Leading science, pioneering therapies
Join us

Available PhD's

University funded PhD positions are advertised below. Please use the specific link on each project to apply.

Understanding how progenitor cell-niche interactions alter during development and with adult ageing through Next-Generation techniques 

Apply here (deadline Friday 10th February 2017)

  1. 1st Supervisor - Dr Elaine Emmerson
  2. 2nd Supervisor - Dr Abdenour Soufi

Embryonic tissues can regenerate following injury, yet this ability is lost with age, a process that is incompletely understood. Ageing is commonly associated with a loss of homeostatic and regenerative replacement of cells required to maintain tissue integrity and subsequently a loss of tissue function. Many epithelial organs, such as the pancreas, lung, skin and salivary glands are affected with advanced age, leading to many of the hallmark pathologies of aging. Recently, many studies have attributed this decline to degenerative changes in resident progenitor cells and their niches. Of importance all these organs are highly innervated and a functional nerve supply is essential to the development, function and regeneration of organs.

My research has previously demonstrated that peripheral nerves are an essential component of the progenitor cell niche, where they serve to maintain progenitor cells during development, homeostasis and regeneration, where I used the salivary gland as a model organ. The salivary gland acts as an excellent model system to address such a research question: a) It contains defined progenitor cell populations; b) quantitative measures of functionality are easily obtained (eg. saliva flow); c) fresh mouse and human tissue (both fetal and adult) is easily obtained; d) the gland can be cultured ex vivo; and e) it undergoes defined atrophy with increasing age. We have demonstrated that the transcription factor SOX2 marks a progenitor population, is vital for lineage specification during salivary gland development and adult homeostasis and is maintained by cholinergic signals from the parasympathetic nervous system (Emmerson, et al. in submission). However, the mechanisms by which this occurs and the changes the progenitor cells themselves undergo during the course of development and ageing are largely unknown.

This PhD project will utilise both mouse and human salivary gland tissue and will investigate how SOX2+ progenitor cells themselves and their interactions with the niche change throughout development and adult ageing and in the presence of absence of neuronal signals, using Next Generation sequencing techniques and single cell analyses.

Techniques to be used 
Microdissection and ex vivo organ culture of both mouse and human tissue
Immunohistochemistry, immunofluorescence, confocal microscopy
Quantitative PCR, RNA-seq, single cell RNA-seq
Fluorescence activated cell sorting (FACS)
High-throughput Chromosome Conformation Capture (4C-seq)
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq)

Learning outcomes
Independent working and teamwork
Organisational skills and timekeeping
Critical thinking
Oral and poster presentation skills
Manuscript preparation

References

    1. Nedvetsky, Emmerson, et al. Parasympathetic innervation regulates tubulogenesis in the developing salivary gland. Developmental Cell. 2014. 30(4): 449-62
    2. Arnold, et al. Sox2(+) adult stem and progenitor cells are important for tissue regeneration and survival of mice. Cell Stem Cell. 2011. 9(4): 317-29
    3. Dixon, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015. 9(518): 331-6

    Integrated hypoxia signalling network analysis for stratified medicine in acute myeloid leukaemia - Precision Medicine Doctoral Training Programme

    Applications are no longer accepted for this project (deadline Monday 9th January 2017)

    Supervisor(s): Prof Kamil Kranc, Prof Owen Sansom, Dr Vignir Helgason & Dr Simon Tomlinson 

    Lifelong haematopoiesis critically depends on self-renewing haematopoietic stem cells (HSCs) that replenish progenitor cells and give rise to all blood lineages. Acute myeloid leukaemia (AML) is a clonal disorder of HSCs and progenitor cells, which acquire mutations and form treatment-resistant leukaemic stem cells (LSCs) that propagate the disease. Since current therapies often fail to fully eradicate LSCs, leading to high relapse rates in patients, it is essential to understand how LSCs are generated, sustained, and to identify new therapeutic targets for LSC elimination.

