Research Opportunities

The skin epidermis provides a protective barrier against external insults. To ensure its maintenance, specialised cells located in its basal layer, known as stem cells, divide and differentiate to replace cells lost through exhaustion and damage. However, the mechanisms that control stem cell renewal and the pathways that lead to their dysregulation in disease remain controversial.

While studies have highlighted the role of stochastic renewal programs where stem cells are constantly lost and replaced by neighbouring cells, the underlying biological and physical mechanisms governing stochastic cell fate decisions remain poorly understood. Recent investigations in skin inflammatory diseases, such as psoriasis or atopic dermatitis, where the balance between proliferation and differentiation is typically disrupted have emphasized the influence of tissue mechanics in priming stem cells for renewal or differentiation and the crucial role niche signals from immune, stromal, and neuro-glial cells in modulating stem cell self-renewal and tissue dynamics.

In this project, you will use the latest spatial transcriptomics methods combined with machine learning to characterise simultaneously the mechanical, biochemical and cellular niches of epidermal stem cells, and how their composition, properties and spatial organisation might be altered in inflammatory skin diseases. You will also have the opportunity to contribute to follow-up experiments and hypothesis testing using mouse models and human epithelial organoids co-cultures, combined with advanced live imaging, AFM, mathematical modelling, genetic lineage tracing and functional genomics approaches such as CRISPR-based gene editing.

Ultimately, the results of this interdisciplinary project will transform our understanding of the mechanisms regulating epithelial tissue dynamics, and lay the foundation for the development of more effective therapeutic interventions targeting the causes, rather than the symptoms, of skin inflammatory diseases.

There is an unmet need for repair following injury in humans, particularly in the brain where endogenous stem cell activity is minimal. An understanding of neural progenitor diversity and flexibility in their fate choices is crucial for understanding how complex organs like the brain are generated or undergo repair. The neonatal mouse cerebellum is a powerful model system to uncover regenerative responses due to its high regenerative potential.   We have previously shown that the cerebellum can recover from the loss of at least two types of neurons via distinct regenerative mechanisms (Wojcinski, 2017; Bayin, 2018; Bayin, 2021). In one case, a subpopulation of the nestin-expressing progenitors (NEPs) that normally generate astroglia undergoes adaptive reprogramming and replenishes the lost neurons. However, the molecular and cellular mechanisms that regulate neonatal cerebellar development and adaptive reprogramming of NEPs upon injury are unknown.   Interestingly, the regenerative potential of the cerebellum decreases once development ends, despite the presence of NEP-like cells in the adult cerebellum that respond to cerebellar injury by increasing their numbers. However, neuron production is blocked. We hypothesize that the lack of regeneration is due to a lack of pro-regenerative developmental signals in the adult brain in addition to epigenetic silencing of stem cell differentiation programs and inhibitory cellular mechanisms as development is completed.  

Our lab is interested in answering two overarching questions:  
1)    What are the cellular and molecular mechanisms that enable regeneration in the neonates and inhibit in the adult?
2)    Can we facilitate regeneration in the brain?  

This project involves interdisciplinary approaches ranging from in vivo mouse genetics, in vitro modelling and stem cell assays, and single cell and other genomics technologies. Our system allows us to interrogate fundamental stem cell biology questions in a systematic manner and unravel the molecular mechanisms that govern neural stem cells during development, homeostasis and upon injury. The student taking on this project benefit from our multidisciplinary approach and participate in our collaborative work locally and internationally.

This team is interested in the development and repair of musculoskeletal tissues. Diseases of the musculoskeletal system include those that arise during development, including inherited connective tissue diseases such as Marfan Syndrome and chondrodysplasias, as well as the highly prevalent age-related disease of joints, osteoarthritis. The team uses model systems as well as large human datasets to explore molecular drivers of disease and mechanisms that underly chondrogenesis and cartilage repair, including stem cell biology and deciphering intrinsic cartilage repair mechanisms.

