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Epidemiology & genetics

Dietary factors and all-cause and cardiovascular mortality in Eastern European cohort studies

Supervisor: Prof Martin Bobak

Department: Research Department of Epidemiology and Public Health

Project outline:
Background. Unhealthy diet, particularly low fruit and vegetable consumption, has been proposed as an important reason for the high cardiovascular disease (CVD) mortality in Central and Eastern Europe (CEE) and the former Soviet Union (FSU). However, individual-level food and nutrient intake data in these regions and direct comparisons with Western European populations are sparse, and estimates of their health effects are not available.

Aims. The aim of this thesis was to compare dietary intake habits between adults who live in Eastern and Western European countries, and to assess the relationships between selected dietary habits and all-cause and cause-specific mortality in Eastern Europeans.

Methods. Data collected from the Czech, Polish and Russian participants of the Health, Alcohol and Psychosocial Factors in Eastern Europe (HAPIEE) prospective cohort study (n=28,947) were used. The comparison of food and nutrient intakes with British participants in the UK Whitehall II study was carried out using quantile regression analysis after dietary data harmonization. The associations between dietary habits and mortality outcomes in the Eastern European cohorts were assessed by Cox regression models. Missing data was imputed using multiple random imputation procedures.

Results. Compared to the British participants, fruit and vegetable intakes were significantly lower in the pooled Eastern European sample but not in all country cohorts. In the pooled HAPIEE sample, the healthy diet indicator score and the Mediterranean diet score were significantly and inversely associated with CVD mortality after multivariable adjustments. Regarding fruit and vegetable intake, the inverse association appeared to be the strongest with stroke mortality and especially among smokers.

Discussion. The findings of this thesis support the hypothesis that unhealthy diet has played a role in the high CVD mortality in Eastern Europe. Public health interventions which target fruit and vegetable consumption and/or other dietary factors should be considered in this region.

Key references:

  1. Ambring A, Johansson M, Axelsen M, Gan L, Strandvik B, Friberg P. Mediterranean-inspired diet lowers the ratio of serum phospholipid n-6 to n-3 fatty acids, the number of leukocytes and platelets, and vascular endothelial growth factor in healthy subjects. Am J Clin Nutr. 2006;83:575-81
  2. Mente A, de Koning L, Shannon HS, Anand SS. A systematic review of the evidence supporting a causal link between dietary factors and coronary heart disease. Arch Intern Med. 2009;169:659-69.
  3. Estruch R, Ros E, Salas-Salvadó J, Covas MI, Corella D, Arós F, Gómez-Gracia E, Ruiz-Gutiérrez V, Fiol M, Lapetra J, Lamuela-Raventos RM, Serra-Majem L, Pintó X, Basora J, Muñoz MA, Sorlí JV, Martínez JA, Martínez-González MA; PREDIMED Study Investigators. Primary prevention of cardiovascular disease with a Mediterranean diet. N Engl J Med. 2013;368:1279-90.

The role of psychosocial wellbeing and biological stress processes in linking type II diabetes and cardiovascular disease

Supervisor: Prof. Andrew Steptoe

Department: Epidemiology and Public Health

Project outline:
Type 2 diabetes (T2D) is chronic disorder with increasing prevalence that contributes to the risk of cardiovascular disease (CVD). Epidemiological and clinical evidence suggests that psychosocial stress is involved in both conditions, but the pathways involved remain unclear. This project aimed to contribute to the evidence linking T2D and CVD by examining the role of psychosocial wellbeing, as well as the underlying pathophysiological effects of stress in T2D through a laboratory study and secondary analysis of large longitudinal datasets. The laboratory study assessed biological responses to acute mental stress and psychosocial adversity in people with T2D. The secondary data analysis study used longitudinal data from the Whitehall II cohort to examine the associations between diurnal cortisol patterns and risk of T2D.

Key references:

  1. Sarwar, N. et al. (2010). Diabetes mellitus, fasting blood glucose concentration, and risk of vascular disease: a collaborative meta-analysis of 102 prospective studies. Lancet, 375(9733), 2215-22.
  2. Dimsdale, J. E. (2008). Psychological stress and cardiovascular disease. Journal of the American College of Cardiology, 51(13), 1237-1246.
  3. Novak, M., Björck, L., Giang, K. W., Heden‐Ståhl, C., Wilhelmsen, L., & Rosengren, A. (2013). Perceived stress and incidence of Type 2 diabetes: a 35‐year follow‐up study of middle‐aged Swedish men. Diabetic Medicine, 30(1), e8-e16.
  4. Steptoe A., Hackett R. A., Lazzarino A. I., Bostock S., La Marca R., Hamer M., (2014), Disruption of multisystem responses to stress in type 2 diabetes: Investigating the dynamics of allostatic load. Proc. Natl. Acad. Sci., 111(44), 15693-15698.
  5. Hackett, R. A., Kivimaki, M., Kumari, M., & Steptoe, A., (in press). Diurnal cortisol patterns, future diabetes and impaired glucose metabolism in the Whitehall II cohort. Journal of Clinical Endocrinology and Metabolism

Use of smartphone applications to enhance smoking cessation support

Supervisors: Prof. Robert West and Dr Lion Shahab

Department: Epidemiology and Public Health

Project outline:
The most effective method of stopping smoking is to use a combination of face-to-face behavioural support together with pharmacotherapy. However, numerous barriers exist in provision, access and adherence to treatment. Smartphones could support the delivery of some of the support and thus improve quit rates. However, we still lack data on effectiveness of such programmes, or how they could facilitate cessation. This PhD programme is employing mixed-methods and a theoretical framework provided by Behaviour Change Wheel (Michie et al, 2014) to develop, as well as to conduct preliminary evaluation of smartphone-delivered programmes to support quitting and the use of cessation medications. The research will also help to identity and address some of the key challenges involved in evaluation of such programmes.

In the first instance this PhD focuses on two projects involving development and evaluation of two stop smoking apps. The first one revolves around Bupa Quit – an app supporting craving management. Bupa Quit is the flagship project of the new Global Institute for Digital Health Excellence, GLIDHE – a collaborative initiative between UCL and Bupa. This project involves one of the largest randomized controlled trials of cessation apps to date (www.bupa.com/bupaquit), as well as an international release of the app and data collection. The second project focuses on NRT2Quit - an app that addresses non-adherence to over-the-counter nicotine replacement therapy during quit attempts (www.nrt2quit.com). The final phase of the PhD will assess the potential behind smartphone-delivered programmes to support cessation interventions initiated by health professionals. 

Key references:

  1. Cahill, K., Stevens, S., Perera, R., & Lancaster, T. (2013). Pharmacological interventions for smoking cessation: an overview and network meta-analysis. Cochrane Database Syst Rev, 5(5).
  2. Chen, Y.F., Madan, J., Welton, N., Yahaya, I., Aveyard, P., Bauld, L., Wang, D., Fry-Smith A, & Munafo, M.R. (2012). Effectiveness and cost-effectiveness of computer and other electronic aids for smoking cessation: a systematic review and network meta-analysis. Health Technology Assessment, 16:1-205
  3. Dayer, L., Heldenbrand, S., Anderson, P., Gubbins, P.O., & Martin, B.C. (2013). Smartphone medication adherence apps: potential benefits to patients and providers. Journal of the American Pharmacists Association: JAPhA,. 53:172-81.
  4. Foulds, J., Hughes, J., Hyland, A., Le Houezec, J., McNeill, A., Melvin, C., ... & Zeller, M. (2009). Barriers to use of FDA-approved smoking cessation medications: implications for policy action. Society for Research on Nicotine and Tobacco. March.
  5. Michie S, Atkins L, &West R, (2014). The Behaviour Change Wheel: A guide to designing interventions. Silverback Publishing
  6. Pulverman, R., & Yellowlees, P. M. (2014). Smart devices and a future of hybrid tobacco cessation programs. Telemedicine and e-Health, 20(3), 241-245.
  7. Stead, L. F., & Lancaster, T. (2012). Combined pharmacotherapy and behavioural interventions for smoking cessation. Cochrane Database Syst Rev, 10(10).

