systemic drug delivery from reaching the brain and brain tumor tissue. While previous studies have mainly focused on circumventing the BBB, very few agents or mechanisms have been explored that modulate the tumor microenvironment to enhance effective therapies for malignant brain tumors. Our studies focus on understanding the heterogeneity of BBB permeability amongst malignant tumor cells and the role of the supportive BBB in tumor growth. Our collaborative laboratory and clinical investigations center around BBB biology, cancer biology, pharmacokinetics and pharmacodynamics related to optimal CNS drug delivery.

Using a clinical/translational approach, we aim to:

1) Evaluate the efficacy of targeted tumor and BBB directed therapy

2) Define the mechanisms that drive differences in neuropharmacokinetics of agents to the CNS

3) Identify exquisite parameters via neuro-imaging of CNS permeability amongst malignant brain tumors.

Our overall goal is to enhance our understanding of the heterogeneity of blood-brain barrier permeability among tumor cells and develop mechanism-based therapeutic interventions to treat affected brain tumor patients at the NIH Clinical Center. We use a combination of cell biology, molecular biology, imaging, pharmacokinetics and animal tumor models.

During development, brains grow rapidly as behaviors develop. Impairment in early brain development often leads to neurodevelopmental conditions, including a number of neuropsychiatric disorders. From early postnatal period throughout adulthood, learning leads to important and dynamic changes in brain circuitry, and in an animals’ behaviors to adapt and sense the environment. The hierarchical yet reciprocal interaction between thalamus and cortex is one of the key brain circuits that are involved in learning-related changes from early development to adulthood.

To investigate the development of thalamocortical connection in the context of sensory learning, this project aims to understand 1) the specificity and plasticity in the interaction between thalamus and cortex during both early development and later life, and 2) how the impairment in this functional connection during early development results in long lasting effects on the capacity for learning in the adult brain. Specifically, we will study how different neuronal types and neuromodulators play a role in the developmental and adult plasticity of thalamocortical connectivity.

To address these questions, we will use the rodent whisker-related sensory-motor system because it is ecologically relevant and critical to the animal’s abilities to navigate and engage in goal-directed behavior. We will apply a multidisciplinary approach that combines molecular and genetic techniques with in vivo intracellular and extracellular electrophysiology, in vivo longitudinal calcium imaging, viral tracing, optogenetic and pharmacogenetic methods, and quantitative behavior and anatomical analyses.

Lee’s lab at NIH will focus on early developmental studies and Bruno’s lab at Oxford will focus on adult plasticity. The two labs will use complementary approaches. A student working with Drs. Lee and Bruno will have a unique opportunity to learn conceptual perspectives from both labs, as well as a wide range of experimental and analytical methodologies in the field of system neuroscience. 

There has been increasing interest in applying computational methods in medicine, to make sense of cancer’s ‘big data’ problem by exploiting recent advances in data-processing and machine learning to capture and integrate clinical, genomic, and image data collated from hundreds of cancer patients in real-time. Such methods can be applied to digital clinical images to extract image information about patterns of pixels that are not perceivable to the human eye, allowing characterisation of tumour.  Prostate cancer is the 2nd commonest male cancer worldwide, and MRI is the diagnostic tool of choice, however, MRI can miss 10% of significant tumours and leads to unnecessary (invasive) biopsy in around 1/3rd patients who do not have cancer.  

We will use a prototype AI system (Pi) developed with Lucida Medical on retrospective data, in a prospective clinical study. We plan to link histological data to imaging features derived from MRI (including texture analysis) to identify predictors of lesion aggressiveness and need for sampling, using biopsy cores and surgical specimens from the prospective cohort. Further work will link biopsy tissue to MRI data to identify radiogenomic markers of disease aggressiveness. The project presents an opportunity for AI to answer key clinical questions at the intersection of interpretation, imaging and biopsy.  

The project will involve working with an established interdisciplinary programme of researchers and help in the assessment of cross-cutting “multi-omic” approaches to cancer assessment, involving integration of advanced image analysis, transcriptomic, genomic, tissue, and patient outcomes to inform the design of diagnostic strategies.

We are developing artificial multi-valent proteins capable of liquid-liquid phase separation (LLPS) with the aim of building multi-functional biomolecular condensates and thereby harnessing specific cellular enzymes to target disease-associated proteins for destruction. We propose to design condensates that contain a class of proteins known as tandem-repeat proteins (RPs). We have shown that RPs are strikingly amenable to rational design and can be engineered to simultaneously bind multiple proteins, bringing them into specific spatial proximity in such a way as to enable a chemical modification of the target protein. The rational design of LLPS systems capable of selectively recruiting client proteins into them to drive specific biological reactions would enable both a deeper understanding of the role of biomolecular condensates in nature as well as the exploitation of their remarkable physico-chemical properties for therapeutic effect. 

Key areas of interest include: 
 

1. Understanding the molecular grammar of protein phase separation to define rules for creating designer LLPS systems. 

2. Developing novel hetero-bifunctional phase-separating proteins to recruit disease-associated targets to the protein degradation machinery. 

3. Translating the designed LLPS proteins into biomolecular condensates in the cell capable of enhancing targeted protein degradation. 

“Life will find a way….” In a now famous quote from the 1993 movie Jurassic Park, the “chaotician” Ian Malcolm nicely captures the essence of adaptation through evolution. But series evolutionary change often requires multiple mutations to arise – the changes arising from SNPs and indels in single genes usually amount to little more than phenotypic “tinkering”. So what would happen if we could “step on the evolutionary gas pedal” and accelerate the pace of change? Or alternatively, what would be the consequences of “slamming on the evolutionary brakes” to prevent adaptation? Well, these are just the kind of approaches that we have developed in the Welch lab, and we are applying these to look at how the opportunistic bacterial pathogen, Pseudomonas aeruginosa, adapts to the presence of infection-relevant selection pressures. Essentially, we’ve engineered the mismatch-repair system to come under the control of an inert chemical inducer, and so can “rheostatically” modulate the rate of mutation from very high (1000 x the wild-type level) to very low indeed (eliciting a state of “hypomutation” in which evolutionary change essentially grinds to a halt).

Using this system, we aim to investigate the evolutionary trajectories of P. aeruginosa when challenged with intense selection pressures e.g., in a polymicrobial environment, or upon exposure to antimicrobial agents or nutrient limitation. Project will involve elements of synthetic biology, microbiology, evolutionary biology, modelling and genomics. A stable polymicrobial culture system has recently been developed by the lab and is available for use.  

Accumulation of vascular smooth muscle cells (VSMCs) is a hallmark of cardiovascular diseases such as atherosclerosis, which cause heart attack and stroke. In healthy vessels, VSMC contraction regulate blood flow and blood pressure but loose their contractile function and undergo extensive transformation upon vasuclar insult. This process results in the generation of a wide spectrum of phenotypically changed cells within atherosclerotic lesions, which are predicted to impact differently on disease progression. Using clonal lineage tracing in mouse models of atherosclerosis, we demonstrated that disease-associated cell accumulation result from extensive proliferation of a small subset of VSMC that can generate the full range of distinct cells. By combining lineage tracing with single cell RNA sequencing (sc-RNAseq) in mouse models, we have identified signatures of VSMC-derived cells subpopulations. Interestingly, cells displaying mesenchymal stem cell character are rare in healthy vessels and their numbers increase in disease models. The aim of this project is to understand how specific VSMC-derived cell populations in human disease arise, using a combination of genomics and functional assays, in order to allow efficient cell targeting in atherosclerotic lesions.