PGT to PGR Project List

The scholarships mentioned on this page will cover home fees and stipend at the UKRI rate for 3.5 years. Overseas candidates are welcome to apply, but would need to cover the fee difference.

Study a PhD at the University of Sheffield
Study a PhD at the University of Sheffield
On

The deadline to apply for one of the listed PGR Projects is Thursday 22nd June 2023.

Clinical Medicine

Getting to the heart of cardiac infection using zebrafish models

Primary Supervisor: Philip Elks (p.elks@sheffield.ac.uk)

Second Supervisor: Emily Noel (e.s.noel@sheffield.ac.uk)

Project Description: 

Inflammatory heart diseases are major causes of mortality worldwide and often result from infections in the heart, which fall into three main classes. Endocarditis is inflammation of the inner lining of the heart (endocardium), typically caused by circulating bacteria such as Staphylococcus aureus, becoming lodged in the heart through unknown mechanisms. Staphylococcus aureus can also cause myocarditis (inflammation of the myocardium, the contractile cells of the heart) and pericarditis (the sac around the heart). Cardiac infection can cause lasting damage to the heart, and the recent identification of myocarditis in patients with Sars-Cov2 infection highlights a need to better understand the mechanisms underlying heart infections. Despite this, few animal models of cardiac infection exist.


You will use zebrafish embryos infected with Staphylococcus aureus to understand the tissue and immune cell mechanisms involved in the development of heart infections. We hypothesise that the innate immune system plays key roles in the instigation of heart infections that can be therapeutically manipulated to improve infection outcomes.
You will use state-of-the-art fluorescence microscopy to:


1. Identify when, where and how Staphylococcus aureus infects the heart in a systemic infection model.
2. Determine whether innate immune cells participate in establishing heart infections.
3. Investigate mechanisms to improve innate immunity and reduce heart infection.
This project will exploit recently-established transgenic fish lines and cutting edge methodologies in the recently opened Wolfson Zebrafish Infection Laboratory. Zebrafish larvae will be infected systemically with fluorescent Staphylococcus aureus by microinjection into the caudal vein, around 20% of which develop cardiac infection. You will use cutting-edge confocal and lightsheet microscopy to define which cell types and cardiac structures are the primary site of infection, and to establish how infection progresses. Fluorescent microscopy will identify whether infected immune cells enter the heart. Innate immunity will be modulated to investigate whether heart infection can be controlled.


This project synergises the expertise of two successful groups from the Faculties of Medicine and Science, using techniques that are well-established in our groups that have so far produced exciting results and requires an enthusiastic PhD student to take forwards. You will join two vibrant research groups here and here and you will be well trained in zebrafish biology and microscopy techniques, as well as writing and presenting your science.
 

How to apply:

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Infection, Immunity and Cardiovascular Disease as the department.

Engineered enzymes for improved diagnosis of infectious diseases

Primary Supervisor: Jon Sayers (j.r.sayers@sheffield.ac.uk)

Second Supervisor: Thushan de Silva (t.desilva@sheffield.ac.uk)

Other Supervisors: Dr Laura Kemp

Project Description: 

BACKGROUND
Flap endonucleases (FENs) are enzymes that process branched DNA (Okazaki fragments) by an unusual threading mechanism (AlMalki et al, 2016). Gene knock-outs suggest they are essential for all cells (Fukushima et al, 2006;Kucherlapati et al, 2002). Importantly, recombinant FENs are key players in modern molecular biology techniques e.g. in ligase-free cloning methods such as SLIC and Gibson assembly, (Xia et al., 2019: Gibson et al., 2009) and the ~$20 billion nucleic acids diagnostics industry (Grand View Research 2021). The Thermus aquaticus Taq polymerase used for PCR, possesses a FEN domain which is crucial in many assay formats (Zauli 2019).
This project sets out to explore and exploit mechanisms of FEN enzymology and to use this knowledge to engineer proteins for improved diagnostic devices. The studentship is a collaborative venture with binx health Ltd. Their point-of-care device (the binx io) for rapidly detecting pathogens. relies upon FEN activity for detection and is FDA approved. This project will impact on our understanding of critical DNA replication mechanisms and aims to apply this knowledge to creating improved diagnostic devices.
Objectives
This project has three main objectives which are to;
• Develop mechanistic understanding of the FEN enzymes
• Reduce test turnaround time for the binx health IO device
• Identify alternative/improved enzymes to increase flexibility and robustness to expand applications

TRAINING AND EXPERIENCE
You will be trained in a range of specific research skills including; cloning, protein engineering, protein production, FPLC chromatography, molecular-interaction analysis, bio-informatics and structural biology. The academic supervisors (Prof. Jon Sayers & Prof. Thushan de Silva) have expertise in recombinant enzyme technology, assay development, production scale-up of enzymes and pathogen sequencing and detection. The industry supervisor (Dr Laura Kemp) will bring practical experience in biophysical techniques and diagnostic applications.
This studentship will primarily be based in the laboratory of Prof Jon Sayers at the Department of Infection, Immunity and Cardiovascular Disease at the University of Sheffield, where the research environment was graded 100% 4* in the recent REF2021 exercise. Additionally, you will be part of the vibrant Florey Institute for Host-Pathogen Interactions (http://www.floreyinstitute.com) and the Sheffield Institute for Nucleic Acids (https://tinyurl.com/fmwvkfuh. Both provide opportunities to attend regular meetings hosted by these institutes (in addition to Departmental research meetings) to further their scientific training. Students will also undertake an institutionally approved Doctoral Development Programme.
As part of this studentship, you will undertake industrial placements at Binx Health Ltd to gain hands-on experience in industry and to further the development of the binx I/O device. This studentship, therefore, offers a brilliant opportunity train in both industrial and academic environments.
We foster an inclusive, diverse, and high-performing culture leads to more engaged students, greater creativity and innovative research.
 

How to apply:

Masters level (must be from FMDH masters course for this scheme).

Please complete a University Postgraduate Research Application form available here.
 

Please clearly state the prospective main supervisor in the respective box and select Infection, Immunity and Cardiovascular Disease as the department.

Regulation of RNA stability in inflammation - a new route to pro-resolution therapeutics.

Primary Supervisor: Prof Stephen Renshaw (s.a.renshaw@sheffield.ac.uk)

Second Supervisor: Catherine Loynes (c.loynes@sheffield.ac.uk)

Other Supervisors: Roger Thompson

Project Description: 

Uncontrolled inflammation causing irreversible tissue damage is driven by the white blood cell the neutrophil, and is known to be a major driver of pathology in many common disabling diseases, including Chronic Obstructive Pulmonary Disease (COPD), which causes over 3 million deaths globally each year (WHO). There is a pressing need for pro-resolution therapies that target persisting inflammatory neutrophils, while leaving circulating neutrophils able to respond to infectious threats. Our lab (https://renshaw.sites.sheffield.ac.uk/home) seeks to determine the molecular mechanisms behind the regulation of neutrophil function and to identify drug targets to develop their translational potential.