Evaluating the role of rare variants in disease causation

Supervisors: Prof. David Balding and Dr Dace Ruklisa

Department: UCL Genetics Institute

Project outline:
This computer-based project will focus on studying rare variants and their role in the aetiology of hereditary heart disease (Long QT syndrome, Brugada syndrome and others). One class of rare variants with high potential for causing disease are copy number variants (CNVs). However, detection of CNVs can be challenging, especially in targeted resequencing data. We aim at comparison of several methods for accomplishing this task and of assessing the impacts of the CNVs. Within this project data sets describing specific heart disease related gene families are available for analysis from a BHF-funded project that combines UCL with Royal Brompton Hospital and the European Bioinformatics Institute. It is of interest to look at the characteristics of these gene families, like the distribution of rare variants across the regions coding different protein domains. Then there are numerous opportunities to use this information for improvement of rare variant detection or the functional interpretation of rare variants.

Key references:

  1. Jordan, D.M. et al., Development and Validation of a Computational Method for Assessment of Missense Variants in Hypertrophic Cardiomyopathy, Am J Hum Genet 2011; 88:183-192
  2. Kapa, S. et al., Genetic Testing for Long-QT Syndrome, Circulation 2009; 120:1752-1760
  3. Plagnol, V. et al., A robust model for read count data in exome sequencing experiments and implications for copy number variant calling, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts526

Epigenetic Regulation of Arterial Smooth Muscle Phenotype in Chronic Kidney Disease Associated Vascular Disease

Supervisors: Ben Caplin and Jill Norman

Department: UCL Centre for Nephrology Royal Free (UCL CfN)

Project outline:
Chronic Kidney Disease (CKD) represents a critical risk factor for vascular death.1 Arterial structure is altered in CKD, smooth muscle cells (SMCs) are activated, leading to increased extracellular matrix, wall thickening and calcification2, eventually causing reduced end-organ perfusion and clinical events. Epigenetic changes3, such as DNA-methylation, are important in mediating sustained alterations in cell phenotype. DNA-methylation is altered in CKD patients4 but as yet there has been no investigation of the epigenetic changes in the cells of the arterial wall.

Taking advantage of the unique UCL CfN resource of arteries retrieved from patients undergoing renal transplant surgery, this project will characterise the impact of local DNA methylation in arterial SMCs in CKD. An initial study would explore the relationship between differential methylation (epigenome-wide3) and (immuno)histochemical abnormalities in CKD arteries. This would then be a basis for a substantive project focused on in vitro interrogation of the relevant pathways and exploration of the effect of methylation inhibitors using in vivo models of CKD.

Key references:

  1. Chronic Kidney Disease Prognosis C, Matsushita K, van der Velde M, Astor BC, Woodward M, Levey AS, de Jong PE, Coresh J, Gansevoort RT: Association of estimated glomerular filtration rate and albuminuria with all-cause and cardiovascular mortality in general population cohorts: a collaborative meta-analysis. Lancet 2010, 375:2073-81.
  2. Pai A, Leaf EM, El-Abbadi M, Giachelli CM: Elastin degradation and vascular smooth muscle cell phenotype change precede cell loss and arterial medial calcification in a uremic mouse model of chronic kidney disease. Am J Pathol 2011, 178:764-73.
  3. Bell CG, Beck S: The epigenomic interface between genome and environment in common complex diseases. Briefings in functional genomics 2010, 9:477-85.
  4. Wing MR, Devaney JM, Joffe MM, Xie D, Feldman HI, Dominic EA, Guzman NJ, Ramezani A, Susztak K, Herman JG, Cope L, Harmon B, Kwabi-Addo B, Gordish-Dressman H, Go AS, He J, Lash JP, Kusek JW, Raj DS, Chronic Renal Insufficiency Cohort S: DNA methylation profile associated with rapid decline in kidney function: findings from the CRIC study. Nephrol Dial Transplant 2014, 29:864-72.

Iron regulation of lipid metabolism in a model of atherosclerosis

Supervisors: Dr Ann Walker, Prof. Philippa Talmud and Prof. Steve Humphries

Department: Institute of Cardiovascular Science

Project outline:
Plasma low density lipoprotein cholesterol (LDL-C) concentration is a risk factor for atherosclerosis, in which fatty material progressively accumulates within macrophages, which become foam cells in the artery wall, predisposing to coronary heart disease. GWAS of plasma lipid traits in 100,000 individuals of European descent found that the main variant which is found in haemochromatosis (hereditary primary iron overload), rs1800562 (HFE p.(C282Y))(1) is associated with lower LDL levels.(2)  The mechanism whereby increased iron absorption may be associated with lower LDL-C levels is unknown.  However, the molecular regulation of iron metabolism pathways has been elucidated by the identification of many genes underlying single gene disorders of iron overload and deficiency.  Furthermore, iron overload is treatable.(3, 4)

This project will use a relevant cell culture model to test the hypothesis that iron concentrations modulate the expression of LDL-C associated genes,(2) as a potential mechanism underlying the association of rs1800562 with LDL-C.

Macrophage THP-1 cells, aortic smooth muscle or endothelial cells will be cultured in control medium and compared to cells grown in media with increased (ferric ammonium citrate, hemin) or decreased (desferrioxamine, deferiprone) iron concentrations for isolation of total RNA.  RNA will be reverse transcribed to cDNA for quantitative PCR of LDL-C associated genes using reliable TaqMan gene expression assays.  If time allows, the pathway whereby iron regulates LDL-C associated gene expression may be further characterised by investigation of either candidate bioinformatically-predicted iron responsive elements, or microRNAs or transcription factors involved in iron and lipid metabolism.    

Key references:

  1. The UK Haemochromatosis Consortium. A simple genetic test identifies 90% of UK patients with haemochromatsis. Gut 1997 Dec;41(6):841-844.
  2. Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, Koseki M, et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 2010 Aug 5;466(7307):707-713.
  3. Swinkels DW, Fleming RE. Novel observations in hereditary hemochromatosis: potential implications for clinical strategies. Haematologica 2011 Apr;96(4):485-488.
  4. Evstatiev R, Gasche C. Iron sensing and signalling. Gut 2012 Jun;61(6):933-952

An annotation approach to improving the interpretation of GWAS datasets

Supervisor: Dr Ruth Lovering

Department: Institute of Cardiovascular Science

Project outline:
Gene Ontology (GO) is now an established standard for the functional annotation of gene products (www.geneontology.org/).

This project will involve in depth literature review and annotation of specific genes, identified as associated with lipid traits through GWAS. Thus creating detailed annotations of a limited number of genes. The student will then use a comparative genomics approach to transfer appropriate annotations to orthologous gene family members. Finally, the student will use functional analysis tools to investigate the impact of the annotations on the analysis of several relevant datasets.

This project is especially suitable for students wanting to gain experience in the use of a wide range of bioinformatic resources and to gain an understanding of the applications of Gene Ontology annotations and protein interaction datasets.

Key references:

  1. Asselbergs, F. W., Lovering, R. C., & Drenos, F. (2013). Progress in genetic association studies of plasma lipids. Curr Opin Lipidol, 24 (2), 123-128.
  2. The representation of heart development in the gene ontology. Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC. Dev Biol; 2011 Jun 1;354(1):9-17
  3. The impact of focused Gene Ontology curation of specific mammalian systems. Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. PLoS One; 2011;6(12):e27541.

A bioinformatics approach to understanding heart development

Supervisors: Dr Ruth Lovering and Dr Anna Melidoni

Department: Institute of Cardiovascular Science

Project outline:
Gene Ontology (GO) is now an established standard for the functional annotation of gene products (www.geneontology.org/).

This project will involve in depth literature review and annotation of specific genes, with a known role in a signalling pathway relevant to embryonic heart development. Thus creating detailed annotations of a limited number of genes. The student will then use a comparative genomics approach to transfer appropriate annotations to orthologous gene family members. Finally, the student will use functional analysis tools to investigate the impact of the annotations on the analysis of a relevant dataset.

This project is especially suitable for students wanting to gain experience in the use of a wide range of bioinformatic resources and to gain an understanding of the applications of Gene Ontology annotations and protein interaction datasets.

Key references:

  1. The representation of heart development in the gene ontology. Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC. Dev Biol. 2011 Jun 1;354(1):9-17.
  2. The impact of focused Gene Ontology curation of specific mammalian systems. Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. PLoS One. 2011;6(12):e27541.
  3. Coordinating tissue interactions: Notch signaling in cardiac development and disease. de la Pompa JL, Epstein JA. Dev Cell. 2012 Feb 14;22(2):244-54.
  4. The role of Wnt signalling in cardiac development and tissue remodelling in the mature heart. Brade T, Männer J, Kühl M. Cardiovasc Res. 2006 Nov 1;72(2):198-209.

