Theme 1 Molecules, Cells and the Basis for Disease€¦ · 19.1 Identifying effective drugs to...
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Theme 1 Molecules, Cells and the Basis for Disease 2017/2018
Transcript of Theme 1 Molecules, Cells and the Basis for Disease€¦ · 19.1 Identifying effective drugs to...
Theme 1
Molecules, Cells and the Basis
for Disease
2017/2018
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1.1 Dissecting antigen presentation to T lymphocytes using dendritic cells derived from genetically
modified induced-pluripotent stem cells ................................................................................................... 5 2.1 Mapping the PTPN22 interactome. .................................................................................................... 6 3.1 MicroRNAs as biomarkers of liver regeneration and their link to tumour biology ........................... 7 4.1 Whole organ bioengineering for tooth replacement ........................................................................... 8 5.1 Applying single-cell RNA sequencing technologies to establish cardiac stem/progenitor cell
heterogeneity ............................................................................................................................................. 9 6.1 Developing nanomedicines for immunosuppression in liver transplantation ................................... 10 7.1 Manipulating the stem cell state in vivo ............................................................................................ 11 8.1 Mechanisms of bacterial inhibition by interferon-stimulated genes ................................................. 12 9.1 The role of post-translational modification of self proteins in breaking immune tolerance in type 1
diabetes .................................................................................................................................................... 13 10.1 Gestational Diabetes, the epigenome and the health of the next generation ................................. 14 11.1 Tackling hearing loss: development, regeneration and reconstruction of the ear .......................... 15 12.1 Mechanism of membrane remodelling in cell biology and replication of HIV-1 and Ebola virus . 16 14.1 E Gene expression in skin in subjects with reduced biological ageing compared to their
chronological ageing ................................................................................................................................ 18 15.1 Adhesion receptor signalling regulating lung cancer progression .................................................. 19 16.1 Developing novel, conventional and nanoparticle, inhibitors of the Wnt signaling pathway as a
treatment for prostate and breast cancers ............................................................................................... 20 17.1 Roles of the RNA-binding proteins LARP4A and LARP4B in cancer cell migration and invasion
................................................................................................................................................................. 21 18.1 Membrane remodelling during cell division ................................................................................... 22 19.1 Identifying effective drugs to treat oral squamous cell carcinoma. ................................................ 23 20.1 Interventions to improve maternal metabolic profile in obese pregnancy and prevent cardio-
metabolic and behavioural deficits in future generations ....................................................................... 24 21.1 Molecular dissection of epigenetic signals controlling muscle stem cell behaviour during
regeneration ............................................................................................................................................. 25 22.1 A Bioengineering Approach To Polarise Glioma Tumour Initiating Cells and Induce Asymmetric
Cell Division In Order To Limit Their Tumorigenic Potential ............................................................. 26 23.1 Mesenchymal Stromal cells – a novel therapy for Crohn’s disease ................................................ 27 24.1 HIV-1 mediated reprogramming of T cell gene expression networks ........................................... 28 25.1 The role of the pro-FLG Ca2+-binding domain in the formation of the skin barrier and pathogenesis
of atopic dermatitis .................................................................................................................................. 29 26.1 Exploring the general mechanisms of mammalian neural crest migration in vivo using live cell
imaging and how it is altered in neuroblastoma cancer cells ................................................................. 30 27.1 Functional interrogation and therapeutic intervention of the molecular pathways driving cutaneous
T-cell lymphoma ..................................................................................................................................... 31 28.1 In-silico design and identification of novel antiviral drugs targeting vector borne viruses (Zika,
Dengue & Chikungunya) ........................................................................................................................ 32 29.1 Defining the role of circulating fibrocytes in the pathogenesis of renal fibrosis; a study of cell-
signalling crosstalk .................................................................................................................................. 33 30.1 Structural characterisation of a novel cytolytic peptide toxin ........................................................ 34 31.1 MS1 - a cardiac regulator of development and stress ..................................................................... 35
32.1 Identifying novel molecular mechanisms involved in the generation of new insulin-producing beta
cells from adult stem/ progenitor cells………………………………………………………………………………36 33.1 Therapeutic use of regulatory T cells in liver disease: Immunoregulation and tissue
regeneration ............................................................................................................................................. 37 34.1 Understanding regulation of cellular energy metabolism ............................................................... 38 35.1 Mechanism of action of a cancer-selective protein toxin ................................................................ 39
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36.1 Mitochondrial microRNA (MitomiRs) and their relationship to mitochondrial bioenergetics ..... 40 37.1 Using chemical modification of anticancer drug scaffolds to study efflux mediated chemoresistance
in cancer stem cells .................................................................................................................................. 41 38.1 Role of sphingosine-1-phosphate (S1P) signalling in cochlear homeostasis and progressive hearing
loss ........................................................................................................................................................... 42 39.1 Characterising the epigenome in mice after exposure to environmental carcinogens ................... 43 40.1 Understanding immune responses in intestinal homeostasis and disease ....................................... 44 41.1 Broadly neutralizing antibody responses against HIV ................................................................... 45 42.1 The CXCL8-producing T cell: function in health and carcinogenesis ........................................... 46 43.1 Elucidating the crosstalk between lymphocytes and intestinal epithelial cells using human mini-
guts ........................................................................................................................................................... 47 44.1 Elucidating the molecular mechanisms of peanut allergies ............................................................. 48 45.1 Targeting PSK kinases for breast cancer therapy ........................................................................... 49 46.1 How do mutations in MYO18B lead to muscle diseases? ............................................................... 50 47.1 Developmental basis of skin diversity ........................................................................................... 51 48.1Molecular mechanisms underlying the contractile dysfunction in ageing-related muscle
weakness .................................................................................................................................................. 52 49.1 Linking Genotype to Phenotype in Psoriatic Arthritis: determining the role of disease-associated
genes in Tc17 cell function and development ......................................................................................... 55 50.1 TRPV1 and TRPA1 ligands as P-gp substrates: a wide-reaching investigation from basic molecule
through to animal models of disease ....................................................................................................... 57
51.1 Role of genetic regulation of gene expression in Type 2 Diabetes and Obesity………………………59
52.1 Identifying novel therapeutics to target pancreatic cancer metastasis………………………………..60
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Molecules, Cells and the Basis for Disease
This theme brings together stem cells and regenerative medicine (inc. cellular
therapies), immunology, genetics, cellular biology (particularly relating to
cancer), and biophysics. These areas – and particularly the interfaces between
them – are current strengths and priorities for King’s.