Although neutrophils are resistant to the anti-inflammatory effects of current treatments, our lab has shown that targeting neutrophil phenotype can drive inflammation resolution. Gene transcription, through regulation of RNA stability, is important in controlling neutrophil phenotype. RNA editing and RNA binding proteins are 2 ways in which RNA stability can be altered. Our lab has shown that the RNA stabilising protein, ELAVL1, controls the phenotype of the neutrophil by regulating expression of pro-inflammatory genes and we are currently investigating the mechanisms of a pro-resolution drug, already in clinical trials, that targets ELAVL1. RNA editing can lead to changes in RNA sequence, which in turn can affect the abundance and function of the RNA molecule. ADARs are an RNA editing enzyme family that are necessary for the binding of ELAVL1. You will investigate the relationship between ADAR family members and ELAVL1 in neutrophils and utilise neutrophil transcriptomics and neutrophil function to explore further genes for drug target development.

In our lab you will experience a happy, inviting environment with a hardworking ethos balanced with social events and friendly, helpful, inclusive colleagues. This project would allow you to use in vivo (zebrafish) and in vitro (human neutrophils) models to manipulate neutrophil phenotype to reveal the downstream targets of ELAVL1, identifying new drug targets for the treatment of inflammatory disease. Using our zebrafish model of tailfin transection, we can visualise the behavioural dynamics of neutrophils at wound sites in several transgenic zebrafish lines and using various live stains, following gene manipulation or pharmacological treatment. You will learn to culture human neutrophils and to generate and analyse transcriptomic data. We will provide you with training in molecular biology techniques and in vivo imaging, both of which are sort-after transferable skills. This work involves generating and analysing large data sets so we will send you on a Bioinformatic/Data Analysis course, involving R- programming, again, a skill that is becoming more widely needed in research. We strongly encourage students to attend international conferences, and we operate a publication-focussed lab culture that allows students to publish manuscripts at an early stage.
 

How to apply:

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Infection, Immunity and Cardiovascular Disease as the department.

Accelerated diagnostics of multi-drug resistant Neisseria gonorrhoeae in sexual health samples

Primary Supervisor: Luke Green (l.r.green@sheffield.ac.uk)

Second Supervisor: Jonathan Shaw (j.g.shaw@sheffield.ac.uk)

Other Supervisors: Dr Joby Cole

Project Description: 

Neisseria gonorrhoeae is the causative agent of gonorrhoea, the second most common sexually transmitted disease in the UK. In 2016, the World Health Organisation (WHO) estimated the incidence of gonorrhoea at 86.9 million, however, cases are increasing sharply across the world, for example, cases rose by 26% in the UK between 2017-2018. To compound this problem, the WHO global gonococcal antimicrobial surveillance programme has highlighted the rise in multidrug resistant gonorrhoea infections around the world. There are increasing reports of clinical isolates demonstrating resistance to the first-line antibiotics. This inexorable increase in antibiotic resistance coupled with a sharp rise in cases identifies N. gonorrhoeae as a major public health burden with a clear need for the development of rapid diagnostics to improve antibiotic stewardship.

Currently, conventional diagnostic methods for gonorrhoea, including culture and nucleic acid amplification tests (NAATs), have limitations in terms of sensitivity, specificity, and the time required for results. Recently, whole genome sequencing (WGS), and in particular long-read sequencing technologies, have been employed to support the diagnostic process for sexually transmitted diseases by providing an accurate and rapid identification of the causative agent. WGS of N. gonorrhoeae can provide a comprehensive picture of the genetic makeup of the strain, identifying antimicrobial resistance (AMR) markers and consequently informing appropriate treatment decisions. This also allows epidemiological tracing of outbreaks and therefore more effective public health interventions.

This project seeks to utilise long-read sequencing technology to improve gonorrhoea diagnostics, allowing the rapid identification of N. gonorrhoeae, informing appropriate treatment decisions in a timely manner and thus improving antibiotic stewardship. Clinical isolates from a series of global locations will be sequenced using a variety of WGS platforms to enable the direct design of multi-plex PCR to analyse primary clinical samples. Bioinformatic analysis of sequences will enable analysis of AMR associated alleles and fine-typing of bacteria to determine epidemiological relatedness and potential transmission.

Student support: The project provides a vast array of techniques to develop the student’s technical repertoire. You will benefit from the supervision and mentorship of a cross-disciplinary team of researchers. You will give weekly presentations and lab meetings and would be invited to present at monthly clinical and departmental meetings. You will be provided one-to-one training with both Dr Green and Dr Shaw. You will also have the opportunity to attend both national and international conferences.

How to apply:

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Infection, Immunity and Cardiovascular Disease as the department.

Additional sex combs as a model for ASXL-related disorders in the fly: Unravelling neurodevelopmental disease mechanism

Primary Supervisor: Meena Balasubramanian (m.balasubramanian@sheffield.ac.uk)

Second Supervisor: Dr Iwan Evans (i.r.evans@sheffield.ac.uk)

Project Description: 

Asx is the sole ASXL family member in Drosophila but has not been exploited to study ASXL-related disorders including Bohring-Opitz (ASLX1); Shashi-Pena (ASXL2) and Bainbridge-Ropers (ASXL3) syndromes which share common phenotypes. Asx encodes a chromatin-binding protein required for segment identity during development. Asx encodes a Polycomb protein, necessary for stable repression of homeotic and other loci. Understanding disease mechanisms using Drosophila will decipher mechanisms of ASXL-related disorders.

With increasing use of whole genome sequencing as a first line of investigation into developmental delay (DD) and intellectual disability (ID), we are finding ASXL1-3 are one of the top-hitting genes. Although it is thought that the disorder is caused by haplo-insufficiency, disease mechanisms remain unclear and research to find new treatments are hampered by lack of understanding of pathophysiology.

Drosophila melanogaster is a fruit fly species that has been used in research for many years and are a successful model due to their short reproduction cycle, simple genome which is easy to alter and the fact that 75% of human diseases have a recognisable genome match with flies.

The additional sex combs gene (asx) in flies encodes a chromatin-binding protein involved in antennal development, the embryonic cell cycle and functions in the repression of homeotic gene transcription. Homeotic genes control the development of body segments of the fly. Understanding disease mechanisms using Drosophila will decipher mechanisms of ASXL-related disorders.

