Fully funded 4 Year PhD studentships in Biomedical Sciences

Project location 

QMRI, Bioquarter

Contact

Matt.Brook@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Prof. Nicola Gray (CRH/IRR) Email: Nicola.Gray@ed.ac.uk

Prof. Robert Semple (CVS) Email: rsemple@exseed.ed.ac.uk

Project description

PABPC4 is a poorly characterised RNA-binding protein whose genetic locus is strongly associated in human genetic association studies to metabolic disease traits (e.g. cholesterol and triglyceride levels, type 2 diabetes), with some associations sexually dimorphic. Population genetic studies (gnomAD) moreover indicate clear selection against heterozygous loss of function in the wider population. PABPC4 is a close homologue of PABPC1, which binds to mRNA poly(A) tails and regulates multiple facets of mRNA translation and turnover, but PABPC4 molecular functions, RNA targets, and role in mammalian physiology remain to be determined.

Importantly, our (Brook/Gray) unpublished work has revealed sexually-dimorphic dysregulation of growth, body composition, and response to high-fat diet (HFD) of Pabp4-/- mice, with male, but not female, Pabpc4-/- mice being profoundly protected from HFD-induced obesity, insulin resistance and non-alcoholic fatty liver disease (NAFLD). Collectively these findings establish that genetic alteration of PABPC4 function and/or expression predisposes to the development of impaired lipid metabolism, obesity and associated pathologies in response to HFD. 

We hypothesise that PABPC4 is a master post-transcriptional regulator of sexually dimorphic metabolic gene expression programs. We will take advantage of complementary expertise in the new collaborative team to test this hypothesis via 3 major aims:

Aim 1: Elucidate the metabolic/physiological mechanisms and tissue aetiology of the obesity resistant/dyslipidaemic phenotype of Pabpc4-/- mice. Aim 2: Identify cell types and cellular pathways underlying the PABP4-dependent regulation of lipid/lipoprotein profiles and metabolic traits in mice. Aim 3: Identify functionally relevant PABPC4 mRNA targets and characterise their dysregulation in Pabpc4-/- mice.

Approaches used in project

The student will receive training in cutting-edge methods to study mouse in vivo metabolism (e.g. Sable Promethion indirect calorimetry/behaviour system) and ex vivo/in vitro cell metabolism (e.g. cellular respiration). The identification of PABP4 targets and regulated pathways will require combinations of transcriptomics, proteomics (proteome regulation, protein interactome mapping) and post-transcriptional regulation of gene expression studies (e.g. RNA-binding protein function, RNA target identification).

The supervisory team encompasses all the required expertise and will fully support method training and deployment. In addition, training will be provided in bioinformatics approaches to data handling/analysis and use of human genetic association data, as required.

Relevant references for project background

1.    J. Wu, R. X. Yin, T. Guo, Q. Z. Lin, S. W. Shen, J. Q. Sun, et al. (2015) Gender-specific association between the cytoplasmic poly(A) binding protein 4 rs4660293 single nucleotide polymorphism and serum lipid levels. Mol Med Rep. 12: 3476-3486 [PMID:26005159]

2.    L. A. Passmore and J. Coller (2022) Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol. 23(2): 93-106. [PMID:34594027]

3.    Fátima Gebauer, Thomas Schwarzl, Juan Valcárcel & Matthias W. Hentze (2021) RNA-binding proteins in human genetic disease. Nature Reviews Genetics. 22:185–198 [PMID: 33235359]

4.    Kelaini S, Chan C, Cornelius VA, Margariti A. (2021) RNA-Binding Proteins Hold Key Roles in Function, Dysfunction, and Disease. Biology (Basel). 10(5):366. [PMID: 33923168]

5.    Van Nostrand EL, Pratt GA, et al. (2020) Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. Genome Biology. 21(1):90. [PMID: 32252787]

Project location 

QMRI, Bioquarter

Contact

Matt.Brook@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Dr. Di Chen (ZJE) Email: dichen@intl.zju.edu.cn

Project description

PABPC1 is central to normal regulation of mRNA translation and decay. By binding mRNA poly(A) tails and interacting with a suite of partner proteins, PABPC1 confers disparate regulatory outcomes to mRNAs. However, despite many protein partners binding at overlapping or shared sites, the regulation of PABPC1-partner interactions is very poorly understood.