Characterising the mechanism of GWAS variants for coronary heart disease and related traits

Supervisor: Dr Andrew J P Smith

Department: Institute of Cardiovascular Science

Project outline:
Genome-wide association studies (GWAS) have identified many genetic loci associated with cardiovascular disease and related biomarkers. The majority of signals arise from non-coding regions of the genome, often not close to an obvious candidate gene. One of the primary goals of GWAS is to identify novel disease pathways to aid the design of new therapeutics. The student will select a GWAS locus to examine and aim to characterise a) the functional variants at the locus, and b) the potential mechanism by which these variants lead to CHD pathology (or a related trait, such as type 2 diabetes, blood pressure, lipids etc.). Methods used for the project may include: electrophoretic mobility shift assay, luciferase reporter assay, formaldehyde-assisted isolation of regulatory elements, next-gen sequencing, chromatin immunoprecipitation, bioinformatics, epidemiological analysis, gene expression arrays, chromosome conformation capture, genome-editing, tissue culture, induced pluripotent stem cells.

Key references:

  1. Deloukas, P., S. Kanoni, C. Willenborg, et al, 2013. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet 45: 25-U52.
  2. Smith AJP, Howard P, Shah S, Eriksson P, Stender S, et al. (2012) Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays. PLoS genetics 8: e1002908.
  3. Smith AJP, Palmen J, Putt W, Talmud PJ, Humphries SE, et al. (2010) Application of statistical and functional methodologies for the investigation of genetic determinants of coronary heart disease biomarkers: lipoprotein lipase genotype and plasma triglycerides as an exemplar. Human molecular genetics 19: 3936-3947.
  4. Smith AJP, Zheng D, Palmen J, Pang DX, Woo P, et al. (2012) Effects of genetic variation on chromatin structure and the transcriptional machinery: analysis of the IL6 gene locus. Genes and immunity 13: 583-586.
  5. Pang DX, Smith AJP, Humphries SE (2012) Functional analysis of TCF7L2 genetic variants associated with type 2 diabetes. Nutrition, metabolism, and cardiovascular diseases : NMCD.

Study of CHD and T2D loci on chromosome 9p21.3, and divergent effects of proximal enhancers in disease

Supervisor: Dr Andrew J P Smith

Department: Institute of Cardiovascular Sciences

Project outline:
Chromosome 9p21.3 is a region highly enriched in transcriptional enhancers, and contains susceptibility loci for a number of different diseases including coronary heart disease, stroke, type 2 diabetes and a number of cancers. We have generated preliminary data to localise the causal genetic variants at the CHD and T2D loci. The project will aim to confirm the functional variants at this locus, and to identify why these variants, which occur in close proximity on the genome, are having such diverse effects with regards to disease. The ultimate goals are to identify novel pathways leading to disease, which can be targeted by novel or existing drugs, and to understand the behaviour of enhancers in greater detail. Techniques may involve: stem cell genome-editing/differentiation, gene expression analysis, electrophoretic mobility shift assay, luciferase reporter assay, chromosome conformation capture, bioinformatics (ENCODE databases).

Key references:

  1. Deloukas, P., S. Kanoni, C. Willenborg, M. et al, 2013. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet 45: 25-U52.
  2. Smith AJP, Howard P, Shah S, Eriksson P, Stender S, et al. (2012) Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays. PLoS genetics 8: e1002908.
  3. Smith AJP, Palmen J, Putt W, Talmud PJ, Humphries SE, et al. (2010) Application of statistical and functional methodologies for the investigation of genetic determinants of coronary heart disease biomarkers: lipoprotein lipase genotype and plasma triglycerides as an exemplar. Human molecular genetics 19: 3936-3947.
  4. Smith AJP, Zheng D, Palmen J, Pang DX, Woo P, et al. (2012) Effects of genetic variation on chromatin structure and the transcriptional machinery: analysis of the IL6 gene locus. Genes and immunity 13: 583-586.
  5. Pang DX, Smith AJP, Humphries SE (2012) Functional analysis of TCF7L2 genetic variants associated with type 2 diabetes. Nutrition, metabolism, and cardiovascular diseases : NMCD.

Cell & developmental biology

Altered gene targeting by the myocardial regulatory factors GATA4 and TBX5 during heart development

Supervisor: Richard Jenner1 and Pete Scambler2

Departments: 

  1. UCL Cancer Institute
  2. Developmental Biology of Birth Defects, UCL Institute of Child Health

Project outline:

The transcription factors TBX5 and GATA4 control cardiac development through regulating the transcription of genes such as cardiac myosin-binding protein C (Mybpc3) and ryanodine receptor 2 (Ryr2) (He et al., 2011). Together with MEF2C, TBX5 and GATA4 can reprogram cardiac fibroblasts into cardiomyocyte-like cells (Ieda et al., 2010). Mutations in TBX5 are associated Holt-Oram syndrome, whereas mutations in GATA4 cause septal defects (reviewed in McCulley & Black, 2012). The two transcription factors also directly interact and this interaction is disrupted by septal-defect-associated GATA4 mutations (Garg et al., 2003). The role of the interaction between TBX5 and GATA4 is unclear. We have previously discovered that the related transcription factors T-bet (TBX21) and GATA3 also interact and that T-bet uses this interaction to redistribute GATA3 to a new set of target genes in T-cells (Kanhere et al., 2012). The student will use ChIP-seq to discover if a similar mechanism operates for TBX5 and GATA4 in heart and, using mutant forms of these proteins, reveal the role for TBX5-GATA4 interaction in cardiomyocyte development.

Key references:

  1. Garg V, Kathiriya IS, Barnes R, Schluterman MK, King IN, Butler CA, Rothrock CR, Eapen RS, Hirayama-Yamada K, Joo K, Matsuoka R, Cohen JC, Srivastava D. (2003). GATA4 mutations cause human congenital heart defects and reveal an interaction with TBX5. Nature 424: 443-7.
  2. He A, Kong SW, Ma Q, Pu WT. (2011). Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A. 108: 5632-7. 
  3. Ieda M, Fu JD, Delgado-Olguin P, Vedantham V, Hayashi Y, Bruneau BG, Srivastava D. (2010). Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142: 375-386.
  4. Kanhere ., Hertweck A, Bhatia U, Gokmen R, Perucha, E, Jackson I, Lord GM, and Jenner RG (2012). T-bet and GATA3 orchestrate Th1 and Th2 cell differentiation through lineage-specific targeting of distal regulatory elements. Nat. Commun. 3:1268.
  5. McCulley DJ, Black BL. (2012). Transcription factor pathways and congenital heart disease. Curr Top Dev Biol. 100: 253-77.

Cholesterol traffic into mitochondria

Supervisor: Dr Tim Levine

Department: UCL Institute of Ophthalmology

Project outline:

Very many major questions about the shared, fundamental cellular functions in all eukaryotes have not been answered. One unsolved puzzle is how cholesterol traffics inside cells. Mitochondrial cholesterol is important in many cell types including cardiac myocytes [1], but traffic of cholesterol to mitochondria is poorly understood [2]. We have applied structural bioinformatics tools to predicting key proteins in membrane and lipid traffic [3,4], and have now used these to discover a family of previously unstudied cholesterol transfer proteins that are on mitochondria. This project will use a wide range molecular cell biology and genetic techniques to study mitochondrial cholesterol and these new proteins, in particular using the simplest eukaryotic model system, budding yeast, to make rapid progress.

Key references:

  1. Monteiro JP et al. (2013) Prog Lipid Res, 52:513.
  2. Mesmin B et al. (2013) Cell Mol Life Sci, 70:3405.
  3. Hayes MJ et al. (2011) Traffic, 12:260.
  4. Levine TP et al. (2013) Bioinformatics, 29:499.