The spinocerebellar ataxias (SCAs) are a complex group of neurodegenerative diseases that affect the cerebellum and result in the loss of motor coordination. No effective treatments exist for the SCAs, and there is a pressing need for better models in which to study the underlying disease-causing mechanisms and to identify potential therapies.

The aim of this project will be to develop novel stem cell-derived models to identify common pathological mechanisms in SCA that could be targeted therapeutically. The Becker group has identified several novel SCA mutations that highlight mGluR1-TRPC3-IP3R1 signaling as a key pathway affected in disease. Both research groups have developed complementary stem cell-derived and primary cerebellar models that provide unique systems to investigate the functional consequences of gene mutations affecting this pathway in the Purkinje cells, which are the neurons that are primarily affected in SCA.

The project will employ patient-derived induced pluripotent stem cells (iPSCs) as well as introduce gene mutations into iPSCs using CRISPR gene editing technology. Pluripotent stem cells will be differentiated into cerebellar neurons and three-dimensional organoids and deeply phenotyped using a combination of functional experiments including calcium imaging, super-resolution imaging, and morphological analyses. In addition, functional analyses will be carried out in primary Purkinje cells. Identified disease phenotypes will subsequently be screened for potential therapeutics.

Becker Group website: https://www.ndcn.ox.ac.uk/research/cerebellar-disease-group

Hammer Group website: https://irp.nih.gov/pi/john-hammer

The presence and role of neural stem cells (NSCs) in the adult human brain is a long-debated issue in neuroscience. Recent work has demonstrated that stem-like cells exist in the embryonic, foetal, and human adult brain where they persist well into adulthood and can even contribute to neurogenesis. However, their role in neurodegenerative disease is unknown. Ongoing work in the lab has led to the hypothesis that NSCs may become dysfunctional in neurodegenerative disease resulting in senescence chronic inflammation, and thereby acting as pacemaker cells driving neuronal demise. This ambitious project aims to identify disease-associated NSCs and their phenotype in the context of human neurodegeneration using spatial biology approaches, including imaging mass cytometry, RNA scope and single nuclear RNA sequencing. Relying on post-mortem brain tissue of different stages of Alzheimer’s disease, traumatic brain injury, vascular dementia and chronic stroke, this project will study NSCs in a range of human diseases characterised by neurodegeneration and neuronal injury. Ongoing work in the lab identifies NSC-specific markers based on transcriptomics and protein profiling experiments in brains with progressive multiple sclerosis, enabling to investigate the distribution of NSCs in a wide range of diseases. Spatial transcriptomics and proteomic approaches will allow to study their phenotype and dysfunction in relation to other cell types and local pathology. This project will shed light on the role of NSCs in neurodegeneration and has the potential to identify an entirely novel mechanism of neurodegeneration in human disease.

This project will be co-supervised by Prof. A. Quaegebeur.

Multipotent self-renewing hematopoietic stem cells (HSCs) support life-long blood system homeostasis and play essential roles in human disease and its therapy. HSC transplantation is an important cell therapy for a range of hematological diseases including immunodeficiencies, beta-globinopathies, and blood cancers. Through their ability for self-renewal and multipotency, HSCs can reconstitute the hematopoietic system following transplantation. Most HSC transplants are performed using allogeneic HSCs but there is also a growing interest in the development and use of autologous HSC transplantation gene therapies for a range of non-malignant blood diseases. A major unresolved question in the field is what regulates the fitness of an HSC. High fitness HSCs display durable and balanced blood system reconstitution activities. By contrast, low fitness HSCs have weak or biased activities. The accumulation of low fitness HSCs is thought to contribute to various disease pathologies and their use in HSC transplantation can result in engraftment failure. Building on research interests in the Muljo lab at the NIH and the Wilkinson lab at the University of Oxford, this project will focus on characterizing transcriptional and post-transcriptional mechanisms regulating HSC fitness. Biological mechanisms identified here will be used to devise new strategies to enhance life-long hematopoietic system health and to improve the safety and efficacy of HSC transplantation therapies.
 

