Research Opportunities

Hematopoiesis is a finely tuned process by which mature blood cells of multiple lineages are constantly generated throughout life from hematopoietic stem cells. In humans, definitive hematopoiesis commences in the fetal liver (FL) at around five weeks of gestation, and remains the main site of hematopoiesis throughout fetal life. Hematopoiesis in the bone marrow (BM) starts around 11-12 weeks of gestation, but does not take over as the primary site of hematopoiesis until just after birth. Recent evidence suggests that fetal hematopoiesis is distinct from postnatal hematopoiesis in many ways. Most of these studies have been done on mouse models, but whether these differences exist in, or are a true reflection of hematopoiesis in the human setting, remains to be determined. We, and others have begun to investigate unique features of human fetal hematopoiesis and this project will determine fetal specific programmes that change through ontogeny. This may depend on the physiological processes or demands of that particular developmental stage, and/or in response to specific microenvironmental cues. This research is clinically relevant since the transplantation of hematopoietic stem cells from donors of different ages vary in their regenerative and differentiation potential. Studying hematopoiesis throughout the human lifespan may be important not only to understand normal developmental processes, but also to understand the pathogenesis of postnatal haematological diseases that may have their origins in fetal life. Research by the Roy laboratory particularly focuses on properties of fetal cells that contribute to leukemia initiation in utero and how these might change after birth, and we have recently developed a unique infant acute lymphocytic leukemia (ALL) model. We are particularly interested in ‘oncofetal’ genes that might define the biology of infant and childhood leukemias; and whether they can be manipulated for therapeutic interventions.

*This project is available for the 2021 Oxford-NIH Pilot Programme*

A previous infection with one of the four dengue viruses increases future risk of severe dengue disease, including hemorrhagic fever, upon infection with a different dengue virus. For this reason, dengue viruses 1-4 are challenging vaccine targets because sub-protective vaccines can increase risk the disease vaccines are designed to prevent. In the Viral Epidemiology and Immunity Unit (Chief, Dr. Katzelnick), we aim to identify correlates of natural and vaccine protection and antibody-dependent enhancement in order to develop better next generation vaccines, extend the longevity of vaccine-induced immunity, and characterize how vaccines may affect viral evolution and transmission.  Our work combines immunology, virology, and epidemiology, including close collaborations with research teams leading longitudinal cohort and vaccine studies in Nicaragua, Sri Lanka, Thailand, Ecuador, the Philippines, and other sites. Specific projects include studying quaternary ‘super-antibodies', which bind epitopes across viral envelope proteins, and testing whether these antibodies provide enduring protection against dengue and other viral diseases. We will also study antigenic evolution away from existing immunity for flaviviruses and coronaviruses. Dr. Katzelnick was part of the NIH OxCam program (2012-2016) and is open to collaborating with research groups at both Oxford and Cambridge to mentor Ph.D. students.

Neurons are specially shaped cells that have an extremely polarized structure. They contain protrusions called dendrites and a long axon extending from cell body that connect to neighbouring cells forming a neural network. Axons and dendrites retain a dynamic plasticity throughout the whole lifespan of a neuron to ensure the ability to adjust and adapt neural network connections.  The polarity and plasticity of neurons is maintained by a cytoskeleton of actin filaments and microtubules together with associated motors and other essential proteins.

This PhD project aims to elucidate the molecular organization of axons and dendrites using in situ cryo-electron tomography (cryo-ET) of primary neurons.  We will address how cytoskeletal filaments and motors drive the branching, elongation and neural network formation. To this end we form a strong collaboration between the lab of Andrew Carter at the Laboratory of Molecular Biology (LMB), Cambridge University and Mizuno Naoko at the National Heart, Lung and Blood Institute at NIH. Mizuno’s lab’s expertise is visualizing cell shape formations controlled by remodelling of cytoskeleton and the Carter lab has a long-standing interest in how trafficking is carried out by cytoskeletal motors.

Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) bridge the resolution gap between light-microscopy and conventional structural methods for gaining information on a molecular level (X-ray crystallography/NMR).  Current technical developments further facilitate in-depth analysis of cells on a molecular level that has not been possible before. The skillset obtained in this PhD project will be highly relevant to the field of newly emerging structural cell biology.

The formation of neural network is essential for building a nerve system and to maintain its dynamic function. Neuronal cells extend their axons to connect to dendrites of partner neurons. The process is facilitated by axonal migration and controlled by the balance of the search for partner neurons vs the locking of axon-dendrite connections. This balance is maintained by two signaling pathways relying on the integrin receptor (mode of neurite migration) and the semaphorin receptor (mode of axon-dendrite locking). The inter-regulation between both pathways is mediated by the intracellular signaling factor Rap1. However, the mechanism of this interconnection is unknown.

This PhD project aims to elucidate the nature of this crosstalk using a bottom-up reconstitution of integrin, semaphorin and Rap1 by developing a cell-surface mimicking membrane system. We aim to establish a functional membrane system that allows us to control the two modes, i.e. attachment/detachment of two neighboring membranes representing dendrite and axon connections. The uniqueness of the project lies in the exact control of communication through membranes by the bottom-up strategy, which would be otherwise extremely challenging to elucidate. Moreover, the system will allow us to probe receptor interactions using biophysical, light microscopic as well as cryo-EM methods to understand the underlying principles of neural network formation and neuronal regeneration.

Our collaborative team has expertise in a wide variety of interdisciplinary techniques to facilitate the proposed PhD research, such as X-ray crystallography, cryo-EM, biophysical analysis, membrane biology and light microscopy. Mizuno lab is leading in the use of cryo-EM in combination with cellular methods to visualize cell shape formations controlled by the integrin signaling pathway and the remodeling of cytoskeleton components. Jones lab has a long-standing interest in axon guidance and structural biology of membrane proteins. Yvonne Jones co-heads the Structural Biology Division of the Wellcome Centre for Human Genetics at the University of Oxford.