Identification of different macrophage subsets in symptomatic, asymptomatic and haemorrhagic human atherosclerotic carotid plaques

Supervisor(s): Dr Ines Pineda-Torra, Prof. Kaila Srai and Dr Toby Richards

Department: Division of Medicine and Div of Biosciences

Project outline:

Atherosclerosis is the main cause of cardiovascular disease and premature death in the western world. This condition is characterised by the thickening of major arteries as the result of a build­up of lipids, cells and extracellular matrix. Macrophages are key cells in the initiation and development of the lesion as they orchestrate a wide variety of inflammatory and anti-inflammatory processes throughout atherogenesis (1). Cultured and tissue macrophages exhibit pronounced heterogeneity and plasticity in response to various environmental cues (M1, M2, Mhem) (2, 3). Despite the fairly extensive characterisation of macrophage subsets in vitro, evidence of their patho-physiological relevance in a human atherosclerotic setting remains scarce (4, 5). Our ultimate goal is to identify differences in the expression, localization and function of different macrophage subtypes in human carotid lesions and key transcription factors involved in phenotype switching in order to understand how these cells can influence the development of the plaque. This relies on the differential expression of selected surface markers that are used to identify these macrophage subsets. Although a number of markers have been used in similar studies, there is a considerable discrepancy on which are the most appropriate (4, 5). We aim to confirm that a given protein is specifically expressed upon activation by a particular stimuli. In order to aid in the selection of the best markers for our studies, human macrophages exposed to different stimuli (growth factors M-CSF and GM-CSF with or without heme) will be cultured and expression of markers and transcription factors will be assayed by and real time PCR, immunocytochemistry and flow cytometry. When not available, specificity of commercial antibodies will be tested by immunocytochemistry/flow cytometry in cells with a partial or total knock down of the protein being targeted (achieved by RNA interference via nucleofection). Ultimately, selected specific antibodies will be used to detect markers of specific activation states in human carotid plaques. This will provide a better understanding of the contribution of different macrophage subsets to the inflammatory and metabolic (lipid and iron handling) environment that is predominant in different types of atherosclerotic plaques.

Key references:

  1. K. J. Moore, F. J. Sheedy, and E. A. Fisher. 2013. Macrophages in atherosclerosis: a dynamic balance. Nature reviews. Immunology 13:709-721.
  2. J. J. Boyle. 2012. Heme and haemoglobin direct macrophage Mhem phenotype and counter foam cell formation in areas of intraplaque haemorrhage. Current opinion in lipidology 23:453-461.
  3. F. O. Martinez, and S. Gordon. 2014. The M1 and M2 paradigm of macrophage activation: time for reassessment. F1000prime reports 6:13.
  4. I. Brocheriou, S. Maouche, H. Durand, V. Braunersreuther, G. Le Naour, A. Gratchev, F. Koskas, F. Mach, J. Kzhyshkowska, and E. Ninio. 2011. Antagonistic regulation of macrophage phenotype by M-CSF and GM-CSF: implication in atherosclerosis. Atherosclerosis 214:316-324.
  5. M. Jaguin, N. Houlbert, O. Fardel, and V. Lecureur. 2013. Polarization profiles of human M-CSF-generated macrophages and comparison of M1-markers in classically activated macrophages from GM-CSF and M-CSF origin. Cellular immunology 281:51-61.

Control of brain blood flow by neurotransmitters

Supervisor(s): Prof. David Attwell

Department: Physiology (NPP)

Project outline:

Neural activity leads to increased blood flow in the brain, as a result of neuronally released glutamate generating messengers such as NO, adenosine, prostaglandins and other arachidonic acid derivatives which relax arteriole smooth muscle. We have shown that, in addition to this control of blood flow at the arteriole level, contractile cells called pericytes can also regulate brain blood flow. The project will involve studying how neurotransmitters regulate the contractile tone of these cells in brain slices.

Key references:

  1. Peppiatt, C.M., Howarth, C., Mobbs, P. & Attwell, D. (2006) Bidirectional control of CNS capillary diameter by pericytes. Nature 443, 700-704.
  2. Peppiatt, C. & Attwell, D. (2004) Food for thought. Nature 431, 137-13

The effect of substrate topography on secretion of angiogenic growth factors

Supervisor: Dr Richard Day

Department: Applied Biomedical Engineering Group, UCL Division of Medicine

Project outline:

Mesenchymal stem cell (MSC) behaviour can be manipulated by substrates with modified surface topographical features such as groves, ridges and pits [1-4]. Likewise substrate stiffness and dimension have been shown to play a role in regulating the proliferation, morphology and differentiation of MSCs and as consequence are likely to affect the profile of secreted factors [5]. The project will involve fabricating a selection of polymer based substrates and characterizing their physical properties. MSCs will be cultured on the surface of the substrates and the secretion of angiogenic growth factors measured. Extracted data will be used to generate invariant metrics of the physical feature of each substrate and correlated with the cell secretome.

Key references:

  1. Watari et al. Biomaterials 2012;33:128-36.
  2. Kolind et al. Biomaterials 2010;31:9182-91.
  3. Teo et al. Biomaterials 2011;32:9866-75.
  4. Bettinger et al. Angew Chem Int Ed Engl. 2009;48:5406-15.
  5. Li et al., 2013 Biomaterials 2013;34:7616-7625.

How is the levels of phosphatidylinositol-4,5-bisphosphate maintained after phospholipase C activation in cardiomyocytes?

Supervisor: Prof Shamshad Cockcroft

Department: Neuroscience, Physiology, and Pharmacology (NPP)

Project outline:

Gqa-protein-coupled receptor (GPCR) agonists such as angiotensin II, endothelin-1 and phenylephrine activate phospholipase C-mediated hydrolysis of phosphatidylinositol 4,5-bisphosphate which produces inositol 1,4,5-trisphosphate and diacylglycerol (DAG). DAG functions as a potent activator of protein kinase C, and is known to play an important role in the development and progression of cardiac hypertrophy. One major route for terminating DAG signalling is the phosphorylation by DAG kinase to phosphatidic acid (PA) at the plasma membrane (see Fig). PA has to be transported to the endoplasmic reticulum where it can be converted to phosphatidylinositol (PI). Intense stimulation by GPCR agonists also dramatically increases the expression of CDS1, the rate limiting enzyme for PI resynthesis. How PIP2 hydrolysis by phospholipase C is co-ordinated with resynthesis of PI at the endoplasmic reticulum remains a mystery. The working hypothesis is that PITPNC1, a PI/PA binding protein may couple the events at the plasma membrane with the endoplasmic reticulum by either acting as a LIPID TRANSPORTER or a LIPID SENSOR (see Figure) [1-5].

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Key references:

  1. Cockcroft, S. and Garner, K. (2011) Function of the phosphatidylinositol transfer protein gene family: is phosphatidylinositol transfer the mechanism of action? Crit.Rev.Biochem.Mol.Biol. 46, 89-117
  2. Cockcroft, S. and Garner, K. (2012) 14-3-3 protein and ATRAP bind to the soluble class IIB phosphatidylinositol transfer protein RdgBbeta at distinct sites. Biochem.Soc.Trans. 40, 451-456
  3. Cockcroft, S. and Garner, K. (2013) Potential role for phosphatidylinositol transfer protein (PITP) family in lipid transfer during phospholipase C signalling. Adv.Biol.Regul. 53, 280-291
  4. Garner, K., Li, M., Ugwuanya, N., and Cockcroft, S. (2011) The phosphatidylinositol transfer protein, RdgB binds 14-3-3 via its unstructured C-terminus, whereas its lipid binding domain interacts with the integral membrane protein, ATRAP (Angiotensin II Type I receptor-associated protein). Biochem.J. 439, 97-111
  5. Garner, K., Hunt, A. N., Koster, G., Somerharju, P., Grover, E., Li, M., Raghu, P., Holic, R., and Cockcroft, S. (2012) Phosphatidylinositol transfer protein, Cytoplasmic 1 (PITPNC1) binds and transfers phosphatidic acid. J Biol.Chem. 287, 32263-32276

Role of mitochondrial calcium uptake pathways in cardiomyocyte life and death

Supervisor: Prof Michael Duchen

Department: Cell and Developmental Biology

Project outline:

Mitochondria take up calcium from the cytosol through a pathway called the mitochondrial calcium uniporter.  The increase in intramitochondrial calcium helps to sustain oxidative phosphorylation through the calcium dependent activation of enzyme pathways but can also drive cell death if accompanying oxidative stress. The proteins that mediate and regulate mitochondrial calcium handling have only very recently been identified. We will there knockout the proteins – MCU – the channel former – MICU1 and MICU2 which regulate the calcium sensitivity of uptake to determine the specific role of mitochondrial calcium uptake in cardiomyocyte life and death.