Lead: Professor Rebecca Oakey
When choosing a project from this catalogue in the funding section of the online
application form please enter MRCDTP2017_Theme1
Deadline for application: Sunday 7th
May 2017
Shortlisted candidates will be contacted in early June and invited to an interview on June
15th
.
Interviews: 15 June 2017
The 2017/18 studentships will commence in September 2017.
For further Information or queries relating to the application process please contact
Projects listed in this catalogue are subject to amendments, candidates invited to interview
will have the opportunity to discuss projects in further detail.
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1.1 Dissecting antigen presentation to T lymphocytes using dendritic cells derived from
genetically modified induced-pluripotent stem cells
Co-supervisor 1: Pierre GUERMONPREZ
Research Division or CAG: DIIID
E-mail: [email protected]
www.kcl.ac.uk/lsm/research/divisions/diiid/departments/immunobiology/research/guermonprez/i
ndex.aspx
Co-supervisor 2: Timothy TREE
Research Division or CAG: DIIID
Email: [email protected]
Website:http://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/immunobiology/research
/Tree/index.aspx
Project Description:
Depending on environmental cues, dendritic cells (DCs) can induce the functional inactivation of T
cells (i.e. tolerance) or their differentiation in effector/memory T cells (i.e. immunity). Regulatory
“immune checkpoints” molecules (PDL1/PDL2, e.g.) or co-stimulatory molecules
(CD80/CD86/OX40-L/CD40, e.g.) expressed by DCs determine T cell fate after DC-T cell
interactions. DC-based immunotherapies are currently limited by the difficulty to obtain large
amounts of DCs of immunogenic phenotype to infuse in patients. Human Induced Pluripotent Stem
Cells (iPSCs) represent an inexhaustible source of immunologically compatible cells opening novel
iPSCs (termed as iPSCDCs) by recapitulating the physiological differentiation pathway of DCs from
hematopoietic stem cells. We intend to apply this technology to iPSCs, genetically modified using
CRISPR/Cas technology, in which inhibitory signalling molecules are inactivated and/or activator
pathways activated. The ultimate goal of this approach is to generate iPSCDCs with increased
potential to activate T cells. iPSCDCs might serve as a proof-of-concept for the development of new
cellular immunotherapies in cancer patients.
Two representative publications from supervisors:
Cross-Presentation of Cell-Associated Antigens by MHC Class I in Dendritic Cell Subsets. Gutiérrez-
Martínez E, Planès R, Anselmi G, Reynolds M, Menezes S, Adiko AC, Saveanu
L, Guermonprez P. Front Immunol. 2015 Jul 17;6:363.
Inflammatory Flt3l is essential to mobilize dendritic cells and for T cell responses during Plasmodium
infection. Guermonprez P*, Helft J, Claser C, Deroubaix S, Karanje H, Gazumyan A, Darasse-Jèze
G, Telerman SB, Breton G, Schreiber HA, Frias-Staheli N, Billerbeck E, Dorner M, Rice CM, Ploss
A, Klein F, Swiecki M, Colonna M, Kamphorst AO, Meredith M, Niec R, Takacs C, Mikhail F, Hari
A, Bosque D, Eisenreich T, Merad M, Shi Y, Ginhoux F, Rénia L, Urban BC, Nussenzweig MC. Nat
Med. 2013 Jun;19(6):730-8. * corresponding author
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2.1 Mapping the PTPN22 interactome
Co-supervisor 1: Andrew P. Cope
Research Division or CAG: DIIID
E-mail: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/diiid/centres/cmcbi/research/cope/index.aspx
Co-supervisor 2: Dylan M. Owen
Research Division or CAG: Randall Institute
Email: [email protected]
www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/cell/owen/index.aspx
Project Description:
Scientific background: PTPN22 encodes a protein tyrosine phosphatase that negatively regulates
antigen receptor signalling by targeting Src and Syk family kinases. The PTPN22-R620W genetic
variant is strongly associated with susceptibility to RA, T1D and lupus through mechanisms that are
poorly understood. We have demonstrated that PTPN22 is a negative regulator of adhesion receptor
signalling; the disease-associated variant promotes integrin-dependent cell adhesion. We also
discovered that PTPN22 is sequestered in large clusters in the steady state that disperse following
receptor stimulation, permitting association of the phosphatase with its substrates. In this project we
will study mechanisms of PTPN22 clustering and de-clustering in T cells, informed by proteomic
profiling and high resolution imaging of PTPN22 and its interacting partners. This will offer new
insights into pathways regulated by PTPN22 that underpin susceptibility to autoimmunity.
Skills training: Cell signalling and protein purification; generation of mutant proteins for functional
analysis; imaging by confocal and super resolution microscopy; Bayesian cluster analysis; functional
analysis of T lymphocytes.
Objectives:
Year 1: The PTPN22 interactome will be defined using the BioID system. PTPN22 constructs will
be generated for transfection of T cells, interacting proteins purified using streptavidin beads and
identified by mass spectrometry.
Year 2: Super resolution microscopy will be used to visualise cluster assembly and disassembly of
PTPN22 and key interacting partners; transfecting cells with fluorescent fusion proteins will permit
imaging of live cells.
Year 3/4: Functional analysis of T cells expressing mutants of PTPN22 and its interacting partners,
including cell adhesion and migration, and effector function.
Two representative publications from supervisors:
Rubin-Delanchy P, Burn GL, Griffié J, Williamson DJ, Heard NA, Cope AP, Owen DM. Bayesian
cluster identification in single-molecule localization microscopy data. Nat Methods 2015;12:1072-
1076.