This project will give a candidate a tremendous opportunity to apply cutting-edge in vitro reconstitution methods in the field of structural- and neuro- biology.

Age-related macular degeneration (AMD) is one of the leading causes of blindness among the elderly affecting over 30 million individuals world-wide. AMD initiates in the back of the eye because of dysfunctions in the retinal pigment epithelium (RPE), a monolayer of cells that maintains vision through maintenance of photoreceptor healthy and integrity. AMD can lead to severe vision loss and blindness in advanced stages – “dry” and “wet” forms. In the dry stage, the death of RPE cells triggers photoreceptor cell death and atrophy of the choroidal blood supply causing vision loss. It is thought that RPE cell death in AMD is triggered by the formation of sub-RPE protein/lipid deposits called drusen. Our recent work shows that drusen formation is initiated by reduced autophagic flux in RPE cells resulting in reduced ability of RPE cells to process intracellular “debris” that eventually gets secreted as drusen deposits. TFEB, a member of MiT family of transcription factors is a known master regulator of autophagy. Here, we propose to investigate the activity of transcription factor TEFB in our AMD cellular models of iPSC-derived RPE cells. We hypothesize that autophagy downregulation is triggered by post-translational changes in TFEB that affect its sub-cellular localization and reduce its transcriptional activity. Here, we propose to identify those changes in TEFB and discover signaling pathways that lead to its altered activity. Lastly, we will test the ability of our recently discovered FDA-approved drugs that stimulate TEFB activity to reduce drusen formation by increasing autophagy in iPSC-RPE AMD models. This work will lead to a better understanding of AMD pathogenesis and potentially retool existing  drugs to treat AMD patients.

The BL research is organized into four focus areas: a) epidemiology; b) infections; c) genetics, and d) tumor studies. The epidemiological studies seek to characterize the macro- and micro-geographical and spatial-temporal  patterns of endemic Burkitt lymphoma to generate new hypotheses about environmental risk factors. The infection focus seek to discover infection-related biomarkers of risk, focusing on unique serological profiles or discovery of high-risk genetic variants for EBV or Pf infection associated with eBL risk. The genetic studies (GWAS, exome, HLA) provide a powerful approach to complement questionnaire and serological methods with less concern for measurement error, reverse causality, and imperfect correlation with biology to disentangle the genetic architecture of eBL risk.  Finally, BL is a molecular disease with identifiable molecular sub-groups. The EMBLEM study provides an opportunity to collaborate with others on studies to develop a blood-based assay for BL diagnosis and molecular characterization. Students will be given the opportunity to spend time in East Africa with collaborating partners to be involved with data and sample collections.

The primary goals of EMBLEM are to investigate:

a) risk factors of BL in endemic populations in East Africa;

b) EBV and Pf immuno-profiles and other biomarkers associated with BL;

c) molecular characteristics of BL tumor genomes, B-cell receptor, and EBV variants; and

d) germline risk factors of BL using genome-wide association studies (GWAS) and exome sequencing

e) the association between BL and human leukocyte antigen (HLA) class I and II loci.

The tumour suppressor p53 is encoded by the most mutated gene in human cancers and there is extensive knowledge of its vital role in tumour suppression. However, the contribution of p53 to immune surveillance is less well understood. Cancer initiation and progression is influenced by inflammation, and it is increasingly important to understand interactions between inflammatory and tumourigenic pathways to improve cancer prevention and patient responses to immunotherapy. p53 activity is known to intersect with key inflammatory signalling pathways, including NFB, AP1, MAPK and JAK/STAT, suggesting p53 could have a pivotal role in immune surveillance. To expand knowledge in this important area, this project will investigate crosstalk between the p53 pathway and inflammation.

The project will use cutting edge technologies, including ex vivo 3D organoid co-culture models, to study interactions between cancer-initiating epithelial cells and immune cells. It will also harness recent advances in RNA-sequencing, single cell analysis and ChIP-sequencing, as well as a broad range of molecular cell biology techniques, to address the crosstalk between p53 and inflammation. The student will be able to leverage access to expertise and clinical samples in chronic inflammatory conditions – such as Barrett’s Oesophagus – that predispose patients to cancer. Oesophageal cancer and stomach cancer may be used as exemplar cancer types; these cancers have important unmet clinical needs and strong links to inflammation. This project may also extend to crosstalk of p53 with the immune system, such as in the context of immunotherapy for cancer: an emerging therapeutic strategy that is showing great success in some patients. The study will offer exciting opportunities to understand the details of the relationship between p53 and inflammation, which will be crucial for developing new approaches for early intervention to prevent cancer progression and for understanding responses to therapy.

In order to maintain homeostasis in response to environmental changes such as nutrient availability, eukaryotic cells have evolved intricate mechanisms to quickly increase or decrease the activity of fundamental processes such as gene expression, protein expression and degradation. Indeed, several metabolites act as cofactors for important cellular enzymes that regulate e.g. chromatin state and serve as templates for posttranslational modifications flagging proteins for proteolysis via the ubiquitin-proteasome system. Consequently, the identification of metabolites and complementary binding domains has broadened our understanding of human physiology and contributed to the development of new medicines to treat malignant and inflammatory disease. The aim of this project is to systematically map protein-metabolite interactions on a proteome-wide scale by combining the development of specific metabolite-inspired affinity reagents with unbiased approaches such as thermal profiling to dissect metabolite signalling in the context of protein degradation pathways in various cell types. Applicants will have the opportunity to take advantage of a unique combination of synthetic organic chemistry and cell biology techniques to identify new potential drug targets and develop first-in-class ligands for key regulators of protein homeostasis.