Wellcome Trust Combined Training Programme
3 year PhD proposals starting October 2011
Prof. David J. Blackbourn
Cancer Sciences
Dr Jorge Caamaño and Dr Cecile
Benezech
Immunology and Stem Cell Biology
Dr Martyn Chidgey and Prof.
Effects E effects of plakoglobin mutations
Michael Overduin
Dr S John Curnow
T cell immunology
Dr Chris Dawson and Prof.
Lawrence Young
Dr. Paul Foster and Prof. Chris
McCabe
Dr RJA Grand and Prof. David
Blackbourn
Viral Oncology
Dr Andrew Hislop
Immunity to the oncogenic human herpesviruses
Dr Charlotte Inman, Dr Joanne
Croudace and Prof. Paul Moss
Allogeneic stem cell transplant
Prof Ann Logan & Wg Cmdr Rob
Scott
B
Vitreous Biomarkers of neural retinal cell death
Prof. Chris McCabe and Prof.
Jayne Franklyn
Hormones and Cancer
Dr Matthew Morgan and Prof.
Lorraine Harper
Prof. Paul Moss and Dr Annette
Pachnio
Prof. Paul Moss and Prof. Mark
Kilby
Prof. Paul Murray
Renal inflammation, Vasculitis, Autoimmunity
Oestrogen metabolism in colorectal cancer
Cell biology, protein biochemistry and virology.
anti-viral Immunology, Cytomegalovirus
Study of the cellular alloreactive immune response in pregnancy
and its relation to fetal loss
Chronic inflammation and lymphomagenesis
Prof. Gerard Nash and Dr. Helen Inflamation Biology: What controls leukocyte entry, transit through
McGettrick
and exit of tissue?
Prof. Phil Newsome & Prof. Jon
Frampton
Prof. Mark Pallen and Prof.
Gurdyal Besra
Dr Graham Taylor, Dr Heather
Long and Prof. Alan Rickinson
Mesenchymal stem cells and inflammatory injury
Dr Kai Michael Toellner
B cell differentiation, Vaccination and memory
Steve Watson and Neena Kalia
Platelets in the maintenance of the lymphatic system and in
atherosclerotic plaque formation in adult mice fed on a high fat diet
Lymphangiogenesis in ocular inflammation
Prof. Steve Watson and Dr Graham
Wallace
Dr Steve Young
Dr Jianmin Zuo and Prof. Martin
Rowe
Esx protein secretion in diverse bacteria
Epstein-Barr Virus (EBV) – fundamental and translational research
on an important human pathogen
Chronic Inflammatory Disease
Virology/Immunology/Cancer
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Prof David J. Blackbourn
Contact details: d.j.blackbourn@bham.ac.uk
School: Cancer Sciences
Area of Research: Cancer Sciences
Brief description of research carried out in your team:
Work in this laboratory concerns (1) understanding virus host relationships with a view to understanding
virus mechanisms of disease and immune evasion. In other work, we have interests in (2) characterising
tumour microenvironments in order to understand immune responses to tumours and how they can be
augmented.
1. Virus-host interactions
Kaposi’s sarcoma-associated herpesvirus (KSHV) causes two malignancies: Kaposi’s sarcoma (KS)
and primary effusion lymphoma (PEL). We use this virus as a model to investigate virus-host
interaction, especially at the level of escape from the immune response, to learn about the role and
mechanisms of anti-viral immunity. We are particularly interested in understanding how KSHV
evades innate immune responses and how the cell senses infection by a virus in order to trigger
innate immune responses.
2. Tumour microenvironments
Merkel cell carcinoma (MCC) is a particular aggressive cancer with a poor prognosis. It is believed
to be caused by a newly identified virus, Merkel cell polyomavirus (MCV). Currently, we are
characterising the reasons for inefficient T cell infiltration in to Merkel Cell Carcinoma with a view
to correcting this deficiency and improving prognosis.
Plans are in place to extrapolate this work to the study of melanoma.
Key references:
Areste, C., and D. J. Blackbourn. 2009. Modulation of the immune system by Kaposi's
sarcoma-associated herpesvirus. Trends Microbiol 17:119-129.
Feng, H., M. Shuda, Y. Chang, and P. S. Moore. 2008. Clonal Integration of a Polyomavirus in Human
Merkel Cell Carcinoma. Science 319:1049-1050.
Training provided:
Cancer biology, immunology (innate and adaptive), virology
Techniques to be used in the project:
Cell culture; Virus propagation & quantification
Quantification of virus-infected cells (flow cytometry)
Reverse transcription (RT)-PCR and quantitative RT-PCR; Immunocytochemistry; Confocal microscopy
Names of other researchers who may also be involved in the project:
Rachel Wheat, Drs Andrew Hislop &/or Neil Steven
Are PhD projects in this area likely to require the student to hold a personal home office licence?
No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Jorge Caamano and Cecile Benezech
Contact details: J.Caamano@bham.ac.uk or C.Benezech@bham.ac.uk (x44077)
School: Immunity and Infection
Area of Research: Immunology and Stem Cell Biology
Brief description of research carried out in your team:
Title: Lymphotoxin Beta Receptor Signalling Effects on Adipogenic Differentiation
Inflammation is regarded as an important process underlying metabolic diseases in obese individuals. Thus,
understanding the influence of the immune system in adipose tissue formation and the correlation between
inflammation and obesity is a very important area of study under the current spread of obesity. We have shown that a
specific member of the Tumour Necrosis Factor (TNF) family of receptors, Lymphotoxin Beta Receptor (LTbR), is
required for the maturation and homeostasis of secondary lymphoid tissue stromal “organizer” cells (1-2). More
recently, we have shown that LTbR signalling impairs the differentiation of progenitor cells to adipocytes by blocking
the up-regulation of a several genes essential for this process in vivo during the development of secondary lymphoid
tissues (3). We have taken ex vivo approaches to understand the LTbR signalling mechanism in this context and
shown that this pathway block mesenchymal stem cell differentiation towards osteoblasts and chondrocytes lineages
as well.
Aim: This project aims to uncover the specific function of the TNF-R-NF-kB signalling axis in mesenchymal stromal
cell differentiation toward adipocytes during inflammation.
Hypothesis: The TNF-Rs act as a switch to regulate stromal cell differentiation into adipocytes in vivo. During
inflammation TNF-R signalling will induce stromal cells to become lymphoid tissue organizer cells and support
lymphocyte survival and contribute to the formation of ectopic lymphoid tissues. In contrast, absence of TNF-R will
result in large numbers of stromal cells becoming adipocytes and contributing to obesity.
The student will investigate the function of TNF-R-NF-kB during adipogenic differentiation to identify the cells that
respond to these pathways and characterize the target genes that are induced or repressed during this process. In
addition, the function and gene targets of these pathways ex vivo in human cells will be also investigated.
Understanding the role of the TNF Receptors in adipocyte differentiation might have far reaching importance to
understand the links between adipose tissue formation, inflammation and obesity.
Key references:
1- White, A., et al. (2007). Lymphotoxin a-dependent and -independent signals regulate stromal organizer cell
homeostasis during lymph node organogenesis. Blood 110, 1950-1959.
2- Bénézech C, et al. (2010). Ontogeny of stromal organizer cells during lymph node development. J Immunol.
184:4521-30.
3- Bénézech et al. (2012). Lymphotoxin Beta Receptor Signalling through NF-kB2/RelB Reprograms Adipocyte
Precursors to Become Lymphoid Tissue Stromal Cells. Immunity (In Press).
Training provided: The student will work in close collaboration with a postdoctoral graduate and PhD students in
our group. She/he will receive training in cell and molecular biology techniques listed below. The student will be able
to discuss his/her data during informal daily meetings, and more formally in weekly meetings and joint lab meetings
with other groups at the IBR. The student will benefit from our ongoing collaborations in different projects with
Laura O’Neill’s, Peter Hewett’s, and Ed Rainger’s groups and the Liver labs at the IBR as well as groups at the Inst of
Metabolic Sciences, MRC LMB and Babraham Inst in Cambridge.
Techniques to be used in the project: FACs analysis, immunostaining and immunofluorescence staining and
confocal microscopy, PCR, QPCR and gene arrays, cell transfection and siRNAs. Preparation of primary cells, cell
and organ cultures. Southern, Northern and Western blotting, Electro Mobility Shift Assays.
Names of other researchers who may also be involved in the project: Dr Laura O’Neill, Prof. Graham
Anderson, Dr Peter Hewett, Dr Dave Withers, Prof. Vidal-Puig (Univ. of Cambridge).
Are PhD projects in this area likely to require the student to hold a personal home office licence?
No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Martyn Chidgey, Michael Overduin
Contact details: M.A.Chidgey@bham.ac.uk; M.Overduin@bham.ac.uk
School: Cancer Sciences
Area of Research: Effects of plakoglobin mutations
Brief description of research carried out in your team:
Background: Desmosomes are intercellular junctions formed by multi-protein complexes. They are located at the
cell membrane where they rivet cells together. They are essential for the maintenance of the integrity of muscle and
epithelial tissue. Loss of desmosomal function in cardiomyocytes results in arrhythmogenic right ventricular
cardiomyopathy (ARVC), one of the most common inherited cardiomyopathies, and a cause of heart failure and
sudden death in young adults, particularly competitive athletes. Loss of desmosomal adhesion in the epidermis causes
lethal acantholytic epidermolysis bullosa, a distressing skin blistering condition that results in catastrophic fluid loss
and infant death. Finally, loss of desmosomal adhesion has been implicated in cancer. Nonetheless the precise effects
of the hundreds of mutations which have been identified in desmosomal proteins have not yet been elucidated,
limiting our ability to provide accurate diagnostic or treatment options.
Aim: The goal of this project will be to determine the biophysical and delocalising effects of inherited mutations
within the desmosomal protein plakoglobin (preliminary structure depicted above). Wild-type and ARVC mutant
plakoglobin proteins will be expressed in bacteria and purified using established techniques. A variety of biophysical
techniques will then be used to investigate the specific effects of the mutations on plakoglobin structure and stability.
The interactions of the wild-type and mutant plakoglobin proteins to with the ligands desmocollin and desmoglein
will be compared in biochemical and cell based experiments, providing the first mechanistic information about how
these genetic alterations cause disease.
Progress: We have just received Wellcome Trust grant support for this research, and have already purified all the
desmosomal proteins including plakoglobin in full length and truncated forms. We have identified protein interactions
using pull-down assays, revealing novel complexes. The structures of component domains are in progress by NMR
spectroscopy, X-ray crystallography and small angle X-ray scattering, providing a rich opportunity for determining
the specific effects of specific disease-causing mutations.
Long term: We plan to initiate a new system of designating ARVC mutations as ‘red’, ‘amber’ or ‘green’ based on
their abilities to completely, partially or insignificantly compromise the integrity of desmosomal structures and
complexes, thus aiding clinicians and genetic counsellors in making informed decisions and recommendation for
patients carrying desmosomal gene mutations.
