2023 summer projects
Enhancing mRNA vaccine delivery using lipid nanoparticle formulations: a study on optimizing LNP formulation for increased GFP expression in cells
Supervisor: César López-Camacho
Location: Jenner Institute, Old Road Campus, Headington, Oxford
The summer internship project will focus on optimising lipid nanoparticle (LNP) formulation conditions for mRNA delivery, to enhance green fluorescent protein (GFP) expression in cells. The project will involve designing and testing various LNP formulations with different ratios of mRNA and lipid components, as well as exploring different conditions for LNP formulations such temperature, formulation and incubation time.
The intern will be responsible for preparing LNPs and testing their transfection efficiency in vitro using cell culture models. GFP expression levels will be measured using fluorescence microscopy and flow cytometry, and the intern will analyse and present the results to the team in weekly meetings.
This project aims to provide the intern with hands-on experience in optimising LNP formulation for mRNA delivery and assessing the efficiency of gene expression.
Mapping the epigenetic modifications of DNA and RNA
Supervisor: Chunxiao Song
Location: Oxford Ludwig Institute, NDM Research Building, Old Road Campus, Headington, Oxford
Our genome is not a static state; it contains dynamic epigenetic modifications that play crucial roles from development to pathogenesis. Recently, there has been an explosion of new information in the field of epigenetics, thanks to the discovery of many new nucleotide variants in DNA and RNA. The chemical and biological transformations of these nucleotide variants have always been at the core of crucial methodologies in epigenetic research. Our group is focused to advancing the field of epigenetics and epitranscriptomics through technology development, functional studies, and clinical applications. We employ a combination of chemical biology and genome technologies to develop novel tools to analyse the epigenome. In this project, you will be working to develop new chemistry for use in epigenetics and epitranscriptomics, with the goal of advancing our understanding of these crucial processes.
References:
Liu, Y.et al. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat. Biotechnol. 37, 424-429 (2019).
Siejka-Zielińska, P. et al. Cell-free DNA TAPS provides multimodal information for early cancer detection. Sci. Adv. 7, eabh0534 (2021).
Modelling gastric reflux using stomach stem-cell driven cultures
Supervisor: Francesco Boccellato
Location: Oxford Ludwig Institute, NDM Research Building, Old Road Campus, Headington, Oxford
Background
Epidemiology suggests that Helicobacter pylori infection and reflux correlate with an increased incidence of gastric cancer development. While the role of Helicobacter pylori in stomach pathogenesis has been studied extensively, the role of reflux is less clear.
Aim of the project
To develop an in-vitro model to study the effect of gastric reflux on the stomach epithelium.
Methods
We developed “mucosoid cultures”: a stem cell-driven model for the stomach epithelium. Healthy human stomach cells in the mucosoid form a monolayer of polarised cells with tight junctions with regenerative capacity. The mucosoids accumulate mucins on the apical side and their cells can differentiate to produce digestive enzymes and gastric acid. As such, the mucosoids are a unique, advanced cell culture model that mimics most of the features of a real healthy gastric mucosa. Mucosoids were successfully used to model Helicobacter pylori infection. We propose to model the effect reflux on the stomach epithelium by treating the gastric mucosoids with human gastric juices from patients with reflux.
Expectations and future plans
We expect reflux to impact on cell viability and epithelial barrier integrity. We will investigate how regeneration and differentiation is altered in the presence of gastric reflux
Hypoxia inducible factors: a therapeutic target for the treatment of Respiratory viral infections
Supervisor: Jane McKeating
Location: NDM Research Building, Old Road Campus, Headington, Oxford
Respiratory viral infections in humans are responsible for a significant proportion of global deaths, approximately 4.25 million/year, mostly in children and older adults. Respiratory syncytial virus (RSV) is the leading cause of infant hospitalisation worldwide, infecting approximately 34 million children each year and a major cause of morbidity and mortality in elderly and immunosuppressed adults. The only approved prophylactic treatment is Palivizumb (a neutralising anti-RSV Fusion antibody) and currently there are no approved vaccines, highlighting an urgent need for antiviral agents.