Objectives:

1. Characterise a Drosophila model to decipher ASXL3-related disorder mechanisms
2. Use patient variants in combination with loss/gain-of-function approaches to dissect pathophysiology of this disorder
3. Identify modifiers of disease and avenues for development of therapeutic interventions

Next generation sequencing has expanded our patient cohort and range of mutations driving DD. As a clinician within an international network coordinating study of these patients, the primary supervisor’s group is well placed to capitalise on this new data. Coupling this with Drosophila expertise (from the secondary supervisor’s group) with access to this patient data will enable the student to bring the powerful genetics/high-throughput capacity of the fly to understand pathophysiology underscoring ASXL-related disorders.

References:

1. Delineating the phenotypic spectrum of Bainbridge-Ropers syndrome: 12 new patients with de novo, heterozygous, loss-of-function mutations in ASXL3 and review of published literature. J Med Genet. 2017 Aug;54(8):537-543. doi: 10.1136/jmedgenet-2016-104360. Epub 2017 Jan 18. Review.

2. ASXL3-Related Disorder. 2020 Nov 5. In: Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Stephens K, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993–2020. PMID: 33151654.

3. Expanding the phenotype of ASXL3-related syndrome: A comprehensive description of 45 unpublished individuals with inherited and de novo pathogenic variants in ASXL3. Am J Med Genet A. 2021 Nov;185(11):3446-3458. PMID: 34436830.

How to apply:

Fly experience desirable

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Oncology and Metabolism as the department.

Targeting dormant myeloma cells with Karonudib

Primary Supervisor: Alanna Green (a.c.green@sheffield.ac.uk)

Second Supervisor: Helen Bryant (h.bryant@sheffield.ac.uk)

Project Description: 

Multiple myeloma is the second most common blood cancer and remains essentially incurable. Chemotherapy is effective at reducing tumour and extends survival, but it never fully eradicates disease, so patients face inevitable relapse. To find a cure for myeloma, new treatments that can target minimal residual disease (MRD) are needed.

One reason myeloma is difficult to treat, is that as myeloma tumours grow in the bone marrow some cancer cells become dormant when in contact with bone. While dormant and not cycling, they are resistant to most conventional chemotherapeutics.

Our team has exciting new data that a novel anti-cancer therapy can kill dormant myeloma cells. Our next goal is to identify the mechanism through which these drugs kill dormant myeloma cells to identify drug combinations that enhance killing of dormant myeloma cells.

This project will (1) identify vulnerabilities of dormant myeloma cells and (2) determine how to exploit vulnerabilities therapeutically. We will use cutting-edge in vivo models of myeloma dormancy and chemotherapy-resistant relapse, alongside 2D and 3D co-culture and models of dormancy to discover mechanisms and test therapeutics.

How to apply:

Candidates must have a first or upper second class honors degree or significant research experience.

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Oncology and Metabolism as the department.

Deconvoluting the spatial multi-omic landscape of high-grade glioma to target post-surgical residual disease

Primary Supervisor: Dr Spencer Collis (s.collis@sheffield.ac.uk)

Second Supervisor: Ola Rominiyi (o.rominiyi@sheffield.ac.uk)

Other Supervisors: Dr Mark Dunning

Project Description: 

High-grade gliomas are the most common cancers arising within the brain and contribute to ~190,000 brain tumour related deaths/year globally. These tumours demonstrate extraordinary intratumoural heterogeneity, however increasing understanding of genetic diversity within tumours has not yet led to tangible improvements in patient survival, which has improved little over the last 40 years. Most patients receive surgical resection followed by DNA damaging radiotherapy and temozolomide chemotherapy.

However, despite standard-of-care treatment, average survival remains around 1 year, highlighting an urgent need to improve outcomes. Critically, tumours harbour diverse subpopulations of glioma stem cells (GSCs), which possess unlimited regenerative potential and enhanced DNA repair capabilities. Although recent studies clearly demonstrate regional genetic differences within individual tumours, whether these translate to functional differences in response to DNA damaging therapy remains unproven.

Our team have developed a ‘living biobank’ of surgically-relevant preclinical high-grade glioma models, through sampling multiple distinct tumour regions to recapitulate the native features and heterogeneity of parental tumours. These models provide a unique capability to understand how spatial variation shapes resistance to current DNA damaging treatments, and construct patient-specific drug combinations targeting the DNA damage response, designed to tackle the range of functional diversity within a given tumour. We have recently generated whole exome sequencing (WES) and transcriptomic (RNASeq) data for a number of these models within our Biobank. Hypothesis: Residual and resected GSCs have genetic and transcriptomic differences that could be exploited to improve the clinical management of these currently incurable tumours. Methods: These computationally-focused studies leverage our existing and expanding database of omic data generated from SLB to uncover distinct, targetable features of the disease left-behind after surgery.

In Year 1 the genomic and transcriptomic landscapes of resected and residual disease will be contrasted using ‘Cancer Hallmarks’(15) and cell state-based(7,20) frameworks to prioritise targetable cancer vulnerabilities before generating experimental drug-response data to iteratively refine pharmacogenomic predictions using our leading expertise in ex vivo therapeutic drug screening(21).

Years 2-3 will focus on bioinformatics analyses to further expand our understanding of residual GSCs, including through data integration with emerging single-cell (10x Genomics RNA+ATACseq) data generated in our laboratory and large external datasets (including TCGA and GLASS cohorts) – before final experimental evaluation of the most promising treatment strategy/strategies in our patient-derived 3D intratumoural heterogeneity models. Collectively, the studies will systematically identify and validate new treatment strategies most likely to be effective against difficult-to-treat post-surgical residual disease in patients.

How to apply:

Candidates must have a first or upper second class honours degree or significant research experience. Previous experience with R and/or bioinformatics analyses is desired.

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Oncology and Metabolism as the department.

Brain and bone: deciphering the connection [BRONE study]

Primary Supervisor: Meena Balasubramanian (m.balasubramanian@sheffield.ac.uk)

Second Supervisor: Duncan Baker (duncan.baker@nhs.net)

Project Description: 

Purpose of proposed investigation:

We have a cohort of patients within the Highly Specialised Severe, Complex & Atypical OI service who present with ‘atypical OI’; further genetic investigations have identified pathogenic variants in genes known to be associated a syndromal intellectual disability phenotype. Through this study, we will explore the underlying mechanism for why individuals with these disorders present with fractures and determine whether there is a link between type 1 collagen production or processing and defects in underlying genes. We plan to undertake collagen species analyses, RNA sequencing and in-depth analyses of skin biopsies through electron microscopy and histology to compare data with OI (published by my group) and determine common genetic mechanisms.

