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Projects available for October 2020

Abstracts of research projects offered for October 2020

The research interests of all the members of the Department are available at www.phar.cam.ac.uk/research.

Candidates are advised to read these research interest pages in conjunction with this information.

 

Dr Matthew Harper:


Mechanisms of arterial thrombosis

Platelets play a critical role in the pathogenesis of arterial thrombosis and myocardial infarction, which is a major cause of death in the UK. ADP is a major platelet activator, acting through P2Y1 and P2Y12 receptors. P2Y12 inhibitors are widely-used as anti-thrombotics. ADP is degraded by CD39, an ectonucleosidase. CD39 inhibitors have been proposed as novel immune checkpoint inhibitors for use in treating cancer. However, CD39 inhibition may also exacerbate arterial thrombosis by increasing ADP and reducing anti-thrombotic adenosine concentrations.

Platelets are not the only cells in thrombosis, however. Leukocytes and erythrocytes are increasingly recognised as playing important roles and may provide new targets for preventing arterial thrombosis.

Examples of projects available:

  1. What are the pro-thrombotic consequences of inhibiting CD39?
  2. How does adenosine signalling affect platelets and leukocytes?
  3. What are the roles of leukocytes and erythrocytes in arterial thrombosis?

Note that these projects are currently unfunded. We particularly welcome applicants who would make strong candidates for prestigious scholarships, such as Gates Cambridge, Cambridge Trust, Vice Chancellor’s Awards, or similar (see www.graduate.study.cam.ac.uk/finance/funding for more details and deadlines). Funded PhD studentships will be advertised separately.

Keywords: cardiovascular disease; heart attack; cell signalling;thrombosis

 

Dr Catherine Wilson:


Harnessing Myc transcription to drive proliferation in non-regenerative organs

Myc is a transcription factor deregulated in the vast majority of cancers, its expression drives cells into cycle and, if unchecked, this deregulation leads to uncontrolled growth. We use acutely switchable models of Myc to assess the immediate molecular and pathological effects of switching Myc on and off. Using these systems, we have shown that Myc binds to a large set of genes common to all tissues that are involved in cell cycle entry; suggesting Myc is able to drive cell cycle progression in any type of cell. However, we found that despite acutely overexpressing Myc in all tissues, non-regenerative tissues like the heart remained almost entirely resistant to cell cycle entry, due to an inability of ectopic Myc to activate transcription of its target genes once bound.  We have established that Myc driven transcription, and consequently cell proliferation, is critically dependent on the level of P-TEFb activity within a specific tissue. Using the heart as a model system that has very limited capacity for proliferation, we have reactivated Myc transcription and proliferation by increasing the activity of P-TEFb. The aim of this project is to establish if restoring Myc driven transcription and proliferation in non-regenerative cells can be harnessed to stimulate endogenous tissue repair.

Please contact Dr Wilson to discuss the projects offered. Please see www.graduate.study.cam.ac.uk/finance/funding for funding opportunities.

 Keywords: Myc, transcription, cell cycle, cardiomyocyte, cardiovascular disease, cancer, regeneration, myocardial infarction.

 

Dr Ewan Smith:


Project 1. Changing the gain in pain

The ability to detect potentially damaging stimuli provides a vital protective function, but in chronic pain syndromes (e.g. osteoarthritis and inflammatory bowel disease) the gain in pain goes wrong and the pain experienced has a major impact on an individual’s well-being. In our lab, we employ a range of molecular biology, electrophysiology and behaviour techniques to understand how sensory neurones function and how they have behaviour changes in chronic pain states, the overall aim being to identify new targets for the treatment of pain.Recent work has used single-cell RNA-sequencing to describe 7 distinct sensory neurone subsets innervating the distal colon (a prime source of visceral pain) and shown that upregulation of TRPV1 in knee-innervating sensory neurones is a good target for ameliorating inflammatory joint pain. Future research projects will involve continuing to further our understanding of chronic pain.