Key references:

  1. De Stefani D, Raffaello A, Teardo E, Szabò I, Rizzuto R. A forty-kilodalton protein of the inner membrane is the mitochondrial calcium uniporter. Nature. 2011 Jun 19;476(7360):336-40. doi: 10.1038/nature10230.
  2. Pan X, Liu J, Nguyen T, Liu C, Sun J, Teng Y, Fergusson MM, Rovira II, Allen M, Springer DA, Aponte AM, Gucek M, Balaban RS, Murphy E, Finkel T. The physiological role of mitochondrial calcium revealed by mice lacking the mitochondrial calcium uniporter. Nat Cell Biol. 2013 Dec;15(12):1464-72. doi: 10.1038/ncb2868. Epub 2013 Nov 10.
  3. Logan CV, Szabadkai G, Sharpe JA, Parry DA, Torelli S, Childs AM, Kriek M, Phadke R, Johnson CA, Roberts NY, Bonthron DT, Pysden KA, Whyte T, Munteanu I, Foley AR, Wheway G, Szymanska K, Natarajan S, Abdelhamed ZA, Morgan JE, Roper H, Santen GW, Niks EH, van der Pol WL, Lindhout D, Raffaello A, De Stefani D, den Dunnen JT, Sun Y, Ginjaar I, Sewry CA, Hurles M, Rizzuto R; UK10K Consortium, Duchen MR, Muntoni F, Sheridan E. Loss-of-function mutations in MICU1 cause a brain and muscle disorder linked to primary alterations in mitochondrial calcium signaling. Nat Genet. 2014 Feb;46(2):188-93. doi: 10.1038/ng.2851. Epub 2013 Dec 15.
  4. Patron M, Checchetto V, Raffaello A, Teardo E, Vecellio Reane D, Mantoan M, Granatiero V, Szabò I, De Stefani D, Rizzuto R. MICU1 and MICU2 finely tune the mitochondrial Ca2+ uniporter by exerting opposite effects on MCU activity. Mol Cell. 2014 Mar 6;53(5):726-37. doi: 10.1016/j.molcel.2014.01.013.

CXCL12: Generation and Regeneration of Coronary Arteries

Supervisor(s): Prof. Peter Scambler and Dr Sarah Ivins

Department: UCL-ICH (Developmental Biology of Birth Defects)

Project outline:

The chemokine ligand CXCL12 (also known as SDF1) and its cognate receptor CXCR4 play essential roles in multiple processes during development.  We have discovered that this signaling axis acts downstream of VEGF in the formation of coronary arteries during development, and lack of CXCL12 is embryonic lethal.  There are also defects of large vessel formation, semilunar valve formation and closure of the interventricular septum.  Several projects emerge from this work and would be available studying

  1. How CXCL12 controls coronary artery development and whether this can potentially be used to stabilize neovasculogenesis post infarct
  2. The developmental role of the axis in great vessel formation, valve formation and septum formation
  3. How CXCl12 influences cell migration of endothelial and neural crest cells
  4. Whether CXCL12 has a role in defective microvessels found in the brains of Tbx1 mutant mice and whether this could affect interneurone migration

Training would be dependent upon the project but could involve confocal microscopy (including live imaging), optical projection tomography, maintenance of mouse colonies, conditional mutagenesis, dissection of embryos and hearts, mouse surgery, tissue sectioning, staining and gene expression studies, FACS, linage tracing.

Key references:

Our recently submitted paper will be made available to anyone interested

  1. Kokovay, E., Goderie, S., Wang, Y., Lotz, S., Lin, G., Sun, Y., Roysam, B., Shen, Q., and Temple, S. Adult SVZ lineage cells home to and leave the vascular niche via differential responses to SDF1/CXCR4 signaling. Cell Stem Cell. 7(2), 163-173. 6-8-2010.
  2. Wen, J., Zhang, J. Q., Huang, W., and Wang, Y. SDF-1alpha and CXCR4 as therapeutic targets in cardiovascular disease. Am.J.Cardiovasc.Dis. 2(1), 20-28. 2012.
  3. Zhu, B., Xu, D., Deng, X., Chen, Q., Huang, Y., Peng, H., Li, Y., Jia, B., Thoreson, W. B., Ding, W., Ding, J., Zhao, L., Wang, Y., Wavrin, K. L., Duan, S., and Zheng, J. CXCL12 enhances human neural progenitor cell survival through a CXCR7- and CXCR4-mediated endocytotic signaling pathway. Stem Cells 30(11), 2571-2583. 2012.
  4. Escot, S., Blavet, C., Hartle, S., Duband, J. L., and Fournier-Thibault, C. Misregulation of SDF1-CXCR4 signaling impairs early cardiac neural crest cell migration leading to conotruncal defects. Circulation Research 113(5), 505-516. 16-8-2013.

The chromatin remodeler CHD7 during heart development

Supervisor: Prof Peter Scambler

Department: UCL-ICH (Developmental Biology of Birth Defects)

Project outline:

The gene encoding the chromatin remodelling protein CHD7 is haploinsufficient in the CHARGE association, a multisystem birth defect including cardiovascular malformation.  We have determined that CHD7 is required in several distinct lineages required for cardiac development.  A rotation project will examine aspects of CHD7 regulation in the neural crest cell linage with a view to publication.  This may involve work with conditionally mutnat embryos (in sut hybridization and other expression analysis) or cultured cell lines (possibly chromatin immunoprecipitation, siRNA knockdown).  PhD projects could be elaborated on exploration of the TBX1 (DiGeorge syndrome gene): CHD7 interaction and/or the TCOF1 gene (Treacher Collins syndrome) :CHD7 interaction.  Each of these syndromes is a haploinsufficiency lending weight to the idea that such genes are at hubs of important developmental networks.  The network components and developmental roles would be explored.

Key references:

  1. Van Nostrand, J. L., Brady, C. A., Jung, H., Fuentes, D. R., Kozak, M. M., Johnson, T. M., Lin, C. Y., Lin, C. J., Swiderski, D. L., Vogel, H., Bernstein, J. A., Attie-Bitach, T., Chang, C. P., Wysocka, J., Martin, D. M., and Attardi, L. D. Inappropriate p53 activation during development induces features of CHARGE syndrome. (2014) Nature.
  2. Liu, Y., Harmelink, C., Peng, Y., Chen, Y., Wang, Q., and Jiao, K. CHD7 interacts with BMP R-SMADs to epigenetically regulate cardiogenesis in mice. Human Molecular Genetics (2014) 23(8), 2145-2156.
  3. Yu, T., Meiners, L. C., Danielsen, K., Wong, M. T., Bowler, T., Reinberg, D., Scambler, P. J., van Ravenswaaij-Arts, C. M., and Basson, M. A. Deregulated FGF and homeotic gene expression underlies cerebellar vermis hypoplasia in CHARGE syndrome. (2013) Elife. 2, e01305.
  4. Bajpai,R., Chen,D.A., Rada-Iglesias,A., Zhang,J., Xiong,Y., Helms,J., Chang,C.P., Zhao,Y., Swigut,T., and Wysocka,J. (2010). CHD7 cooperates with PBAF to control multipotent neural crest formation. Nature. 463, 958-962.
  5. Randall, V., McCue, K., Roberts, C., Kyriakopoulou, V., Beddow, S., Barrett, A. N., Vitelli, F., Prescott, K., Shaw-Smith, C., Devriendt, K., Bosman, E., Steffes, G., Steel, K. P., Simrick, S., Basson, M. A., Illingworth, E., and Scambler, P. J. Great vessel development requires biallelic expression of Chd7 and Tbx1 in pharyngeal ectoderm in mice. Journal of Clinical Investigation 119(11), 3301-3310. 2009.

NB: V. Randall a BHF PhD student

A submitted paper from final year BHF student Sophie Payne will be made available to interested students

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Addressing the impact of a genetic modifier in the predisposition for congenital heart defects in various mouse models of Down syndrome

Supervisor(s): Dr Victor Tybulewicz and Prof. Elizabeth Fisher

Department: Immune Cell Biology, MRC National Institute for Medical Research

Project outline:

Congenital heart defects, in particular atrio-ventricular septal defects (AVSD), affect around half of individuals with Down Syndrome (DS) (1), suggesting that trisomy of human chromosome 21 (Hsa21) alone might not be sufficient to cause congenital heart defects (CHD) and other genetic modifiers might be required. Human association studies have identified inactivating mutations in CRELD1 that may increase the likelihood for the presence of AVSD in the DS population (2, 3). An interesting study from Reeves’ lab showed that crossing the Ts65Dn mouse model for DS with Creld1+/- mice, the frequency of CHD was significant increased (4). However, one of the limitations of the Ts65Dn model is that it does not present with AVSD. We previously reported that the Tc1 mouse model of DS recapitulates many of the cardiac phenotypes observed in humans with DS, including AVSD (5, 6). By using the best imaging technique available to detect CHD in embryos -High Resolution Episcopic Microscopy (HREM)- we propose to study the impact of the modifier Creld1 in the incidence and typology of CHD in the Tc1 mouse and in a number of new models of DS that we have recently generated in the lab.