Background of the project:

Inherited bone fragility disorders are rare of which Osteogenesis Imperfecta (OI), is the commonest. These disorders are complex, require a multidisciplinary approach, and often go unrecognised outside specialised settings, increasing patient burden. The clinical expression of OI varies across life and between individuals both in severity and qualitatively different complications such as deafness, valvular incompetence, and hypermobility. Over 90% of patients have a mutation in either the COL1A1 or COL1A2 genes resulting in either qualitative or quantitative defect in collagen production. The consequence is an abnormal collagen matrix within the bone. Current therapy for improving bone strength is not optimal and even though bisphosphonates significantly improve lumbar spine bone mineral density, there is no effect on hip BMD, bone pain or fracture rate in adults with Type I and children with moderate to severe OI. Teriparatide, a potent anabolic, while increasing BMD, also failed to demonstrate a reduction in fracture reduction. This has led to the search for novel pathways and therapies to treat this condition better.

This programme aims to study in-depth patients with ‘atypical OI’ caused due to genes that are known to cause unexplained fractures in the background of a neurological phenotype and explore novel pathways and therapeutic options for this rare, combined presentation. The comprehensive description of the disease and how it manifests will aid in translation of this knowledge to clinical care.

Sheffield has the strongest basic science and clinical base targeting bone disease across all ages in the UK, particularly the Paediatric age group. This project will integrate clinical and laboratory approaches in OI and provide further insight into disease mechanism. Consequently, this will help bring this translational research into a clinical setting and create a platform for better management in patients presenting with a brain and bone phenotype.

How to apply:

Research experience and experience on RNAseq data analyses desirable.

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Oncology and Metabolism as the department.

Precision Therapy for NBAS-related disorder using a zebrafish model

Primary Supervisor: Meena Balasubramanian (m.balasubramanian@sheffield.ac.uk)

Second Supervisor: Catherine Loynes (c.loynes@sheffield.ac.uk)

Project Description: 

Background: NBAS mutations causes SOPH syndrome (Short stature; Optic atrophy; Pelger-Huet anomaly), fractures and acute-onset liver failure [1-3.] Majority of patients with NBAS-related disorder have a homozygous recurrent missense variant c.5741G>A,p.Arg1914His [4-5]. We have now generated a stable F2 Crispant knock-in missense zebrafish model for nbas and a homozygous nonsense nbas mutant model and analysing the phenotype. The next step is to develop a precision therapy for treating these zebrafish models which is the focus of this project.

Aim: Developing druggable targets using screening assays will rescue nbas activity in homozygous mutant fish model

Methods: nbas mutant fish will provide a platform for chemical screens to identify candidate small molecules. The PhD student will develop a mutant rescue assay for screening using tools and test this on existing nbas mutant models. We have extensive experience of different drug screening assays using gene expression and fluorescence read outs with methods for high through-put screening with zebrafish.

1. Development of the drug screening assay. The screening assay will either be based upon morphological changes (e.g., using zebrafish skeletal stains in 5 dpf embryos) or readouts (collagen:GFP fusions or using in situ hybridisation for targets). The morphology assay will involve a quantitative measurement of the angles of the ceratohyal and Meckel’s cartilage structures that widen in the mutant embryos (Fiji, Danioscope). Markers identified that are absent or significantly reduced in the mutant embryos will be used for quantifiable primary or secondary assays.

2. Systematic testing of compound libraries. The primary focus will be on compound repurposing using the Spectrum library (Microsource Discovery Systems) of FDA-approved drugs (2000 compounds). Libraries of known bioactives (Tocris Total, 1120 compounds; Sigma LOPAC 1280 compounds) will be used for identifying target pathways that can rescue nbas mutants. We will screen compounds at 10microM concentration which we have found to be the best combination of high efficacy and low toxicity with the largest range of compounds.

3. Validation of results. Potential hits will be rescreened using the primary assay and counter screened for off target and toxic effects using a selection of markers of skeletal development. The validated hits will be tested to determine if they can rescue the disease-specific fish generated. Chemoinformatic analysis will determine compounds with similar structures and functions to be taken forward for further analysis.

Translational Aspect: It is very well recognised that rare diseases offer the potential to uncover new information about mechanisms underlying a range of phenotypes. Mechanistic insights benefit patients suffering from the disease in question, but also provide information with the potential for wider benefit. Understanding disease mechanism and identifying druggable targets for NBAS, will help treat NBAS-related phenotypes with potential wider utility.

How to apply:

Zebrafish experience desirable.

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Oncology and Metabolism as the department.

Understanding the mitotic response to DNA damage and cell confinement to overcome cancer drug resistance.

Primary Supervisor: Ruth Thompson (r.h.thompson@sheffield.ac.uk)

Second Supervisor: Dr Helen Matthews (h.k.matthews@sheffield.ac.uk)

Project Description: 

There were 18.1 million new cases of cancer in 2020 and 1 in 2 of us will be diagnosed with cancer at some point in our lifetime (Cancer Statistics UK). 80-90% of cancer deaths are attributable either directly or indirectly to cancer drug resistance and for this reason, new drugs are urgently needed to improve response to chemotherapy.

Many anti-cancer drugs kill rapidly growing and dividing cells by inflicting excessive amounts of DNA damage. If the level of damage is too high for the cells to repair prior to division they will die. Our own DNA repair systems can work against us in this situation as if cancer cells can repair the damage inflicted by the drugs they will not die and will go on to form drug resistant tumours. For this reason, inhibitors to our DNA damage repair pathways are currently in development for use alongside standard anti-cancer treatment.

The process of cell division where one cell becomes two is known as mitosis. The human DNA damage repair pathways are well characterised in the replication and resting phases of the cell cycle, however, our lab have discovered that there is a previously unidentified DNA recognition and repair signaling pathway in mitosis acting as a final “fail safe” for the cell to identify and repair damage prior to cell division. This previously unidentified checkpoint does not utilize the same proteins as the known interphase DNA damage checkpoints and could result in resistance to anti-cancer drugs even when combined with inhibitors of our known DNA repair systems. It is therefore vital that we understand the inner workings of this pathway in order to develop successful, effective anti-cancer drugs.

A major feature of cancers is limited space and nutrient availability due to a large amount of cells growing rapidly in one place without control. As part of this project we intend to assess how cell squashing due to confined space impacts cell division.

Through unbiased screening approaches, we have identified proteins necessary for the mitotic DNA damage checkpoint. This project will focus on these protein, how they are involved in the checkpoint and the impact that inhibiting them has on the cancer. We have demonstrated that inhibition of some of the proteins of leads to loss of mitotic DNA repair and therefore could sensitise cells to cancer chemotherapy. This project will fully characterize the role of these protein in DNA damage induced mitotic arrest and test whether drugs which inhibit this pathway can sensitise cancer cells to standard anti-cancer drugs.