Keywords: pain, electrophysiology, behaviour

 

Project 2. Healthy ageing with the naked mole-rat – dealing with reactive oxygen species

Lipid peroxidation occurs as a result of reactive oxygen species (ROS) activity. Accumulative peroxidative damage is one hypothesis underpinning ageing-induced decline in bodily function. Mice are short lived, but naked mole-rats are long-lived and thus we hypothesise that naked mole-rat lipid membranes are more resistant to ageing-related damage. Ion channels embedded in the plasma membrane are fundamental to controlling cellular excitability and their function is regulated by their lipid environment. The transient receptor potential (TRP) ion channel family are particularly susceptible to lipid modulation, certain lipid peroxidation products potently activating TRP vanilloid 1 (TRPV1) and TRP ankyrin 1 (TRPA1), ion channels linked to longevity. We will heterologously express mouse and naked mole-rat TRPV1/TRPA1 and determine how their responses are modulated by lipid peroxidation and disruption of lipid rafts. We will also perform experiments in primary dorsal root ganglion (DRG) neurones due to their high TRPA1/TRPV1 expression. Using real tissue enables comparison of peroxidation and lipid raft modulation responses at different ages to enable us to test the hypothesis that naked mole-rat lipid membranes are less influenced by ageing than mice. We will also determine the effects of lipid peroxidation and lipid raft modulation on key factors regulating neuronal excitability, e.g. the resting membrane potential, and examine how modulation of lipid raft components to build a more general picture of species differences.

 Keywords: electrophysiology, cell biology, ion channels

 

Professor Laura Itzhaki:


Tandem-repeat proteins: Physiological and pathological functions, therapeutic intervention, synthetic biology and drug development

The major focus of our research is a class of proteins with very distinctive architecture, known as tandem-repeat proteins (e.g. ankyrin, tetratricopeptide and armadillo repeats), which are frequently deregulated in human diseases such as cancers and respiratory and cardiovascular diseases. These proteins function as scaffolds for molecular recognition and binding hubs for assembling large macromolecular machines. The term ‘scaffold’ implies a rigid architecture; however, as suggested by their Slinky spring-like shapes, it is thought that repeat proteins utilise much more dynamic and elastic modes of action. For example: stretching and contracting to regulate the activity of a bound enzyme; reversible nanosprings to operate ion channels; proteins that wrap around their cargoes to transport them in and out of the nucleus. The modular architecture of repeat proteins makes them uniquely amenable to the dissection of their biophysical properties as well as the rational redesign of these properties. The following PhD projects are available:

1. Exploiting the design-ability of repeat proteins to build artificial proteins with applications in synthetic biology (multivalent and multi-functional repeat proteins designed to rewire signalling pathways), repeat-protein therapeutics as alternatives to antibodies (designed repeat proteins to trigger the destruction of disease-associated targets pathways), and nanotechnology (self-assembling repeats proteins to build functional nanomaterials).

2. Peptide inhibitors to target disease-associated repeat proteins for therapeutic benefit. 

3. Protein engineering and design to determine how the distinctive structures of repeat proteins control their functions in the cell - e.g. building artificial repeat proteins to act as cellular force sensors. 

Research in our group is at the interface between biology and chemistry; we also have close collaborations with computational groups and synthetic chemistry groups in Cambridge, and therefore students will be able to learn a broad range of techniques and approaches, including protein engineering, biochemistry and biophysical analysis including single-molecule techniques, cell biology and medicinal chemistry.

Keywords: protein engineering, protein degradation, cancer, biotherapeutics, mechanobiology 

 

Prof. Colin Taylor:


Structure and function of Ca2+ channels within dynamic organelles

How does Ca2+, an element and the simplest of all intracellular messengers, selectively regulate so many cellular activities? We address this question by examining how the behaviour of intracellular Ca2+ channels, notably IP3 receptors, and the organelles in which they reside lead to complex changes in intracellular Ca2+ concentration. We are exploring the structural basis of IP3 receptor gating and the contribution of dynamic intracellular organelles to shaping cytosolic Ca2+ signals. The ER, where most IP3 receptors reside, forms intimate contacts with most other organelles. Dynamic regulation of these interactions may be as important as receptor-regulated formation of IP3 in determining how cells generate and respond to cytosolic Ca2+ signals. Furthermore, IP3 receptors move within the ER. We do not understand the relationships between these dynamic IP3 receptors and the much smaller number of immobile IP3 receptors that appear to generate most Ca2+ signals. What licences immobile IP3 receptors to respond? We apply super-resolution optical and electrophysiological methods alongside gene-editing with CRISPR/cas9 of native signalling proteins to explore, often at the single-molecule level, the structural basis of IP3 receptor activation and the dynamics of Ca2+-handling organelles. We apply these methods to both 'work-horse' cells like HEK293 cells, and to primary cells: bronchial and vascular smooth muscle (cAMP/Ca2+ interactions controlling contraction), fibroblasts, astrocytes (spatial organization of intracellular ATP provision) and glioma cells (migration and invasion). Our work, including that of PhD students, is supported by extensive national and international collaborations with chemists, structural biologists and mathematicians, and with partners in industry.

