PhD projects in Integrated Bioscience

We have a number of PhD projects area available in the group and enquiries from highly motivated and talented indivuduals are encouraged (preferably with a plan for funding the work).   Please follow the links below to projects in the three subject areas to view example projects. However, general enquiries via our form are welcome as are direct enquiries to supervisors.

Enquiries are welcome and can be made via the PhD Enquiry Form (click here) or by contacting supervisors directly.

Please also see our new Dental School Postgraduate Research Degree Hub for information on the timeline of applications, what to expect in the school and to get an idea of our current student population.

Infection and Immunity

1. Effect of fluid flow on both the invasive ability of the periodontal pathogen P.gingivalis and the host cell uptake of this bacteria.

Supervisors: Dr Simon Whawell & Dr Graham Stafford

P.gingivalis is thought to play a key role in periodontal disease and has the ability to invade host cells where it can survive and avoid host defences and therapeutic interventions. Recent work in our laboratory has shown that low levels of fluid flow (150µl/min) enhances endocytosis of eukaryotic cells and uptake of labelled dextrans and thus invasion of bacteria may similarly be affected. Previous studies have shown that microenvironmental conditions such as similar levels of fluid flow can have a significant impact on P.gingivalis biofilm morphology and growth behaviour. Furthermore, a recent comparison between planktonic and biofilm grown P.gingivalis has identified changes in a number of genes that may be important in invasion and or intracellular life as a number are common to those identified by our group in hyper-invasive strains. We thus hypothesise that fluid flow may enhance both the ability of bacteria to invade host cells and the susceptibility of such cells. Biofilm growth may also favour development of this invasive phenotype.

2. The effects of ultrasonic treatment on bacterial biofilms
Supervisors: Dr Joey Shepherd & Dr Graham Stafford

The overall aim of this project is to investigate the potential of treating bacterial biofilms with ultrasound, in order to increase the efficacy of antibiotics against persister cells within the biofilm. We will test our theory using planktonic and biofilm bacteria, both in culture and as part of 3D tissue engineered models of skin wound infection (Fig.1) (Shepherd et al., Tissue Engineering Part C: Methods., 15(3):475-484) and infected 3D tissue engineered models of oral mucosa. The project will involve practical work encompassing microbiology, cell culture, histology, tissue engineering, microscopy and sonochemistry.

3. Innate immunity in tissue engineered skin and oral mucosa
Supervisors: Dr Joey Shepherd & Craig Murdoch

Human skin and oral epithelial cells (keratinocytes) produce antimicrobial peptides, such as human β-defensins (hBD), as part of the innate immune defence system. Keratinocytes produce hBD in vitro and after incorporation into cultured human skin substitutes (Supp et al., 2004). There is evidence that dermal fibroblasts may also produce hBD. This project will identify and compare the levels of hBD expression in human skin and oral mucosa cells, and test whether production of hBD can be manipulated by stimulating the cells with inflammatory agents. The levels of hBD in tissue engineered skin and oral mucosa, both infected with bacteria and uninfected, as well as stimulated with agents such as bacterial lipopolysaccharide, will also be measured. Techniques used will include cell culture, tissue engineering, histology, microbiology, microscopy, and molecular biology techniques.

4. Investigating glycans and glycosidases in periodontal infection as a route to novel antimicrobials

Supervisors: Dr Graham Stafford

Periodontitis (often known as gum disease) is a common condition affecting 700 million people worldwide, characterized by receding gums and loss of supporting structures of the teeth. Its chronic and inflammatory nature mean it is also associated with other diseases such as diabetes, heart disease and rheumatoid arthritis as well as being a disease of ageing. Periodontal disease is caused by a group of bacteria that our recent work has shown may damage gum tissue by attacking the sugars (glycans) that coat cells lining the mouth. The bacteria use these sugars as a fuel to allow them to grow in the mouth and cause disease but removal of these by bacterial action also affects the way our cells react to infection- called the immune response. This project will investigate the mechanisms of how the bacteria utlise these sugars for causing infections with a specific focus on the most common surface sugar- sialic acid. The work will focus on how the bacteria change the levels of these sugars on cell surfaces using enzymes they produce called sialidases (a glycosidase) and a related enzyme called a Sialate o-acetylesterase and how this allows them to manipulate our immune response during infections and cause the symptoms of peridontal disease. On top of this the project will test how effective potential drugs to combat these infections (via sialidase inhibition) might be, while also creating new knowledge of this microbial infection that will allow design of other new antimicrobial drugs aimed at combatting periodontal disease and other infections of humans.