We have previously demonstrated PABPC1 to be extensively post-translational modified (PTM); ranging from S/T/Y phosphorylation and R methylation to more unusual K acetylation/methylation switches and Q/D methylation. To date, the functional relevance, regulatory mechanism, and upstream signalling pathways of almost all these PTMs remains unknown.

However, we have determined that PABPC1 is subject to regulation in response to nutrient status, cell cycle stage, and viral infection, indicating that full understanding of PABPC1 PTM-mediated regulation may uncover novel pathways of gene expression regulation.

To reveal novel systems of post-transcriptional regulation of gene expression that underpin nutrient responsiveness and metabolic homeostasis, we will quantitatively determine PABPC1 PTM responses to nutrient availability and perform mechanistic studies of PTM effects on (for e.g.) protein partner binding, mRNA target selection/mRNA binding, and utilisation/fate of target mRNAs (e.g. translation, poly(A) tail status, decay), and we will delineate upstream signalling pathways of nutrient-responsive PTMs.

Aim 1: PTM-omics analysis of PABPC1 to fully characterise its post-translational regulation in response to nutrient availability. Aim 2: Mechanistic characterisation of the effects of nutrient-responsive PTMs on PABPC1 protein partner and/or mRNA interactions. Aim 3: Mapping of upstream regulatory signalling pathways that modulate nutrient-responsive PABPC1 PTMs to affect metabolic gene expression.

Approaches used in project

The student will receive training in cutting-edge methods to study: The identification of PABPC1 PTMs and regulated outcomes, interactions and upstream pathways will require combinations of proteomics/PTMomics, biophysical and structural studies (e.g. SPR, crystallography/NMR), transcriptomics, post-transcriptional regulation of gene expression studies (e.g. RNA-binding protein function, RNA target identification) and in vitro cell metabolism methods (e.g. cellular respiration).

The supervisory team encompasses all the required expertise and will fully support method training and deployment. In addition, training will be provided in bioinformatics approaches to data handling/analysis, as required

Relevant references for project background

1.    Brook M, McCracken L, Reddington JP, Lu ZL, Morrice NA, Gray NK. (2012) Biochem J. 441(3):803-12. The multifunctional poly(A)-binding protein (PABP) 1 is subject to extensive dynamic post-translational modification, which molecular modelling suggests plays an important role in co-ordinating its activities. [PMID: 22004688]

2.    Friend K, Brook M, Bezirci FB, Sheets MD, Gray NK, Seli E. (2012) Embryonic poly(A)-binding protein (ePAB) phosphorylation is required for Xenopus oocyte maturation. Biochem J. 445(1):93-100. [PMID: 22497250]

3.    Shan P, Fan G, Sun L, Liu J, Wang W, Hu C, Zhang X, Zhai Q, Song X, Cao L, Cui Y, Zhang S, Wang C. (2017) SIRT1 Functions as a Negative Regulator of Eukaryotic Poly(A)RNA Transport. Curr Biol. 27(15):2271-2284.e5. [PMID: 28756945]

4.    Passmore LA, Coller J. (2022) Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol. 23(2):93-106. [PMID: 34594027]

Project location 

Hugh Robson Building, George Square.

Contact

P.J.Brunton@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Prof. Ruth Andrew (Centre for Cardiovascular Science) Email: Ruth.Andrew@ed.ac.uk

Project description

Maternal stress during pregnancy ‘programs’ long-lasting neuroendocrine and behavioural changes in the offspring[1,2]. Often this ‘programming’ is maladaptive and sex-specific[1,2]. How the effects of maternal stress are transmitted from the mother to the fetuses is not known. Direct transfer of maternal glucocorticoids to the fetuses is often proposed to mediate the programming effects. However, we have shown that although corticosterone secretion is significantly greater in stressed dams compared with controls, there is no impact on corticosterone concentrations in the fetal circulation or brain[3].

In addition, maternal stress upregulates placental 11β-hydroxysteroid dehydrogenase-2 (the enzyme that inactivates glucocorticoids, limiting mother-to-fetus glucocorticoid transfer), suggesting this protective mechanism is intact[3]. These findings suggest a factor(s) other than glucocorticoids mediate fetal programming.

