Research Opportunities

Sympathetic neurons have a wide range of physiological functions and their hypoactivity contributes to obesity and diabetes, among other syndromes. Sympathomimemic drugs rescue this deficiency but this drug class, mostly composed of brain-penetrant amphetamines and adrenergic agonists, is both cardiotoxic and highly controlled. Our recent publication puts forward new class of drugs  named Sympathofacilitators that do not enter the brain and have an anti-obesity and cardio-neutral effect in vivo. The first-in-class was published in Mahu I et al Domingos, Cell Metabolism 2020; Fig. 3C of this paper demonstrated a neuro-facilitatory effect, rather than neuro-excitatory one. 

This new class is in needed of novel chemical entities which can be screened in vitro on cultured iPSC-derived sympathetic neurones. The screen would be based on fluorescent readouts of calcium activity reporter, screening for a facilitation of responses to acetylcholine (similar to Fig. 3C of Mahu I et al). 

The prospect of identifying natural compounds that have a Sympathofacilitatory effect is tangible when performed in collaboration with the laboratory of Barry O’Keefe. The student will learn lab how to grow and scale-up iPSC-derived sympathetic neurones in Domingos lab, and optimize an in vitro assay based on Fig. 3C. The student will then transfer this knowledge to the lab of Barry O’Keefe where the screen will be performed using a fluorescent plate reader, robotic liquid handling, and a library of natural compounds.

While X-ray crystal structures of proteins are terrifically informative, both in basic research (6 Nobel prizes in 25 years) and drug design, the major stumbling block remains the need to obtain crystals of the biological sample (protein, protein complex, virus) suitable for X-ray analysis.  Even for a biochemically well-behaved sample, the likelihood of it crystallizing is always low, and there are no rules or reliable protocols to improve this.  Structure-based drug discovery similarly requires diverse crystal forms to be available for the protein; this too cannot currently be easily induced.

This project addresses the pressing need for rapid and simple protein engineering techniques to make samples crystallize routinely.  This will entail, depending on the student's background, skills and preferences:

• Develop streamlined protocols for parallel generation of large numbers of crystallization chaperones, e.g. using in vivo selection directly coupled to over-expression, with DNA libraries of binding scaffolds;
• Evolve binders that favour crystallization, by adapting existing motifs through iterative design supported by high-throughput crystallization, e.g. Gluebodies [Ye et al, 2024]; 
• Adapt protein design algorithms to find surface mutations that better allow the protein to pack into crystals, e.g. by machine learning of crystal contacts in the PDB;
• Streamline protocols for rapid large-volume parallel expression, purification and crystallization of large numbers of diverse protein variants; 
• Develop generic scaffolds that crystallize robustly, and ways of tethering target proteins to the scaffold.

Cardiometabolic disease (CMD) remains the leading cause of global mortality, contributing to a heavy burden on healthcare systems. It is well accepted that lifestyle factors, such as poor diet, physical inactivity, smoking, and excessive alcohol consumption, are important contributors to CMD incidence and mortality but underlying biological mechanisms linking lifestyle factors with cardiometabolic health are largely unknown. Research on such mechanisms may uncover novel biomarkers that more accurately predict disease onset, progression, and response to lifestyle interventions. 

The China Kadoorie Biobank study (CKB) is a large prospective cohort study with >0.5 million Chinese adults from 10 different locations in China (www.ckbiobank.org). Over the past 20 years, CKB has accumulated multi-dimensional data on lifestyle and other exposures, physical and other measurements (e.g. adiposity, blood pressure, liver steatosis and fibrosis, ECG, carotid artery intima media thickness and plaque, bone mineral density, and retinal images), incidence and mortality of major diseases including CMD, as well as multi-omics data including genomics (GWAS genotyping as well as WGS), proteomics (>10,000 proteins from Olink and Somalogic), metabolomics (>220 NMR and >5400 Metabolon metabolites, which cover 8 super biological pathways, e.g. amino acid metabolism, nucleotide metabolism, and microbiome metabolism, and 70 major pathways) and gut/oral metagenomics (shotgun sequencing). This large and rich resource will enable us to investigate the potential relevance of different lifestyle factors, as well as their interplay, for a range of cardiometabolic health conditions. Findings from CKB could be compared with those from the UK Biobank, which is an open resource for global researchers.