Burn GL, Cornish GH, Potrzebowska K, Samuelsson M, Griffie J, Minoughan S, Yates M, Ashdown
G, Pernodet N, Morrison VL, Sanchez-Blanco C, Purvis H, Clarke F, Brownlie RJ, Vyse TJ,
Zamoyska R, Owen DM, Svensson LM, Cope AP. Super-resolution imaging of the cytoplasmic
phosphatase PTPN22 links integrin-mediated adhesion with autoimmunity. Sci Signaling
2016;9:ra99.
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3.1 MicroRNAs as biomarkers of liver regeneration and their link to tumour biology
Co-supervisor 1: Dr. Varuna R. Aluvihare
Research Division or CAG: Transplantation Immunology & Mucosal Biology
E-mail: [email protected]
Co-Supervisor 2: Dr Siamak Salehi
Research Division or CAG: Transplantation Immunology & Mucosal Biology
Email: [email protected]
Project Description:
Regenerative competence is species and tissue specific. In higher eukaryotes efficient solid
organ regeneration is restricted to the liver. Regeneration competence encompasses regulated cell
proliferation, differentiation and remodelling to enable replacement of tissue or whole complex body
parts. In our previous studies we identified microRNAs (miRNA) that regulate successful and failed
human liver regeneration in an auxiliary transplant model. We also demonstrate that miRNA
associated with successful regeneration drive more aggressive tumour behaviour. Conversely miRNA
linked to failed regeneration can inhibit tumour growth.
Our goal is to understand the processes that regulate liver regeneration or prevent it. We will
use a variety of clinical settings which involves regeneration such as transplantation or acute liver
failure to identify the responsible miRNAs and investigate their link to tumour behaviour and its
aggressiveness. It may lead to the development of novel biomarkers that better predict both the
spontaneous liver regeneration/recovery and potential novel treatment strategy for human cancers by
deploying regulatory miRNA inhibitors of regeneration thereby improving patient survival.
Y1: Establish experience in lab techniques (sample collections, RNA and DNA extraction
protocols, molecular biology techniques PCR, qPCR, micro- arrays and vector design and
construction)
Y2: Analyse and interpret data obtained from a tissue samples and invitro validation of
clinical observations
Y3: In vivo experiments to validate invitro findings using animal models for regeneration and
cancer
Y4: Explore putative miRNA clinical applications + Write up
Techniques to be utilized will range from basic molecular biology techniques to FACS,
microRNA arrays, NGS, transfection of microRNA mimics and inhibitors by construction of
Lentiviral and Adenoviral vectors. Tissue culture techniques and primary human hepatocyte isolation
and culture. In vivo techniques such as partial hepatectomy and xenograft tumor models, In vivo
imaging techniques … Liver Studies at King’s College Hospital provides a unique combination of
clinicians and scientists working together allowing strong collaboration on translational research. The
clinical material available for analysis will be obtained from adult patients according to human tissue
act guidelines.
Two representative publications from supervisors:
Human Liver Regeneration Is Characterized by the Coordinated Expression of Distinct
MicroRNA Governing Cell Cycle Fate
S. Salehi, †, H. C. Brereton, †, M. J. Arno, D. Darling, A. Quaglia, J. O’Grady, N. Heaton and V. R.
Aluvihare †Contributed equally American Journal of Transplantation 2013; 13: 1282–1295093
The microRNA Expression Profile in Donation after Cardiac Death (DCD) Livers and Its Ability
to Identify Primary Non Function
Shirin Elizabeth Khorsandi☯, Alberto Quaglia☯, Siamak Salehi☯, Wayel Jassem‡, Hector Vilca-
Melendez‡, Andreas Prachalias‡, Parthi Srinivasan‡, Nigel Heaton*☯☯ = These authors contributed
equally to this work. ‡ = These authors also contributed equally to this work.
Published: May 15, 2015 DOI: 10.1371/journal.pone.0127073 PLOS ONE
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4.1 Whole organ bioengineering for tooth replacement
Co-Supervisor 1: Professor Paul Sharpe
Research Division or CAG: CFDSCB, Dental Institute
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/paul.sharpe.html
Co-Supervisor 2: Prof Agi Grigoriadis
Research Division or CAG: Craniofacial Development and Stem Cell Biology, Dental Institute Email: mailto:[email protected]
Website: https://kclpure.kcl.ac.uk/portal/agi.grigoriadis.html
Project Description:
Replacement of missing teeth currently involves a prosthesis or a dental implant. We are developing
a method to bioengineer an entire tooth organ rudiment in vitro that following transplantation into the
mouth will develop into a complete functional tooth. Whole organ bioengineering faces a number of
significant challenges that need to be overcome before translation into viable and affordable clinical
therapies. This project will focus on the main challenge, namely how to generate an “embryonic-like”
tissue (a tooth rudiment) from cultured adult cells. The project will involve a transcriptomics analysis
of cell populations that when isolated have tooth formatting ability that is lost following in vitro culture
but can be subsequently restored. Single RNA sequencing of these different cell fates will be used to
determine a profile of transcriptional changes associated with tooth formation. Cell re-programing
approaches will then be used to convert adult cells in tooth-inducing embryonic-like cells that can be
used in our bioengineering system to generate whole organ rudiments. An additional goal will be to
use robotics to automate the bioengineering system as a prelude to scale-up prior to clinical translation.
Two representative publications from supervisors:
Sharpe PT (2016) Dental mesenchymal stem cells. Development 143, 2273-2280.
Kaukua N, Khatibi Shahidi M, Konstantinidou C, Assaife Lopes N, Pachnis V, Suter U, Clevers H,
Sharpe PT, Thesleff I, Ernfors P, Fried K and Adameyko A (2014). Glial origin of mesenchymal stem
cells in a tooth model system. Nature 513, 551-554
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5.1 Applying single-cell RNA sequencing technologies to establish cardiac stem/progenitor cell
heterogeneity
Co-Supervisor 1: Dr. Georgina M. Ellison-Hughes
Research Division or CAG: Centre of Human and Aerospace Physiological Sciences, Centre for Stem
Cells & Regenerative Medicine
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/georgina.ellison.html
Co-Supervisor 2: Prof. Juha Kere
Research Division or CAG: Genetics and Molecular Medicine
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/juha.kere.html
Project Description:
We and others have shown that the adult myocardium, including human, harbours a population of
resident (endogenous) multi-potent cardiac stem cells (eCSCs). A variety of markers (i.e. c-kit, Sca-
1, MDR1/2, PDGFrα, Mesp1) have been used to identify and delineate eCSCs in different species
and throughout development, causing conceptual uncertainty because of heterogeneous definition.