The aim of this project is to investigate the factor(s) that signal maternal stress to the fetus. The placenta has several functions that make it a likely central player in mediating the effects of maternal stress[4]. As well as nutrient transport, the placenta also actively produces and secretes factors (e.g. steroids, monoamines, growth factors, cytokines) that can influence fetal brain development. We will perform a metabolomic screen of secretions from male and female placentae from stressed and non-stressed pregnancies.

We will test whether identified candidate factors can mimic changes in gene expression observed in the prenatally stressed offspring brain. We will also investigate sex-dependent changes in placental gene expression induced by maternal stress, (in particular those involved in nutrient transport and allocation) and investigate whether these contribute to the programmed offspring phenotype. 

Approaches used in project

Behavioural observations will be used to monitor social stress induction in pregnant rats. Blood samples will be collected and immunoassays used to determine plasma hormone concentrations (primarily corticosterone). Mass spectrometry will be used for metabolomic profiling of placental secretions. Neuronal cell culture will be used to screen whether candidate placental factors can mimic changes in gene expression observed in the fetal/offspring brain.

Altered gene expression in the fetal brain, placentae neuronal cultures induced by maternal stress will be quantified by RNAscope/qPCR, while changes in protein expression will be assessed using immunocytochemistry/Western blotting.

Relevant references for project background

1.    Brunton, P. J. & Russell, J. A. 2010. Prenatal social stress in the rat programmes neuroendocrine and behavioural responses to stress in the adult offspring: Sex specific effects. J Neuroendocrinol, 22, 258-271. 10.1111/j.1365-2826.2010.01969.x

2.    Maccari, S., Krugers, H. J., Morley-Fletcher, S., Szyf, M. & Brunton, P. J. 2014. The consequences of early-life adversity: Neurobiological, behavioural and epigenetic adaptations. Journal of Neuroendocrinology, 26, 707-23. 10.1111/jne.12175

3.    Sze, Y., Fernandes, J., Kołodziejczyk, Z. M. & Brunton, P. J. 2022. Maternal glucocorticoids do not directly mediate the effects of maternal social stress on the fetus. J Endocrinol, 255, 143-158. 10.1530/JOE-22-0226

4.    Bronson, S. L. & Bale, T. L. 2016. The placenta as a mediator of stress effects on neurodevelopmental reprogramming. Neuropsychopharmacology, 41, 207-18. 10.1038/npp.2015.231

Project location

CDBS, 1 George Square.

Contact

Gedi.Luksys@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Robin Hill (Edinburgh Informatics) Email: r.l.hill@ed.ac.uk

Project description

In today's society, people often find it difficult to receive information outside their social circle or comfort zone. The questions of whether limited availability or active avoidance of such information determines its limited reach and which neurocognitive factors contribute to this outcome are of huge importance, but they have not been sufficiently studied, especially at the basic level. MyNewsScan.eu is a news aggregator platform that we developed to tackle this problem.

We also developed the Paintings/Quotes experiment to investigate the role of schemas (prior information) and modulatory factors (e.g. risk, novelty) in decision making as well as the associated computational models that use error-based learning, motivation, and drift-diffusion model components. The PhD will build upon preliminary findings from both experiments that also included collection of biometrics such as eye movements, heart rates and emotional expressions.

The core doctoral research will employ a newly upgraded version of the website as a community-driven platform for large-scale collection of data, with some Edinburgh-based participants recruited for biometric, EEG and/or fMRI studies. We will also employ computational modelling, neuroeconomics and/or natural language processing methods, depending on student’s expertise and interests.

The ultimate aim is to understand factors affecting decision making at different levels: e.g. how biometric and neuroimaging data relate to behavioural metrics and questionnaire-based data, whether participant decisions and attitudes may be predicted by such information (including factors like stress, motivation and sleep), and whether easily collected online digital markers could be predictive of neuropsychiatric conditions that require lengthy and costly clinical assessments.

Approaches used in project

Depending on the expertise and interests of the student, the project will include (but is not limited to) a number of the following methods: behavioural/cognitive experiments in humans, both online and in laboratory, collection and analysis of biometrics and/or neuroimaging data, management and further development of MyNewsScan platform and its user community, computational modelling of learning and decision making (e.g. reinforcement learning, drift diffusion, motivation models) and their parameter estimation, advanced statistics (e.g. mixed effects models), machine learning and natural language processing, questionnaire-based and clinical characterisation of neuropsychiatric disorders.