Epigenetic regulation plays a crucial role in maintaining homeostasis by fine-tuning gene expression. As we age, epigenetic patterns become deregulated, contributing to age-related conditions such as senescence, metabolic disorders (e.g. diabetes, atherosclerosis), immune dysfunction, and cancer, which collectively decrease life expectancy and quality of life in the elderly. Histone deacetylases (HDACs), enzymes that remove acetyl groups from lysine residues thus promoting chromatin condensation, are key regulators of gene expression and their activity contributes to age-related deficiencies in homeostasis. HDAC inhibitors offer potential to reverse aging by restoring health-promoting and anti-senescence acetylation patterns, improving both cellular and systemic functions and alleviating the aging process. Our previous research demonstrated that HDAC inhibition has strong immunomodulatory effects in aging mice where it is able to revitalise the immune response, and potentially overcome immune related senescence. Specifically, enhanced MHC I and II expression, increased activity of immune cells and infiltration into the tumour microenvironment. This project will investigate the effects of clinical HDAC inhibitors on immune aging, with a focus on restoring healthy immune responses and protection against cancer and age-related diseases, both in vitro and in vivo. The DPhil student will be trained in cutting-edge molecular, biochemical, genomic, bioinformatic and immunological techniques including but not limited to ChIP-seq, single cell RNA seq, CRISPR/Cas9 gene editing, flow cytometry, and ELIspot.

Liu G, Barczak W, Lee LN, Shrestha A, Provine NM, Albayrak G, Zhu H, Hutchings C, Klenerman P, La Thangue NB. The HDAC inhibitor zabadinostat is a systemic regulator of adaptive immunity. Commun Biol. 2023 Jan 26;6(1):102.

Blaszczak W, Liu G, Zhu H, Barczak W, Shrestha A, Albayrak G, Zheng S, Kerr D, Samsonova A, La Thangue NB. Immune modulation underpins the anti-cancer activity of HDAC inhibitors. Mol Oncol. 2021 Dec;15(12):3280-3298.

This collaboration between the Altan-Bonnet (NCI), Buckley and Coles (Oxford) labs addresses how organs generate distinct inflammatory responses despite sharing common components like immune cells, fibroblasts, and the extracellular matrix. In collaboration with additional teams from the Netherlands, and Canada, we aim to uncover the molecular, cellular, and tissue-level rules governing organ-specific inflammation.

We hypothesize that (1) organ context and cellular experience shape the perception of inflammatory signals, and (2) organ-specific hierarchies integrate responses into coordinated outcomes. Using a data-driven approach, we will combine ex vivo and in silico models of mouse and human tissues to explore these mechanisms. High-throughput robotics will generate diverse tissue models with varying sensitivities to infection or immunopathology. Multimodal datasets from these models will be analyzed using machine learning to build computational models, to guide iterative cycles of discovery.

This project will revolutionize tissue biology by creating a unified framework for understanding tissue-specific inflammation, paving the way for new treatments. We are seeking researchers with expertise in bioengineering, computer science, or immunology to join this interdisciplinary effort.

Project keywords: immunology, systems biology, biomedical engineering. 

This collaboration between the Altan-Bonnet (NCI), Buckley and Coles (Oxford) labs addresses how organs generate distinct inflammatory responses despite sharing common components like immune cells, fibroblasts, and the extracellular matrix. In collaboration with additional teams from the Netherlands, and Canada, we aim to uncover the molecular, cellular, and tissue-level rules governing organ-specific inflammation.

We hypothesize that (1) organ context and cellular experience shape the perception of inflammatory signals, and (2) organ-specific hierarchies integrate responses into coordinated outcomes. Using a data-driven approach, we will combine ex vivo and in silico models of mouse and human tissues to explore these mechanisms. High-throughput robotics will generate diverse tissue models with varying sensitivities to infection or immunopathology. Multimodal datasets from these models will be analyzed using machine learning to build computational models, to guide iterative cycles of discovery.