Recent publications:

Wang, S., Chim, B., Su, Y., Khil, P., Wong, M., Wang, X., Foroushani, A., Smith, P. T., Liu, X., Li, R., Ganesan, S., Kanellopoulou, C., Hafner, M. and S. A. Muljo. Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3. Genes & Development, 33: 1048–1068. DOI: 10.1101/gad.325100.119.

Wilkinson, A.C., Ishida, R., Kikuchi, M., Sudo, K., Morita, M., Crisostomo, R.V., Yamamoto, R., Loh, K.M., Nakamura, Y., Watanabe, M., Nakauchi, H. and S. Yamazaki. (2019). Long-term ex vivo haematopoietic-stem-cell expansion allows nonconditioned transplantation. Nature, 571: 117–121. DOI: 10.1038/s41586-019-1244-x.

Haney, M.S., Shankar, A., Hsu, I., Miyauchi, M., Palovics, R., Khoo, H.M., Igarashi, K.J., Bhadury, J., Munson, C., Mack, P.K., Tan, T., Wyss-Coray, T., Nakauchi, H., Wilkinson, A.C. Large-scale in vivo CRISPR screens identify SAGA complex members as a key regulators of HSC lineage commitment and aging. bioRxiv 2022. DOI: 10.1101/2022.07.22.501030

The Rayon’s lab (www.rayonlab.org) overall aim at the Babraham Institute in Cambridge is to investigate the molecular and metabolic pathways that control biological timing and lifespan. To answer these questions, we work with mouse and human stem cells and embryos and employ a variety of quantitative and genomic techniques. We are looking for applicants that are curious about evolution, developmental biology and embryonic stem cells.

We are interested in the following topics:
1.    Understanding the regulation of enhancer timing. We want to test the existence of species-specific enhancers and their dynamics.
2.    Exploiting genetic variation to investigate dynamics of regulatory networks in stem cell models.  
3.    To develop a high-content imaging assay to screen for modulators of timing. Develop a screen to explore if epigenetic, metabolic, and turnover factors impact the pace of differentiation.

A background on cell culture or molecular biology, as well as skills in bioinformatics or computational approaches would be useful, but ample opportunities for training will be provided.

Virus infection of brain stem cells represents a major global health concern, but also offers treatment possibilities in neurodegenerative diseases and in malignant brain tumours. For example, Zika Virus targets SOX2+ neural progenitors in the developing brain to cause microcephaly in babies born to mothers infected during pregnancy; likewise, it targets SOX2+ glioma stem cells in the most common and lethal malignant brain tumour, glioblastoma (GBM) (https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4135719). Stem cells have been shown to exploit a distinct set of antiviral mechanisms compared to somatic cells (https://doi.org/10.1016/j.cell.2017.11.018), and viral permissivity varies widely between example developing brain and glioblastoma stem cell populations. Understanding and manipulating the cell-intrinsic mechanisms underpinning antiviral resistance in brain stem cells will inform approaches to protect and exploit neural stem cell function and to ablate cancer stem cells in GBM.

This project will seek to understand and modify viral permissivity and antiviral defence mechanisms in developing brain and brain tumours, focusing on stem cell intrinsic pathways. In the first place we will  address the hypothesis that immune selection pressure on glioma stem cells during tumour development results in expansion of a mesenchymal/injury-response cell population (https://www.cell.com/cell/pdf/S0092-8674(21)00351-2.pdf) refractory to virus infection, then proceed to examine underlying mechanisms.

You will be working with human patient-derived and mouse defined mutation glioma cell models, treated with viruses and viral mimetic compounds. You will be assaying transcriptional identity and responses using qPCR and RNA sequencing, immunofluorescence and RNA smFISH, and cytokine secretion using immunoassays. The lab has access to the state-of-the-art Cambridge Stem Cell Institute imaging, FACS, sequencing and bioinformatic facilities, and to additional specialist facilities (e.g. imaging mass cytometry) in the CRUK Cancer Institute next door. We will validate results in mice in vivo and/or slice cultures prepared from  human developing brain and patient brain tumour tissue, models we have established and use routinely in the lab.