In this project you will apply innovative and state-of-the art technologies, such as laser capture
microdissection (LCM), enzymatic digestion and micromanipulation, to isolate single cells from the
heart. Then you will apply single-cell RNA sequencing utilising the single-cell tagged RT (STRT)
protocol, with unique molecular identifiers (UMIs), to explore transcriptome heterogeneity of the
eCSCs, and their relationship between each other. You will utilise computational methods to leverage
the full complexity within single-cell transcriptome data, and will mine the eCSC transcriptome data
for specific, novel marker genes in order to better characterise the eCSCs. You will determine multi-
lineage priming, which reflects the cells competency (based on the presence of multi-lineage affiliated
genes) to adopt one of several fates and will employ computational prediction to determine their
relationship to each other, multipotency and cardiomyogenic commitment.
Objective 1: Optimising single-cell isolation techniques from heart tissue.
Objective 2: Single-cell transcription profiling of eCSCs utilising single-cell tagged RT (STRT)
protocol.
Objective 3: Addressing the heterogeneity inherent in the Sca-1pos/c-kitpos eCSCs.
Two representative publications from supervisors:
Ellison GM, Vicinanza C, Smith AJ, Aquila I, Leone A, Waring CD, Henning BJ, Stirparo GG,
Papait R, Scarfò M, et al. Adult c-kit(pos) cardiac stem cells are necessary and sufficient for
functional cardiac regeneration and repair. Cell. 2013, 154:827-842.
Smith AJ, Lewis FC, Aquila I, Waring CD, Nocera A, Agosti V, Nadal-Ginard B, Torella D,
Ellison GM. Isolation and characterization of resident endogenous c-Kit(+) cardiac stem cells from
the adult mouse and rat heart. Nat Protoc. 2014, 9:1662-1681.
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6.1 Developing nanomedicines for immunosuppression in liver transplantation
Co-Supervisor 1: Dr Khuloud T Al-Jamal
Research Division or CAG: IPS
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/en/persons/khuloud-aljamal(4e743c3a-574c-4ef2-b205-
12211b409e05)/projects.html
Co-Supervisor 2: Prof. Giovanna Lombardi
Research Division or CAG: DTIMB
Email: [email protected]
www.kcl.ac.uk/medicine/research/divisions/timb/about/people/profiles/giovannalombardi.aspx
Project Description:
Immunosuppression is an important strategy used in the medical field in cases of organ
transplantation and auto-immune diseases. Current approaches to control unwanted immune
responses involve administration of immunosuppressant drugs of known side-effects. Cell-based
therapy including the use of pluripotent stem cells and allogenic stem cells is an emerging new field
used in tissue regeneration and/or tissue transplantation. These suffer from poor survival or rejection
following implantation. Potential solutions involve the use of cell-substitutes (e.g. exosomes) or the
use of immuno-modulators. Immuno-modulators are generally biological molecules, relatively large in
size molecules with poor kinetics in vivo.
Nanomedicine has emerged as a new field utilises nano-sized carriers that can deliver small
drug molecules (immunosuppressants) or larger proteins (immuno-modulators) in a more controlled
and targeted manner. This overall reduces the dose, improve efficiency and reduce side effects of the
delivered drugs. Nanomedicines accumulate passively in liver tissues due to presence of sinusoids able
to tarp these nanoparticles.
This 4-year project will focus on developing nanomaterials to induce immunosuppression in
liver transplant animal model, with the clinical translation to man in mind. A biodegradable
nanoparticle (NP) (polymer or lipid-based) will be loaded with therapeutic agent(s) and used as an
implant or in an injectable form. During this project, therapeutic strategies include using NP
encapsulating immunosuppressant agents (e.g. rapamycin) which is hypothesised to increase drug
half-life, tissue specificity which reduce the side effect of the proposed drug(s). The second strategy
to be exploited involves using nanocarriers encapsulating therapeutic agents (immune-modulators) to
be used alone or in combination with implanted cells (or tissues) with the aim of improving cell survival
or reduce their immunogenicity.
The project consists of the following stages: (i) preparation and characterisation of the
nanocarriers containing the immunosuppressant/immunomodulatory drug(s); (ii) in vitro studies
(cytotoxicity assays, intra-cellular uptake and immune suppression); (iii) in vivo imaging and therapy
studies in relevant mouse model.
Two representative publications from supervisors:
Safinia N, Vaikunthanathan T, Fraser H, Thirkell S, Lowe K, Blackmore L, Whitehouse G,
Martinez-Llordella M, Jassem W, Sanchez-Fueyo A, Lechler RI, Lombardi G. Successful expansion
of functional and stable regulatory T cells for immunotherapy in liver transplantation. Oncotarget.
2016 Feb 16;7(7):7563-77. doi: 10.18632/oncotarget.6927.
El-Gogary R, Rubio N, Wang JT, Al-Jamal WT, Bourgognon M, Kafa H, Naeem M, Klippstein R,
Abbate V, Leroux F, Bals S, Van Tendeloo G, Kamel AO, Awad GA, Mortada ND, Al-Jamal KT.
Polyethylene glycol conjugated polymeric nanocapsules for targeted delivery of quercetin to folate-
expressing cancer cells in vitro and in vivo. ACS Nano. 2014 Feb 25;8(2):1384-401. doi:
10.1021/nn405155b. Epub 2014 Jan 23.