Key references: [1] Garrod D, Chidgey M (2008) Desmosome structure, composition and function. BBA 1778,
572-87. [2] Kami K, Chidgey M, Dafforn T, Overduin M (2009) The desmoglein-specific cytoplasmic region is
intrinsically unstructured in solution and interacts with multiple desmosomal protein partners. J Mol Biol 386, 53143. [3] Al-Jassar C, Knowles T, Jeeves M, Kami K, Bikker H, Overduin M, Chidgey M (2011) Nonlinear structure of
the desmoplakin plakin domain and the effects of cardiomyopathy-linked mutations, J Mol Biol, 411:1049-61
Training provided: The student will gain expertise in cell microscopy and structural biology and gain training in
molecular biology, protein biochemistry, biophysical and computational methods.
Techniques to be used in the project: recombinant protein expression, protein purification, RT-PCR, pulldown assays, SDS-PAGE, Western blotting, immunofluorescence, NMR spectroscopy, X-ray scattering
Names of other researchers involved: Caezar Al-Jassar (PhD student), Claudia Fogl (PDRA), Prof. Paulus
Kirchhof & Dr Larissa Fabritz, U Birmingham, Hennie Bikker (Academic Medical Center, Netherlands)
Are PhD projects in this area likely to require the student to hold a personal home office licence? no
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Dr John Curnow
Contact details: s.j.curnow@bham.ac.uk
School: Immunity & Infection
Area of Research: T cell immunology
Brief description of research carried out in your team:
My research group is currently interested in the differentiation, inter-relationships and pathological role of a
number of different CD4+ T helper subsets. Most of our work involves the analysis of peripheral blood
from healthy individuals, but importantly we translate our findings to disease contexts, particularly multiple
sclerosis, where we also study cells from the inflamed CNS through analysis of cerebrospinal fluid (CSF)
samples. Current projects within the group include:
1. Analysis of dual cytokine-secreting T cells. This project aims to determine, for example, whether a T
cells that secretes both IFN+ and IL-17 is derived from a Th1 or Th17 progenitor. Recent data from
animals models has also suggested that Th17 cells can switch to a purely Th1 phenotype, and we are
trying to identify these switched cells in human peripheral blood.
2. Our studies of the CSF have confirmed that there is a resident population of T cells in healthy
individuals dominated by CD4+ and CD8+ central memory (CCR7+) T cells. Our analysis suggests
that these cells are unable to respond to a normal stimulus, failing to produce any of the common
effector cytokines. We are now hunting for the equivalent population of cells in the peripheral blood.
3. In multiple sclerosis the CNS is infiltrated by inflammatory T cells. We have an ongoing project
analysing prospective CSF and blood samples at the time of diagnostic sampling, examining the
numbers and spectrum of T cells and how they differ between MS and other neurological diseases
and healthy controls.
Key references:
For a history of previous projects please carry out a PubMed search for Curnow SJ.
For current projects: O'Shea JJ, Paul WE. Mechanisms underlying lineage commitment and plasticity of
helper CD4+ T cells. Science. 2010 Feb 26;327(5969):1098-102.
Mechanisms underlying lineage commitment and plasticity
Training provided: Everything you’ll
need to know,
and more!
of helper
CD4+
T cells.
O'Shea JJ, Paul WE.
Techniques to be used in the project: Cell isolation and culture, qRT-PCR, multi-colour flow cytometry
Names of other researchers who may also be involved in the project: Most of the group
Are PhD projects in this area likely to require the student to hold a personal home office licence? No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Dr Chris Dawson and Professor Lawrence Young
Contact details: c.w.dawson@bham.ac.uk
School: Cancer Sciences
Area of Research: Viral Oncology
Brief description of research carried out in your team:
Although best known for its association with tumours of B cell origin, Epstein-Barr virus (EBV) is also implicated in
the aetiology of certain epithelial malignancies, which include nasopharyngeal carcinoma (NPC) and a proportion of
gastric carcinomas. As a transforming virus, EBV is causally linked to the pathogenesis of various B cell
malignancies; however, the role that EBV plays in the aetiology of epithelial cancers is completely unknown. Unlike
B cells where viral infection is associated with cell transformation, infection of epithelial cells is accompanied by
virus loss through lytic replication, findings which reflect the propensity of EBV to replicate in epithelial tissue. The
virus can, however, establish stable latent infections in undifferentiated epithelial cell lines cultured in vitro, and in
undifferentiated carcinomas in vivo, as exemplified by the universal association of EBV with NPC. These findings
suggest that stable latent infection of epithelial cells with EBV is either (i) a rare event, or (ii) that cells capable of
supporting a latent infection constitute a small fraction of the cell or tissue population. We hypothesise that viral
latency is a prerequisite to malignant transformation and occurs as a consequence of stable latent infection of early
progenitor cells, likely candidates of which might be stem cells or cancer stem cells (CSCs). We propose that stable
infection of such populations not only supports viral latency, but also allows EBV to ”drive” epithelial transformation
through the inappropriate activation of various onco-developmental signalling pathways.
Our research focuses on three main inter-related areas associated with the role of EBV infection in the pathogenesis of
nasopharyngeal carcinoma (NPC), namely (i) studies on the function of individual EBV latent genes, (ii) EBV
infection in in vitro model systems and (iii) the analysis of NPC biopsies. The long-term aims of our work are to
understand: (i) How viral infection contributes to the malignant transformation of an epithelial cell (ii) What insights
can be gained into the oncogenic process by studying the cellular pathways targeted by EBV latent genes? (iii) What
cellular and viral factors influence the outcome of EBV infection in human epithelial cells (iv) how relevant are these
observations to the pathogenesis of EBV-associated tumours in vivo? (v) What novel targets for therapeutic
intervention can be identified?
Key references:
(1). Young, L.S. and Rickinson, A.B. (2004). Nat. Rev. Cancer 4:757-768.
(2). Dawson, CW, Port, RJ, Young, LS. (2012). Seminars in Cancer Biol. 22:144-53.
(3). Wang, J., Guo, L.P., Chen, L.Z., Zeng, Y.X. and Lu, S.H. (2007). Cancer Res. 67:3716-24.
(4). Kong QL, Hu LJ, Cao JY, Huang YJ, Xu LH, Liang Y, Xiong D, Guan S, Guo BH, Mai HQ, Chen QY, Zhang X, Li MZ,
Shao JY, Qian CN, Xia YF, Song LB, Zeng YX, Zeng MS. (2010). PLoS Pathog. 6:e1000940.
(5). Katoh, M. (2007). Stem Cell Reviews and Reports 3:30-38.
Training provided:
The student will be trained by members of the group to become proficient in all of the techniques outlined below. Training will be
provided in preparing oral presentations for public engagement and conference talks, and guidance in the preparation of reports
and manuscripts for publication.
Techniques to be used in the project:
Cell culture (Cell proliferation/apoptosis/sphere formation assays), immunohistochemical staining, indirect immunofluorescence
staining and confocal imaging, western blotting, RT-PCR, quantitative real-time RT-PCR, Luciferase reporter assays,
Fluorescence activated cell sorting (FACS).
Names of other researchers who may also be involved in the project:
Miss Rebecca J.Port (PhD student), Miss Sonia P. Maia (Research technician), Dr John R. Arrand (Senior Research Fellow)
Are PhD projects in this area likely to require the student to hold a personal home office licence? No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Dr. Paul Foster, Prof. Chris McCabe
Contact details: p.a.foster@bham.ac.uk
School: Clinical and Experimental Medicine
Area of Research: Oestrogen metabolism in colorectal cancer
Brief description of research carried out in your team:
Colorectal cancer (CRC) is the second most common cancer in the UK and a significant health burden. Consequently,
new treatments for this malignancy are urgently required. One area, the metabolism of oestrogen, has been generally
overlooked in regards to CRC and consequently a better understanding of oestrogenic action may hold potentially new
therapeutic avenues against this malignancy. Uncertainty surrounds the actions of oestrogen in CRC. Although it is
now recognised that oestrogens are beneficial against CRC, how these protective effects manifest remains obscure.
What is clear is that the regulation of oestrogen synthesis and metabolism are important. Numerous studies indicate
oestrone (E1
suggests a significant role for the enzyme pathways involved in E1 synthesis. Consequently, down-regulation of the
-HSD-2, which oxidises oestradiol (E2) to E1, is a negative prognostic factor for CRC mortality, and the
ratio between steroid sulphatase (STS) and sulphotransferase (EST), enzymes that de-sulphate and sulphate E1
respectively, is a potent prognostic factor for CRC clinical outcomes (Fig. 1)
.
This project aims to further our understanding of oestrogen metabolism in CRC. By utilising novel steroidobolomic
LC/MS techniques, various molecular methodologies, radio-labelled biochemical assays, and animal models of
cancer, this research will probe exactly how CRC cell lines and human colon tissue samples metabolise oestrogen and
whether this action mediates tumour proliferation. This information, once ascertained, would clarify how oestrogens
influence CRC, potentially leading to new therapeutic targets for this disease.
Key references: Sato R, Suzuki T, Katayose Y, et al 2009 Steroid sulfatase and estrogen sulfotransferase in colon carcinoma:
regulators of intratumoral estrogen concentrations and potent prognostic factors. Cancer Research 69 914-22.
Hogan AM, Collins D, Baird AW, Winter DC. 2009 Estrogen and gastrointestinal malignancy. Mol Cell Endocrinol. 307 19-24.
Kennelly R, Kavanagh DO, Hogan AM, Winter DC. 2008 Oestrogen and the colon: Potential mechanisms for cancer prevention.
Lancet Oncol. 9 385-91.
English MA, Stewart PM, Hewison M. 2001 Estrogen metabolism and malignancy: analysis of the expression and function of
17beta-hydroxysteroid dehydrogenase in colonic cancer. Mol Cell Endcocrinol. 171 53-60.
Training provided: Cell culture, qRT-PCR, Western blot, siRNA, LC/MS, Enzyme bio-chemical assays, animal
handling, animal models of cancer, immunohistochemistry, FACS, publishing research, presentation skills, critical
analysis.
Techniques to be used in the project: Cell culture, qRT-PCR, Western blot, siRNA, LC/MS, Enzyme biochemical assays, rodent xenograft, immunohistochemistry, FACS.
Names of other researchers who may also be involved in the project: Prof. Wiebke Arlt, Dr. Vivek Dhir,
Dr. Angela Taylor, Miss Anne-Marie Hewitt (technically support).
Are PhD projects in this area likely to require the student to hold a personal home office licence? Yes
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Dr RJA Grand and Prof. David Blackbourn
Contact details: R.J.A.Grand@bham.ac.uk
School: Cancer Sciences
Area of Research: Cell biology, protein biochemistry and virology.