For further information contact Dr Ruth Thompson at r.h.thompson@sheffield.ac.uk

How to apply:

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Oncology and Metabolism as the department.

An untargeted metabolomic approach to biomarker discovery in primary bone cancers

Primary Supervisor: Prof. A Gartland (A.gartland@sheffield.ac.uk)

Second Supervisor: Dr Karan Shah (k.shah@sheffield.ac.uk)

Other Supervisors: Dr Luke Tattersall

Project Description: 

Primary bone cancers (PBC) are a rare malignant tumors that arise in the bone and account for around 0.2% of all cancer diagnosis worldwide. There are multiple subtypes of PBC with osteosarcoma (OS) and chondrosarcoma (CS) being the most common in adolescents and adults respectively. These cancers are frequently aggressive with little improvement in patient survival for decades and surgical resection still being the main curative treatment. Diagnosing bone tumors is notoriously difficult and sometimes time‐consuming, with prolonged duration of the symptoms being associated with increased metastasis and thus poorer outcomes.

In this project, we propose to use cutting edge liquid spectrometric techniques in combination with in vitro and in vivo pre-clinical models to map the metabolomic profile of OS and CS progression, treatment response and metastasis in biofluids (serum and urine). In order to ensure the clinical translatability of the biomarker discovery, a proof of principle study will be performed with patient samples to validate any features identified by the metabolomic analysis.

This research will help identify a non-invasive biomarker for common PBCs and help enable earlier detection of malignancy and better inform the clinical management of patients.

The project will be conducted in Gartland Bone Group, in collaboration with researchers from University of Liverpool.

How to apply:

Candidates must have a first or upper second-class honours degree or significant research experience in biological sciences.

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Oncology and Metabolism as the department.

Exploiting extracellular vesicles as biomarkers and for drug delivery in solid cancers.

Primary Supervisor: Dr Gareth Richards (g.richards@sheffield.ac.uk ) 

Second Supervisor: Dr Karan Shah (k.shah@sheffield.ac.uk)

Project Description: 

Adrenomedullin (AM) is a multifunctional peptide that exerts its actions through two receptor complexes: adrenomedullin-1 receptors (AM1Rs – a complex of CLR+RAMP2) which are expressed ubiquitously and regulate blood pressure; and adrenomedullin-2 receptors (AM2Rs; CLR+RAMP3) with pathophysiological roles in tumorigenesis with largely cancer-associated expression.

Extracellular vesicles (EVs) are membrane-bound vesicles that transport functional biomolecules between cells for intercellular communication, and their role in pathophysiology is an emerging field. In cancer, tumour-derived EVs (tEVs) can provide a sequestered environment for bio-active cargo that can affect the phenotype of cells present locally in the tumors microenvironment to facilitate cancer progression, as well as cells at distant sites of metastasis for colonization. In fact, AM and its receptor components are expressed in tEVs and mediate pro-tumorigenic effects.

In this study, we aim to use a two-pronged approach utilizing tEVs and novel tools developed to target AM receptor components to improve patient outcomes - 1) develop biomarkers for early diagnosis of cancers, and 2) target metastatic disease in distant organs.

The supervisory team has unrivalled expertise in the field with breadth of knowledge including chemistry, biology and pharmacology and so the student has a real opportunity to graduate with literacy in cross-disciplinary science.

We welcome applicants from all backgrounds, particularly those underrepresented in science, who have curiosity, creativity and a drive to learn new skills.

How to apply:

Candidates must have a first or upper second class honours degree or significant research experience

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Oncology and Metabolism as the department.

Defining the role of glycosylation enzyme ST6GAL1 in the prostate cancer bone metastasis

Primary Supervisor: Dr Ning Wang (n.wang@sheffield.ac.uk)

Second Supervisor: Shelly Lawson (m.a.lawson@sheffield.ac.uk)

Project Description: 

Prostate cancer is the most frequently diagnosed cancer in men and most commonly metastasizes to the skeleton with up to 90% of patients with advanced disease having bone metastases. Once clinically detectable bone metastases have been established, the disease is considered incurable. Current understanding of the mechanisms underlying bone metastasis remains incomplete. Glycans, the essential building blocks of life involved in every biological process, change dramatically in prostate cancerous tissues and potentially hold significant clues to fight this deadly disease.

However, their structural complexity means that glycans have been difficult to target. Therefore targeting enzymes involved in aberrant glycosylation could be a more feasible options than directly targeting glycans themselves. This PhD project is aimed to examine whether targeting specific glycosylation enzymes identified previously in our group could affect the arrival, colonisation, and growth of prostate cancer cells in bone, using a set of cutting-edge in vitro, in vivo, and ex vivo techniques. The proposed project will be carried out in the Department of Oncology & Metabolism, The University of Sheffield, in collaboration with Newcastle University. Sheffield offers a unique combination of infrastructure and expertise for the planned project that is not available elsewhere in the UK. The University of Sheffield is a Centre of Excellence for musculoskeletal research, which means that there are unique and unrivalled facilities in Sheffield for carrying out studies in the area of bone oncology which the University has committed to continuously support and expand.

This will warrant students who are interested in this project to acquire special techniques and skills in bone oncology and bone biology, as well as a broad spectrum of techniques in the fields of cancer biology, cell and molecular biology, biochemistry, and immunology.

How to apply:

Talented and motivated applicants are expected to hold a Master’s degree in Cancer Biology or a related discipline, and/or Bachelor’s degree with good marks. The applicants are also expected to have experience in working with experimental animals and good communication skills in English.

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Oncology and Metabolism as the department.

Neuroscience

The exciting brain: personalised neural stimulation for motor neurone disease

Primary Supervisor: James Alix (j.alix@sheffield.ac.uk)

Second Supervisor: Alekhya Mandali (a.mandali@sheffield.ac.uk)

Other Supervisors: Professors Pamela Shaw and Christopher McDermott

Project Description: 

Motor neurone disease is a fatal neurological condition in which certain cells in the brain are said to ‘hyperexcitable’. This important feature could be a therapeutic target for non-invasive brain stimulation. In this project you will develop personalised non-invasive brain stimulation for patients with motor neurone disease using cutting edge techniques such as transcranial electrical stimulation (tES), transcranial magnetic stimulation (TMS) and electroencephalography (EEG). You will join a vibrant postgraduate research community based at the Sheffield Institute for Translational Neuroscience and have enhanced training opportunities through the University Neuroscience Institute and NIHR Biomedical Research Centre. We are looking for a highly motivated student to join our team and the fight against motor neurone disease.

How to apply:

Candidates should have a first or upper second-class degree, or a Masters degree in a biology-based subject (e.g. biology, neuroscience, psychology). Candidates with physical science degrees (e.g. physics, computer science) may be considered if they have some appropriate research experience. Familiarity with some of the techniques to be used would be advantageous but not essential as full training can/will be provided.