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7.1 Manipulating the stem cell state in vivo
Co-Supervisor 1: Cynthia Andoniadou
Research Division or CAG: Dental Institute
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/cynthia.andoniadou.html
Co-Supervisor 2: Isabelle Miletich
Research Division or CAG: Dental Institute
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/isabelle.miletich.html
Project Description:
The pituitary gland is essential for the regulation of key physiological processes such as growth,
metabolism, fertility and the stress response. This organ can fail to produce hormones at any stage of
life, or develop tumours, both with devastating consequences. Our lab focuses on the stem cell
involvement in both of these processes. The project will study the function of novel determinants that
regulate stem cell potential and homeostasis. We have identified the Hippo kinase cascade to be active
in the pituitary gland and in the stem cells, but its function in this organ is currently unknown. This
pathway regulates organ size in other tissues and when downregulated, promotes stem cell potential,
increases proliferation and prevents apoptosis. We will manipulate this pathway to address the impact
on stem cells, if their potential can be reactivated after loss and if it can be inhibited when overactive
such as during neoplastic disease. This is applicable to regenerative medicine approaches with the
ultimate goal to open new avenues for safer and better treatments for human conditions.
Objectives
1. Through use of genetic tools, to establish the function of individual pathway components in
pituitary stem cell regulation.
2. To establish interactions between Hippo and other signalling pathways in the gland that influence
proliferation.
Laboratory skills training provided
Mouse genetics, developmental biology, dissection, immunofluorescence, ex vivo organ culture, in
vitro culture, confocal microscopy, molecular biology, RNAscope in situ hybridisation.
Two representative publications from supervisors:
Lodge EJ, Russell JP, Patist AL, Francis-West P and Andoniadou CL. (2016) Expression analysis of
the Hippo cascade indicates a role in pituitary stem cell development. Front. Physiol. Mar 31;7:114.
Andoniadou CL et al, (2013) Sox2+ stem/progenitor cells in the adult mouse pituitary support organ
homeostasis and have tumor-inducing potential. Cell Stem Cell, Oct;13(4):433-45.
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8.1 Mechanisms of bacterial inhibition by interferon-stimulated genes
Co-Supervisor 1: Charlotte Odendall
Research Division or CAG: DIIID
Email: [email protected]
Co-Supervisor 2: Stuart Neil
Research Division or CAG: DIIID
E-mail: [email protected] http://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/Neil/index.aspx
Project Description:
Type I and III interferons (IFNs) are produced in response to non-self by the innate immune
system. Although better described as inhibitors of viral infections, we found that IFNs block the
growth of Salmonella within host cells. IFNs function by inducing a large family of 300 proteins
termed Interferon stimulated genes (ISGs), with a wide range of different functions. This project seeks
to determine which ISG(s) are responsible for IFN-mediated inhibition of bacterial growth, using
Salmonella Typhimurium and Shigella sonnei as models. These pathogenic bacteria cause disease
using type III secretion systems (T3SS), molecular needles that enable the transport of virulence
proteins into host cells.
We will first perform an expression screen using an ISG library. Individual ISGs will be
expressed and their ability to block bacterial replication will be assessed. In parallel we will perform
siRNA screens of known ISGs. ISGs will be knocked down and infection assays will be carried out in
the presence of IFNs. Positive hits will be cells that no longer control bacterial infection in the presence
of IFN (Year 1 and 2). In parallel, we will test well-characterised ISGs that could have effects on the
known lifecycles of bacteria (Year 1 and 2). For example, IFITM proteins affect membrane fluidity,
and could potentially affect the lifecycle of Salmonella (that replicates in membrane-bound vacuoles)
or Shigella (that requires vacuolar lysis and escape). Identified ISGs will be further studied to
determine which step of the bacterial intracellular lifecycle is affected (Year 3). The roles of ISGs in
inhibition of bacterial virulence will potentially then be studied in vivo in well-established models
(Year 3). This project will investigate both aspects of host pathogen interactions, as well as bridge the
fields of virology and bacteriology as IFNs and ISGs are normally considered as antiviral factors.
Work involving bacterial virulence, replication and pathogenesis assays will be done with Charlotte
Odendall while Stuart Neil will be mostly involved with the ISG screens.
Techniques involved will be:
- Molecular Biology
- Tissue culture
- Flow cytometry
- Microbiology
- Infection assays with different bacterial pathogens
- Gene knockdowns and knockouts by RNAi and CRISPR/Cas9
- Biochemistry (western immunoblotting, immunoprecipitation)
- Microscopy
- In vivo infection models
Two representative publications from supervisors:
Odendall, C. et al. Diverse intracellular pathogens activate type III interferon expression from
peroxisomes. Nat. Immunol. 15, 717–726 (2014).
Foster et al. Resistance of Transmitted Founder HIV-1 to IFITM-mediated restriction. Cell Host and
Microbe 2016 Oct 12;20(4):429-442. doi: 10.1016/j.chom.2016.08.006
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9.1 The role of post-translational modification of self proteins in breaking immune tolerance in
type 1 diabetes
Co-Supervisor 1: MARK PEAKMAN
Research Division or CAG: DIIID
E-mail: [email protected]
Website: www.kcl.ac.uk/lsm/research/divisions/diiid/.../peakman/index.aspx
Co-Supervisor 2: YUK-FUN LIU
Research Division or CAG: DNS
Email: [email protected]
Website: n/a
Project Description:
Approximately 80 human diseases come under the umbrella term “autoimmune”, and around 1 in 20
of the population will suffer from one of these conditions during their life. Although there is a great
deal known about the genes that predispose to autoimmunity, there is still a very poor understanding
as to how and why the immune system turns on self, and initiates the processes that cause tissue
damage. Recently, a potentially important pathway through which immune tolerance to self can be
broken has been suggested. “Post-translational modifications” (PTMs) of self proteins can alter them
in a way that renders them highly antigenic and circumvents thymic tolerance induction. In the
autoimmune disease Type 1 diabetes, there are new models proposed through which this can occur,
and this PhD project will focus on these pathways. Initial studies will use new techniques we have
developed (cell and molecular) to identify PTMs. In the middle of the PhD the studies will examine
how PTMs can be presented as antigens to the immune system. The final studies will examine how
this is relevant to the autoimmune responses we can detect in patients with Type 1 diabetes. This
highly translational project will include studying patient samples, a range of skill sets (cell biology,
molecular techniques, flow cytometry), and strong interaction (including an exchange visit) with the
Technische Universitat Dresden as part of our KCL: Dresden TransCampus
(http://www.kcl.ac.uk/lsm/research/transcampus/index.aspx).