Brief description of research carried out in your team:
It is now well established that adenovirus-mediated transformation of mammalian cells in culture is
an excellent model for oncogenesis. Indeed, many of the major tumour suppressor genes/proteins which are
most commonly mutated in human cancers, such as Rb and p53, were first identified in the adenovirus
system. The main focus of our research is understanding the intricate relationship between the adenovirus
transforming proteins (oncoproteins) and the host cell. One element of our studies is the investigation of the
ways in which adenoviruses and the host cellular DNA damage response (DDR) network interact.
Maintenance of the integrity of the cellular genome is critical to the well being of multicellular
organisms. To this end, a complex series of interlocking pathways have evolved to detect DNA lesions,
arrest the cell cycle so that the damaged DNA is not replicated, and if the damage is not too severe, and
initiate apoptosis. Mutations which occur in components of the DDR pathway often predispose to cancers.
Similarly individuals who have inherited mutations in damage response genes ( such as Ataxia
Telangiectasia and Fanconi’s Anaemia) often have early onset cancers. The complexity of the DDR
pathways means that our understanding of them is still limited. One of the ways in which we can increase
our knowledge is through examination of the ways in which viral (in this case by adenovirus) infection or
adenovirus-mediated transformation activates and then neutralizes the DDR. In the projects we are
undertaking and offering in this area of research the effects of the virus on particular components of the
DDR will be examined. By introducing the viral proteins into the cell and subsequently activating the
response this places particular stress on the cell and therefore introduces novel effects which allow us to
analyse the pathways in detail and provide insight that is not otherwise available. The experiments will also
help us to understand much better the mode of action of the adenovirus oncoproteins.
Key references:
Regulation of DNA and resection by hnRNPU-like proteins promotes DNA double strand break signalling
and repair. Polo et. al., (2012) Mol. Cell 45, 505-16.
Serotype-specific inactivation of the cellular DNA damage response during adenovirus infection (2011)
Forrester et. al., J. Virol. 85 2201-11.
Adenovirus 12 E4orf6 inhibits ATR activation by promoting TOPBP1 degradation (2010) Blackford et. al.,
Proc. Natl.Acad.Sci. USA,107, 12251-6.
Training provided: The student will be trained in protein biochemistry, cell biology and molecular biology
and, to some extent, virology. Training in scientific writing and presentation will also be given.
Techniques to be used in the project: Cell culture, western blotting, immunoprecipitation, pull down
assays, protein expression, mutagenesis, cloning, immunofluoresence microscopy, virus preparation and
infection.
Names of other researchers who may also be involved in the project: Professor David Blackbourn
Are PhD projects in this area likely to require the student to hold a personal home office licence?
No.
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisor: Dr Andrew Hislop
Contact details: a.d.hislop@bham.ac.uk, 0121 414 7983
School: Cancer Sciences
Area of Research: Immunity to the oncogenic human herpesviruses
Brief description of research carried out in your team:
Our lab examines the T lymphocyte response to the two human oncogenic herpesviruses, namely EpsteinBarr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), how these viruses evade immune
targeting and how we can overcome their evasion strategies. These viruses establish persistent infections
within cells of the immune system and so can teach us much about the workings of the immune system and
control over viral oncogenesis.
Compelling evidence from immunosuppressed patients indicates the T-lymphocyte component of the
immune response controls infection and disease caused by these viruses. Our recent studies have focussed
on the T cell response to KSHV, which causes the most frequently reported malignancy in HIV patients and
sub-Saharan Africans, Kaposi’s sarcoma, as well as other malignancies. We have identified KSHV targets
of the CD8 but especially the CD4 subset of T-lymphocytes; the subset which is depleted in HIV patients
that may make them so sensitive to KSHV-associated disease.
Our preliminary data suggests that the virus encodes effective mechanisms to thwart targeting by CD8+ T
cells. We have then concentrated on CD4 T-lymphocyte control of KSHV-infected cells, mainly primary
effusion lymphoma (PEL); an aggressive KSHV-associated malignancy. In vitro, KSHV-reactive CD4 Tlymphocytes did not recognize PELs and we found that this is in part due to the action of a KSHV-encoded
immune evasion gene. We developed strategies to circumvent the evasion mechanism and restored
recognition by the CD4 T cells, however the virus appears to have secondary mechanisms which prevent
their killing by the T cells. We are now studying how to disrupt this mechanism and have identified a
candidate viral gene product which may be responsible that we will investigate further. More importantly,
we have preliminary in vitro data which suggests treatment of these PELs with an antiviral drug, which
interferes with one of the targets of the candidate gene product, sensitises the PELs to killing by our CD4+
T cells. This finding has the potential for wider application as the candidate gene product is expressed in all
KSHV-associated malignancies and may then be inhibiting effective immune control in these malignancies.
Thus an understanding of whether the antiviral drug can effectively restore killing by CD4+ T cells opens
the avenue for developing an effective therapeutic to restore immune control of KSHV malignancies.
Key references: Sabbah S, Jagne YJ, Zuo J, de Silva T, Ahasan MM, Brander C, Rowland-Jones S,
Flanagan KL, Hislop AD. Blood. 2012 119: 2083-92.
Hislop AD, Palendira U, Leese AM, Arkwright PD, Rohrlich PS, Tangye SG, Gaspar HB, Lankester AC,
Moretta A, Rickinson AB. Blood. 2010 116: 3249-57.
Training provided: The student will be trained in the techniques mentioned below and will learn
transferable skills in experimental design, data interpretation, scientific writing and communication.
Additionally the student will interact with other immunologists and virologists and attend regular seminar
series to extend their understanding of this and related fields.
Techniques to be used in the project: Tissue culture, T cell cloning, T cell recognition assays, ELISA,
ELISpot analysis, flow cytometry, gene cloning, western blot analysis, virus infections.
Names of other researchers who may also be involved in the project: Prof David Blackbourn and Prof
Alan Rickinson
Are PhD projects in this area likely to require the student to hold a personal home office licence? No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Dr Charlotte Inman, Dr Joanne Croudace and Prof Paul Moss
Contact details: c.f.inman@bham.ac.uk, j.e.croudace@bham.ac.uk,
p.moss@bham.ac.uk
School: Cancer Sciences
Area of Research: Allogeneic stem cell transplant
Brief description of research carried out in your team:
One of the major themes of research in the Moss Laboratory is reconstitution of the immune system
following allogeneic stem cell transplant (SCT). SCT is a curative treatment used for high risk leukaemia
and lymphoma and involves replacement of the patient’s immune system with that of a new donor.
One of the major benefits of allo-SCT is the promotion of anti-tumour responses known as the Graft-versusLeukaemia effect (GVL), whereby the donor’s immune system recognises residual tumour cells as ‘nonself’ and destroys them. However in contrast to this, donor immune cells can also recognise patient’s
tissues as ‘non-self’, resulting in destruction of tissues including the skin, gut and liver. This resulting
disease is known as Graft-versus-Host disease (GVHD).
The Moss group is currently undertaking studies to understand the development of both GVL and GVHD,
with a major emphasis being on the first 2-weeks post SCT, a time-point at which we believe priming of
these immune responses occurs. The ultimate goal of the research is to distinguish between the
establishment of GVL and GVHD, in order for the development of treatment strategies to boost GVL,
whilst preventing GVHD. Excitingly our initial studies indicate that it is possible to predict development of
GVHD at least 2 weeks before clinical symptoms. This would have major implications for development of
targeted treatments and intervention strategies which will lead to improvements in outcome post SCT.
One such strategy being explored through clinical trial in the laboratory is the possibility of boosting GVL
by expanding the antigen-specific T cell-pool in the patient using a prime boost vaccination schedule. At
the same time we are also studying the possibility of blocking tissue-migration of antigen-specific T cells
towards the skin, utilising neutralising antibodies directed against chemokine ligands and their receptors.
The successful student would be involved closely in these studies, working alongside Dr Charlotte Inman,
0;p0;
and Dr Joanne Croudace who are both currently postdoctoral researchers in the Moss group.
Key references:
Goodyear OC, Blood. 2012 Jan 10.
McLarnon et al. Haematologica. 2010 Sep;95(9):1572-8.
Nicholls S et al. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3889-94.
Piper KP et al. Blood. 2007 Dec 1;110(12):3827-32.
Training provided: Key laboratory skills including specific training in tissue culture, flow cytometry,
quantitative immuno-histochemistry and immuno-fluorescence and PCR. Critical analysis of published
manuscripts through journal clubs, and small group discussion. Presentation skills through informal lab
meetings and training in data analysis and statistics.
Techniques to be used in the project:
Cell culture, 10-colour flow cytometry, quantitative immuno-histochemistry and fluorescence, PCR.
Names of other researchers who may also be involved in the project:
Dr Charlotte Inman and Dr Joanne Croudace
Are PhD projects in this area likely to require the student to hold a personal home office licence?
No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Prof Ann Logan & Wg Cmdr Rob Scott
Contact details: a.logan@bham.ac.uk
School: CEM
Area of Research: VITREOUS BIOMARKERS OF NEURAL RETINAL CELL DEATH
Brief description of research carried out in your team:
Area of Research:
VITREOUS BIOMARKERS OF NEURAL RETINAL CELL DEATH
Background Surrogate biomarkers for axon and neuron degeneration are used to monitor the progress of cell death
after retinal damage and evaluate the efficacy of potential neuroprotective treatments. Retinal ganglion cells (RGC)
in the RGC layer of the retina and their axons in the fibre layer are separated from the vitreous by the inner limiting
membrane, from the cerebrospinal fluid (CSF) in the subarachnoid space around the lamina cribrosa by the pia mater
of the optic nerve sheath, and from blood by the blood-brain-barrier of the retinal capillaries. The proposition that
intracellular molecules specifically derived from apoptotic RGC and their degenerating axons may leak into the
retinal extracellular fluid and preferentially diffuse through the basal lamina of the inner limiting membrane into the
vitreous, is supported by the observations that, after RGC loss, concentrations of RGC-derived proteins are greater in
the vitreous than in retinal extracts. The observation that rhodopsin (derived from photoreceptors, which comprise
70% of retinal neurons) is not found in the vitreous suggests that the vitreous may represent a sample of proteins
relatively specific to RGC as opposed to other retinal cells (Walsh et al., 2011). Intraneural proteins identical to those
recognised as serum and cerebrospinal fluid (CSF) biomarkers of brain injury, may also accumulate in the vitreous
body after retinal damage. Moreover, proteins released into the subretinal fluid from damaged retinal cells after
rhegmatogenous retinal detachment (RRD), and proliferative vitreoretinopathy (PVR), for example, are also likely to
find their way into the vitreous body.
Generic protein and mRNA biomarkers are detected by proteomic and genomic screening of vitreal fluid
whereas, a more focused approach targets specific molecules known to have raised titres in the vitreous body in
retinal pathology. For example, vitreal biomarkers for RGC degeneration include catalase and the X-linked inhibitor
of apoptosis protein (XIAP) which are raised 25-fold and 9-fold in a mouse glaucoma model (Walsh et al., 2009).