The COVID-19 pandemic has highlighted the importance of understanding fundamental host processes that viruses exploit to infect the respiratory tract. One important factor is local oxygen availability in the microenvironment that can activate hypoxia inducible factors (HIFs) that define the host response to low oxygen (hypoxia). HIFs activate the transcription of genes involved in cell metabolism and immune activity and are key regulators of host defences. We reported that HIFs inhibit SARS-CoV-2 infection and pathology and recent data shows their role in suppressing RSV infection. This project will use state-of-art RSV replication systems and animal models to examine the interplay between HIFs and RSV and this knowledge will inform the discovery of new therapies for the treatment of RSV.
Examining the role of physicians and hospital care as part of Universal Health Coverage in rural Democratic Republic of Congo
Supervisor: Mike English
Location: Peter Medawar Building, Oxford
The Health Systems Collaborative (HSC) links scientists from Oxford with scientists from low and middle-income countries to create new knowledge aimed at strengthening health systems and build capacity in applied, multidisciplinary global health research. We are exploring a partnership with the Vanga Medical Center of Bandundu in the Democratic Republic of Congo. This is the largest hospital in a rural region 500km east of Kinshasa. It welcomes 13,000 patients a year, has more than 400 beds, and employs 13 doctors and hundreds of nurses. The hospital also hosts a medical residency program which continues to grow in size.
Prof. Mike English and the HSC team are developing new work to explore the role of physicians and hospital care as part of Universal Health Coverage (UHC) in a number of settings. This builds on work understanding the provision of neonatal services in Kenya and the critical service planning gaps and skilled nursing staff shortages that prevent access to quality care. It also links with work on the role of specialist physicians, of different forms of task-sharing in providing access to child health services. In the work with the Vanga Medical Centre the aim would be to develop a proposal for work that examines how the hospital engages with the network of smaller facilities and community health workers that it supports to support UHC.
Assessment of Galectin 3 inhibitors as functional modulators of TREM2 signalling in human iPSC macrophages
Supervisors: Paul Brennan and Emma Mead
Location: Centre for Medicines Discovery, Old Road Campus, Headington, Oxford
Alzheimer’s disease (AD) is the most common form of dementia and is thought to comprise 60-70% of the 55.2 million people living with dementia worldwide. Single nucleotide polymorphisms in a number of microglial genes have been identified that confer an increased risk in developing AD, including multiple genes within the TREM2 signalling pathway. This pathway is an important regulator of microglial function and recent evidence has highlighted a link between the TREM2 signalling pathway and another AD risk gene, LGALS3, which encodes Galectin-3 (Gal3).
Gal3 has been found to be elevated in both individuals with AD and microglia exposed to inflammatory and pathogenic stimuli, where it acts as an endogenous ligand to Toll-like receptors and TREM2. Upon binding, Gal3 induces an inflammatory phenotype. As Gal3 appears to modulate inflammation, and inhibition of Gal3 in mouse models enhances microglial phagocytosis, we believe pharmacological inhibition of Gal3 with small molecule compounds may be protective in AD.
This project will use commercially available Gal3 inhibitors as tool compounds to determine whether Gal3 inhibition modulates key functions in human iPSC macrophages. Techniques will include iPSC maintenance and differentiation to macrophages, phagocytosis assays using fluorescent imaging on the Incucyte S3 platform and cytokine/chemokine ELISAs.
Development and validation of a mitophagy fluorescence reporter cell line for drug screening and target validation assays relevant to Alzheimer’s and Parkinson’s diseases
Supervisors: Paul Brennan and Emma Mead
Location: Centre for Medicines Discovery, Old Road Campus, Headington, Oxford
Mitophagy is a process where damaged mitochondria are selectively targeted for degradation in the lysosome. Emerging findings suggest mitophagy is compromised in Alzheimer’s (AD) and Parkinson’s diseases (PD) resulting in accumulation of damaged mitochondria leading to synaptic dysfunction and cognitive deficits. Pharmacological drugs which can enhance the clearance of damaged mitochondria and promote mitophagy flux are seen as promising candidates with therapeutic potential.