    Recent evidence indicated that normal and malignant haematopoiesis occur under hypoxic conditions of the bone marrow. As such, we investigated the role of hypoxia-inducible factor- 1alpha (Hif-1alpha) and Hif-2alpha, the main mediators of cellular responses to hypoxia, in these processes (Gezer et, Stem Cells, 2014). We found that while HSCs do not require Hif- 1alpha and Hif-2alpha to self-renew and sustain haematopoiesis (Guitart et al., Blood, 2013 and Vukovic et al., Blood, 2016), Hif-1alpha and Hif-2alpha synergise to suppress development and maintenance of LSCs (Vukovic et al., J. Exp. Med., 2015 and unpublished data). Our novel findings open up fundamental questions surrounding the molecular mechanisms through which Hifs function as tumour suppressors and the clinical significance of our discovery in AML. 

    Aims
    The central aim of this multidisciplinary project is to address a fundamental question: how do Hifs suppress LSC generation and propagation, and does the level of Hif-dependent signaling determine the clinical outcome of disease in different subtypes of AML? We intend to focus on the following specific aims:

    1. To employ cutting edge genomics (single cell RNA-seq, ATAC-seq and ChIP-seq) and metabolomics coupled with bioinformatics approaches to reveal molecular mechanisms through which Hifs suppress LSC functions;
    2. To use state-of-the-art in vivo approaches to functionally validate the identified pathways that cause aggressive AML upon Hif-1/2alpha deletion;
    3. To employ computational biology approaches to integrate of our datasets with publically available vast resource of human genomic datasets obtained from AML patients to uncover whether and how the Hif system determines the disease severity, drug resistance and prognosis in different subtypes of AML with diverse clinical outcomes.

    Finally, bearing in mind that the haematopoietic system serves as a paradigm for our understanding of cellular hierarchies in many other cancers, we will seek to explore the broad ramifications of our findings in stratified medicine. 

    Training Outcomes
    This project will provide the PhD student with multidisciplinary research training at the interface between experimental cancer and stem cell biology, with integral aspects of molecular pathology, genomics, metabolomics and computational genomics.

    The student will obtain training in gene knockout strategies, in vivo cancer biology approaches, flow-cytometry analyses and cell sorting, high-content/high-throughput imaging, molecular pathology (including genomic profiling) and cancer metabolism. The student will learn how to generate and apply a diverse range of ‘omics’ data resources (including RNA-seq, ChIP-seq and ATAC-seq datasets) and integrate them to address fundamental questions in molecular pathology, and precision medicine.

    The supervisors, Prof. Kamil R Kranc (Edinburgh), Prof. Owen Samson (Glasgow), Dr Vignir Helgason (Glasgow) and Dr Simon Tomlinson (Edinburgh) have expertise and strong track- record in molecular pathology/stem cell biology, cancer/leukaemia metabolism and computational genomics. This unique collaboration will ensure that the student will acquire experimental, quantitative and interdisciplinary skills applicable to many aspects of stratified medicine. 

    References

    1. Vukovic, M., Guitart, A., Sepulveda, C., Villacreces, A., O'Duibhir, E., Panagopoulou, T., Ivens, A., Menendez-Gonzalez, J., Iglesias, J.M., Allen, L., Glykofrydis, F., Subramani, C., Armesilla- Diaz, A., Post, A., Schaak, K., Gezer, D., So, C.W.E., Holyoake, T., Wood, A., O'Carroll, D., Ratcliffe, P. & Kranc, K.R. Hif-1α and Hif-2α synergise to suppress AML development but are dispensable for disease maintenance. J. Exp. Med. 212, 2223-2234 (2015).
    2. Vukovic, M., Sepulveda, C., Subramani, C., Guitart, A., Mohr, J., Allen, L., Panagopoulou, T., Paris, J., Lawson, H., Villacreces, A., Armesilla-Diaz, A., Gezer, D., Holyoake, T.L., Ratcliffe, P. & Kranc, K.R. Adult haematopoietic stem cells lacking Hif-1α self-renew normally. Blood 127(23), 2841-6 (2016).
    3. Guitart, A.V., Subramani, C., Armesilla-Diaz, A., Smith G, Sepulveda, C., Gezer, D., Vukovic, M., Dunn, K., Pollard, P., Holyoake, T.L., Enver, T., Ratcliffe, P.J. & Kranc, K.R. Hif-2alpha is not essential for cell-autonomous hematopoietic stem cell maintenance. Blood 122(10), 1741- 5 (2013).
    4. Gezer, D., Vukovic, M., Soga, T, Pollard, P., & Kranc, K.R. Genetic dissection of hypoxia signalling pathways in normal and leukaemic stem cells. Stem Cells 32(6), 1390–1397 (2014).