Gesslein et al. (2010) recorded elevated levels of tumour necrosis factor alpha (TNF-α) protein in the vitreous fluid of
pigs after retinal ischaemia, and total anti-oxidant capacity (TRAP - an oxidative stress marker) was decreased in the
vitreous of rats by 70% 60 days after the induction of glaucoma (Ferriera et al., 2010). Similarly, interleukin,
interferon, and growth factor proteins and mRNA, accumulating in the subretinal space after RRD and associated
PVR-induced generalised retinal damage (Kenarova et al., 1997; El-Ghrably et al., 1999; Ricker et al., 2011a), also
percolate into the vitreous fluid (Kauffmann et al., 1994; El-Ghrably et al., 2004; Ricker et al., 2011b).
Biomarkers of retinal injury detected in the serum and CSF are also likely to be present in the vitreous fluid
and include: (1), light, medium and heavy chain neurofilament isoforms which appear in the plasma after acute optic
neuritis (Petzold et al., 2004) and in the CSF of MS patients (Lim et al., 2004; Petzold, 2005); and (2),
phosphoglycerate kinase 1, cytokeratin 18 (CK18), Lewis α-3-fucosyltransferase and ephrin receptor A2 which are
transiently raised at 4h and 1d and return to base levels by 3d in a Rhesus monkey photocoagulation model of acute
retinal injury (Dunmire et al., 2011). Moreover, chromatin protein high-mobility group B1 (HMGB1), cyclophilin A
(Christofferson & Yuan, 2010), nucleosomal DNA, Fas ligand, cytochrome C (Greystoke et al., 2008; Ward et al.,
2008), aquaporin 4 antibodies 8 (Janius & Wildemann, 2010), neuron specific enolase, and S100B (Bloomfield et al.,
2007; Kleindienst et al., 2007;Uden &Romner, 2009; Kochanek et al., 2008), which are all serum and CSF
biomarkers of generalised brain injury, may also be found in the vitreous fluid after retinal degeneration.
The relevance of vitreous biomarkers to human diseases is twofold: (1), the vitreous is available for research
in both animal models and in humans (in patients undergoing vitreoretinal surgery) – unlike retinal tissue, which is
only available in animal models. The study of biomarkers in both humans and animal models thus allows
pathological validation of human disease modelling that cannot otherwise take place; and (2), the analysis of vitreous
after vitreo-retinal surgery could be used to make treatment decisions, for example on the need for neuroprotective
therapies or anti-scarring agents, if early biomarkers of cellular injury or fibrotic processes were identified.
Experimental design
Animal Studies
Design: The experiment is comprised 2 groups of adult rats each containing 60 animals. Optic nerves in the
experimental group are transected intra-orbitally and, in the control group, are exposed in the orbit but not transected
(sham operated). Animals are killed at 0d (pre-operative base line data) and, at 3, 8 and 20d post-lesion (dpl) for: (1),
counting of FluoroGold (FG) back filled RGC in retinal whole mounts (total=20 rats/group); and (2), estimation of
titres of mRNA and protein biomarkers from pooled vitreal fluid samples (total=40 rats/group). Five rats are
allocated to each time point (see below for rationale of killing times).
Induction of RGC apoptosis: Berkelaar et al. (1994) plotted the temporal course of RGC death after intraorbital optic
nerve transection and showed that, after a delay of ~3d, the exponential loss of RGC culminated in ~5% remaining at
14d (Fig. 1). This ‘optic nerve transection model of RGC death’ provides sampling times for recording biomarkers of
RGC death at pre-apoptotic (3dpl)), peak apoptotic (8dpl), and post apoptotic death (20dpl) stages.
120
% RGC/mm2
100
80
60
40
20
0
day 0
day 3
day4
day5
day7
day10
day14
day28
dpl
Figure 1. Densities of RGC/mm2 (%) at specific dpl after intra-orbital optic nerve transection (100%=frequency of
RGC in intact retina at 0d). Note the exponential loss of RGC from 4-14dpl.
Surgery: The surgical procedures for intra-orbital access of the optic nerve and crushing within the dural sheath
avoiding damage to the central retinal artery are routine in our laboratory.
FG back filling of RGC: Twenty four hours before killing, the optic nerves of rats in each group are injected with 2µl
of 2% FG in PBS proximal to the site of crush, i.e. mid-way between the lesion and lamina cribrosa. After 24h, FG is
retrogradely transported into all surviving RGC, facilitating accurate RGC counts in the ganglion cell layer of retinal
whole mounts, from which amacrine cells are excluded.
Vitreous fluid sampling: At 0d and 3, 8, and 20dpl, the vitreous body is removed (routine procedure in our
laboratory) and pooled samples centrifuged at 300 rpm for 10min and stored at –80°C until analysis before mRNA
and protein extraction. Vitreous volume is 13µl in the adult rat (Dureau et al), pooling both eyes should be enough
for a Western.
Retinal whole mounts and RGC counts. After removal of the vitreous body, retinae are isolated and whole mounted
(both routine procedures in our laboratory). Counts of fluorogold-labelled RGC are made using
immunohistochemical and image analysis methods.
mRNA detection: (1) Screening; (2), specific mRNAs (such as light, medium and heavy chain neurofilament isoforms,
phosphoglycerate kinase 1, cytokeratin 18 (CK18), Lewis α-3-fucosyltransferase and ephrin receptor A2, chromatin
protein high-mobility group B1 (HMGB1), cyclophilin A, nucleosomal DNA, Fas ligand, cytochrome C, aquaporin 4
antibodies 8, neuron specific enolase and S100B).
Protein detection: (1) Screening; (2), specific proteins (such as light, medium and heavy chain neurofilament
isoforms, phosphoglycerate kinase 1, cytokeratin 18 (CK18), Lewis α-3-fucosyltransferase and ephrin receptor A2,
chromatin protein high-mobility group B1 (HMGB1), cyclophilin A, nucleosomal DNA, Fas ligand, cytochrome C,
aquaporin 4 antibodies 8, neuron specific enolase and S100B).
Human Studies
Similar analyses will be carried out in human vitreous samples and correlated with tissue damage and functional
outcomes of patients.
Key references:
REFERENCES
Berkelaar M, Clarke DB, Wang Y-C, Bray GM, Aguayo AJ (1994) Axotomy results in delayed death and apoptosis of
retinal ganglion cells in adult rats. J Neurosci 14:4368-74.
Bloomfield SM, McKinney J, Smith L, Brisman J (2007) Reliability of S100B in
predicting severity of central nervous system injury. Neurocrit Care 6:121-38.
Christofferson DE, Yuan J (2010)Cyclophilin A release as a biomarker of necrotic cell death.Cell Death Diff 17:1942-3.
Dunmire JJ, Bouhenni R, Mart ML, Wakim BT, Chomyk AM, Scott SE, Nakamura H, Edward DP (2011) Novel serum
proteomic signature in a non-human primate model of retinal injury. Mol Vis 17:779-91.
Dureau P, Bonnel S, Menasche M, Dufier JL, Abitbol M. Quantitative analysis of intravitreal injections in the rat
(2001) Curr Eye Res. 22(1):74-7.
El-Ghrably IA, Dua HS, Orr GM, Fischer D, Tighe PJ (1999) Detection of cytokine mRNA production in infiltrating
cells in proliferative vitreoretinopathy using
reverse transcription polymerase chain reaction. Br J Ophthalmol
83:1296-9.
El-Ghrably IA, Powe DG, Orr G, Fischer D, McIntosh R, Dua HS, Tighe PJ (2004) Apoptosis in in proliferative
vitreoretinopathy. Invest Ophthalmol Vis Sci 45:1473-9.
Ferreira SM, Lerner SF, Brunzini R, Reides CG, Evelson PA, Llesuy SF (2010) Time
course changes of oxidative
stress markers in a rat experimental glaucoma model. Invest Ophthalmol Vis Sci 51:4635-40.
Gesslein B, Håkansson G, Gustafsson L, Ekström P, Malmsjö M (2010) Tumor necrosis factor and its receptors in the
neuroretina and retinal vasculature after ischemia-reperfusion injury in the pig retina. Mol Vis 16:2317-27.
Greystoke A, Cummings J, Ward T, Simpson K, Renehan A, Butt F, Moore D,
Gietema J, Blackhall F, Ranson M, Hughes A, Dive C (2008) Optimisation of biomarkers of cell death for routine
clinical use. Ann Oncol 19:990-5.
Kauffmann DJ, van Meurs JC, Mertens DA, Peperkamp E, Master C, Gerritsen ME (1994) Cytokines in vitreous
humor:interleukin-6 is elevated in proliferative vitreoretinopathy. Invest Ophthalmol Vis Sci 135:900-6.
Kenarova B, Voinov L, Apostolov C, Vladimirova R, Misheva A (1997) Levels of some cytokines in subretinal fluid in
proliferative vitreoretinopathy and rhegmatogenous retinal detachment. Eur J Ophthalmol 7:64-7.
Kleindienst A, Hesse F, Bullock MR, Buchfelder, M (2007) The neurotrophic protein S100B: value as a marker of brain
damage and possible therapeutic implications. Prog Brain res 161:317-25.
Kochanek PM, Berger RP, Bayir H, Wagner AK, Jenkins LW, Clark RS (2008) Biomarkers of primary and evolving
damage in traumatic and ischemic brain injury: diagnosis, prognosis, probing mechanisms, and therapeutic decision
making. Curr Opin Crit Care 14:135-41.
Lim ET, Pashenkov M, Kier G, Thompson EJ, Söderström M, Giovannoni G (2004) Cerebrospinal fluid levels of brain
specific proteins in optic neuritis. Mult Scler 10:261-5.
Petzold A (2005) Neurofilament phosphoforms: Surrogate markers for axonal injury, degeneration and loss. J Neurol
Sci 233:183-98.
Petzold A, Rejdak K, Plant GT (2004) Axon degeneration and inflammation in acute optic neuritis. J Neurol Neurosurg
Psychiat 74:1178-80.
Ricker, LJ, Kijlstra A, Kessells AG, de Jager W, Liem AT, Hendrikse F, La Heij EC (2011a) Interleukin and growth
factor levels in subretinal fluid in rhegmatogenous retinal detachment: a case-control study. PLoS One 27;6(4):e19141.
Ricker, LJ, Altara R, Geoezinne F, Hendrikse F, Kijistra A, La Heij EC (2011b) Soluble apoptotic adhesion molecules
in rhegmatogenous retinal detachment. Invest Ophthalmol Vis Sci 52:4256-62.
Unden J, Romner B (2009) A new objective method of CT triage after minor head injury – serum S100B. Scand J Clin
Lab Invest 69:13-7.
Walsh MM, Yi H, Friedman J, Cho K, Tserentsoodol N, McKinnon S, Searle K, Yeh A, Ferreira PA (2009) Gene and
protein expression pilot profiling and biomarkers in an experimental mouse model of hypertensive glaucoma. Exp
Biol Med 234:918-30.