Keywords: Cell signalling, patch-clamp recording, super-resolution microscopy, gene-editing, ion channel, Ca2+, cyclic AMP, intracellular organelles, smooth muscle, fibroblast, astrocyte, glioma.

 

Dr Hendrik van Veen:
Mechanisms of multidrug transport in microorganisms and cancer cells

Multidrug transporters mediate the extrusion of a broad range of drugs from the cell, away from intracellular targets on which these drugs act. These membrane transporters modulate the toxicity and pharmacokinetics of drugs in organisms ranging from bacteria to man, and are a cause of drug resistance in pathogenic microorganisms and cancers. Using structural, biochemical, biophysical, electrophysiological and microbiological tools, we work on very interesting and relevant questions:

  • How are drugs recognised by multidrug transporters?
  • How is metabolic energy coupled to drug transport?
  • Is drug transport the primary physiological role of these systems? Are other substrates (e.g. lipids) relevant?
  • Can we use these functional and mechanistic insights to generate novel inhibitors and novel drugs that bypass recognition by multidrug transporters, and thus improve the drug-based treatment of infectious diseases and cancer?

 

We currently study important members of the ABC, MFS and MATE transporter families. We collaborate with chemists, structural biologists and biophysicists abroad and within the UK. Please, visit our lab website for further information, and feel free to contact Rik van Veen to discuss the projects offered.

Keywords: Antibiotic resistance and anticancer drug resistance, membrane transporters, drug efflux, multidrug recognition, mechanisms of transport.

 

Dr David Bulmer:

What are the mechanisms of abdominal pain during colitis?

Abdominal pain has a profoundly negative effect on the quality of life experienced by patients with inflammatory bowel disease (IBD). Current immunosuppressant therapies although effective for the treatment of inflammation, are suboptimal for pain with many patients continuing to feel pain during remission.  

To address this problem work in my lab has utilised tissue from patients with IBD to identify mediators and mechanisms responsible for the activation of pain sensing nerves within the gut (see Hockley et al, 2014 PAIN 155 (10): 1962-1975; McGuire et al, 2018 Gut 67(1)). By identifying which mediators are key to the production of pain and how they activate pain sensing nerves we can develop new drugs to switch these processes off and treat pain. This studentship will explore the effects of putative mediators of abdominal pain, identified from a whole transcriptome analysis of IBD patient tissue, on pain sensing neurones that innervate the gut. To do this we will utilise ex vivo electrophysiological recording techniques and calcium imaging to study the effect of selected mediators on neuronal activation.

Keywords: Pain, inflammation, neuroscience, pharmacology

 

Dr Paul Miller:

Ion channels play myriad functional roles in fundamental biology, for example by coordinating and powering muscle contraction, by generating axon potentials, and by mediating synaptic communication between neurones throughout the peripheral and central nervous system (CNS). As such ion channels represent major therapeutic targets with small molecules against them being the third best selling group of prescribed drugs. Despite this only a tiny fraction of channels are currently targeted from the estimated 400 predicted human ion channel genes. In recent decades antibody therapeutics (biologics) have rapidly risen to prominence in the drug market. One reason for the success of these agents is improved target specificity. However, no biologics against ion channels have yet made it into the clinic. Technically, ion channels represent challenging targets for the generation of useful biologic binders and modulators, in part due to difficulties in protein production of native forms, and in part due to a lack of penetrance of biologics into the CNS. The impact of breakthroughs in this area cannot be underestimated. Currently my research is aimed at using electrophysiological, biochemical, protein engineering and structural biology approaches to understand and develop novel antibody (nanobody) modulators with unique pharmacological properties against GABAARs. These receptors are the principal mediators of inhibitory neurotransmission throughout the human brain, and targets for essential clinical drugs such as benzodiazepines, Z-drugs and intravenous anaesthetics. Additionally, I am interested in exploring alternative disease relevant neuronal ion channels from the perspective of structural biology, and to investigate antibodies against them as pharmacological modulators. Naturally, following on from these studies aims are to test these proteins in relevant systems to uncover their impacts in neuronal function and to realise their therapeutic potential. 

These projects are currently unfunded, and so I particularly welcome applicants who would make strong candidates for prestigious scholarships, such as Gates Cambridge, Cambridge Trust, Vice Chancellor’s Awards, or similar (see www.graduate.study.cam.ac.uk/finance/funding for more details and deadlines). 

Keywords: Cryo-EM, ion channels, electrophysiology, antibody modulators