    Illuminating reprogramming mechanisms with DamID-seq- Precision Medicine Doctoral Training Programme

    Applications are no longer accepted for this project (deadline Monday 9th January 2017)

    Supervisor(s): Prof Keisuke Kaji & Dr Pawel Herzyk

    Transcription factors (TFs) not only dominate cellular identities during development, homeostatic and disease conditions, but also can be used to ‘reprogram’ cells and generate desired cell types in vitro and in vivo1. To understand how TFs can achieve these, chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) has been widely used. However, ChIP-seq for TFs usually requires >107 cells as well as good antibodies. Recent technology development has enabled to perform ChIP-seq for histone with various modifications with 500 cells, however the same technique was not successful to map binding sites of a TF, PU.1, with 104 cells2. This represents difficulty to investigate direct targets of TFs when the materials are limited, such as tissue specific or cancer stem cells. To overcome this problem and investigate how TFs control cellular identity, the Kaji lab recently adapted DamID-seq technology, which has mainly been used in Drosophila3, to mouse cell culture system. DamID-seq starts with the exogenous expression of the E.coli DNA adenine methyltransferase (Dam) and DNA/chromatin binding protein of interest fusion protein (Dam-POI). When Dam-POI binds to the POI targets in the genome, Dam methylates adenine of GATC sequences nearby, generating GAmTC. These GAmTC sites can be digested by a GAmTC specific restriction enzyme DpnI and following adapter ligation and PCR amplification enables to make POI target libraries available for next generation sequencing. Since there is no precipitation step where a large amount of DNA can be lost, the required cell number for DamID-seq is much smaller compared to ChIP-seq. Oct4 targets identified with this system using 104 ES cells were comparable to ChIP-seq data obtained from 107 cells. Even with as little as 1,000 cells, ~30% of the Oct4 targets identified in the ChIP-seq data with 107 cells were captured, including 75% of super enhancers (manuscript in preparation). 

    Aims
    The Kaji lab now aims to apply this DamID-seq technology to investigate how binding sites of reprogramming factors (Oct4, Sox2, Klf4, c-Myc) change during the process of induced pluripotent stem cell (iPSC) generation. Since the efficiency of this cellular reprogramming is very low (~1%), it has not been possible to use ChIP-seq against flow-sorted reprogramming intermediate subpopulations. The PhD student will join this project supported by the MRC non-clinical senior fellowship, and study how binding of other TFs and chromatin binding proteins affects reprogramming under close supervision of a senior lab member. The lab has recently performed CRISPR/Cas9-mediated genome-wide knockout screening, and identified several transcription factors/chromatin binding proteins, knockout of which facilitates or blocks reprogramming. The PhD student will aim to reveal 1) direct targets of these proteins, and 2) how knockout of these genes affect reprogramming factor binding, using the DamID-seq technology. 

    Training Outcomes
    The project involves in cell biology (cell culture, reprogramming, flow cytometry, etc), molecular biology (plasmid constructions, DamID-seq library preparation, etc), bioinformatics (sequencing data analysis, etc), under co-supervision of Keisuke Kaji (stem cell biology, molecular biology) and Pawel Herzyk (genomics, bioinformatics). Following the iPSC generation, manipulation of cellular identities by TFs has become a rapidly expanding new research field which would make a large contribution in medicine. Identifying TFs’ direct targets is becoming more and more important to understand how to control cellular identity, and the DamID-seq will be a powerful tool in any other research area where available cell numbers are limited. Importantly, this project also offers the student to gain skills to analyze the large scale sequencing data, which is critical for modern biology. The student will be fully equipped to continue his/her research in a wide range of biomedical research areas after the training.