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Neuroscience as the department.

Using the carer experience to develop an automated assessment of progression of cognitive symptoms in people with Mild Cognitive Impairment (MCI).

Primary Supervisor: Daniel Blackburn (d.blackburn@sheffield.ac.uk)

Second Supervisor: Simon Bell (s.m.bell@sheffield.ac.uk)

Other Supervisors: Dr Traci Walker and Professor Heidi Christensen

Project Description: 

Mild Cognitive Impairment (MCI) is a heterogenous clinical entity that describes patients with demonstrable cognitive deficits but without functional impairment. The aetiology is diverse, though a significant proportion of patients have different types of dementia. In workshops we have run, clinicians, patients and care-partners described the frustration with current pathways. There has been a 682% increase in referral rates to memory clinics resulting in increased waiting times and people with MCI being discharged without adequate follow-up because of insufficient resources, causing anxiety and distress.

CognoSpeakTM (www.cognospeak.org) represents a unique approach to assessing cognition using speech analytics. It is an online tool that engages the patient in a conversation, placing a high demand on cognitive domains. It also tracks levels of depression and anxiety. The Covid-19 pandemic highlighted the need for better, remote assessments. CognoSpeakTM can be done remotely reducing appointment-related travel time, costs and anxiety.

The importance of the carer experience in MCI is often overlooked in research. This project not only focuses on this experience but will incorporate information from carer interviews into the development of the diagnostic pathway for people living with MCI and dementia. Using Cognospeak by the end of the project we will be able to use carer interview experience to help diagnose people with cognitive disorders, track progression and also increase the speed by which a diagnosis of MCI/dementia is made in a semi automated way.

This project will:

1. Develop a semi-structured interview for carers of people with dementia that could be adapted for an Intelligent Virtual agent and would provide information that correlates with standard questionnaires.

2. Develop a digital survey utilising existing tools that the care-partner of a person living with dementia can complete to provide a more complete assessment of cognition and function. This information will be used to help in the develop of differential diagnosis, including subtypes of dementia.

3. Co-design with care-partners from different ethnic minorities groups to ensure carer interview is suitable for all participants.

4. The acceptability and accuracy of repeated caregiver surveys and semi-structured interviews to investigate longitudinal tracking of cognition in people living with MCI (pwMCI).


This project will provide training in the following areas:
• Interdisciplinary skills (in between engineering/computational and clinical (cognitive neurology).
• Co-design development with pwMCI (including those from ethnic minority groups) and clinicians will ensure acceptability and scalability of tool.

• Quantitative skills (computation, data analytics and informatics and developing digital and technology excellence as the student will experience web design and large scale data collection

How to apply:

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Neuroscience as the department.

Identification of gene-environment interactions that enable individualised risk prediction in ALS patients

Primary Supervisor: Andrew Grierson (a.j.grierson@shef.ac.uk)

Second Supervisor: John Cooper-Knock (j.cooper-knock@sheffield.ac.uk)

Project Description: 

At least 90% of amyotrophic lateral sclerosis (ALS) cases are classified as sporadic, where there is no family history supporting transmission of a disease-causing genetic mutation. The causes of sporadic amyotrophic lateral sclerosis (ALS) remain unknown, but most cases are thought to result from complex gene-environment interactions, proposed to occur as sequential hits. Several environmental factors are strongly associated with ALS, and the overall aim of this PhD project is to use zebrafish to develop tractable vertebrate disease models using these factors, and then use these to identify gene-environment interactions allowing individualised risk prediction in ALS patients.


Firstly, you will determine doses for larval exposure of environmental toxins in zebrafish embryos that give an ALS-like phenotype in zebrafish larvae. Secondly you will develop phenotypic readouts of ALS in early exposure experiments, such as swimming behaviour, motor neuron axon length and branching, and neuromuscular junction pathology. Lastly you will investigate gene-environment interactions relevant to genetic risk in individual ALS patients. This will involve RNA sequencing zebrafish larvae to identify genes that show altered expression after environmental exposure. These genes will then be investigated in whole genome sequencing data from thousands of ALS patients to identify genes that show significant enrichment for deleterious variants in ALS patients. We believe these genes are strong candidates to modify an individual’s risk of developing ALS after environmental exposure. To corroborate this, you will use CRISPR/Cas9 to generate F0 mutant zebrafish larvae and determine their ALS phenotypes in environmental exposure dose-response studies compared with wild-type larvae.


We have access to excellent zebrafish facilities and support staff in the Bateson Centre. You will receive training in zebrafish husbandry and genetics, including training for the use of animals in research, and obtain a personal license for zebrafish work. Day-to-day support for zebrafish work will be provided. You will receive specialist training in computational genetic analysis. Methods for investigation of environmental toxin exposure and phenotypic analysis in larval zebrafish are already established in the laboratory.


You will attend lab meetings in the supervisors’ laboratories, present your data monthly, and receive feedback and constructive criticism from the supervisors, lab members, and additional PIs who attend these meetings. You will follow the Neuroscience PhD training programme, and thus benefit from the independent opinions of 2 additional thesis advisors. You will also receive additional training in line with the existing program operating at the University of Sheffield.

How to apply:

Previous experience with zebrafish research, or large-scale genetic datasets, would be helpful, but not essential

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Neuroscience as the department.

Does systemic infection modulate astrocyte function in Alzheimer’s disease?

Primary Supervisor: Julie Simpson (julie.simpson@sheffield.ac.uk)

Second Supervisor: Steve Wharton (s.wharton@sheffield.ac.uk)

Project Description: 

Systemic inflammation in the body can lead to the rapid acceleration of many neurodegenerative diseases such as Alzheimer’s disease (AD). The inflammatory signals produced in response to infection increase blood-brain barrier (BBB) permeability and disrupt homeostasis in the central nervous system (CNS) leading to neuroinflammation and neuronal dysfunction. Similar to microglia, astrocytes also play a key role in the neuroinflammatory response, secreting pro-inflammatory molecules that promote neurodegenerative processes. However, few studies have examined the impact of systemic infection on the astrocyte phenotype in AD.

In response to pathological and physiological stimuli astrocytes engage in morphological and transcriptional changes which ultimately results in a change of function. This PhD will test the hypothesis that systemic inflammation drives astrocytes to a proinflammatory phenotype in AD, contributing to cognitive decline during infection. The study aims to perform a detailed histological characterisation of post-mortem tissue alongside transcriptomic profiling to assess the impact of systemic infection on the astrocyte phenotype in AD.

The proposed research will advance our understanding of the relationship between systemic inflammation, a change in astrocyte function and cognitive decline. Understanding how systemic inflammation contributes to dementia is essential to identify new therapeutic treatments.