Two representative publications from supervisors:
Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity.
Cole DK, Bulek AM, Dolton G, Schauenberg AJ, Szomolay B, Rittase W, Trimby A, Jothikumar P,
Fuller A, Skowera A, Rossjohn J, Zhu C, Miles JJ, Peakman M, Wooldridge L, Rizkallah PJ, Sewell
AK. J Clin Invest. 2016 Jun 1;126(6):2191-204.
Hydrophobic CDR3 residues promote the development of self-reactive T cells.
Stadinski BD, Shekhar K, Gómez-Touriño I, Jung J, Sasaki K, Sewell AK, Peakman M, Chakraborty
AK, Huseby ES. Nat Immunol. 2016 Aug;17(8):946-55.
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10.1 Gestational Diabetes, the epigenome and the health of the next generation
Co-Supervisor 1: Professor Lucilla Poston
Research Division or CAG: Division of Women’s Health
E-mail: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/wh/index.aspx
Co-Supervisor 2: Dr Jordana Bell
Research Division or CAG: Division of Genetics and Molecular Medicine
Email: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/twin/research/bell/index.aspx
Project Description:
The incidence of gestational diabetes mellitus (GDM) is increasing with the rising prevalence of
maternal obesity. Children born to mothers with GDM have heightened risk of obesity and metabolic
disease in adulthood. The purpose of this studentship is to improve understanding of the mechanisms
through which GDM exposure in utero translates to the development of obesity in the children.
Increasing evidence suggests that maternal GDM induces stable modifications of the offspring
epigenome, resulting in persistently changed gene expression and a lifelong increased risk of obesity
and associated disorders. By utilising the biobank of the largest RCT of a lifestyle intervention (low
glycaemic index diet and increased physical activity) in obese pregnant women (UK Pregnancy Better
Eating and Activity Trial, UPBEAT), an RCT which lowered maternal dietary glycaemic index,
increased physical activity) and reduced infant fat mass, this studentship will directly assess the role
of epigenetic processes in the association between maternal GDM and offspring adiposity.
Specifically, the student will address the interaction between the maternal metabolic profile
(metabolome) the neonatal epigenome and childhood adiposity. The student will benefit from an
established collaboration between KCL and the University of Southampton. Dr Karen Lillycrop
(Southampton) an expert in epigenetics will play an important supervisory role in addition to the KCL
supervisors. The student will join a vibrant research group in the KCL Division of Women’s Health.
The student will acquire skills in the fields of women’s health, epigenetics, statistical modelling and
gestational diabetes and benefit from the excellent KCL graduate training.
Two representative publications from supervisors:
Poston L, Bell R, Croker H et al. (2015) Effect of a behavioural intervention in obese pregnant women
(the UPBEAT study): a multicentre, randomised controlled trial. The Lancet Diabetes & Endocrinology
3, 767-777.
Tsai P-C, van Dongen J, Tan Q, Willemsen G, Christiansen L, Boomsma DI, Spector TD, Valdes
AM, Bell JT. (2015) DNA methylation changes in the IGF1R gene in birth weight discordant adult
monozygotic twins. Twin Research and Human Genetics 13, 1-12.
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11.1 Tackling hearing loss: development, regeneration and reconstruction of the ear
Co-Supervisor 1: Prof Abigail Tucker
Research Division or CAG: Craniofacial Development & Stem Cell Biology, KCL
E-mail: [email protected]
http://www.kcl.ac.uk/dentistry/research/divisions/craniofac/ResearchGroups/TuckerLab/Tucker
Lab.aspx
Co-Supervisor 2: Mr Dan Jiang PhD FRCSI(Otol) FRCS(ORL-HNS)
Research Division or CAG: Otolaryngology, Head & Neck Surgery, Guys and St Thomas’s Hospital
Honorary Prof: Craniofacial Development & Stem Cell Biology, KCL
Email: [email protected]
https://kclpure.kcl.ac.uk/portal/en/persons/dan-jiang(cd25e784-010c-4321-a3ac-
7189d23ea839)/publications.html
Project Description:
Birth defects associated with the middle and external ear lead to conductive hearing loss where sound
fails to pass to the inner ear. Our knowledge of how these birth defects arise is limited, hampering our
ability to correct defects. We aim to study the development of the ear taking advantage of mouse
mutants with aberrant ear development and data from patients attending the Ear Clinic at St Thomas’
Hospital. The project is a collaboration between an expert in ear development in mice (Prof Tucker)
and a clinician specialising in ear surgery (Prof Jiang). Overall we aim to understand how the ear
forms and integrates so that ear defects can be more successfully repaired and the ear reconstructed
during surgery.
Aim 1 (year 1): To investigate the normal process of external ear formation during mouse embryonic
development.
Aim 2 (year 1 & 2): To understand the mechanisms behind ear defects using mouse models of human
syndromes associated with external ear defects. These will include 22q11.2 deletion syndrome (Tbx1
mice), Branchio-oto-renal syndrome (Eya1 mice), LADD syndrome (Fgf10 mice), and
holoprosencephaly (Gas1 mice).
Aim 3 (year 2 & 3): To analyse CT scans from patients with ear defects to correlate the findings from
the mouse with humans, and to assess the success of reconstructive surgery.
Skills training: The student will be trained in a range of molecular biology techniques, anatomy and
regenerative biology, while having access to clinical data. In addition critical thinking, presentation
and writing skills will be taught.
Two representative publications from supervisors:
Thompson, H. Tucker, A.S. (2013). Dual origin of the epithelium of the middle ear. Science 339,
1453-1456.
Eze N, Jiang D, O'Connor AF. (2014) The atretic plate – a conduit for drill vibration to the inner
ear. Acta Otolaryngol. 134(1):14-8.