    References
    Cell Stem Cell 2015; 16(2):119-34. 2. Science 2014; 345(6199):943-9. 3. Nat Biotechnol 2000; 18(4):424-8. 

    *EASTBIO* Understanding haematopoietic stem cell development through global single-cell gene expression analysis

    Applications are no longer accepted for this project (closed 5th December 2016)

    1. 1st Supervisor - Prof Alexander Medvinsky
    2. 2nd Supervisor - Prof Chris Ponting

    Although the first blood cells in mammals appear in the yolk sac, haematopoietic stem cells (HSCs) which can self-renew and give rise to the adult haematopoietic system appear separately inside the embryo body within the aorta-gonad-mesonephros (AGM) region (Medvinsky and Dzierzak, Cell, 1996). HSCs emerge through a multi-step process, which involves sequential maturation of intermediate cell types. However, our understanding of genetic mechanisms underlying HSC specification and progression through developmental stages is limited: some genes such as Runx1 and Gfi1 are known to be involved, but the process of HSC development in its entirety remains obscure. Detailed studies are limited partly due to in utero development. To overcome this problem, we have already established an analytical in vitro model system which allows us to replicate the process of HSC maturation in the AGM region (e.g. Taoudi et al., Cell Stem Cell, 2008; Rybtsov et al., Stem Cell Reports, 2014). Although we have characterized several consecutive embryonic HSC precursors by cell surface markers, these markers are shared with other blood progenitors. This hampers precise identification of cells of the developing HSC lineage and specific genes underlying step-wise HSC maturation.

    Recent advancement in single-cell analysis technology is dramatically transforming our understanding of cell types and lineages. It permits exploration of heterogeneity of cell populations and importantly, enables identification of novel cell type markers and otherwise unrecognisable cell sub-types. Using highly parallel barcoding of individual cells and computational tools specifically developed for single-cell data, it is now possible to build developmental/ differentiation trees into which intermediates of cell types and cellular states can be placed (Macosko et al., Cell, 2015).

    In this interdisciplinary project, we aim to explore molecular mechanisms underlying embryonic HSC development in mammals. The student will explore the transcriptional heterogeneity of the developing haematopoietic system in model organisms (mouse and chicken) using system-wide single-cell global transcriptome analysis. Single-cell gene expression analysis will be performed using cell barcoding in a Drop-Seq-like microfluidics device. Using computational biology methods the student will reconstruct the developmental tree of the haematopoietic system and will identify molecular signatures specific to clades of the developing HSC lineage. Candidate genes identified in the molecular signature that could potentially be involved in HSC development will be validated using functional in vitro and in vivo assays and their expression in the embryo will be characterised using confocal microscopy. By contrast to model organisms, analysis of human embryonic HSC development has lagged behind due to the limited availability of material, lack of an in vitro modelling system and poor characterisation of cell type markers. Our data-driven approach using cutting-edge single cell approaches in mouse and chicken is expected to be highly informative for identifying homologous cellular differentiation pathways in human and will have substantial predictive power for analysing mechanisms underlying human HSC development. This project will fill a crucial gap in our mechanistic understanding of HSC development, which could in future inform improved strategies for manipulating HSCs ex vivo.

    This is a collaborative interdisciplinary project addressing important biological questions at the system-wide level, between the groups of Prof. Alexander Medvinsky, an expert in embryonic development of mouse and human HSCs; Prof. Kees Weijer, an expert in chick embryo development and Prof. Chris Ponting, an expert in computational biology and single-cell analysis http://www.hgu.mrc.ac.uk/people/chris.ponting.html. To enhance the outcome of the project we have established a collaboration with Prof. Bertie Gottgens in Cambridge (http://www.cimr.cam.ac.uk/research/affiliated/gottgens), a leading expert in the analysis of blood transcriptional networks.

    The student will work in a highly collaborative environment and will become proficient in advanced methods of early analysis of embryonic HSC development (embryo manipulations, fluorescence activated cell sorting and analysis, HSC culture, qRT-PCR, confocal microscopy) as well as single-cell analysis and computational biology methods. Importantly, UoE has been awarded a £650K MRC Discovery Award (PI: Ponting) to implement Drop-Seq-like approaches to single cell transcriptomics. This creates an excellent opportunity for the student to become an expert in this rapidly evolving cutting-edge technology. The project will allow the student to obtain important insights into the analysis of complex biological systems and to acquire important interdisciplinary skills in systems biology approaches, which should have a highly positive impact on their future career in science.