Our group is interested in uncovering and understanding key mechanisms of disease that affect cardiac muscle function. We have a particular interest in understanding how regulation of cardiac muscle contraction is altered in common acquired and inherited cardiovascular diseases. We do this by using cutting edge techniques in cellular imaging, employing human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs), and CRISPR/Cas-9 to understand human cardiovascular disease in the dish.
 

We have two key focuses in the lab:

1. Understanding how inherited heart conditions including hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) alter cardiomyocyte function. We do this by using CRISPR Cas-9 genome engineering in combination with iPSC-CMs to screen how HCM and DCM causing variants cause disease. We can then use these systems to screen novel therapeutics in the dish. We have designed multiple techniques to make these analyses feasible and rapidly deployable: SarcTrack and CalTrack.
    
2.  Investigate the processes that alter cardiac muscle function in acquired cardiac diseases including myocardial infarction, atrial fibrillation, and heart failure. We are able to use biochemical techniques twinned with fluorescent imaging to assess how cardiac myosin states are altered in disease tissues. This technology allows us to uncover key disease mechanisms that alter heart muscle function, allowing insight into these common heart muscle diseases. 
    

We have multiple key collaborations within the University of Oxford and internationally. Together we focus on pushing the boundaries of understanding in acquired and inherited cardiovascular disorders of the heart muscle. Within the group we have an inclusive and diverse set of researchers who have a wide range of cutting-edge expertise. Within the wider lab environment and our collaboration network we have over 20 researchers in this area.
 

Scientific training opportunities in the lab include but are not limited to:
 

1. Induced pluripotent stem cell culture
2. Techniques for iPSC to cardiomyocyte differentiation
3. CRISPR/Cas-9 genome engineering
4. PCR and genetic sequencing
5. A wide range of standard fluorescent microscopy and confocal microscopy
6. Phenotyping of cardiomyocyte function with fluorescent probes and genetically encoded protein tags
7. RNA sequencing and qPCR
8. Western blotting and phosphoprotein blotting techniques
9. Drug screening using live cell microscopy

Transferrable skills include but are not limited to:
 

1. Learning to interact with MatLab and other computing packages for automating and simplifying data analysis.
2. Using genome viewers and associated software for designing and executing CRISPR/Cas-9 engineering.

References:

1.  Hypertrophic cardiomyopathy mutations in MYBPC3 dysregulate myosin Science Translational Medicine 2019
2. Myosin Sequestration Regulates Sarcomere Function, Cardiomyocyte Energetics, and Metabolism, Informing the Pathogenesis of Hypertrophic Cardiomyopathy Circulation 2020
3. SarcTrack An Adaptable Software Tool for Efficient Large-Scale Analysis of Sarcomere Function in hiPSC-Cardiomyocytes Circulation Research 2019
4. CalTrack: High-Throughput Automated Calcium Transient Analysis in Cardiomyocytes Circulation Research 2021
5. Common genetic variants and modifiable risk factors underpin hypertrophic cardiomyopathy susceptibility and expressivity Nature Genetics 2021

Pluripotent stem cells, such as embryonic stem cells (ESCs), can be used as a model system to study the molecular basis of fate-specification during early mammalian development. They can also be used to derive various types of cells for disease modeling, drug discovery, regenerative medicine, and environmental health sciences. To fully realize these potentials of pluripotent stem cells, it is important to understand the molecular mechanisms that regulate the pluripotent state. We have previously carried out a genome-wide RNAi screen in mouse ESCs and identified a list of novel factors that are important for pluripotency maintenance. Among them, we are currently investigating the function of the Ccr4-Not mRNA deadenylase complex and the INO80 chromatin remodeling complex in ESCs, somatic cell reprogramming, and mouse development using biochemical, genetic, genomic and single cell analysis approaches. In addition, we are developing new genetic and genomic methods to identify and probe genes involved in stem cell fate specification. We are applying these methods in pluripotent and germline stem cells to better understand the maintenance, transition, resolution, and re-establishment of the pluripotent state.

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*