The student will gain a broad training in a range of techniques including molecular microbiology, eukaryotic cell infection models, biochemical analysis and structural biology. This project thus provides an excellent framework on which to build a successful career.

5.The Pathogenesis of Otitis Media (Middle ear infection)

Supervisors: Dr Lynne Bingle and Professor Colin Bingle

Otitis media (OM), a group of inflammatory diseases of the middle ear, is the leading cause of paediatric surgery and the most frequent reason for the prescription of antibiotics. It can have both acute and chronic (recurrent) presentations the consequences of which often continue into adulthood and thus the consequences of OM may be life long.

This project will establish a novel in vitro model of human, primary middle ear epithelial cells (MEECs) using tissue from patients suffering the consequences of chronic OM (commonly known as glue ear) and from those with chronic OM with effusion (COME). The model will be used to study aspects of both infectious (using NTHi) and non-infectious OM, as well as the role of mesenchymal cells.

One of the main characteristics of OM is the differentiation of MEECs into goblet cells in the middle ear leading to the formation of a mucin rich effusion that is not cleared. The phenotype of the MEECs will be modulated to induce goblet cell metaplasia and infected with NTHi to elucidate the pathogenesis of the process. The role of excessive mucin secretion can then be compared with normal cellular morphology. Gene-editing techniques will determine the role of specific genes (identified by transcriptomics/proteomics) in the pathogenesis of disease.

The model will also provide a valuable tool to test novel compounds that may alter cellular phenotypes and modify aspects of OM.

Functional Analysis of BPIFA2 in Human Saliva

Supervisors: Dr Lynne Bingle & Professor Colin Bingle

Saliva acts as a lubricant for mastication, a diluent for food tasting and aids swallowing and speech. It also helps to keep our mouths healthy by washing our mouths, acting as a buffer and contains a number of proteins, which have antibacterial, antifungal and/or antiviral activity. Salivary dysfunction is associated with oral pain, infections (both oral and systemic) and an increased risk of dental caries. We are interested in the role of members of the PLUNC/BPIF protein family in saliva as it is hypothesised they play a role in the innate immune defence of the airways, nose, and ears and, of specific interest to this project, to maintaining health in our mouths. The two proteins that we plan to study in detail are BPIFA2 (SPLUNC2) and BPIFB2 (LPLUNC2) both of which are known to be present in saliva. Our previous immunohistochemical studies have shown that both proteins are expressed in normal, human salivary glands but the expression pattern changes with disease state.

This project will involve the purification of recombinant proteins generated in our lab. Importantly we have transfected expression constructs into mammalian cells to produce a number of isoforms of the proteins so that their functions can be fully elucidated. The functional work will initially focus on putative antimicrobial activities of the proteins and will undertake studies to look at interactions of the proteins with a range of oral microbes. We will also investigate the interaction of microbes, pre-incubated with the PLUNC proteins, with macrophages and neutrophils to determine any opsonising role for the proteins. Understanding the role of these proteins in inflammatory and infectious disease will help us to further understand the pathogenesis of disease and could lead to the development of new treatment regimens.

Head and Neck Cancer

1. Do extracellular vesicles confer drug resistance in oral cancer?
Supervisor: Dr Stuart Hunt, Dr Helen Colley and Professor Paula Farthing

Extracellular vesicles (EVs) are nanosized membrane enclosed particles that are produced by all cells. They contain molecular cargo, including protein and miRNA. There is evidence that cancer cells produce increased numbers of EVs with altered cargo that can facilitate pro-tumorigenic communication between cells in the cancer microenvironment. Oral squamous cell carcinoma (OSCC) has a poor prognosis with a 5 year survival rate of ~50%. Treatment of OSCC usually involves a combination of surgery, radiation and chemotherapy. OSCC has a high rate of recurrence (20-30%), which may be partly due to the development of resistance to chemotherapeutic agents. EV production has been shown to increase in response to cisplatin treatment with reports that EVs export cisplatin as a mechanism of drug-resistance. Furthermore, it is suggested that EV’s can act to confer drug resistance between cells, but to date this has not been investigated in OSCC.