    Further Information 

    Project and application details can be found at the website below. You must follow the instructions on the EASTBIO website for your application to be considered. 

    This opportunity is only open to UK nationals (or EU students who have been resident in the UK for 3+ years immediately prior to the programme start date) due to restrictions imposed by the funding body.

    *EASTBIO* Role of NMPs in axial patterning

    Applications are no longer accepted for this project (closed 5th December 2016)

    1. 1st Supervisor - Dr Val Wilson 
    2. 2nd Supervisor - Prof Kate Storey

    During embryo development, the spinal cord, backbone, and its associated musculature are built in a head-to-tail sequence by a population of bipotent neural/mesodermal progenitors (NMPs) located at the tail end of the embryo, while the brain is likely to be formed by an independent cell population at the head end. While most textbooks describe that the central nervous system is formed by the specification of neural tissue, followed by its subsequent patterning into brain and spinal cord (the ‘activation-transformation’ hypothesis, generated first in amphibians), there is little evidence that this mechanism operates in all vertebrate organisms. Specifically, it is not known whether neural specification precedes the allocation of cells into brain and spinal cord (NMP) progenitors.

    NMPs are characterised by the coexpression of two transcription factors, T(brachyury) and Sox2. These cells have some properties reminiscent of stem cells: they can be retained for long periods as progenitors, continuously giving rise to neural and mesodermal tissue. However, in contrast to the definition of a stem cell as ‘self-renewing’ their transcriptome changes dramatically over time. This raises the question of how these cells mature over time, and how this maturation, in turn, contributes to the patterning of different segments of the anteroposterior axis.

    We have begun to investigate when NMPs and brain progenitors become committed to their fates in mouse and chick, and these experiments suggest that this event occurs at a rather similar stage in both organisms. We also know that NMPs are particularly environment-sensitive, and are flanked by two other progenitor populations that produce the notochord and the lateral mesoderm, which might influence the identity and the fates of individual NMPs.

    In this project, we will investigate, in two model organisms (mouse and chick) with different axial patterning:

    1. What are the mechanisms that operate to specify brain and spinal cord? Do they obey the ‘activation-transformation’ hypothesis?
    2. What aspects of the NMP environment and the intrinsic programming of NMPs govern their maturation?
    3. What role does NMP patterning play in determining the identity of descendant cells in the spinal cord and backbone?

    This will involve in vitro culture and both manual and genetic manipulation of mouse NMPs, ex vivo culture of mouse and chick embryos, and a comparative analysis of the mouse and chick NMP transcriptomes.

    Further Information 

    Project and application details can be found at the website below. You must follow the instructions on the EASTBIO website for your application to be considered. 

    This opportunity is only open to UK nationals (or EU students who have been resident in the UK for 3+ years immediately prior to the programme start date) due to restrictions imposed by the funding body. 

    References

    1. Wilson, V., Olivera-Martinez, I. and Storey, K. G. (2009). Stem cells, signals and vertebrate body axis extension. Development 136, 1591–1604.
    2. Wymeersch, F. J., Huang, Y., Blin, G., Cambray, N., Wilkie, R., Wong, F. C. and Wilson, V. (2016). Position-dependent plasticity of distinct progenitor types in the primitive streak. Elife 5. e10042.
    3. Henrique, D., Abranches, E., Verrier, L. and Storey, K. G. (2015). Neuromesodermal progenitors and the making of the spinal cord. Development 142, 2864–2875.

    Subject Areas

    Embryo, mouse, chick, pluripotent cell, neuromesodermal progenitor

    Understanding haematopoietic stem cell development through global single-cell gene expression analysis

    Applications are no longer accepted for this project (closed 5th December 2016)

    1. 1st Supervisor - Prof Alexander Medvisnky
    2. 2nd Supervisor - Prof Chris Ponting

    Haematopoietic stem cells (HSCs) can self-renew and generate all blood cells of the adult animal. Here, we aim to dissect molecular mechanisms underlying development of embryonic HSCs, which remains a crucial gap in the current understanding of HSCs.