This project will revolutionize tissue biology by creating a unified framework for understanding tissue-specific inflammation, paving the way for new treatments. We are seeking researchers with expertise in bioengineering, computer science, or immunology to join this interdisciplinary effort.

Project keywords: immunology, systems biology, biomedical engineering. 

This collaboration between the Altan-Bonnet (NCI), Buckley and Coles (Oxford) labs addresses how organs generate distinct inflammatory responses despite sharing common components like immune cells, fibroblasts, and the extracellular matrix. In collaboration with additional teams from the Netherlands, and Canada, we aim to uncover the molecular, cellular, and tissue-level rules governing organ-specific inflammation.

We hypothesize that (1) organ context and cellular experience shape the perception of inflammatory signals, and (2) organ-specific hierarchies integrate responses into coordinated outcomes. Using a data-driven approach, we will combine ex vivo and in silico models of mouse and human tissues to explore these mechanisms. High-throughput robotics will generate diverse tissue models with varying sensitivities to infection or immunopathology. Multimodal datasets from these models will be analyzed using machine learning to build computational models, to guide iterative cycles of discovery.

This project will revolutionize tissue biology by creating a unified framework for understanding tissue-specific inflammation, paving the way for new treatments. We are seeking researchers with expertise in bioengineering, computer science, or immunology to join this interdisciplinary effort.

Project keywords: immunology, systems biology, biomedical engineering. 

Population-based cohorts have identified major modifiable risk factors for cardio-metabolic diseases, such as adiposity and physical activity, but the patterns and relevance of these factors varies greatly across populations, and previous evidence is predominantly from high-income countries. There is a high burden of cardio-metabolic diseases in South and Southeast Asian populations. However, the underlying mechanisms are yet to be fully elucidated, with previous evidence suggesting ethnically divergent body fat and muscle mass distribution to be a determining factor. Furthermore, physical activity has a complex relationship with body composition, and different patterns of physical activity between high- and low-/middle-income countries and between urban and rural areas might be an independent or explanatory factor in associations with cardio-metabolic diseases.

The objectives of this DPhil project may be to explore associations between different measures of body composition with objective measures of physical activity between populations and their individual and joint associations with cardio-metabolic diseases across different ethnicities, using data from different large-scale prospective studies. 

This project will use data from three large prospective studies: the Indian Study of Healthy Ageing (ISHA), the Malaysian Cohort, and the South and Southeast Asian participants of the UK Biobank. It will provide unique opportunity for novel insights into disease risks and aetiology to inform global non-communicable disease control and prevention efforts, and the student will have the chance to work collaboratively across the Global Populations Studies Group led by Prof Sarah Lewington, the Oxford Wearables group led by Prof Aiden Doherty, and the Oxford Centre for Diabetes, Endocrinology and Metabolism led by Prof Fredrik Karpe.

Our research group aims to understand unique patterns of hypertensive end organ disease progression of women and their children following a hypertensive pregnancy. This information is used to develop personalised clinical tools to identify, track, and slow end organ disease to prevent early onset cardiac, cerebral and vascular disease in these families.

This project will make use of information from computational modelling to study disease progression related to a hypertensive pregnancy across multiple modalities and organs. The insights into key structural and functional changes at the organ-level that describe stages of disease will be used to help identify potential targeted intervention.

The project will make use of a collection of unique imaging and clinical datasets from clinical trials and observational studies in families with a hypertensive pregnancy history. Furthermore, our clinical trials help us understand how interventions modify the underlying disease development.

Potential areas for a PhD project include: 

• Artificial intelligence - Application of artificial intelligence and machine learning to large research imaging datasets to improve the clinical tools already available to identify those at risk, and to identify next generation imaging and management approaches.
   
• Novel markers of early disease - Using imaging and laboratory studies to identify early cardiac and vascular changes in young people at risk of cardiovascular disease.
   
• Young adult cardiovascular prevention trials - Running trials to understand how novel approaches to lifestyle and clinical management may be able to modify these early risk cardiovascular phenotypes to prevent the development of later disease. 