2. Effects of Cancer-Associated Fibroblasts on Bone Invasion of Oral Cancer using an
Advanced Tissue-engineered 3D Osteo-mucosal Model

Primary Supervisors: Dr. Keyvan Moharamzadeh and Dr. Dan Lambert
Co-supervisor: Dr. Ali Khurram

Cancer-associated fibroblasts (CAFs) play an important role in cancer:stroma interactions and tumorigenesis including development and progression of oral cancer. The experimental models of cancer cell survival, proliferation, migration, and invasion have mostly relied on two-dimensional monocellular and monolayer tissue culture systems. However, these experiments do not precisely reflect the physiological or pathological conditions in a diseased organ. Previously we have developed 3D tissue engineered models of human alveolar bone and oral mucosa for various in vivo and in vitro applications including oral disease modelling. The effects of CAFs on bone invasion of oral cancer have not been previously investigated using a 3D osteo-mucosal in vitro model and this is the main aim of the work in this project.

3. Investigating mechanisms of HPV DNA integration into tonsillar keratinocytes
during HPV-mediated oropharyngeal cancer

Supervisor(s): Dr Craig Murdoch, Dr Vanessa Hearnden, Dr Keith Hunter
To cause cancer HPV must infect epithelial cells that line the back of the throat, in particular the basal epithelial cells that line the tonsil region. The HPV DNA is then inserted into human epithelial cells where it either resides in the cytoplasm or is integrated into the host DNA. Only HPV that is integrated can go on to produce proteins that drive cancer. To date not much is known about how HPV infects and integrates into human DNA in the tonsils because studying HPV infection in the laboratory is difficult. This is because the HPV life cycle relies on epithelial cell maturation that cannot be modelled in monolayer cell culture. To accurately study HPV infection tonsil epithelial cells need to be grown in 3D as multi-layered epithelium to replicate normal human tonsil tissue. We have recently developed a 3D, multi-layered, tissue-engineered tonsil epithelium that can be grown in the lab from human cells. To our knowledge this is the only tonsil epithelial model available. The aim of this study is to use our engineered tissue to establish the first ever laboratory model of HPV infection in tonsil epithelium. This HPV-model can then be used to examine factors that might affect HPV DNA integration and therefore influence cancer progression.

4. Defining the role of HOX genes in HNSCC

Supervisor: Dr Keith Hunter, Dr Dan Lambert
A number of HOX genes have been shown to be aberrantly expressed in upper aero-digestive tract cancers (HNSCC and NSCLC). In general HOX genes are highly expressed in cancers and in some this has been related to poor prognosis. There is extensive functional redundancy in HOX gene expression and it is unclear which are fundamentally important and which are not. The method of altered regulation varies between tumours (e.g. HOXD10 is controlled differently in HNSCC and BC). Strategies exist for inhibition of HOX genes, but these are not selective, as they target the interaction of HOX proteins with co-factors, such as PBX.
The overall project objective is to identify which HOX genes are important in the development of HNSCC and to develop strategies to exploit that knowledge clinically.

5. Exploring the tumour-fibroblast interactome in HPV positive and negative Oropharyngeal SCC

Supervisor: Dr Keith Hunter, Dr Dan Lambert

Ongoing work in the lab has identified a number of candidate molecules secreted by fibroblasts which direct the migration of OP HNSCC cells, particularly HPV-ve ones. These molecules have been identified on their release following the application of SCC conditioned media to the fibroblasts. Whilst we have pursued the resulting fibroblast secretome, we have not explored the candidate molecules which are being released by the OPSCC cells or how their effects are mediated by the fibroblasts.

The overall project objective is to identify which molecules released by HNSCC cells activate the fibroblasts and to understand the molecular pathways which underpin these actions.

Characterisation of in vitro models of human salivary glands and their use in functional studies

Supervisors: Dr Lynne Bingle, Dr Aileen Crawford & Professor Colin Bingle

Saliva is produced by three pairs of major salivary glands and multiple minor glands in the lips, associated with the tongue and also with the palate. Saliva starts the digestion of food, helps to keep the mouth moist so that we can talk, keeps the mouth clean by washing extra material, including food, out and contains proteins able to control the normal flora of the mouth; both the number and types of bacteria present.

There are some clinical situations in which we stop producing saliva, for example if the glands are damaged by radiotherapy or chemotherapy given as treatment for cancer, or if we suffer from the autoimmune disease Sjögren’s syndrome where the glands are irreparably damaged. Reduced salivary flow makes it very difficult to talk, to swallow food and the mouth can become infected with bacteria, viruses and/or fungi. These infections can quickly spread into the blood stream and, in extreme cases, be fatal.
Salivary gland biology is not well understood and any research into any associated diseases is severely hampered by the lack of useful research models and tools.