Ward TH, Cummings J, Dean E, Greystoke A, Hou JM, Backen A, Ranson M, Dive C (2008) Biomarkers of apoptosis.
Br J Cancer 99:841-6.
Training provided:
Animal surgery, histology, immunohistochemistry & a full range of genomics/proteomics/metabolomics methods.
Techniques to be used in the project:
See above
Names of other researchers who may also be involved in the project:
Dr Graham Wallace, Prof Martin Berry, Major Richard Blanch
Are PhD projects in this area likely to require the student to hold a personal home office licence? yes
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors:
Contact details:
School:
Area of Research:
Prof Chris McCabe and Prof Jayne Franklyn
c.j.mccabe.med@bham.ac.uk/ 58713
School of Clinical and Experimental Medicine
Hormones and Cancer
Brief description of research carried out in your team:
The McCabe/ Franklyn group investigates the mechanisms by which hormones drive tumour initiation and
progression, using thyroid, breast and colorectal tumour models. We are the leading thyroid cancer research
group in the UK, and our members include an MRC Clinician Scientist, a CRUK Senior Research Fellow,
an MRC Post Doctoral Fellow, an MRC Surgical Fellow, and 4 MRC and Wellcome funded PhD students.
As Director of Postgraduate Research in the School of Clinical and Experimental Medicine, Chris McCabe
is dedicated to PhD student support and development. Meanwhile, Jayne Franklyn is Head of the School of
Clinical and Experimental Medicine and a world renowned expert on thyroid disease. Overall, our team is a
dynamic and enthusiastic mix of clinical and non-clinical scientists engaged in leading research into
endocrine cancer, via a number of leading in vitro and in vivo approaches:
Key references:
1. RJ Watkins et al (2010). PTTG Binding Factor – a New Gene in Breast Cancer. Cancer Research 70(9); 3739-49
2. Read ML et al (2011). Proto-oncogene PBF/PTTG1IP regulates thyroid cell growth and represses radioiodide
treatment. Cancer Research 71(19):6153-64.
3. Smith et al (2012). PTTG-binding factor (PBF) is a novel regulator of the thyroid hormone transporter MCT8.
Endocrinology (In Press)
Training provided: Supportive and responsive training and supervision will be provided by Professors
Chris McCabe and Jayne Franklyn, as well as by experienced clinical and non-clinical researchers within
the lab, on a daily basis.
Techniques to be used in the project: Transfection, siRNA knock-down, cell culture, Western blotting,
TaqMan RT-PCR, immunofluorescent microscopy, transgenic mouse studies, cell invasion and migration
assays, primary cell culture, data analysis, critical appraisal of literature, scientific writing.
Names of other researchers who may also be involved in the project: Dr Kristien Boelaert, Dr Martin
Read, Dr Vicki Smith, Mr Neil Sharma, Gavin Ryan.
Are PhD projects in this area likely to require the student to hold a personal home office licence?
This is a possibility, and if deemed necessary, the successful PhD student will be helped and guided through
the process of attaining a personal home office licence.
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Matthew Morgan, Lorraine Harper
Contact details: m.d.morgan@bham.ac.uk; l.harper@bham.ac.uk;
School: Immunity and Infection
Area of Research: Renal inflammation, Vasculitis, Autoimmunity
Brief description of research carried out in your team:
The Renal Immunobiology Group is interested in the pathogenesis and treatment of patients with antineutrophil cytoplasm antibody associated vasculitis (AAV).
AAV is a devastating and often fatal autoimmune disease that causes inflammation of predominantly small
blood vessels. Whilst any organ can be affected the kidneys and lungs are most commonly affected and this
can rapidly lead to renal failure. Current treatment involves high dose corticosteroids and cytotoxic drugs.
With this treatment 5 year survival is currently around 80% but there is a huge burden of adverse effects
including infection and cancer. Our aim is to understand the pathogenesis of the disease, the factors causing
adverse events during follow up (including both treatment and disease related problems) and improve
treatment, survival and quality of life for patients.
The major themes of our research are
The role of T-cells in the pathogenesis of vasculitis: previous studies have examined changes in T-cell
phenotype in patients as they change from active disease to remission to identify cells cell populations
potentially involved in disease process, the number and function of regulatory T cells in patients, the role of
CMV in driving expansion of CD28- T-helper cells, the role of BLyS in driving a Th17 autoreactive
population in AAV and the potential role of Th17 and other T-helper subsets in AAV.
The role of stromal cells and cytokine production in glomerular inflammation: We have previously
identified IL-18 in both resident and infiltrating cells in AAV related glomerular inflammation and
established a role for it in priming neutrophils for ANCA activation. More recently we have started to
investigate the role of the inflammasome in resident renal cells in the production and activation of IL-18 and
IL-1b and the way neutrophil activation may influence inflammatory and pro-fibrotic behaviour in stromal
cells. We have also identified IL-17 producing cells in renal biopsy material and started to investigate the
effector mechanisms of IL-17 on stromal cells and the way it may mediate the inflammatory response in the
kidney.
The factors driving infection risk (a major cause of mortality) in AAV patients: We have identified that
hypogammaglobulinaemia (secondary immunodeficiency), chronic CMV infection and the increased CD28T-helper population and a reduced naive CD4 cell count are risk factors for infection in patients with AAV.
We are currently investigating role of functional inhibitory receptors on T-cells and risk of infection and
also the responses to vaccination in patients in AAV.
Key references:
Morris H, Morgan MD, Woods A, Smith SW, Ekeowa UI, Butherus K, Holle JU, Guillevin L, Lomas DA,
Perez J, Pusey C, Salama AD, Stockley R, Wieczorek S, McKnight AJ, Maxwell AP, Miranda E, Williams
J, Savage CO, Harper L. ANCA-associated vasculitis is associated with carriage of the Z allele of
α1antitrypsin and its polymers. Annals Rheum Dis 2011;70:1851-6
Holden NJ, Williams JM, Morgan MD, Challa A, Gordon J, Pepper RJ, Salama AD, Harper L, Savage
COS. ANCA stimulated neutrophils release BLyS and promote B cell survival: a clinically relevant cellular
process. Ann Rheum Dis 2011;70:2229-33
Morgan MD, Pachnio A, Begum J, Roberts D, Rasmussen N, Neil DAH, Bajema I, Savage COS, Moss PA,
Harper L. CD4+CD28- T-cell expansion in Wegener’s granulomatosis is driven by latent CMV and is
associated with an increased risk of infection and mortality. Arthritis Rheum 2011;63:2127-37
Morgan MD, Drayson MT, Savage COS, Harper L. Addition of Infliximab to standard therapy for AntiNeutrophil Cytoplasm Antibody associated vasculitis. Nephron Clin Pract 2010;117:89-97
Morgan MD, Day CJ, Piper KL, Khan N, Harper L, Moss P, Savage COS. Patients with Wegener’s
granulomatosis demonstrate a relative deficiency and functional impairment of T regulatory cells.
Immunology 2010;130:64-73
Hewins P, Morgan MD, Holden N, Neil DAH, Savage COS, Harper L. IL-18: A pro-inflammatory mediator
in ANCA-associated vasculitis Kidney Int. 2006 Feb; 69 (3): 605-15
Training provided:
As below
Techniques to be used in the project:
Techniques routinely available within the laboratory include: Cell culture and co-culture models, western
blotting, flow cytometry, immunohistochemistry, confocal microscopy, PCR, ELISA, multiplex assays,
neutrophil functional studies, T cell isolation and functional studies including T-helper subset
differentiation.
Names of other researchers who may also be involved in the project:
Our group collaborates widely including Paul Moss (Cancer Sciences), Chris Buckley and Stephen
Young (Rheumatology), Mark Drayson and Mark Cobbold (Clinical Immunology), The Binding Site
and GSK
Are PhD projects in this area likely to require the student to hold a personal home office licence? No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Professor Paul Moss, Dr Annette Pachnio
Contact details: p.moss@bham.ac.uk, 0121 414 8324
a.pachnio@bham.ac.uk, 0121 414 4485
School: School of Cancer Sciences
Area of Research: anti-viral Immunology, Cytomegalovirus
Brief description of research carried out in your team:
The main focus of our research lies on the T cell immunity to human cytomegalovirus (HCMV). This virus is a member of the
family of herpes viridae and infects about 60-90% of the population by adulthood. It remains latent within the host for life and is
thought to reactivate intermittently but in healthy individuals the virus is controlled by the immune system. In immune suppressed
individuals on the other hand CMV can cause major complications. Cytomagalovirus induces some of the largest immune
responses observed to date and earlier studies in our lab have shown that these T cell responses accumulate with age and take up a
large space within the immune system which may lead to an impairment of immunity against other pathogens. Screening healthy
CMV carriers using peptide libraries covering the whole virus proteome as well as work using a virus strain deleted for immune
evasion genes have revealed that the immune response is much broader than first thought. On average 10% of CD4+ and CD8+ T
cells in one donor were directed against this virus. Research so far has mainly been focused on the two viral proteins pp65 (the
most abundant virion associated protein) and IE-1 (the first protein made by invading virus genome). A similar phenomenon is
observed in murine CMV infection. Here “inflationary” and stable immune responses can be detected. In the human setting this
distinction has not been confirmed to date.
Using newly identified CD8-restricted peptide epitopes we are now aiming to extend the studies of CD8+ T cell responses beyond
pp65 and IE-1 to determine whether in the human setting such heterogeneity exists. The responses remain to be characterized in
terms of kinetics, phenotype and ability to recognize naturally infected cells. As these epitopes were identified using the immune
evasion-gene deleted virus strain it also is important to establish the role these play in controlling the virus. Therefore, in addition
we would like to address the role of virus-host balance by analyzing the anti-viral responses in different tissues rather then just
peripheral blood. CMV is thought to remain latent in cells of myeloid origin, but is capable of infecting a large variety of tissues
throughout the body. There are studies detecting CMV viral load and we are planning to establish these in our laboratory which
would enable us to investigate correlations between viral load and the T cell response.
Relatively little is know about the CD4+ T cell reactivities against CMV proteins. A response hierarchy has been established but
very few individual peptide epitopes have been described. More recently we have started to extend our studies of virus specific
CD4+ T cell responses. We are identifying new epitopes particularly against glycoprotein B (part of the virus envelope) which is
fed into the MHC class II processing pathway and therefore the immunodominant protein for CD4+ T cell responses. This will
then be compared to T cell responses against other glycoproteins. Furthermore new reagents have become available that will
allow us to analyse and characterize these directly ex vivo. We wish to gain more insight into the nature of these T cell responses
for example what subset of T cell they belong to, their functionality and homing characteristics.
Key references: 1) Morgan MD, Pachnio A, Begum J et al. 2011 Arthritis Rheum. Jul;63(7):2127-37. 2) Crompton L, Khan N,
Khanna R et al. 2008 Blood Feb 15;111(4):2053-61. 3) Pourgheysari B, Khan N, Best D et al. 2007. J Virol. Jul;81(14):7759-65.