Key references:

  1. Vis JC, et al. (2009) Down syndrome: a cardiovascular perspective. J Intellect Disabil Res 53(5):419-425.
  2. Robinson SW, et al. (2003) Missense mutations in CRELD1 are associated with cardiac atrioventricular septal defects. Am J Hum Genet 72(4):1047-1052.
  3. Maslen CL (2004) Molecular genetics of atrioventricular septal defects. Curr Opin Cardiol 19(3):205-210.
  4. Li H, et al. (2012) Genetic modifiers predisposing to congenital heart disease in the sensitized down syndrome population. Circ Cardiovasc Genet 5(3):301-308.
  5. Dunlevy L, et al. (2010) Down's syndrome-like cardiac developmental defects in embryos of the transchromosomic Tc1 mouse. Cardiovasc Res 88(2):287-295.
  6. O'Doherty A, et al. (2005) An aneuploid mouse strain carrying human chromosome 21 with Down syndrome phenotypes. Science 309(5743):2033-2037.

Planar cell polarity and angiogenesis

Supervisor(s): Dr. David A Long (MRC New Investigator) and Dr Eugenia (Jenny) Papakrivopoulou (Wellcome Trust Clinical Fellow)

Department: Nephro-Urology Unit, UCL Institute of Child Health

Project outline:

Planar cell polarity (PCP) is the uniform orientation and alignment of a group of cells within a tissue. Originally described in insects, it is now known that PCP is required for many processes in vertebrates including directional cell movement, polarised cell division, ciliary orientation, neural tube closure, heart development and kidney development.1-2 Recent studies have begun to indicate that PCP may also be important in endothelial function and angiogenesis;3-4 but the molecular mechanisms underlying these effects are unknown. In this studentship, a combination of in-vivo and in-vitro techniques will be used to examine blood vessel formation in models that lack PCP proteins. The vasculature will be assessed using detailed three-dimensional confocal imaging5 as well as endothelial proliferation and migration assays using techniques established in our laboratory. These studies will begin to determine the molecular pathways which control the involvement of PCP in angiogenesis.

Key references:

  1. Wallingford JB. Planar cell polarity and the developmental control of cell behaviour in vertebrate embryos. Annu Rev Cell Dev Biol 2012 28: 627-653.
  2. Yates LL, Papakrivopoulou J, Long DA et al. The planar cell polarity gene Vangl2 is required for mammalian kidney-branching morphogenesis and glomerular maturation. Hum Mol Genet 2010 19: 4663-4676.
  3. Descamps B, Sewduth R, Ferreira Tojais N et al. Frizzled 4 regulates arterial network organisation through noncanonical Wnt/planar cell polarity signaling. Circ Res 2012 110: 47-58.
  4. Ju R, Cirone P, Lin S et al. Activation of the planar cell polarity formin DAAM1 leads to inhibition of endothelial cell proliferation, migration and angiogenesis. Proc Natl Acad Sci U S A 2010 107: 6906-6911.
  5. Baluk P, McDonald DM. Markers for microscopic imaging of lymphangiogenesis and angiogenesis. Ann N Y Acad Sci 2008 1131: 1-12.
Vascular biology

Mechanisms for the high risk of cardiometabolic disease in South Asians: do associations between genetic risk variants for diabetes, circulating amino acids and features of the metabolic syndrome differ by ethnicity?

Supervisor(s): Profs Nish Chaturvedi and Alun Hughes

Department: Cardiometablic Phenotyping Group, Institute of Cardiovascular Science

Project outline:

South Asians have one of the greatest risks of diabetes and coronary heart disease (CHD) in the world.  Moreover, diabetes may increase CHD risk to a greater extent in South Asians than in Europeans. Metabolomic profiling shows circulating amino acids are associated with insulin resistance and hyperglycaemia, and predict diabetes onset, independently of other risk factors.  These associations are in part governed by known genetic risk variants for diabetes.  These analyses have not been performed in South Asians, and we hypothesise that associations may differ, and may contribute to our understanding of their greater risks of cardiometabolic disease.  You will analyse data from the SABRE cohort to test this hypothesis.  This includes GWAS data using a novel chip, and data on >200 metabolites using NMR spectroscopy.  This project will advance your understanding of the associations between insulin resistance, diabetes and CHD, will introduce you to statistical analysis techniques of complex data and enhance your epidemiological and genetic knowledge.   

Key references:

  1. Tillin T, Hughes AD, Godsland IF, Whincup P, Forouhi NG, Welsh P et al. Insulin resistance and truncal obesity as important determinants of the greater incidence of diabetes in Indian Asians and African Caribbeans compared with Europeans: the Southall And Brent REvisited (SABRE) cohort. Diabetes Care 2013; 36(2):383-393.
  2. Tillin T, Hughes AD, Mayet J, Whincup P, Sattar N, Forouhi NG et al. The Relationship Between Metabolic Risk Factors and Incident Cardiovascular Disease in Europeans, South Asians, and African Caribbeans: SABRE (Southall and Brent Revisited)-A Prospective Population-Based Study. J Am Coll Cardiol 2013; 61(17):1777-1786.
  3. Wang TJ, Larson MG, Vasan RS, Cheng S, Rhee EP, McCabe E et al. Metabolite profiles and the risk of developing diabetes. Nat Med 2011; 17(4):448-453.
  4. Stancakova A, Civelek M, Saleem NK, Soininen P, Kangas AJ, Cederberg H et al. Hyperglycemia and a common variant of GCKR are associated with the levels of eight amino acids in 9,369 Finnish men. Diabetes 2012; 61:1895-1902.

Endothelial injury and repair in moyamoya disease related childhood stroke

Supervisor(s): Dr Despina Eleftheriou, Dr Paul Brogan, Prof Nigel Klein and Dr Vijeya Ganesan

Department: Infectious diseases and microbiology unit, Neurosciences Unit

Project outline:

Moyamoya disease (MMD) is associated with the highest risk of recurrence in childhood stroke (1-3). However, patients’ clinical courses are highly variable and this is not currently predictable on the basis of any clinical or radiological parameters (1-3). This project will test the hypothesis that patients with MMD and recurrent strokes have persistent cerebrovascular injury and impaired endothelial repair responses resulting in progressive arteriopathy and further cerebral ischaemia. We will specifically examine: (i) whether biomarkers of endothelial injury (circulating endothelial cells/ microparticles) and related hypercoagulability (thrombin generation assay) differ between children with ongoing symptomatology versus those with a single stroke event (4); (ii) establish whether progressive MMD is mediated in part by abnormalities in repair injury due to altered endothelial progenitor cell responses.

Key references:

  1. Scott RM, Smith ER. Moyamoya disease and moyamoya syndrome. New England Journal of Medicine 2009;360:1226-1237. 
  2. Schoenberg BS, Mellinger JF, Schoenberg DG. Moyamoya disease in children. Southern medical journal 1978;71:237.
  3. Ganesan V, Prengler M, Wade A, Kirkham FJ. Clinical and radiological recurrence after childhood arterial ischemic stroke. Circulation 2006;114:2170-2177.
  4. Eleftheriou D, Ganesan V, et al. Endothelial injury in childhood stroke with cerebral arteriopathy: a cross sectional study. Neurology 2012.Epub.

Sympathetic activation in pulmonary arterial hypertension

Supervisor(s): Dr Naphtali Marina-Gonzalez and Prof Lucie Clapp

Department: Centre for Clinical Pharmacology, Division of Medicine

Project outline:

Pulmonary arterial hypertension (PAH) is a vascular remodeling disease characterised by high pulmonary vascular resistance and right ventricular hypertrophy, leading to heart failure and death. While sympathetic nervous system activation is an independent predictor of clinical deterioration in PAH, the role of sympathetic innervation in the development and progression of this disease is unknown. In this project we will perform an immunohistochemical study to determine the distribution, morphology and abundance of sympathetic postganglionic fibres in the pulmonary artery of naive animals and mice with pulmonary arterial hypertension. Comparisons will be made in human tissue obtained from control and patients with PAH. 