    Although the first blood in mammals appear in the yolk sac, adult HSCs appear later inside the embryo body within the AGM region (Medvinsky and Dzierzak, Cell, 1996). HSCs emerge through a multi-step process, which involves intermediate cell types. The analysis of this process in mammals is hampered by in utero development. To overcome this problem, we developed a powerful analytical in vitro model system which allows us to replicate the process of HSC maturation in the AGM region (Rybtsov et al., Stem Cell Reports, 2014). Although we partly characterized several consecutive HSC precursors, these markers are shared with other blood progenitors and therefore it is currently not possible to define specific genes which are involved in step-wise maturation of HSCs.

    Recent advances in single-cell analysis have opened up novel exciting possibilities. It permits exploration of heterogeneity of cell populations and identify novel markers and cell sub-types, which otherwise could not be distinguished. Using computer tools specifically developed for single-cell databases, developmental/ differentiation trees can be built in which cell intermediates are orderly integrated (Macosko et al., Cell, 2015).    

    In this interdisciplinary project, the student will explore the transcriptional heterogeneity of the developing haematopoietic system in model organisms using system-wide single-cell global transcriptome analysis. Using computational biology methods s/he will generate the developmental tree and identify specific molecular signatures in the developing HSC lineage. Candidate genes identified that are potentially involved in HSC development will be validated using functional in vitro and in vivo assays and their expression in the embryo will be characterised using confocal microscopy. The data generated will have a predictive power for analysis of mechanisms underlying human HSC development.

    Further Information 

    This is a collaborative interdisciplinary project between two laboratories: experts in embryonic development of HSCs: Prof. Alexander Medvinsky and expert in computational biology and single-cell analysis: Prof. Chris Ponting

    To enhance outcome of the project a collaboration has been established also with Prof. Bertie Gottgens in Cambridge, expert in blood transcriptional networks. The UoE has been awarded £650K MRC discovery award (PI, C. Ponting) to implement droplet-based approached to single cell transcriptomics.

    The student will become proficient in methods analysing embryonic HSC development (embryo manipulations, fluorescence activated cell sorting and analysis, HSC culture, qRT-PCR, confocal microscopy), as well as single-cell and computational biology methods.   

    References

    1. Medvinsky, A. and Dzierzak, E. (1996). “Definitive hematopoiesis is autonomously initiated by the AGM region”. Cell,v. 86: 897-906
    2. S. Rybtsov, et al. (2014). Tracing the origin of the HSC hierarchy reveals a SCF dependent, IL-3 independent CD43- embryonic precursor. Stem Cell Reports 3: 489–501, 2014.
    3. Macosko et al., Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 21;161: 1202-14; 2015

    Subject Areas

    Developmental biology, Stem Cell Biology, Systems Biology


    Tissue Repair PhD Programme

    Applications are no longer accepted for this programme (closed 5th December 2016)

    University of Edinburgh/Wellcome Trust Tissue Repair Four Year PhD Programme

    The Centre for Regenerative Medicine is one of five key research centres involved in an innovative and exciting new Wellcome Trust Four-year PhD Programme in Tissue Repair, run by the University of Edinburgh and funded by the Wellcome Trust. The Tissue Repair PhD Programme provides cutting edge, cross-disciplinary PhD training which builds on the breath of world-class biomedical research performed at the University of Edinburgh's College of Medicine & Veterinary Medicine (CMVM).

    Tissue Repair Programme Website



    We encourage enquiries and applications from self-funded basic and clinical scientists and from candidates who intend to apply for external funding all year round.

    Instructions on how to apply as a self funded student can be found here.

    Please contact the relevant PI’s informally to discuss potential projects and visit our funding opportunities page.

    Centre Funded Studentships include:

    • Stipend for 3 or 4 years
    • Tuition Fees
    • Research Training Costs
    • Conference Travel Allowance

    Further information about MRC Studentships.

    Contact us for more information.