4) Khan N, Best D, Bruton R et al. 2007 J Immunol. Apr 1;178(7):4455-65. 5) Khan N, Bruton R, Taylor GS et al. 2005 J Virol.
Mar;79(5):2869-79. 6) Khan N, Hislop A, Gudgeon N et al., 2004 J Immunol. Dec 15;173(12):7481-9.
Training provided: We will provide training in all relevant techniques by experienced staff. Regular meetings with supervisors
and discussion with other researchers will support the student in becoming an independent researcher. In our group we also have a
weekly lab meeting during which members present their work on a regular basis. In addition regular seminars are held in which
external speakers present their work on relevant topics.
Techniques to be used in the project: Cellular Biology – Isolation of PBMC, T cell stimulation using peptides and CMV
antigen, detection of cytokine production using flow cytometry, functional characterisation and phenotyping using flow
cytometry, T cell cloning, typing of CMV-serostatus by ELISA, tissue culture of cell lines (fibroblasts, endothelial cells,
lymphoblastoid cells)
Names of other researchers who may also be involved in the project:
Jusnara Begum – research technician
Are PhD projects in this area likely to require the student to hold a personal home office licence? No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors:
Paul Moss & Mark Kilby
Contact details:
42824
School:
Cancer Sciences & C.E.M.
Title of project:
Study of the cellular alloreactive immune response in
pregnancy and its relation to fetal loss
Outline of Project:
Pregnancy offers a major challenge to the maternal immune system. Indeed, survival of the fetal
allograft, despite maternal awareness of fetal antigen (Tafuri, Science, 1995) and a fetal-specific CD8 T cell
immune response (Piper, Biol Repro, 2007) remains a fascinating yet poorly understood immunological
enigma. Breakdown of this active state of tolerance is thought to be important in problems such as
miscarriage and preterm labour. The parallels between pregnancy and transplantation mean understanding
these processes also has important lessons to translate into improving transplantation.
Villitis of unknown aetiology (VUE) is infiltration of the villous tree of the placenta by maternal
CD8 T lymphocytes. This is a common problem (5-15% at term) associated with fetal growth restriction,
pregnancy loss and stillbirth, yet it is very poorly understood. A recurrence risk of 15-20% in subsequent
pregnancies has been reported. No infectious agent has been found and an alloimmune aetiology is
suggested. The transcriptome of VUE demonstrated multiple immunological pathways involved and
interestingly similarities with graft versus host disease (GVHD) post transplantation (Kim, JI, 2009).
Expression of the chemokine receptors CXCR3, CCR5 and their ligands is increased in VUE governing the
homing of T cells to the site (Kim, JI, 2009) and again this has close similarities with changes we observed
in women who have recurrent miscarriages (manuscript in preparation) and changes we described in GVHD
(Piper, Blood, 2007).
We recently identified that maternal CD8 T cells specific for fetal antigens can be isolated from
maternal blood throughout human pregnancy. We hypothesise that these fetal-specific T cells are
infiltrating the villi and causing VUE.
This project aims to characterise the T cell infiltrate in VUE. We will define if these cells are fetal
antigen specific and investigate how the normal mechanisms of tolerance have been disrupted in women
with VUE. Archived and fresh tissue is provided by the regional perinatal pathology centre (Birmingham
Women’s Hospital).
VUE represents not just a clinically important problem in its own right but a remarkable opportunity
to learn about the interactions of the maternal and fetal immune system and draw analogies with GVHD.
Key references:
Kim MJ, Romero R, Kim CJ, et al. Journal of Immunology 2009; 182: 3919-3927.
Piper K, McLarnon A, Ainsworth J, Kilby M, Martin W, Moss PAH. Biol Reprod 2007; 76: 96-101.
VUE review - in Redline RW, Human Pathology; 2007; 38: 1439-1446.
Training provided: T cell biology, cell separation, immunohistochemistry, flow cytometery, statistical analysis
Techniques to be used in the project: This will predominantly involve multiparameter flow cytometry,
immunohistochemical and molecular techniques to understand the phenotype, function and homing of these
infiltrating T cells and correlate this with histological classification and adverse clinical outcomes.
Names of other researchers who may also be involved in the project: Dr David Lissauer, Lecturer in
Obstetrics and Gynaecology and Dr Phillip Cox, Consultant Perinatal pathologist
Does this project require the student to hold a personal home office licence? No
Do you have all the relevant ethical approval for this study? Application via HBRC
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Paul Murray
Contact details: Tel: 0121 414 4021, e-mail: p.g.murray@bham.ac.uk
School: Cancer Sciences
Area of Research: Chronic inflammation and lymphomagenesis
Brief description of research carried out in your team:
Work in the Murray Group is focussed on understanding how a common virus, the Epstein-Barr virus (EBV),
contributes to the pathogenesis of human lymphomas. Previous work in the Group has shown not only how EBV
contributes to the transformation of human B cells, but also that EBV can induce the recruitment of chronic
inflammatory which in turn support tumour cell growth.
We now wish to address several key questions:
1) What are the early events in EBV-driven lymphomagenesis leading to the establishment of a persistent
chronic inflammatory state in B cells?
2)
How does this chronic inflammatory state contribute to lymphomagenesis?
3) Can inhibition of this chronic inflammation provide an alternative, less toxic, therapy for lymphoma
sufferers?
Several types of EBV-associated lymphoma, particularly those arising in the elderly or in immunosuppressed
patients, have a very poor outcome. The ultimate goal of our studies is to identify novel approaches to treat
lymphoma patients. We are particularly excited about the potential to target the non-malignant chronic
inflammatory cells present in these lymphomas as an alternative therapy for patients with aggressive types of
lymphoma.
Key reference:
Vrzalikova K, Vockerodt M, et al., Down-regulation of BLIMP1α by the EBV oncogene LMP1 disrupts the plasma cell
differentiation program and prevents viral replication in B cells: implications for the pathogenesis of EBV-associated
B cell lymphomas. Blood 2011; 117: 5907-17.
Training provided: Training will be provided in molecular biology and cell biology techniques as well as in novel
approaches to the study of lymphoma pathogenesis, which will include the isolation and analysis of primary human
B cell subsets transduced with viral oncogenes and the development of 3-dimensional in vitro models to study
interactions between lymphoma cells and their microenvironment.
Techniques to be used in the project e.g. magnetic isolation of B cell and other lymphoid subsets, 3dimensional cell culture, gene expression (microarrays, Q-RT-PCR, immunohistochemistry).
Names of other researchers who may also be involved in the project: Dr Martina Vockerodt, Dr Katerina
Vrzalikova, Dr Zumla Cader
Are PhD projects in this area likely to require the student to hold a personal home office licence? No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Prof. Gerard Nash & Dr. Helen McGettrick
Contact details: g.nash@bham.ac.uk (x43670); h.m.mcgettrick@bham.ac.uk (x44043)
School: Clinical and Experimental Medicine & Immunity and Infection.
Area of Research: Inflammation Biology: What controls leukocyte entry, transit through
and exit of tissue?
Regulation of the inflammatory leukocyte infiltrate
Inflammation requires the recruitment of leukocytes by the vascular endothelium and their subsequent
migration into the tissue. Resolution of inflammation requires that they also leave (or undergo apoptosis and are
cleared by macrophages). We and our colleagues have described a number of mechanisms which control leukocyte
recruitment, and are becoming increasingly interested in factors deciding their subsequent fate. From a therapeutic
point of view, one might wish to down-regulate adhesion and migration on vascular endothelium or promote
migration out through lymphatics. We know little about the control of the latter process.
In recent years, we have concentrated on the concept that the state of the local tissue stroma defines the
efficiency with which vascular endothelial cells recruit leukocytes, and also the subsequent fate of these leukocytes 1.
This has involved the development and validation of novel in vitro, multi-cellular, layered culture systems, allied to
flow systems for studying capture of leukocytes. We aim to develop a more complete understanding of the
mechanisms regulating leukocyte recruitment, onward tissue migration and subsequent egress during acute and
chronic inflammation. A novel concept that we are investigating is to manipulate the local stroma to instruct
recruited cells to leave chronically inflamed tissue, in effect to “switch on” resolution, or alternatively to stop
leukocytes entering the inflamed site by “turning off” recruitment.
Our current work in these areas can be divided into 4 main research themes:
1. Characterising the regulatory steps determining efficiency of T-cell migration into tissue2.
2. Understanding endothelial-fibroblast interactions and their ability to influence leukocyte behaviour3-4.
3. Determining how mesenchymal stem cells influence endothelial recruitment and fate of leukocytes.
4. Dissecting crosstalk between vascular and lymphatic endothelial cells and its effects on the balance of
leukocyte infiltrates5.
These processes are all relevant to acute or chronic inflammatory disorders, and their manipulation is potentially
therapeutic. We thus maintain close collaborative ties with clinical colleagues working on rheumatology and
cardiovascular disease.
Key references:
1. McGettrick et al., Stromal tissue as a regulator of leukocyte recruitment in inflammation. J. Leuk Biol, 2012, 91:385-400
2. McGettrick et al., Direct observations of the kinetics of migrating T-cells suggest active retention by endothelial cells with
continual bidirectional migration. J Leuk Biol 2009, 85; 98-107.
3. McGettrick et al., Fibroblasts from different sites may promote or inhibit recruitment of flowing lymphocytes by endothelial
cells. Eur J Immunol 2009, 39; 113-125.
4. McGettrick et al., Stromal cells differentially regulate neutrophil and lymphocyte migration through the endothelium.
Immunol. 2010, 131; 357-370
5. Ahmed et al., Prostaglandin-D2 regulates the traffic of CD4+ memory T cells across blood vascular endothelial cells and primes
the same cells for clearance across lymphatic endothelium. J Immunol. 2011, 187:1432-1439
Training provided: A wide range of laboratory skills (noted below), generic skills in oral and written presentation,
project and time management, analytical skills.
Techniques to be used in the project: Cell culture, isolation of leukocytes, microscopic adhesion and migration
assays, image analysis, immunofluorescence and flow cytometry, basic molecular biology (qPCR, siRNA and over
expression studies for manipulation of gene expression), analysis of cytokines, chemokines and lipids secreted into
supernatants or matrices.
Names of other researchers who may also be involved in the project:
The supervisors’ close collaborators are Prof. Ed Rainger, Prof. Chris Buckley & Prof. Jon Frampton.
Are PhD projects in this area likely to require the student to hold a personal home office licence? No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Phil Newsome & Jon Frampton
Contact details: 45614
School: Immunity & Infection
Area of Research: Mesenchymal stem cells and inflammatory injury
Brief description of research carried out in your team:
Mesenchymal stem cells (MSC) are a predominantly bone marrow and fat derived stem cell, with
immunomodulatory properties. We have unique access to murine and human mesenchymal stem cells in our
laboratories and are focussing on the role of mesenchymal stem cells in suppressing aberrant inflammatory
injury.