The PhD will be based at the Sheffield Institute for Translational Neuroscience (SITraN), a multi-disciplinary institute which brings together scientists with a range of expertise in neuropathology, experimental neuroscience and bioinformatics, with a strong emphasis on neurodegenerative research.

For more information about this exciting PhD opportunity please email julie.simpson@sheffield.ac.uk

How to apply:

Experience of histology, with basic laboratory skills in molecular biology and neuroscience are desirable.

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Neuroscience as the department.

The role of post-translational protein modifications (PTMs) in the regulation of RNP biomolecular condensates in health and motor neuron disease (MND)

Primary Supervisor: Tatyana Shelkovnikova (t.shelkovnikova@sheffield.ac.uk)

Second Supervisor: Mark Dickman (m.dickman@sheffield.ac.uk)

Other Supervisors: Caroline Evans

Project Description: 

Background. Eukaryotic cells contain a whole repertoire of microscopically visible, non-membrane-bound RNA-protein complexes - biomolecular condensates that are maintained through a combination of protein-protein, protein-RNA and RNA-RNA interaction.
Biomolecular condensates are abundant and prominent in neurons – large, long-lived cells. Therefore, it is not surprising that their dysfunction has been linked to the pathology of fatal neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Biogenesis, integrity, dynamics and ultimately, function of stress granule, paraspeckle, gem, P-body and speckle condensates are compromised in ALS making it a disease of disrupted cellular condensate network.
Phase separating properties of many proteins (primarily RNA-binding proteins, RBPs) and their ability to form/enter biomolecular condensates are regulated by post-translational modifications (PTMs), for example, arginine methylation. PTM dysregulation may therefore play a prominent role in diseases with a misbalance of the cellular condensate network, such as ALS.
Paraspeckles are prototypical biomolecular condensates formed by a long non-coding RNA NEAT1_2 that acts as a scaffold, and a set of proteins that stabilise this lncRNA and drive phase separation (paraspeckle proteins, PSPs). These PSPs were found abnormally accumulated, mislocalised and/or aggregated across multiple ALS subtypes. Furthermore, mutations in PSPs can compromise paraspeckle integrity, and motor neurons, the affected neuronal population in ALS, are characterised by paraspeckle hyper-assembly, suggesting a reliance of this neuronal subtype on paraspeckles for survival and potentially depletion of this regulatory mechanism in PSP-linked ALS.
Project hypothesis. We hypothesise that PTMs of ALS-linked PSPs critically regulate and control their physiological and pathological phase separation.
Aim and objectives. The aim of this project is to comprehensively characterise the role of PTMs, in particular, arginine methylation and the antagonistic modification citrullination, of ALS-linked proteins – paraspeckle components – in physiological and pathological phase separation.
Objectives:
1. To identify PSPs whose regulation by PTMs is primarily responsible for paraspeckle clustering/separation, using mass-spectrometry coupled with super-resolution imaging.
2. To characterise the changes in the PSP and paraspeckle stability, dynamics, turnover and function upon manipulation of PSPs’ PTM profile, using pharmacological, molecular biology and super-resolution imaging approaches.
3. To characterise changes in the PTMs profiles in genetic models of ALS (including PSP-linked subtypes) and correlate these to paraspeckle structure and integrity.
Student training. The primary supervisor is a UKRI Future Leaders Fellow based at the Sheffield Institute for Translational Neuroscience (SITraN) – a centre with an outstanding reputation in training PhD students. The student will also spend a significant amount of time in the co-supervisors’ lab in the Department of Chemical and Biological Engineering (CBE). Both labs are actively involved in curiosity-driven research of highest quality, and the multidisciplinary nature of the project will provide a space for research creativity thus offering an excellent training opportunity for an open-minded and flexible candidate.

How to apply:

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Neuroscience as the department.

Assessment of glucose metabolism in Alzhiemer disease cell types to determine new disease biomarkers

Primary Supervisor: Simon Bell (s.m.bell@sheffield.ac.uk)

Second Supervisor: Professor Heather Mortiboys (h.mortiboys@sheffield.ac.uk)

Other Supervisors: Caroline Evans

Project Description: 

Alzheimer’s disease (AD) is the most common form of dementia worldwide with limited treatments available. The condition is characterised by protein accumulation but deficits in cellular metabolism are seen early in the condition too. We have previously shown that astrocytes derived from people with AD have deficits in the glycolytic enzyme hexokinase and that these deficits correlate with neuropsychological features of the disease. Understanding how hexokinase and other glycolytic enzymes change in AD and how this change compares with other established cellular pathologies in AD will help us to develop new treatments and biomarkers for the condition.
In our previous work, funded by the Wellcome trust, we have identified that astrocytes and fibroblasts derived from patients with both sporadic and familial forms of AD have deficits in total cellular ATP, extracellular lactate and have increased mitochondrial reactive oxygen species (ROS). This suggests deficits in both glycolysis and mitochondrial oxidative phosphorylation. AD astrocytes also have deficits in the expression of hexokinase 1 (HK1). Correcting the HK1 deficit in sporadic AD astrocytes, via transfection with an adenovirus vector, ameliorates the ATP, lactate and ROS abnormalities. This suggests that targeting hexokinase activity within the astrocytes could improve brain glucose metabolism which potentially contributes to disease progression. If these deficits are also present in peripheral cells in people living with AD, glycolytic enzymatic change could be investigated as a new disease biomarker.

In this project the student with investigate the expression of glycolytic enzymes, including hexokinase, in different cell types taken from people living with AD, including blood, fibroblasts and derived neurons. They will assess if metabolic stress leads to differential expression of the glycolytic enzymes, and if enzyme expression correlates with other well established AD pathologies. Finally, the student will determine if the expression of glycolytic enzymes in the blood of people living with AD, when combined with other established AD blood biomarkers can determine disease progression when compared to clinical phenotype.

Objectives
1. Determine blood expression/activity levels of glycolytic enzymes in patients with
biomarker confirmed in AD.
2. Correlate blood hexokinase activity/expression with imaging biomarkers.
3. Measure glycolytic enzyme expression responses in relation to physiological stressors
in different cell types derived from the AD patients.
4. Determine if new metabolic blood biomarkers can be developed to monitor disease
progression rates when combined with established AD blood biomarkers.

Skills acquired:
1. Human tissue culture (Astrocyte, fibroblast, neuron) and human cell line reprogramming
2. Techniques in molecular biology, neuroscience and cell culture
3. Exposure to clinical data sets and biomarker development, including MRI, PET, and
neuropsychology.
4. Neurodegenerative disease biomarker development.

How to apply:

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select Neuroscience as the department.