We are interested in understanding how cellular identity is propagated as cells divide. Using advanced flow cytometry combined with mass spectrometry1,2, we have been able to isolate and purify individual mitotic chromosomes from different species (human, mouse and fly) and comprehensively profile the proteins and RNAs that remain chromosome-associated during mitosis. We have also prospectively isolated the active and inactive X metaphase chromosomes from female cells and identified novel factors likely to be important for maintaining their distinctive states3. Although many proteins are evicted from condensing chromosomes, our studies have shown that approximately 10% remain chromosome-associated throughout mitosis1,4. These include specific DNA-binding factors, chromatin repressor complexes, DNA methylation machinery and SMC family proteins. To assess their importance for chromosome structure and epigenetic inheritance, we are systematically degrading or cleaving individual factors in metaphase and examining the biophysical, structural and molecular consequences of this using optical tweezers and Cryo-ET approaches as well as analysing nascent RNA expression in postmitotic cells. These studies bring together expertise in several fields to decipher, at a mechanistic level, how epigenetic memory is propagated. In addition, as the approaches we are developing enable native (unfixed) human chromosomes to be individually isolated and studied ex vivo, we will investigate how disease-associated chromosomal translocations impact mitotic bookmarking and genome stability.

References

1. Djeghloul et al., 2020 Nat Commun. 11, 4118. 
2. Djeghloul et al., 2023 Nat Struct Mol Biol 30, 489.
3. Djeghloul et al.,Research Square https://doi.org/10.21203/rs.3.rs-4687808/v1
4. Dimond et al.,bioRxiv https://doi.org/10.1101/2024.04.23.590758

Immune surveillance plays a formidable role in eliminating cancer cells. At the centre of this process lies an interaction between the T cell receptor (TCR) in T cells and peptides presented by the major histocompatibility complex (pMHC). The biochemical and structural properties that underpin the TCR/pMHC interaction dictate the fate of infected or cancer cells. However, the rules that govern TCR specificity and sensitivity remain unknown. 

We aim to apply cryoEM and cryo-electron tomography (cryoET) including in situ structural studies to determine the structural fingerprints associated with productive TCR/pMHC interactions. We have recently made crucial technical advances in determining the structures of native unmodified TCR/pMHC complexes derived from SARS-CoV-2 infection, which had been intractable due to their intrinsic flexibility and innate low affinity. A robust cryoEM structure pipeline has thus been established for elucidating tumour-reactive TCRs in complex with natural cancer pMHCs. We will examine conserved features and differences among complexes to understand the observed specificity, sensitivity and binding affinity of TCRs recognising cancer antigens. We will also determine the complete, native TCR/CD3 and pMHC complexes from opposing membranes as they are in the immunological synapse formed between the T cell and target cancer cell using in situ cryoET.

These structures will reveal mechanisms underpinning the specificity and affinity for each TCR/pMHC pair and common shared interfaces. Such structural information will make critical contributions to the selection of TCRs for the deployment of robust and safe TCR-based immunotherapies

Human immunodeficiency virus type 1 (HIV-1) is the causative agent behind acquired immunodeficiency syndrome (AIDS) that currently has no cure or vaccine. While antiviral treatments are effective, the rise of drug-resistant strains has become a growing concern. HIV-1 primarily infects the immune system, targeting CD4+ T cells and macrophages and is a lentivirus known to be able to infect non-dividing cells, requiring it to exploit nuclear import mechanisms. This process is dependent on the viral capsid. The HIV capsid is a conical structure that houses the genomic material of the virus. It needs to be metastable in order to be protective while allowing timely disassembly (termed uncoating) to release its genome. The dynamics of the capsid nuclear import and uncoating are still unknown and are modulated by host dependency and restriction factors.