We have recently shown that adoptively transferred human MSC injected into venous blood are recruited to
the injured liver via specific molecular mechanisms activated in the inflamed liver (Aldridge et al,
Hepatology 2012). We have also identified the mechanisms by which mouse and human MSC profoundly
inhibit T cell activation & proliferation in vitro. Preliminary data demonstrates our MSC are able to reduce
immune-mediated pancreas damage.
We have relevant mouse models of inflammatory injury (liver and other), in which we would like to test the
efficacy and mechanisms of action of MSC infusions. We would propose that the successful student would
study the mechanisms by which MSC reduce inflammatory injury.
Options include studying the impact of priming MSC with cytokines to improve their immunomodulatory
function and homing to injured organs. The effects of this can be studied both in vitro and in vivo. The
factors engrafting MSC secrete to exert can be studied by assessing their secretome.
The student would be joining a team of 4 scientists/students working with MSC in this setting.
Key references:
Human mesenchymal stem cells are recruited to injured liver in a β1 integrin and CD44 dependent manner.
Aldridge V, Garg A, Davies N, Bartlett DC, Youster J, Beard H, Kavanagh DP, Kalia N, Frampton J, Lalor
PF, Newsome PN. Hepatology. 2012 Mar 15.
Prospective identification, isolation, and systemic transplantation of multipotent mesenchymal stem cells in
murine bone marrow. Morikawa S, Mabuchi Y, Kubota Y, Nagai Y, Niibe K, Hiratsu E, Suzuki S,
Miyauchi-Hara C, Nagoshi N, Sunabori T, Shimmura S, Miyawaki A, Nakagawa T, Suda T, Okano H,
Matsuzaki Y. J Exp Med. 2009 Oct 26;206(11):2483-96. Epub 2009 Oct 19.
Training provided: As per the techniques below
Techniques to be used in the project: Flow cytometry, Cell sorting, Immunohistochemistry, in vivo
models of injury, cell infusions in vivo, ELISA, Western Blotting
Names of other researchers who may also be involved in the project:
Are PhD projects in this area likely to require the student to hold a personal home office licence?
YES
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Professor Mark Pallen and Professor Gurdyal Besra
Contact details: m.pallen@bham.ac.uk
School: Institute of Microbiology and Research, School of Biosciences
Area of Research: Esx protein secretion in diverse bacteria
Brief description of research carried out in your team:
Tuberculosis is the most important bacterial disease worldwide. This infection is
caused by Mycobacterium tuberculosis, which possesses the most complex cell
envelope of all known bacteria. Professor Gurdyal Besra is a world expert on the
biosynthesis of the mycobacterial cell wall. Crucial to the virulence of M. tuberculosis
are a number of specialised protein secretion systems, known as Esx or Wss secretion
systems. It remains a mystery as to how these systems are deployed in the bacterial
cell envelope and allow protein secretion across the thick cell wall. Some years ago
Professor Mark Pallen, an expert on bacterial protein secretion systems, showed that
Esx secretion systems were not confined to M. tuberculosis and its close relatives, but
instead occur in a wide range of Gram-positive bacteria. More recently, these
observations have been generalised to an even more diverse set of bacteria, including
the Gram-negative pathogen Helicobacter pylori. This opens up the possibility of
investigating this crucial mycobacterial virulence factor in a more tractable Gramnegative host, while also raising the question of what role Esx secretion might play in
the biology of the important human gastric pathogen, H. pylori. This project will thus
explore the functions of the various proteins involved in Esx secretion in these two
contexts, together with relevant protein-protein interactions, mainly through
molecular biological methods in pathogens and model organisms (e.g. E. coli, M.
smegmatis). Attempts will also be made to locate and visualise the Esx secretion
apparatus in situ in the cell wall.
For more information on our research see:
http://pathogenomics.bham.ac.uk/staff/mpallen.html
http://www.birmingham.ac.uk/staff/profiles/biosciences/besra-gurdyal.aspx
Key references:
http://www.ncbi.nlm.nih.gov/pubmed/11973144,21045286,21521247
Training provided in molecular biology techniques and electron microscopy
Techniques to be used in the project: PCR, cloning, sequencing, SDS-PAGE, Western blotting, protein
expression, protein-protein interaction techiques, mutant construction and complementation
Names of other researchers who may also be involved in the project:
Dr Chrystala Constantinidou; Professor Charles Penn, Dr Luke Alderwisk, Dr Apoorva Bhatt
Are PhD projects in this area likely to require the student to hold a personal home office licence?
No
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors:
Dr Graham Taylor, Dr Heather Long and Prof Alan Rickinson
Contact details: g.s.taylor@bham.ac.uk 0121 4147458
h.m.long@bham.ac.uk 0121 4142808
School:
School of Cancer Sciences
Title of project: Epstein-Barr Virus (EBV) – fundamental and translational research
on an important human pathogen
Outline of Project:
A major focus of research conducted by the Rickinson/Taylor/Long laboratories is studying the immunology
of Epstein-Barr Virus infection (EBV). This virus is important in two respects.
First, as a common human infection EBV allows fundamental aspects of human immunity to be explored.
Rickinson has been instrumental in characterising the evolution of the CD8 T cell response to EBV, work
that has been extended by Taylor and Long to the CD4 T cell response. Taylor has shown how protein
localization affects antigen processing by autophagy, and is continuing to research this novel antigen
processing pathway. Long has demonstrated the broad spectrum of proteins targeted by the CD4+ T cell
response, shedding new light on this area.
Second, EBV is associated with several different cancers. Therefore, the laboratories also perform
translational research seeking to improve patient outcomes. Rickinson and Taylor have successfully taken
a new therapeutic cancer vaccine through phase I clinical trials in cancer patients and the results have led
to two subsequent international phase 2 trials that are currently underway. Long has identified exciting
novel immune targets within cancer cells and is currently characterising these for therapeutic use. EBV is
also increasingly recognized as playing a role in the development of the autoimmune disease Multiple
Sclerosis. Rickinson and Taylor, in collaboration with leading neurologists, are working to identify the
immunological mechanisms underpinning EBV’s role in the development of MS, work that is funded by the
Wellcome Trust.
Key references:
Long HM, Leese AM, Chagoury OL, Connerty SR, Quarcoopome J, Quinn LL, Shannon-Lowe C, Rickinson AB.
Cytotoxic CD4+ T cell responses to Epstein-Barr virus contrast with CD8 responses in breadth of lytic cycle antigen
choice and in lytic cycle recognition. J Immunol. 2011;187(1):92-10
Long HM, Taylor GS, Rickinson AB. Immune defence against EBV and EBV-associated disease. Curr Opin
Immunol. 2011; 23(2):258-64.
Leung, CS, Haigh TA, Mackay LK, Rickinson AB, Taylor GS. Nuclear location of an endogenously expressed
antigen, EBNA1, restricts access to macroautophagy and the range of CD4 epitope display. Proc Nat Acad Sci (USA)
2010; 107(5):2165-70.
Hislop AD, Taylor GS, Sauce D, Rickinson AB. Cellular responses to viral infection in humans: lessons from
Epstein-Barr virus. Annu Rev Immunol. 2007;25:587-617.
Training provided: This project will provide the student with a wealth of skills in advanced laboratory techniques.
Additionally, the student will have the opportunity to further their knowledge of viral and tumour immunology by
attending group meetings, journal club presentations and internal, external and cross-departmental seminars.
Essential transferable skills will also be developed.
Techniques to be used in the project:
Recombinant virus technology, cell biology techniques, immunological cytotoxicity and cytokine assays
Names of other researchers who may also be involved in the project:
Prof Alan Rickinson
Does this project require the student to hold a personal home office licence? No
Do you have all the relevant ethical approval for this study? Yes
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Kai-Michael Toellner
Contact details: K.M.Toellner@bham.ac.uk, Tel 58687, IBR room 432
School: Immunity and Infection
Area of Research: B cell differentiation, Vaccination and memory
Brief description of research carried out in your team:
Vaccine or pathogen induced B cell activation results in a complex differentiation programme, before cells
become plasma cells that secrete large amounts of high affinity protective antibody. This involves B cell
migration through different compartments of lymphoid tissues, interactions with accessory cells, and
differentiation events such as immunoglobulin class switching and hypermutation. Our team tries to
understand the sequence and location of these events, and how they are regulated by the environment. We
were one of the first groups to show when and where B cells are activated initially and where they interact
with T cells 1,2, and we developed a transgenic mouse model with which large numbers of differentiating B
cells can be followed in vivo 3,4. More recently we have used this model to characterize the initial steps
leading to early plasma cell formation, which is regulated by a balance of transcription factors that either
induce differentiation to plasma cells, or induce affinity maturation of B cells in germinal centres 5. An
important transcription factor regulating Ig class switching, plasma cell, and germinal centre differentiation
is interferon regulatory factor 4 (IRF4) 6. Using our own mouse model we recently have shown that IRF4 is
involved in regulating initial Ig class switching, as well as regulating plasma cell output from GCs
(unpublished).
Currently we try to understand which signals regulate B cells to produce plasma cell, and to produce plasma
cell output from the germinal centre. This work is done using mice deficient in transcription factors,
cytokines or costimulatory molecules regulating B cell differentiation. Isolation of B cells followed by
analysis of gene and protein expression on single cell level, and microscopy to trace specific B cells give us
information what happens inside B cells while they migrate through different microanatomical
compartments.
A range of signals has been identified – signals that may be produced by T cells, dendritic cells, stromal
cells, or come from lymphoid tissue inducer cells. To address where these signals come from stroma we
currently develop a transgenic mouse model in which stromal cells can be specifically deleted at specific
times after vaccination. This model will be used to address when and whether stromal cells interact with B
cells to induce high affinity germinal centre derived plasma cells.
Key references:
(1) Toellner et al. J. Exp. Med. 183, 2303-2312, (1996). (2) Toellner et al. J. Exp. Med. 187, 1193-1204, (1998). (3)
Garcia de Vinuesa et al. J. Exp. Med. 191, 485-494, (2000). (4) Toellner et al. J. Exp. Med. 195, 383-389, (2002). (5)
Marshall et al. Eur. J. Immunol. 41, 3506-3512, (2011). (6) Sciammas et al. Immunity 25, 225-236, (2006).
Training provided: Training in all techniques necessary to perform the project will be provided by experienced
team members (postdocs or PhD students). Analysis of data, discussion of the progress of the project, and oral or
written presentation of data will be practiced in at least weekly group or individual meetings with the supervisor.
Techniques to be used in the project:
Vaccination of mice and adoptive transfer of B cells, ELISA, immunoenzymatic and immunofluorescence
histology, stereological analysis of tissues, flow cytometry, real time RT-PCR, statistical analysis.
Names of other researchers who may also be involved in the project:
Dr. Yang Zhang, Dr. Jennifer Marshall, Dr. Francesca Barone, Prof. Chris Buckley
Are PhD projects in this area likely to require the student to hold a personal home office licence?