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12.1 Mechanism of membrane remodelling in cell biology and replication of HIV-1 and Ebola
virus
Co-Supervisor 1: Prof. Juan Martin-Serrano
Research Division or CAG: DIIID
E-mail: [email protected]
www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/Martin-
Serrano/indexJD.aspx
Co-Supervisor 2: Dr. Jorge Bernardino de la Serna
Research Division or CAG: Department of Physics
Email: [email protected]
Project Description:
The Endosomal Sorting Complex Required for Transport (ESCRT) pathway catalyses the scission of
thin membranous stalks found in diverse cellular processes, including multivesicular body (MVB)
formation, cytokinetic abscission and nuclear envelope reformation. These fundamental events share
a common topology and they all require ESCRT-III, a filament forming multi-protein complex that
promotes membrane deformation and scission. In other words, the ESCRT complexes form the only
cellular machinery capable of inducing membrane invaginations that protrude away from the
cytoplasm, and this unique property explains why these proteins are hijacked by enveloped viruses,
such as HIV-1 and Ebola virus, to facilitate their budding.
In this project the student will take advantage of existing cell lines that express physiological levels of
fluorescently tagged ESCRT-III subunits. These cells will be used to visualise ESCRT-III filament
formation by live-cell microscopy under strict physiological conditions. The combination of this
experimental setting with bespoke biophysical analysis will allow the study of the dynamics of
ESCRT-III polymerization, and how the biogenesis of these polymers facilitates membrane
remodeling. A complementary approach will take advantage of super-resolution microscopy (SIM an
STED) that are available in the host labs. Advanced quantitative fluorescence microscopy techniques
and imaging analysis tools will be employed to reveal the role of ESCRTs in membrane remodelling
during viral budding at the spatial and temporal nanoscale, including the tracking of single viral
budding events.
Two representative publications from supervisors:
Host factors involved in retroviral budding and release. Martin-Serrano J, Neil SJ. Nature Reviews in
Microbiology. 2011 Jun 16;9(7):519-31. doi: 10.1038/nrmicro2596
ESCRT machinery: Damage control at the nuclear membrane. Ventimiglia LN, Martin-Serrano J.
Cell Res. 2016 Jun;26(6):641-2. doi: 10.1038/cr.2016.52.
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14.1 Gene expression in skin in subjects with reduced biological ageing compared to their
chronological ageing
Co-Supervisor 1: Dr Mario Falchi, PhD
Research Division or CAG: Genetics Division, Kings College, Twin Research Unit, St Thomas
Hospital London
E-mail: [email protected]
Co-Supervisor 2: Dr Veronique Bataille, MD PhD FRCP
Research Division or CAG: Genetics Division, Kings College, Twin Research Unit, St Thomas
Hospital London
Email: [email protected]
Project Description:
The TwinsUK cohort includes 12,000 twins used to study the genetic and environmental aetiology
of age-related complex traits. Measures of biological ageing comprise cataract score, strength, muscle
mass on DEXA scan, lung function, telomere length, bone mineral density, naevus count, creatinine
and others, as well as measures derived from epigenetics and glycomics data. The final aim of this PhD
is to identify novel gene and pathways involved in skin ageing and skin cancer (one of the most
common cancers in the world).
1st year: Integrate phenotypic and –omics data already available in the TwinsUK cohort to define
reliable biological ageing scores. Gene expression data in skin are available on more than 700 twins:
the student will learn how to analyse the RNA sequencing data. Differential expression analysis will
be used to identify genes associated with reduced and accelerated biological ageing.
2nd: Gene network analysis will be used to identify modules of co-expressed genes correlated with
the observed gap between biological and chronological age, to identify pathways associated with
decelerated biological ageing. Modules and hub genes (genes exerting the main control within each
module) will be investigated for their role in risk to skin cancer, skin, and systemic ageing.
3rd: The biological function of identified genes and modules will be investigated through whole-
genome sequencing, metabolomics, metagenomics, and epigenetics data.
4th: During the fourth year, the student will write their thesis.
The student is expected to write manuscripts for peer review as well as presenting his work at national
and international meetings.
Two representative publications from supervisors:
Falchi M et al Genome-wide association study identifies variants at 9p21 and 22q13 associated with
development of cutaneous nevi. Nat Genet. 2009 41:915-9
V Bataille et al Nevus size and number are associated with telomere length and represent potential
markers of a decreased senescence in vivo Cancer Epidemiol Biomark Prev 2007 16:1499-1502
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15.1 Adhesion receptor signalling regulating lung cancer progression
Co-Supervisor 1: Professor Maddy Parsons
Research Division or CAG: Randall Division
E-mail: [email protected]
Website:
www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/motility/parsons/index.aspx
Co-Supervisor 2: Professor George Santis
Research Division or CAG: AALB Division/Cancer CAG
Email: [email protected]
Website: www.kcl.ac.uk/lsm/research/divisions/aalb/about/people/profiles/santisg.aspx
Project Description:
The Coxsackie and Adenovirus Receptor (CAR) is a transmembrane receptor that plays a key role in
controlling adhesion between adjacent epithelial cells. CAR is expressed in normal epithelial cells,
but has also been shown to be upregulated in a number of human tumours including lung carcinomas.
However, the potential mechanisms by which CAR contributes to cancer cell growth remain unclear.
Our recent data has shown that CAR increases recruitment of immune cells during lung inflammation.
Further unpublished data demonstrated an important role for CAR in promoting lung cancer cell
proliferation in vitro and in vivo. In this context, CAR is also important for maintaining junctions
between proliferating human lung cancer cells and this promotes optimal signaling downstream of the
epidermal growth factor receptor (EGFR) to perpetuate cell division. However, whether CAR plays
an additional role in immunomodulation within tumours to promote cancer cell growth remains
unknown. CAR has never before been studied as a potential therapeutic target for inflammation, and
as the CAR knockout mouse is embryonic lethal, this receptor has also not previously been studied in
the context of the adult lung. The aim of this project is to use biochemistry, cell biology, advanced
imaging and in vivo analysis to define how CAR depletion from tumour cells in non-
immunocompromised mice impacts tumour growth and stromal organization. This data will provide
novel insight into the role of CAR in homeostasis and disease, and provide a solid foundation for future
in vivo studies of this receptor as a potential therapeutic target. The two supervisors have collaborated
closely for many years and their complementary expertise in basic and translational research will
provide the student with an excellent training opportunity.