Relevant references for project background

1. Vosoughi et al., “The spread of true and false news online”, Science 2018; Huckvale et al., “Toward clinical digital phenotyping: a timely opportunity to consider purpose, quality, and safety”, npj Digital Medicine 2019;

2. Strasser et al., “Glutamine-to-glutamate ratio in the nucleus accumbens predicts effort-based motivated performance in humans”, Neuropsychopharmacology 2020;

3. Shinn et al., “A flexible framework for simulating and fitting generalized drift-diffusion models”, eLife 2020;

4. Luksys et al., “Stress, genotype and norepinephrine in the prediction of mouse behavior using reinforcement learning”, Nature Neuroscience 2009

Project location

IRR, Bioquarter

Contact

Vasso.Makrantoni@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Dr Mikael Bjorklund (ZJE, China) Email: mikaelbj@intl.zju.edu.cn

Dr Richard Sloan (CIR-IRR, UoE/ZJE) Email: richard.sloan@ed.ac.uk;  

Dr Arno Alpi (Institute for Cell Biology, UoE) Email: aalpi@ed.ac.uk

Project description

Fungal pathogens kill over a million people every year. The most common human fungal pathogen is Candida albicans, a WHO-priority target. With only three classes of antifungal drugs available and increasing drug-resistant infections in clinical settings, understanding the mechanisms of resistance is a priority. Candida’s survival in the complex and dynamic host environment depends on the ability to efficiently control its metabolism, which involves the production and breakdown of numerous different small biological chemicals collectively called "metabolites". Candida is known to assimilate glucose and alternative carbon sources simultaneously, thereby providing growth advantages [1]. However, how this remarkable metabolic flexibility is regulated during infection, remains largely unknown.

Cellular responses to metabolic stress stimuli are mediated through gene regulatory networks and post-translational modifications. One such network, the Ubiquitin-Proteasome-System (UPS), is known to be responsible for eliminating unwanted proteins that would otherwise damage Candida cells. Molecular machines, called E3 ubiquitin ligases, ensure that the UPS destroys only those proteins whose functions should be terminated, and spares the majority of those required for ongoing cellular functions. One of the first UPS-dependent mechanisms identified in metabolic regulation is mediated by the budding yeast GID E3 ligase complex, which targets superfluous metabolic enzymes for proteasomal degradation upon changes in carbon sources [2,3]. Evidence from the Makrantoni lab suggests that Candida employs the GID E3 complex during host infection to rewire metabolic pathways in order to enhance its virulence. This project aims to uncover the molecular mechanism by which GID E3 ligase regulates metabolic flexibility in Candida.

Approaches used in project

This interdisciplinary PhD project is supported by cross-institutional collaborations between the Institutes for Regeneration and Repair and of Cell Biology in Edinburgh, and the ZJE Institute in China, providing state-of-the-art technologies.

Approaches used include:  

(1) Sophisticated genetics (CRISPR-Cas9 editing) to generate Candida mutants to assess functional links between viability and metabolome changes upon stress (in collaboration with Bjorklund lab, ZJE);

(2) Mass spectrometry-based proteomics to identify GID E3 substrates, and biochemical approaches utilizing reconstituted GID-substrate ubiquitylation systems (in collaboration with Alpi lab, UoE);

(3) Use of human macrophages to reconstitute in vitro host-pathogen systems for assessing virulence (in collaboration with Sloan lab, UoE).

Relevant references for project background

[1] Childers DS et al. (2016). The Rewiring of Ubiquitination Targets in a Pathogenic Yeast Promotes Metabolic Flexibility, Host Colonization and Virulence. PLOS Pathogens.  DOI: 10.1371/journal.ppat.1005566;

[2] Shuai Qiao et al. (2020). Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly. Molecular Cell 77: 150–163;

[3] Langlois CR et al (2022). A GID E3 ligase assembly ubiquitinates an Rsp5 E3 adaptor and regulates plasma membrane transporters. EMBO Reports, 23: e53835

Project location 

CDBS, Hugh Robson Building, George Square.