We have successfully developed lysosomal pH biosensor cell lines to measure lysosomal luminal pH and we are now interested in developing similar tools that will be sensitive and robust enough to measure mitophagy flux in cellular models of AD and PD. Many fluorescent reporter systems are now available for investigating mitophagy in cells, including the mito-QC, mt-Keima and mito-timer. The mito-QC fluorescence reporter consists of a tandem mCherry-GFP fused protein selectively targeted to the outer mitochondrial membrane. The fluorescence of the GFP portion of the reporter is quenched in lysosomes due to sensitivity to acidic pH, allowing to measure the mitophagy flux by ratiometric imaging of mCherry and GFP signals.
You will be producing a stable cell line expressing the mito-QC reporter (or another alternative), testing for its mitochondrial localization and performance, by subjecting cells to various mitochondrial-damaging agents and lysosomal inhibitors with view to assess its use in our drug screening and validation studies.
You will potentially use techniques such as tissue culture, high-content imaging, and molecular biology.
Generating evidence to inform schistosomiasis elimination as public health problem
Supervisors: Piero Olliaro and Michel Vaillant
Location: Pandemic Sciences Institute, Old Road Campus, Headington, Oxford
Background: The new WHO/NTD roadmap has set as target the global elimination of schistosomiasis as public health problem by 2030 in all 78 endemic countries.
This project: To understand if intensity of Schistosoma infection can be used as a proxy for morbidity, a systematic review of the literature and meta-analysis of published and unpublished databases will be conducted. PubMed, EMBASE, the Cochrane Library and LILACS literature database will be searched for specific keywords for epidemiological studies on prevalence, morbidity and infection intensity of schistosomiasis. After data extraction of selected articles, meta-analytic estimates will be derived using random-effects modelling. Individual patient data from studies available to WHO/NTD will also be analysed with random-effects models. Assessment of methodological quality will be carried out by using the NOS checklist and the GRADE methodology.
The role sought: The student will be involved in literature review, data assessment and extraction, and possibly analysis and interpretation, depending on timelines. Both supervisors have extensive experience in schistosomiasis including generating data informing WHO/NTD recommendations.
Significance of the work: The project is commissioned by WHO/NTD, that will support the study and facilitate access to relevant databases. Results of these analyses will be reported to a WHO advisory committee.
Viral factors influencing Cell-to-Cell transmission of HIV
Supervisors: Sarah Rowland-Jones, Ester Gea-Mallorquí
Location: Centre for Immuno-Oncology, Old Road Campus Research Building, Headington, Oxford
HIV is a pandemic virus that affects more than 38M people worldwide. In the lab, we compare the virological characteristics of HIV-1 and HIV-2. While HIV-1 is a pandemic virus, HIV-2 is endemic and better controlled by the immune system. By understanding the means of control of HIV-2, we aim to infer mechanisms of viral and immune control that can help in future therapy or cure strategies for HIV-1. We have recently discovered key differences in the role of some viral proteins in the way HIV-1 and HIV-2 interact with Dendritic Cells. In this project, we will make molecular constructs of these proteins to address their role in subsequent steps of cell-to-cell transmission and viral spread. Work in the Cat level 3 lab will be performed by the supervisor and training will be provided for all the techniques, which include primary cell isolation and culture, flow cytometry and RT-qPCR.
The role of Trip4 mutations in cancer drug resistance
Supervisor: Yang Shi
Location: Oxford Ludwig Institute, NDM Research Building, Old Road Campus, Headington, Oxford
Trip4, initially identified as a co-activator of thyroid hormone receptor, is a poorly characterized transcriptional factor reported to cause congenital muscular dystrophy. Our group discovered that trip4 binds to tRNA genes and possibly indirectly regulates the translation of key myosin proteins in the process of muscle fiber maturation. Interestingly, loss-of-function mutations of trip4 have been implicated in drug resistance in cancers. We are interested in investigating if Trip4 mutations promote the acquisition of drug resistance in cancers through a similar mechanism involving the regulation of protein metabolism via tRNA.
This project will survey the role of trip4 mutations in cancer drug resistance in a cohort of cancer cell lines and dissect the underlying mechanisms with the combination of genetic, genomic, and biochemistry tools. The student will receive trainings in all related experiment techniques, analysis skills, as well as scientific thinking.
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