We aim to apply multi-imaging modalities to investigate uncoating and nuclear import of HIV. These will include super-resolution fluorescence microscopy (including the newest MINFLUX technology), Focused Ion Beam and Scanning electron microscopy (cryoFIB/SEM), cryo-electron microscopy and cryo-electron tomography (cryoEM/ET). The viral core and host factors will be fluorescently tagged, and infection will be monitored from viral attachment to nuclear import. The sample will be cryo-preserved and imaged by cryoEM/ET and cryoFIB/SEM. The combination of these imaging techniques, paired with molecular biology and virology tools, will yield unparalleled knowledge of the HIV infection process within the native cells, providing the framework for development of novel therapeutics targeting HIV infection in the future.

Forces are important in the cardiovascular system, acting as regulators of vascular physiology and pathology. Vascular endothelial cells are constantly exposed to mechanical forces, such as shear stress, due to the flowing blood. Patterns of blood flow depend on blood vessel geometry and type and can range from uniform blood flow (which is protective) to disturbed blood flow (which is pathologic). Although we know that endothelial cells can sense and respond differently to different types of flow, the mechanisms by which they sense and respond to blood flow remain a mystery. Our laboratory has pioneered the studies of endothelial mechanosensing and has championed the use of a multi-disciplinary approach to this scientific problem. 

The focus of the proposed studentship is to identify mechanisms by which endothelial cells sense and respond to blood flow.  The student will have the opportunity to be exposed to a wide range of techniques based on the student’s individual interests that include: 
1) use of imaging and genetic approaches to characterize how mechanosensing affects disease intitiation and progression ; 
2) applying high throughput RNA sequencing and proteomics approaches to globally dissect steps involved in disease aetiology; and 
3) use of bioinformatics and biochemical experimental approaches to understand the role of blood flow forces in cardiovascular disease.

Reference:
Mehta V, Pang K, Rozbesky D, Nather K, Keen A, Lachowski D, Kong Y, Karia D, Ameismeier M, Huang J, Fang Y, Hernandez A, Reader JS, Jones EY, Tzima E. The Guidance Receptor Plexin D1 moonlights as an endothelial mechanosensor.2020 Nature Feb 5. https://pubmed.ncbi.nlm.nih.gov/32025034/

Ribosomes are fascinating protein-making factories. Ribosomes and the entourage of associated factors are responsible for translating the genetic information encoded within mRNA into amino acid sequences joined together to make proteins. Surprisingly, components of the ribosomal machinery have been recently discovered to have additional roles in eukaryotic cells, including regulation of endothelial cell health. Work from our group has identified a strong genetic link between a ribosomal factor and cardiovascular disease but we do not understand how this works. How do ribosomes regulate endothelial cell health and protection from disease? What is the connection between faulty ribosomes and cardiovascular disease? These are some of the fundamental questions that this project will tackle. Our ultimate goal is to identify novel players in cardiovascular disease and design new therapies that target these pathways.

The student will have the opportunity to be exposed to a wide range of techniques based on the student’s individual interests. The student will be supervised on a daily basis by a postdoctoral fellow and will be trained in cell culture, siRNA/CRISPR techniques, protein gels and western blotting, ribosomal and polysome profiling, subcellular fractionation, molecular cloning, confocal microscopy, protein structure analysis, and bioinformatics. 

Understanding eukaryotic replication is important, because during our lifetimes we copy approximately a lightyear’s worth of DNA, and how the different components of the molecular machinery (the replisome) work together to achieve this successfully is an area of highly active research.  In our lab, we take on the exciting challenge of understanding the dynamics of DNA replication of this process by studying the activity of eukaryotic replisome at the single-molecule level on both bare DNA and chromatin.

In this PhD project, you will learn a diverse set of techniques (synthesizing DNA constructs, purifying proteins, state-of-the-art single-molecule microscopy and measurements, in-depth quantitative analysis) and work together with others in an interdisciplinary team comprised of biologists, (bio)physicists, biochemists, and data scientists.  You will be taught how to perform high-quality experiments and then you will be invited to develop new ones of your own, making use of your training and insights! This research, carried out together with collaborators at the University of Oxford, the Francis Crick Institute, the Hubrecht Institute, and elsewhere, should lead to new discoveries and insights that inform our quantitative understanding of DNA replication and advance this exciting field while contributing to the next generation of in vitro single-molecule methods.