Key references:

  1. Wensel R, Jilek C, Dörr M, Francis DP, Stadler H, Lange T, Blumberg F, Opitz C, Pfeifer M, Ewert R. Impaired cardiac autonomic control relates to disease severity in pulmonary hypertension. Eur Respir J. 2009;34(4):895-901.
  2. Marina N, Tang F, Figueiredo M, Mastitskaya S, Kasimov V, Mohamed-Ali V, Roloff E, Teschemacher AG, Gourine AV, Kasparov S. Purinergic signalling in the rostral ventro-lateral medulla controls sympathetic drive and contributes to the progression of heart failure following myocardial infarction in rats. Basic Res Cardiol. 2013;108(1):317. doi: 10.1007/s00395-012-0317-x.
  3. Mastitskaya S, Marina N, Gourine A, Gilbey MP, Spyer KM, Teschemacher AG, Kasparov S, Trapp S, Ackland GL, Gourine AV. Cardioprotection evoked by remote ischaemic preconditioning is critically dependent on the activity of vagal pre-ganglionic neurones. Cardiovasc Res. 2012 1;95(4):487-94.
  4. Marina N, Abdala AP, Korsak A, Simms AE, Allen AM, Paton JF, Gourine AV.Control of sympathetic vasomotor tone by catecholaminergic C1 neurones of the rostral ventrolateral medulla oblongata. Cardiovasc Res. 2011;91(4):703-10.
  5. Falcetti,E, Hall SM, Phillips PG, Patel JA, Morrell NW, Haworth SG, Clapp LH. Smooth muscle proliferation and role of the prostacyclin (IP) receptor in idiopathic pulmonary arterial hypertension. Am J Respir Crit Care Med, 182:1161-70, 2010.

Analysing transcription factors that affect vascular function using zebrafish and mouse models.

Supervisor: Dr V. Budhram-Mahadeo

Department: Medical Molecular Biology Unit, UCL Institute of Child Health

Project outline:

Background: We have recently identified transcription factors (TFs) that may have crucial roles in regulating vascular function since mutant mice have marked vascular defects such as abnormal blood pressure and reduced arterial resistance. Furthermore, targeted reduction of these TFs can give rise to branching defects in the vasculature of zebrafish. Since vascularisation is vital for normal development/function and responses to cardiac stress/injury, it is imperative that we understand how these transcription factors control vascular function.

Experimental plan for 3 month project:

(i) Analyse blood vessels such as the aorta from existing knock-out (KO) mouse mutants to identify the basis for changes in vascular function compared with wild type controls.

(ii) Analyse potential roles in vascular development and function using loss- or gain-of-function in zebrafish

No key references



Exploring downstream targets of angiopoietin signalling

Supervisor(s): Dr David A Long (MRC New Investigator) and Dr Elisa Vasilopoulou (MRC Research Associate)

Department: Nephro-Urology Unit, UCL Institute of Child Health

Project outline:

The formation and maintenance of blood vessels is controlled by cells near the endothelium releasing vascular growth factors1. One such family of growth factors are the Angiopoietins (Ang); Ang1 activates Tie2 leading to endothelial survival and intracellular adhesion, while Ang2 acts as an antagonist2. To date, little is known about the downstream pathways by which Ang exerts its biological effects. To identify potential candidate genes, we performed microarray analysis on transgenic mice which overexpressed Ang2 in a site and temporal specific fashion3. In this rotation project, the student will follow-up some of these genes by determine localisation in Ang2 overexpressing mice and utilising cultured cells incubated with Ang2. These studies will begin to determine novel downstream targets of Ang signalling which will be examined in more detail in future functional experiments.

Key references:

  1. Carmeliet P, Jain RK. Molecular mechanisms and clinical applications of angiogenesis. Nature 2011 473: 298-307.
  2. Woolf AS, Gnudi L, Long DA. Angiopoietins in development and disease. J Am Soc Nephrol 2009 20, 239-244.
  3. Davis B, Dei Cas A, Long DA, White KE, Hayward A, Ku CH, Woolf AS, Bilous R, Viberti G, Gnudi L. Podoctye-specific induced overexpression of Angiopoietin-2 causes proteinuria and apoptosis of glomerular endothelia. J Am Soc Nephrol 2007 18, 2320-2329.

Microvascular permeability

Supervisor(s): Dr Patric Turowski and Dr Mosharraf Sarker

Department: Cell Biology, UCL Institute of Ophthalmology

Project outline:

Excessive microvascular permeability and subsequent interstitial fluid accumulation are at the root of or exacerbate many different pathologies. The aim of this project is to study the permeability response in two completely different vascular beds, namely the retinae and the mesentery. Tissues from rats and mice will be dissected out and prepared for measurements of vascular permeability. The permeability response to key molecules such as vascular endothelial growth factor (VEGF), histamine and lipids will be measured. Concomitant molecular changes in endothelial and mural cells will be studied by whole mount antibody staining. By combining pharmacological, molecular and cytological approaches these experiments will provide mechanistic insight into a key pathophysiological response of the microvasculature.

Key references:

  1. Hudson et al. (2014). Differential apicobasal VEGF signaling at vascular blood-neural barriers. Dev Cell, 8 Sept 2014
  2. Warboys et al. (2009). Role of NADPH oxidase in retinal microvascular permeability increase by RAGE activation. Invest Ophthalmol Vis Sci50(3):1319-28.

Molecular control of trachea vascularisation

Supervisor: Prof Christiana Ruhrberg

Department: Department of Cell Biology, UCL Institute of Ophthalmology

Project outline:

Understanding the mechanisms of tissue vascularisation is a prerequisite for the rational design of pro-angiogenic therapies in ischemic disease. For example, the vascularisation of tracheal scaffolds is currently a rate-limiting step in regenerative medicine programmes at UCL. Moreover, the trachea provides an ideal model to study physiological angiogenesis in a postnatal setting. Thus, the trachea assembles a vascular network to support tissue growth during embryogenesis, but this network collapses after birth concomitantly with cartilage remodelling and then regrows to support the adult organ. For this project, the student will use immunolabelling of tracheal tissue after disruption of signalling pathways implicated in angiogenesis and include further techniques if continued into a PhD project. Alternative projects: Elucidating molecular mechanisms in lung vascularisation or lymphangiogenesis.

Key references:

  1. Raimondi, R., Fantin A., Lampropoulou, A., Denti, L., Chikh, A. and Ruhrberg, C. (2014) Imatinib inhibits VEGF-independent angiogenesis by targeting NRP1-dependent ABL1 activation in endothelial cells. Journal of Experimental Medicine 211(6): 1167-1183
  2. Lanahan, A., Zhang, X., Fantin, A., Zhuang, Z.W., Rivera-Molina, F., Speichinger, K.R., Prahst, C., Zhang, J., Wang, Y., Davis, G.E., Toomre, D., Ruhrberg, C.* and Simons M.* (2013). The Neuropilin-1 cytoplasmic domain is required for VEGF-A-dependent arteriogenesis. Developmental Cell 25(2): 156-68. *co-corresponding
  3. Fantin, A., Vieira, J. M., Plein, A. R., Denti, L., Fruttiger, M., Pollard, J. W. and Ruhrberg, C. (2013). NRP1 acts cell autonomously in endothelium to promote tip cell function during sprouting angiogenesis. Blood 121(12): 2352-62.
  4. Fantin, A., Vieira, J. M., Plein, A. R., Maden, C. H. and Ruhrberg, C. (2013). The embryonic mouse hindbrain as a qualitative and quantitative model to study the molecular and cellular mechanisms of angiogenesis. Nature Protocols  8(2): 418-29.
  5. Fantin, A., Schwarz, Q., Davidson, K., Normando, E.M., Denti, L. and Ruhrberg, C. (2011). The cytoplasmic domain of neuropilin 1 is dispensable for angiogenesis, but promotes the spatial separation of retinal arteries and veins. Development 138 (19):4185-91.