It has not previously been possible to study the onset or early stages of disease and thus our recent research has involved the development of 3D in vitro models of both major and minor salivary glands with the aim of using them to further our understanding of salivary gland development and to investigate the pathogenesis of salivary gland diseases. The models have been characterised in terms of cell genotype and phenotype and culture conditions have been adapted to allow the models to mimic, as closely as possible, the in vivo situation.
This follow-on project will use the 3D models to study the development of salivary glands, and thus provide vital information needed to "grow" new glands to replace those irreparably damaged. We also aim to use the models to study the development and progression of salivary gland disease, particularly the damage caused by bacterial and viral infections, and to determine how cancers develop in salivary glands. Currently there is no immune component to the model but this project will involve the addition of inflammatory cells such as macrophages, neutrophils and lymphocytes.

Salivary gland disease is a very understudied area but one where the consequences of disease can be extremely serious.

Salivary Profile of Children and Young Adults and the Impact of Health and Lifestyle

Supervisors: Dr Lynne Bingle, Dr Sarah Baker & Dr Stuart Hunt

Our population is ageing and we know that globally the number of older individuals is increasing at a greater rate than that of young people. We hypothesise that with age saliva composition and output alters and can have a significant impact on our health and well-being. Significantly saliva can give us information not only about oral diseases but also diseases affecting other areas of our bodies. For example, saliva plays an important role in our nutritional status allowing us to taste and smell food, to swallow and to start digestion. Age-related salivary changes negatively impacting our nutritional status might increase the risk of disease development and/or recovery time. To fully assess the impact of ageing, we must first understand normal, ageing-associated changes, from birth onwards, and compare this with changes due to disease.

A further, very novel, field of study which is of great interest to us is the study of salivary extracellular vesicles (EVs) and their potential as a novel source of biomarkers of both oral and systemic disease, especially cancer.
Saliva and salivary EVs will be subjected to proteomic and glycomic analyses and an assessment of the oral microbiome. Oral health quality of life questionnaires will also be completed to relate the impact of health and lifestyle on biological changes.

Do extracellular vesicles confer drug resistance in head and neck cancer?

Supervisor: Dr Stuart Hunt and Dr Helen Colley

Extracellular vesicles (EVs) are nano-sized membrane enclosed particles that are produced by all cells. They contain molecular cargo, including protein and miRNA. There is evidence that cancer cells produce increased numbers of EVs with altered cargo that can facilitate pro-tumorigenic communication between cells in the cancer microenvironment. Head and neck squamous cell carcinoma (HNSCC) has a poor prognosis with a 5 year survival rate of ~50%. Treatment of HNSCC usually involves a combination of surgery, radiation and chemotherapy. HNSCC has a high rate of recurrence, which may be partly due to the development of resistance to chemotherapeutic agents. EV production has been shown to increase in response to cisplatin treatment with reports that EVs export cisplatin as a mechanism of drug-resistance. Furthermore, it is suggested that EV’s can act to confer drug resistance between cells, but to date this has not been investigated in HNSCC.

Oral Neuroscience

The role of inflammatory cytokines in the initiation of neuropathic pain after peripheral nerve repair

Supervisors: Mr Simon Atkins, Dr Emma Bird, Professor Fiona Boissonade

This project investigates whether modification of the inflammatory cytokine profile at a site of peripheral nerve repair reduces ectopic neural discharge, and will hence reduce or prevent the development of neuropathic pain. This translational research will clarify the peripheral and central mechanisms underlying injury-induced neuropathic pain, and help identify potential therapeutic approaches.

The role of anti-scarring agents on regeneration following nerve trauma and repair

Supervisors: Mr Simon Atkins, Dr Emma Bird, Professor Fiona Boissonade

This translational research is investigating the effect of scar reducing agents on functional regeneration following peripheral nerve injury and repair with the aim of delivering a clinically effective agent.

Identification of molecules linked with chronic neuropathic and inflammatory pain in man

Supervisors: Dr Emma Bird, Professor Fiona Boissonade, Mr Simon Atkins

Chronic pain, including that from the oro-facial region, represents a major public health issue, impacting primarily on health and quality of life, but also on economic and employment issues. Despite improved knowledge of underlying mechanisms and better treatments, chronic pain is still poorly understood and many people have chronic pain for which there is no reliable treatment. Previous studies have shown that changes which occur in damaged nerve fibres and surrounding tissue at the site of a nerve injury and inflammation, maybe responsible for the onset and cause of pain.
The aims of this study are to employ genomic, proteomic and immunohistochemical methods to screen human nerve tissues and biological samples to identify genetic and protein profile modifications that are explicitly linked with the presence of neuropathic and inflammatory pain in man. These findings will further our understanding of the cause of nerve injury-induced and inflammatory pain and will help identify targets for new treatments of chronic pain.