Contact

Duncan.macgregor@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Weiwei Qiu (Zhejiang) Email: weiweiqiu@intl.zju.edu.cn

Project description

We will use computational modelling in tandem with in vivo approaches to explore how the brain integrates sensory, gut, and energy homeostasis signals to regulate feeding behaviour and maintain energy stores. Our computational model will take a systems approach, combining knowledge of brain-body mechanisms to better define mechanistic interactions within a whole-body system. The performance of this brain-body model will be tested in simulations of published behavioural experiments. The model will be kept simple, adding complexity only as necessary to match the data being tested against, but using a modular structure that will also allow the integration and testing of more detailed model components. Critically, this approach facilitates the interpretation of existing data and the generation of new, quantitative predictions for behavioural and physiological parameters such as body weight, blood glucose, and gut signalling that can be tested in the Qiu lab. 

We have already developed a basic version of the model to study how appetite is regulated by competition between sensory and physiological signals, with model output closely aligned with published behavioural data. Modelling of appetite regulation is a competitive field, but most models represent a limited, single paradigm for the relationship between eating behaviour and energy stores. Our modular approach will build on a skeleton of essential components (energy stores, digestion, metabolism, etc) that is ‘control paradigm neutral’ and therefore broadly adaptable to different experimental contexts. For example, investigations of the cognitive basis for decision-making are often based on foraging behaviour, for which our model would be an ideal partner. 

Approaches used in project

This will primarily be a computational modelling-based project but will also include in vivo experimental work, potentially in both Edinburgh and Zhejiang.

In particular, ongoing translational work exploring the endocrine and neural circuit signalling in the hypothalamus and brain stem that regulates eating behaviours and energy balance. The modelling will use our own software tools designed to make modelling rapid and accessible both for model development, and for dissemination and teaching.

Relevant references for project background

1. Final Report Summary - NUDGE-IT (The Neurobiology of Decision-Making in Eating - Innovative Tools) https://cordis.europa.eu/project/id/607310/reporting

2. Hume, Jachs, Menzies. Homeostatic responses to palatable food consumption in satiated rats. Obesity 2016 24(10):2126. doi: 10.1002/oby.21606

3. MacGregor, Leng. Modelling the hypothalamic control of growth hormone secretion. Journal of Neuroendocrinology 2005, 17 (12): 788-803. doi: 10.1111/j.1365-2826.2005.01370.x

4. MacGregor, Leng. Emergent decision-making behaviour and rhythm generation in a computational model of the ventromedial nucleus of the hypothalamus. PLoS Computational Biology 2019 15(6). doi: 10.1371/pcbi.1007092.

5. Qui, W., Hutch, C. R., Wang, Y., Rucker, R. A., Wloszek, J., Myers Jr, M. G., & Sandoval, D. (2022). Multiple NTS Neuron Populations Synergistically Suppress Physiologic Food Intake but are Dispensable for the Response to VSG. bioRxiv, 2022-12.

Project location 

Hugh Robson Building, George Square.

Contact

John.Menzies@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Dr Celine Caquineau (BMTO) Email: c.caquineau@ed.ac.uk

Project description

We anticipate this distinctive project will have wide-spread influence in the field of TNE research by providing key foundational evidence to better understand T&L practices at ZJE and across the many other UK-China TNE partnerships. Being exploratory in nature, we believe this project provides a unique, pioneering and potentially transformative opportunity for a PhD researcher to develop a strategic direction for research into intercultural learning. 

The supervisory team has extensive experience in T&L in both UK and China. Both supervisors have Advance HE accreditations and have supported numerous PhD researchers in the development of their teaching practices. The supervisory team has strong links with the Institute for Academic Development at the University of Edinburgh, which has international recognition in T&L research.

Approaches used in project

First, the student will carry out a systematic review of TNE research to identify knowledge gaps. Informed by the review and in alignment with ZJE’s research priorities, the student will then identify the focus of their investigation.

Their project will likely encompass mixed quantitative and qualitative methods to directly address specific research questions. The project will use different ways of generating and analysing data to provide an in-depth and inclusive understanding of the ZJE community, and thus to identify potential challenges and opportunities in enhancing student and staff experiences. 

Relevant references for project background

1. www.ed.ac.uk/biomedical-sciences/connections-outreach/international-activities/zje-institute

2. www.britishcouncil.cn/en/programmes/education/higher/TNE

Project location

CDBS, Hugh Robson Building, George Square. 