To investigate the effect of LRG1 on BMP9 signalling in endothelial cells and its effect on angiogenesis

Supervisor(s): Prof. John Greenwood and Prof. Stephen Moss

Department: Cell Biology, UCL Institute of Ophthalmology

Project outline:

We have shown that LRG1 is a potent pro-angiogenic secreted glycoprotein that mediates its effect through redirecting TGFβ signalling (see reference Wang et al below). In a similar manner to TGFβ1, BMPs also signal through type II receptors (BMPRs) in association with the ALKs. Moreover, BMP activation of ALK1 has been reported both to promote and suppress endothelial cell proliferation and migration. In this project we will ask whether LRG1 modifies BMP-mediated signalling. If LRG1 modifies BMP9 signalling we will expand then investigate the individual and combinatorial effects of LRG1, TGFβ1 and BMP9 on endothelial cell function in both in vitro and ex vivo proliferation and angiogenesis assays.

Key references:

  1. Wang, X., Abraham, S., McKenzie, J.A.G., Jeffs, N., Swire, M., Tripathi, V.B., Luhmann, U.F.O., Lange, C.A.K., Zhai, Z., Arthur, H.M., Bainbridge, J., Moss, S.E. and Greenwood, J. (2013). LRG1 promotes angiogenesis by modulating endothelial TGFß signalling. Nature (in press, July 18th publication).
  2. McKenzie, J.A., Fruttiger, M., Abraham, S., Lange, C., Stone, J., Gandhi, P., Wang, X., Bainbridge, J., Moss, S.E. and Greenwood, J. (2012). Apelin is required for non-neovascular remodelling in the retina. Am. J. Pathol. 108:399-409.

Making blood vessels from stem cells

Supervisor: Dr Marcus Fruttiger

Department: UCL Institute of Ophthalmology

Project outline:

Vascular precursor cells are suitable for cell therapy approaches in vaso-degenerative diseases such as diabetes. The project will investigate the factors that are involved in driving cell differentiation down the vascular lineage pathway. Students will also culture different cells types in combination to explore their potential to establish vascular structures in vitro. The project will be integrated in a collaborative effort within the UCL Institute of Ophthalmology (Dr. Fruttiger and Prof. P. Coffey), Industry and Moorfields Eye Hospital.

Key references:

  1. Scott A, Powner MB, Fruttiger M. Quantification of vascular tortuosity as an early outcome measure in oxygen induced retinopathy (OIR). Exp Eye Res. 2014 Mar;120:55-60.
  2. Ramsden CM, Powner MB, Carr AJ, Smart MJ, da Cruz L, Coffey PJ. Stem cells in retinal regeneration: past, present and future. Development. 2013 Jun;140(12):2576-85. doi: 10.1242/dev.092270. Review. PubMed PMID: 23715550; PubMed Central PMCID: PMC3666384.
  3. Reis M, Czupalla CJ, Ziegler N, Devraj K, Zinke J, Seidel S, Heck R, Thom S, Macas J, Bockamp E, Fruttiger M, Taketo MM, Dimmeler S, Plate KH, Liebner S. Endothelial Wnt/β-catenin signaling inhibits glioma angiogenesis and normalizes tumor blood vessels by inducing PDGF-B expression. J Exp Med. 2012 Aug 27;209(9):1611-27.
  4. Powner MB, Vevis K, McKenzie JA, Gandhi P, Jadeja S, Fruttiger M. Visualization of gene expression in whole mouse retina by in situ hybridization. Nat Protoc. 2012 May 10;7(6):1086-96.
  5. Kuhnert F, Mancuso MR, Shamloo A, Wang HT, Choksi V, Florek M, Su H, Fruttiger M, Young WL, Heilshorn SC, Kuo CJ. Essential regulation of CNS angiogenesis by the orphan G protein-coupled receptor GPR124. Science. 2010 Nov 2;330(6006):985-9.
Translation & therapeutics

A Microparticle Based Angiogenic Delivery System

Supervisor: Dr Richard Day

Department: Applied Biomedical Engineering Group, UCL Division of Medicine

Project outline:

Controlled, sustained and targeted delivery of active pharmaceutical ingredients, such as pro-angiogenic factors for cardiovascular disease, is challenging and new methodologies are sought. The project will investigate a novel delivery system consisting of degradable microparticles that contain a bioactive load. Experimental work will involve microparticle fabrication with encapsulation of active ingredients combined with biological and chemical assays to determine release and activity of the encapsulated compound.

No key references



Imaging microparticles intended for therapeutic angiogenesis

Supervisor: Dr Richard Day

Department: Applied Biomedical Engineering Group, UCL Division of Medicine

Project outline:

Therapeutic angiogenesis based on transplantation of cells that secrete angiogenic growth factors could provide an effective new treatment for cardiovascular disease. Persistence of the transplanted cells and retention of the correct cell lineage are important parameters that need to be addressed before regulatory approval can be obtained. The project will explore the use of different imaging modalities for tracking mesenchymal stem cells (MSC) in vivo following their delivery on polymer microparticles.

No key references



Microparticles for therapeutic angiogenesis

Supervisor(s): Dr Richard Day and Prof. Ian Zachary

Department: Centre for Cardiovascular Biology & Medicine, UCL Division of Medicine

Project outline:

Very little information exists on the perivascular delivery of microparticles for use as a delivery vehicle of pro-angiogenic compounds. The project will use an established model of hind limb ischaemia to determine whether transplantation of microparticles encapsulated with bioactive compounds improve restoration of post-ischaemic reperfusion compared with delivery of unloaded microparticles. The primary endpoint of treatment will be superficial blood flow recovery (laser Doppler imaging) and secondary endpoints of local clinical outcome (occurrence of necrotic toes) and neovascularization (immunohistochemical staining for capillary and arteriole density). Retention of microparticles at the delivery site, together with the expected tissue response and degradation of the microparticles, will be confirmed by histology.


Image guided cardiac regeneration: Visible bioscaffolds functionalised to increase stem cell-mediated repair and improved cardiac function

Supervisor(s): Prof Mark Lythgoe and Dr Daniel Stuckey

Department: Centre of Advanced Biomedical Imaging, Division of Medicine

Project outline:

Cell therapy offers a promising approach for regenerating the infarcted heart, yet benefits are limited as the majority of injected cells are lost shortly after grafting. This problem could be effectively address if it were feasible to serially track grafted cell and nurturing bioscaffold location and function in vivo. This project will develop an injectable, image detectable, cardiac stem cell encapsulating biomaterial that will mechanically support the myocardium and augment cell retention, proliferation and differentiation, subsequently improving post-infarct remodelling and stem cell-mediated regeneration. Importantly, this strategy will be guided by novel multimodality in vivo preclinical imaging to permit for the first time serial tracking of cell and biomaterial retention, together with accurate assessment of cardiac function after grafting into infarcted mouse hearts.

Key references:

  1. Stuckey DJ, Ishii H, Chen QZ, Boccaccini AR, Hansen U, Carr CA, Roether JA, Jawad H, Tyler DJ, Ali NN, Clarke K, Harding SE. Magnetic resonance imaging evaluation of remodeling by cardiac elastomeric tissue scaffold biomaterials in a rat model of myocardial infarction. Tissue Eng Part A. 2010;16:3395-3402
  2. Stuckey DJ, Carr CA, Martin-Rendon E, Tyler DJ, Willmott C, Cassidy PJ, Hale SJ, Schneider JE, Tatton L, Harding SE, Radda GK, Watt S, Clarke K. Iron particles for noninvasive monitoring of bone marrow stromal cell engraftment into, and isolation of viable engrafted donor cells from, the heart. Stem Cells. 2006;24:1968-1975
  3. Smart N, Bollini S, Dube KN, Vieira JM, Zhou B, Davidson S, Yellon D, Riegler J, Price AN, Lythgoe MF, Pu WT, Riley PR. De novo cardiomyocytes from within the activated adult heart after injury. Nature. 2011;474:640-644
  4. Chen IY, Wu JC. Cardiovascular molecular imaging: Focus on clinical translation. Circulation. 2011;123:425-443
  5. Makkar RR, Smith RR, Cheng K, Malliaras K, Thomson LE, Berman D, Czer LS, Marban L, Mendizabal A, Johnston PV, Russell SD, Schuleri KH, Lardo AC, Gerstenblith G, Marban E. Intracoronary cardiosphere-derived cells for heart regeneration after myocardial infarction (caduceus): A prospective, randomised phase 1 trial. Lancet. 2012;379:895-904