Clinical Dentistry

Diagnostic, prognostic and predictive biomarkers for head and neck cancer

Primary Supervisor: Professor Syed Ali Khurram (s.a.khurram@sheffield.ac.uk)

Second Supervisor: Professor Daniel Lambert (d.w.lambert@sheffield.ac.uk)

Project Description: Head and Neck cancer (HNC) is a significant cause of mortality and morbidity worldwide, ranking as the 6th most common cause of cancer incidence and mortality in the world. In the UK alone, it accounted for over 12000 new cases and 4000 deaths in 2019-20 whereas in developing countries the incidence is even higher contributing up to 25% of all reported cancer cases. In Western Europe, HNC incidence has increased in recent decades, with the UK reporting a 68% increase in incidence and 22% increase in mortality during the last decade indicating that it is a significant and pertinent clinical problem. In comparison to other common cancers, the molecular landscape of HNC is poorly understood, hampering the development of novel treatments and prognosticators informing treatment options. The pathogenesis of HNC is complex and multifactorial and our previous work has shown that tumour microenvironment (TME) in particular fibroblasts play a key role in progression. Further characterisation of these fibroblasts and comparison between different types of HNC (oral, oropharyngeal and laryngeal) has the potential for therapy as fibroblasts remain genetically stable unlike the epithelial cancer cells.

This project aims to re-create the HNC TME using a range of invitro and ex vivo methods and modular organ-on-a chip system to develop better understanding of HNC pathogenesis and treatment.

Useful links:
1. Cancer Research UK
2. Dr Ali Khurram’s Virtuathon 2020
3. Professor Dan Lambert - We need to talk about the fibroblasts: key players in cancer, ageing and tissue engineering
4. Global Cancer Observatory

How to apply:

Candidates must have a first or upper second class honors degree and experience or awareness of cell culture and molecular biology.

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select School of Clinical Dentistry as the department.

Vaulting the void: The vault particle as a novel mediator of intercellular communication in the tumour microenvironment

Primary Supervisor: Dr Stuart Hunt (s.hunt@sheffield.ac.uk)

Second Supervisor: Professor Daniel Lambert (d.w.lambert@sheffield.ac.uk)

Project Description: 

Background
The vault particle is the largest known eukaryotic ribonucleoprotein complex. It is composed of 78 copies of major vault protein (MVP) as well as two associated proteins (TEP1 and PARP4) and vault RNA (vtRNA) [1,2].

The function of the vault particle remains elusive. However, it has been implicated in intracellular transport and multidrug resistance. VtRNA have been linked to resistance to apoptosis and chemoresistance, independent of the vault particle [3].

Cancer cells release a complex mixture of soluble factors and extracellular particles into the tumour microenvironment (TME), which have been implicated in driving tumorigenesis. In recent decades, extracellular vesicles (EVs) have attracted attention due to their role in intercellular communication in the TME. MVP and vtRNA have repeatedly been reported as EV cargo. However, a recent report [4] (and our unpublished data) demonstrated the presence of intact vault particles in the extracellular space. We have shown that vault particles are frequently co-isolated with EVs.

Experimental approach
In collaboration with our industrial partner, NanoFCM, we will utilise the state-of-the-art NanoAnalyzer to characterise the extracellular particles released from wild-type oral cancer cells and a vault particle deficient cell line (already generated in house). You will receive full training to use the NanoAnalyzer whilst working at the NanoFCM laboratory in Nottingham. You will also become proficient in cell culture, enrichment of extracellular particles (using techniques such as size exclusion chromatography and ultracentrifugation) and fluorescent labelling of extracellular particles.

We will investigate the mechanism of vault particle release using advanced microscopy techniques such as confocal microscopy and transmission electron microscopy coupled with immunogold labelling. We will use small interfering RNA and CRISPR Cas9 gene editing to perturb putative export machinery. You will also utilise quantitative PCR and western blotting to analyse gene expression and protein abundance, respectively.

We will use in vitro cell culture to investigate if transfer of vtRNA via uptake of vault particles can endow an apoptosis resistant phenotype in cells that would be found in the TME. Vault particles will be tagged by genetic manipulation to allow tracking of release and uptake.

Supervisor one: Dr Stuart Hunt

Supervisor two: Prof Dan Lambert

How to apply:

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select School of Clinical Dentistry as the department.

Delivery of anti-cancer therapeutic drugs using oral mucoadhesive patches

Primary Supervisor: Craig Murdoch (c.murdoch@sheffield.ac.uk)

Second Supervisor: Helen Colley (h.colley@sheffield.ac.uk)

Other Supervisors: Prof Malcom Clench

Project Description: 

There is increasing interest in the development of needle-free, self-administered drug delivery systems for a number of diseases. A multidisciplinary team at The University of Sheffield, in collaboration with AFYX Therapeutics, have developed a polymer-based patch that can adhere tightly to the oral epithelium that lines the inside of the mouth and deliver drugs (e.g., corticosteroids, anaesthetic, peptides) directly to oral lesions (Colley 2018, Clitherow 2020, Said 2021). The patch has successfully completed phase 2 clinical trials. This project aims to incorporate anti-cancer agents into these novel patches for the treatment of oral cancer, the incidence of which has risen by 60% in the UK in the last decade.

To progress further, the oral patch technology requires fine-tuning in terms of controlled drug release and understanding drug absorption, distribution in tissues, as well as drug metabolism and excretion. In this project you will produce oral patches to contain anti-cancer drugs at therapeutically relevant concentrations and determine the drug release profiles from the patch over-time using a number of analytical techniques (Franz Chamber/HPLC). We have previously developed tissue-engineered in-vitro models of human oral cancer (Colley 2011) that accurately mimic cancer in vivo. You will adhere patches to oral cancer models and visualise drug permeation through the 3D tissue using Mass Spectrometry (MS) Imaging, a powerful label-free analytical technique that allows visualisation and spatial location of any specific molecule within tissues (Russo 2018, Handler 2021). You will also measure oral cancer cell death and rates of drug metabolism as the anti-cancer drug is de-activated by enzymes within cancer cells. The use of MS imaging combined with tissue-engineered oral cancer to develop oral patch-delivered drugs has not been performed previously.

This project will deliver extensive training in cell culture, tissue-engineering and 3D biology. This will be combined with training in advanced tissue imaging and analytical techniques. Complementing these core techniques, the student will also obtain training in biomaterial fabrication using polymers (University of Sheffield) and network with other researchers that make-up the wider multidisciplinary team, allowing first hand insight into other disciplines and how these interact at the cutting edge of science.

How to apply:

Please complete a University Postgraduate Research Application form available here.

Please clearly state the prospective main supervisor in the respective box and select School of Clinical Dentistry as the department.