Contact

Nicola.romano@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Dr Duncan McGregor (UoE/ZJE) Email: duncan.macgregor@ed.ac.uk 

Dr Peter Duncan (UoE) Email: peter.duncan@ed.ac.uk

Project description

Recent technological advances enabled scientists to study biological processes at the single-cell level with unprecedented amount of detail. These techniques highlighted a previously unknown level of heterogeneity in several biological tissues, but whether and how this translates to altered function is still poorly understood. The idea that cell populations are much more heterogeneous than previously thought changes how we think about our body functions and questions the traditional definitions of what is a "cell type". This project will focus on the pituitary gland, a key organ in controlling critical hormonal responses in the body, and specifically on corticotrophs, which regulate stress responses. We and others have gathered evidence for a high level of heterogeneity in corticotrophs at the functional level (e.g. electrical activity, calcium responses) and at the level of the transcriptome. These results brought us to ask how such a heterogeneous group of cells works like a coherent population to drive stress responses and what would be the function of it. One hypothesis is that heterogeneity increases the dynamic range of the system, allowing it to respond to a variety of different types, lengths and magnitudes of stress. We have recently shown that corticotrophs exist in a variety of dynamic cell states, that might be contributing in different ways to stress responses. This project will investigate the link between transcriptional and functional heterogeneity using state-of-the-art techniques, ranging from mathematical modelling and bioinformatics approaches to "wet lab" techniques such as imaging and electrophysiology to map transcriptomic state to functional outcomes.

Approaches used in project

The laboratories of the Supervisory Team use a range of complementary approaches, from bioinformatics (e.g. scRNAseq), imaging (IHC, calcium imaging, in vivo), electrophysiology, optogenetics, and mathematical modelling which can be integrated at different stages of the project.

Relevant references for project background

1. Romanò et al., 2017 - Heterogeneity of Calcium Responses to Secretagogues in Corticotrophs From Male Rats - https://pubmed.ncbi.nlm.nih.gov/28323954/

2. Duncan et al., 2022 - Chronic stress facilitates bursting electrical activity in pituitary corticotrophs - https://pubmed.ncbi.nlm.nih.gov/34855218/

3. Walker and Romanò, 2022 - Fast dynamics in the HPA axis: Insight from mathematical and experimental studies - https://pubmed.ncbi.nlm.nih.gov/36632146/

4. MacGregor and Leng, 2013 - Spike triggered hormone secretion in vasopressin cells; a model investigation of mechanism and heterogeneous population function - https://pubmed.ncbi.nlm.nih.gov/23966850/

5. Le Tissier et al., 2016 - An updated view of hypothalamic-vascular-pituitary unit function and plasticity - https://pubmed.ncbi.nlm.nih.gov/27934864/

Project location 

CDBS, Hugh Robson Building, George Square.

Contact

Nicola.Romano@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Dr Peter Duncan (UoE) Email: peter.duncan@ed.ac.uk

Dr KuanYoow Chan (ZJE) Email: kychan@intl.zju.edu.cn

Paul Le Tissier (UoE/ZJE) Email: Paul.letissier@ed.ac.uk

Project description

Most hormones are stored in vesicles, allowing release in large amounts in response to stimulation.  Differential release of vesicles dependent on the time stored thereby allowing release of different cargoes (both endocrine and potentially autocrine signalling molecules), has been shown in several non-pituitary endocrine cells.  

The aim of this project is to study the importance of this temporal encoding of secretory vesicles using the endocrine cells of the pituitary regulating stress and growth as model systems.     

As well as being storage organelles, dynamic modification can occur within vesicles (processing of cargo by intra-vesicle enzymes /recruitment of additional proteins) and on the organelle surface (directing cytosolic location).  We hypothesise that this allows encoding of vesicle function, allowing a readout of the history of secretion and/or differential effects by release of specific pools of vesicles.  Using TIMER, a fluorescent cargo protein that changes colour with age, individual secretory vesicles will be labelled to determine whether there is differential release of secretory vesicles dependent on their age or the pattern of secretagogue(s) stimulation. 

Secretory vesicles of different ages will be isolated from cells using FACs and mass spectroscopy to identify the proteins packaged within a vesicle and on its membrane, determining if vesicles change with time and/or the physiological state of the cells.  Manipulation of the cargo will then allow us to test the physiological regulation of vesicle release based on age, as well as the consequences for physiology.