Yes – can be obtained during project
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Steve Watson and Neena Kalia
Contact details: s.p.watson@bham.ac.uk
School: CEM and II
Area of Research:
Platelets in the maintenance of the lymphatic system and in atherosclerotic plaque
formation in adult mice fed on a high fat diet
Brief description of research carried out in your team:
The last few years have seen major advances in our understanding of the development and maintenance of
the lymphatic system. This includes the demonstration from our own group of a critical role of the ITAM
receptor, CLEC-2, on platelets in the separation of the lymphatics from the cardinal vein during
development and in the maintenance/repair of the lymphatics following radiation (Finney et al., 2012). In
addition, we have shown that the ligand for CLEC-2, podoplanin, is present on inflammatory macrophages
and that these can stimulate powerful platelet activation (Kerrigan, Journal of Thrombosis and
Haemostasis in press). Significantly, podoplanin is expressed on inflammatory macrophages in advanced
atherosclerotic plaques.
This project will build on these observations using three new adult mouse models that have been made in
Birmingham: namely mice deficient in the platelet lectin receptor CLEC-2, the CLEC-2 ligand, podoplanin
and the CLEC-2 signalling partner Syk. Using a tamoxifen-inducible system, we are able to knock out all
three proteins in the adult animal. The goal of this project is to
(i)
(ii)
study the maintenance and function of the lymphatic system upon feeding of the mice on a high
fat diet given the critical role of the lymphatics in fat absorption;
investigate the role of these three proteins on an ApoE background to investigate the role of this
pathway in plaque formation.
Key references: Finney, B.A., Schweighoffer, E., Navarro-Núñez, L., Bénézech, C., Barone, F., Hughes, C.E.,
Langhan, S., Lowe, K.L., Pollitt, A.Y., Mauro-Sa, D., Sheardown, S., Nash, G.B., Smither, N., Reis e Sousa, C.,
Tybulewicz, V.L.J. and Watson, S.P. (2012) CLEC-2 and Syk in the megakaryocytic/platelet lineage are essential for
development. Blood 119:1747-1756
Training provided: We are a large group and so can provide training in basic techniques but the student
will be encouraged to develop new techniques of their own.
Techniques to be used in the project: histology; mouse breeding; various in vivo techniques including
intravital imaging of both the blood and lymphatic systems.
Names of other researchers who may also be involved in the project: Ed Rainger.
Are PhD projects in this area likely to require the student to hold a personal home office licence?
Yes
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Professor Steve Watson, Dr Graham Wallace
Contact details: watsonsp@bham.ac.uk; g.r.wallace@bham.ac.uk
School: Imminuity and Infection
Area of Research: Lymphangiogenesis in ocular inflammation
Brief description of research carried out in your team:
Corneal transplantation is one of the most successful operations in the field. However graft rejection does
occur and acceptance depends on the level of vascularisation in the recipient tissue. To date the role of
neovascularisation has been well investigated and many of the mechanisms involved identified. By
comparison, the growth of new lymphatic vessels has only recently been discovered and their contribution
to acceptance/rejection is not known. This project will address lymphangiogenesis in mouse models of
corneal inflammation. Human corneal tissue will also be available for validation of molecules and pathways
involved in the process. The project will involve analysing mechanisms and molecular pathways in normal
mice and animals in which key control molecules of lymphangiogenesis are deficient. Inhibition of
lymphabgiogenesis by pharmaceutical therapy will also be addressed. The project provide the opportunity to
study an important human process in animal models, then translate back to human tissue. The role and
control of lymphangiogenesis is regeneration and disease progression is relevant to many others tissues as
well as the cornea and therefore will encourage interaction with other researchers.
Key references:
Tshionyi M. et al Cornea 2012 31;74
Steele MM. et al Cornea 2011 30;1442
Chauhan SK. et al Blood 2011 118;4630
Kerrigan AM. et al J Thromb Haemost 2012 10;484
Liu L. et al Invest Ophthalmol Vis Sci 2011 52;7282
Training provided:
The student will be given instruction in all the techiques described which are all currently available in the
laboratories of the supervisors progress will be assessed by regular weekly meetings.
Techniques to be used in the project:
Cell culture, animal experimentation, PCR, signalling analysis, flow cytometry
Names of other researchers who may also be involved in the project:
Ms Saaeha Rauz – human corneal tissue and
Are PhD projects in this area likely to require the student to hold a personal home office licence?
Yes
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Dr Stephen Young
Contact details: s.p.young@bham.ac.uk
School: Immunity & Infection
Area of Research: Chronic Inflammatory Disease
Brief description of research carried out in your team:
Chronic inflammatory diseases such as rheumatoid arthritis have a complex aetiology with strong contributions from
both genes and environmental factors such as age, gender, diet, smoking and infection. The most significant genes are
MHC class II and PTPN 22, which strongly suggest that signalling through immune cell receptors is key to the
susceptibility to these diseases. Work in our laboratory is focused on how environmental factors may synergise with
polymorphic genes to give rise to altered immune cell signalling and function and thus give rise to chronic disease.
One important characteristic of the rheumatoid joint, which may also be true of other tissues susceptible to chronic
disease, is that oxygen levels are very low which may have profound effects on the function of immune cells,
contributing to a disease phenotype.
Projects currently underway in the laboratory are investigating metabolomic profiling of samples from patients with
early arthritis, coupled with in vitro analysis of metabolism of fibroblasts taken from the joints of patients. Fibroblasts
and macrophages take up an aggressive phenotype in rheumatoid arthritis and are responsible for much of the joint
destruction, and so we are investigating how the hypoxic inflammatory environment of the joint alters the metabolism,
differentiation and function of these cells. Altered signalling through the T-cell receptor within the inflammatory joint
may also deviate cells down a route which supports chronic inflammation and so we are also investigating the effects
of hypoxia and inflammatory mediators on the differentiation of T cells with a particular focus on TH 17 and Tregs.
We are also studying how the oxidative joint environment together with exogenous oxidative stress resulting from
cigarette smoke and dietary insufficiency in antioxidant intake may synergise with polymorphic variants of the key
phosphatase PTPN 22 to contribute to aberrant T cell signalling and differentiation. Many questions still the wait to be
addressed in this area which could form the basis of a PhD project, some of which are listed below:
What is the role of the Lyp phosphatase (PTPN22) in phagocyte signalling and function?
Do variants of PTPN22 give rise to altered monocyte and neutrophil function?
Does the decline in antioxidants in age give rise to altered PTP function and promote auto-inflammation?
Does tissue hypoxia regulate immune cell function giving rise to pro-inflammatory cells?
Do smokers have altered immune cell function which underpins RA and COPD?
Does the Warburg effect drive autoimmunity as well as cancer?
Does expression of variant PTP22 or depletion of GSH in RA patients explain immune dysfunction?
In mice expressing variant PTP which cells contribute to arthritis?
Key references:
Kapoor, S., M. Fitzpatrick, et al. (2012). Metabolomics in the analysis of inflammatory diseases. Metabolomics. U. Roessner.
Rijeka, Intech: 269-288.
Rider, D. A., A. J. Sinclair, et al. (2003). "Oxidative inactivation of CD45 protein tyrosine phosphatase may contribute to T
lymphocyte dysfunction in the elderly." Mechanisms Of Ageing And Development 124(2): 191-198.
Young, S. P., M. Nessim, et al. (2009). "Metabolomic analysis of human vitreous humor differentiates ocular inflammatory disease."
Molecular Vision 15: 1210-1217. The
Training provided: This will depend on the project, but training in the techniques below will be available.
Strong encouragement to attend meeting such as the BSI is given to ensure a broad background knowledge
is maintained.
Techniques to be used in the project: This will depend on the project, but a range of specialist techniques
are available from Biacore interaction analysis, NMR-based metabolite profiling, Ca signalling imaging,
hypoxic cells culture, along with standards such as FACS analysis of cell signalling and PTP assays.
Names of other researchers who may also be involved in the project: Rachel Bayley, Beth Clay, Martin
Fitzpatrick, Sabrina Kapoor, Graham Wallace, Chris Buckley.
Are PhD projects in this area likely to require the student to hold a personal home office licence? Yes,
if work on a PTPN22 variant mouse model is part of the project.
Wellcome Trust Combined Training Programme
PhD Project Request Form
Supervisors: Dr Jianmin Zuo, Prof Martin Rowe
Contact details: j.zuo@bham.ac.uk / m.rowe@bham.ac.uk
School: Cancer Sciences
Area of Research: Virology/Immunology/Cancer
Brief description of research carried out in your team:
Epstein-Barr virus (EBV) is carried as a lifelong latent infection in the B cell compartment. The majority of
adults worldwide are infected with EBV, and usually with no obvious symptoms. However, the virus has the
potential to growth-transform cells, and in some circumstances can be pathogenic; primary infection may
manifest as infectious mononucleosis and persistent infection can cause cancer. Successful asymptomatic
persistence that occurs in the vast majority of people depends on the establishment of a balance between
host immune responses and viral immune evasion.
Our group is studying the factors that regulate the virus:host balance. A number of immunevasins targeting
the MHC-I and MHC-II antigen presentation pathways from EBV have recently been identified. Using a
reductionist in vitro approach (i.e. transfection of single viral genes into EBV-negative cells) we identified
EBV-encoded BGLF5, BNLF2a and BILF1 as immunevasins of MHC-I antigen presentation, and BZLF1
as an immunevasin of MHC-II antigen presentation. We have currently cloned most of the viral genes into a
pCDNA3-IRES-GFP vector, which will enable us to systematically identify any additional immunevasins
by screening with functional EBV-specific immune T cells.
With regards to the known evasion genes of the MHC-I pathway, we know that they are expressed at
different time points in the life-cycle of EBV. We hypothesise that they cooperatively contribute to
establishment of the virus-host balance in vivo. To test this, we are using recombinant EBVs deleted for one
or more immunevasins to establish therir significance in the context of whole virus infections. One arm of
this work involves collaboration with Prof Münz’s lab (Zurich) where a humanized mouse model of EBV
infection has been established; this will enable us to examine the impact of immunevasins on infections in
vivo to complement our in vitro studies.
Key references:
Zuo, J., A. Currin, et al. 2009. PLoS Pathog, 5:e1000255.
Zuo J., Thomas WA, et al. 2011 PLoS Pathog, 7: e1002455
Training provided:
The student will join an internationally recognised and highly active research group. In this environment,
the student will learn how to develop creative ideas and plan appropriate well-controlled experiments to test
relevant hypotheses. Communication, networking, and other transferrable skills will also be developed.
Techniques to be used in the project: Recombinant virus engineering and other general molecular biology
techniques. Cloning of virus-specific T cells, and functional assays. Multi-colour flow cytometry and
confocal microscopy. Biochemical assays of MHC-antigen processing.
Names of other researchers who may also be involved in the project:
Dr Andrew Hislop, Prof Alan Rickinson
Are PhD projects in this area likely to require the student to hold a personal home office licence?
Possibly, depending on student’s interests.