These studies will be done in cell lines and in ex vivo pituitary slices.  

Approaches used in project

This project will allow extensive training in tissue culture, transfection, primary cell transduction, live cell confocal microscopy, FACs, proteomic analysis with mass spectroscopy, protein modification and physiological assays.  Initially, studies will be optimised in cell lines in vitro but once optimised ex vivo primary pituitary cells and tissue slices will allow analysis in a more physiologically relevant context.  

Relevant references for project background

1.Duncan, R., Greaves, J., Wiegand, U. Matskevich, I.  Bodammer, G, Apps, D.K., Shipston, M.J., Chow, R.H.  (2003)  Functional and spatial segregation of secretory vesicle pools according to vesicle age. Nature 422, 176–180.  https://doi.org/10.1038/nature01389  

2. Yau, B., Hays, L., Liang, C., Laybutt, D.R., Thomas, H.E., Gunton, J.E., Williams, L., Hawthorne, W.J., Thorn, P., Rhodes, C.J., Kebede, M.A. (2020)  A fluorescent timer reporter enables sorting of insulin secretory granules by age.  Journal of Biological Chemistry 295, 8901-8911.  https://doi.org/10.1074/jbc.RA120.012432

Project location 

Hugh Robson Building, George Square. 

Contact

Robert.young@ed.ac.uk

Name, location and email of co-applicants (Supervisory Team)

Dr KuanYoow Chan (ZJE) Email: kychan@intl.zju.edu.cn

Dr Sara Macias Ribela, (Institute of Immunology and Infection Research, UoE) Email: sara.maciasribela@ed.ac.uk

Project description

Over 100,000 genetic variants have already been associated with various medical phenotypes by genome-wide association studies (GWAS). However, the majority of these studies have been performed in European populations. This bias limits the utility of these results and the ability to translate this knowledge into under-represented global populations. There is therefore an urgent need to understand population differentiation to inform the development of medical therapeutics for currently underserved populations. 

In this project, you will use bioinformatics to identify genome features that determine differential susceptibility to disease across European and Asian populations. You will then test their biological relevance in the laboratory. While most your time will be spent in Edinburgh, you will have the opportunity to spend time performing research at our international campus at Haining, China.

The project has three elements: 1) Initial characterisation of publicly available GWAS and drug-gene interaction datasets obtained from European and Asian populations to identify phenotypes and genomic features of population-specific variants.  2) Variants identified in the first stage will be engineered using CRISPR-Cas9 genome editing in cell models isolated from both the European and Asian populations. You will quantify the transcriptomic differences across genotypes and populations using the functional genomics technology Cap Analysis of Gene Expression (CAGE).  3) Differentially expressed targets will be investigated using standard bioinformatics analyses, e.g. Gene Ontology enrichment, and integrated omics data available from related populations, including UK Biobank and the China Kadoorie Biobank. Follow-up experiments will determine whether known drug-gene interactions for these targets are effective across populations. 

Approaches used in project

We will use a combination of various computational software (BEDTools, Bowtie, CAGEr) and statistical analyses (in the R programming language) to investigate the genomic and transcriptomic datasets involved in this project. Subsequently, the student will learn cellular and molecular techniques (PCR, western blotting, CRISPR-Cas9 editing, growth assays) required to manipulate the cellular models studied here.

Relevant references for project background

1. Fitipaldi H, Franks PW. Ethnic, gender and other sociodemographic biases in genome-wide association studies for the most burdensome non-communicable diseases: 2005-2022. Human Molecular Genetics 32, 3: 520-532(2023). https://doi.org/10.1093/hmg/ddac245  

2. Kindt ASD, Navarro P, Semple CAM, et al. The genomic signature of trait-associated variants. BMC Genomics 14, 108 (2013). http://www.biomedcentral.com/1471-2164/14/108  

3. Young RS, Talmane L, Marion de Procé S, et al. The contribution of evolutionarily volatile promoters to molecular phenotypes and human trait variation. Genome Biology 23(1), 89 (2022). https://doi.org/10.1186/s13059-022-02634-w  

4. Fernandez N, Cordiner RA, Young RS, et al. Genetic variation and RNA structure regulate microRNA biogenesis. Nature Communications 3(8), 15114 (2017). https://doi.org/10.1038/ncomms15114