Two representative publications from supervisors:
Morton PE et al. -dependent migrations of leukocytes across epithelial
monolayers. Sci Reps. 2016. 19;6:26321
Kiuchi T et al. The ErbB4 CYT2 variant protects EGFR from ligand-induced degradation to enhance
cancer cell motility. Sci Signal. 2014 Aug 19;7(339):ra78. doi: 10.1126/scisignal.2005157.
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16.1 Developing novel, conventional and nanoparticle, inhibitors of the Wnt signaling pathway as
a treatment for prostate and breast cancers
Co-Supervisor 1: Aamir Ahmed
Research Division/Department or CAG: Molecular Medicine and Genetics
E-mail: [email protected]
Website: www.kcl.ac.uk/lsm/research/divisions/gmm/departments/stemcells/people/Dr-Aamir-
Ahmed.aspx
Co-Supervisor 2: Prokar Dasgupta, , Professor of Urological Innovation, Hon. Consultant Urologist,
KCL Research Division/Department or CAG: DTIMB
Liver, Renal, Urology, Transplant, Gastro/Gastro Intestinal Surgery Clinical Academic Group
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/prokar.dasgupta.html
Project Description:
The Wnt signalling pathway plays a key role in carcinogenesis of prostate, penile, colon and breast
cancers. Wnt signalling is transduced by two key transducers, intracellular free calcium ([Ca2+]i) and
ß-catenin, a potent transcription factor co-activator. We have shown that the activation of Wnt
signalling first increases [Ca2+]i that depolarizes the cell and nuclear electrical potential to facilitate
ß-catenin translocation into the nucleus to activate gene (including numerous proto-oncogenes)
transcription. We have a described a novel mechanism for the Wnt signaling pathway that involves
cell membrane potential and inhibition of free [Ca2+]i. Very recently we have identified inhibitors
that can reduce Wnt induced: 1. free [Ca2+]i 2. ß-catenin translocation into the nucleus where it
activates gene transcription which is implicated in carcinogenesis. A patent (GB2014/053138) for
targeting the Wnt pathway as a treatment for cancer was awarded recently.
The purpose of this project will be to develop these novel Wnt pathway inhibitors, organic compounds
and specifically designed nanopraticles (with London Centre for Nanotechnology), and to identify
the mechanisms by which these may act to inhibit Wnt signaling in vitro and tumorigenicity in vivo.
The following techniques, established in our laboratory, will be used:
1. Design and synthesis of specific nanoparticles using chemical techniques
2. [Ca2+]i release and cell membrane currents by simultaneous patch clamp electrophysiology
and live calcium imaging using confocal microscopy
3. ß-catenin translocation into the nucleus using immunocytochemistry
4. Cell growth ± Wnt ligands and ±Wnt inhibitors using live cell imaging
5. Using human models of cancer in mice
Two representative publications from supervisors:
Arya M, Thrasivoulou C, Henrique R, Millar M, Hamblin R, Davda R, Aare K, Masters JR,
Thomson C, Muneer A, Patel HR, Ahmed A. Targets of wnt/ß-catenin transcription in
penile carcinoma. PLoS One 10:e0124395, 2015
Thrasivoulou, C, Millar, M and Ahmed, A. Activation of intracellular calcium by multiple Wnt
ligands and translocation of ß-catenin into the nucleus: a convergent model of Wnt/Ca2+ and Wnt/ß-
catenin pathways. J. Biol.Chem. 288: 35651–35659, 2013
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17.1 Roles of the RNA-binding proteins LARP4A and LARP4B in cancer cell migration and
invasion
Co-Supervisor 1: Anne Ridley
Research Division or CAG: Randall
E-mail:[email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/motility/ridley/index.aspx
Co-Supervisor 2: Sasi Conte
Research Division or CAG: Randall
Email: [email protected]
www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/structural/conte/index.aspx
Project Description:
Cancer metastasis is associated with poor prognosis and is difficult to treat. To metastasize, cancer
cells invade surrounding tissues, then enter blood vessels and spread to other sites. Using RNAi screens
we have identified novel regulators of cancer cell migration and invasion, including the RNA-binding
protein LARP4A. LARP4A and its close relative LARP4B are mutated in several cancers, and our
recent data identified mutations that affect LARP4A function (Seetharaman et al., 2016).
LARP4A/B are believed to bind to mRNA poly(A) tails and thereby regulate translation, although
their mRNA targets are not known. They also interact with Poly(A)-binding protein (PABP) and
RACK1, both of which are involved in mRNA translation. This project aims to determine how
LARP4A/B regulate cancer invasion, and whether they could be targets for cancer therapy.
Skills training: cell culture, siRNA/plasmid transfection, CRISPR/Cas9, site-directed mutagenesis,
confocal microscopy, biochemical/biophysical analysis of protein-protein interactions, in vitro and in
vivo cancer migration/invasion.
Year 1: Roles of LARP4A/LARP4B mutants found in cancers in regulating their interactions with
PABP, RACK1 and poly(A), using biochemical and biophysical approaches. Effects of these mutants
on intracellular localization of LARP4A/B and cancer cell migration.
Year 2: Effects of LARP4A/B depletion and overexpression on translation of Rho GTPase signalling
network proteins that have a similar phenotype to LARP4A/B in our RNAi screen results. Determine
if LARP4A/B cancer-associated mutants alter expression or localization of these Rho network
proteins.
Year 3: Test selected LARP4A/B mutations for effects on cancer cell-cell adhesion, invasion and
metastasis in cells and in animal models.
Two representative publications from supervisors:
Seetharaman, S., Flemyng, E., Shen, J., Conte, M.R., Ridley, A.J. (2016) The RNA-binding protein
LARP4 regulates cancer cell migration and invasion. Cytoskeleton, doi: 10.1002/cm.21336.
Reymond, N., Im, J.H., Garg, R., Cox, S., Soyer, M., Riou, P., Colomba, A., Muschel, R.J., Ridley,
A.J. (2015) RhoC and ROCKs regulate cancer cell interaction with endothelial cells. Mol. Oncol. 9,
1043-1055.
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18.1 Membrane remodelling during cell division
Co-Supervisor 1: Dr Jeremy Carlton
Research Division/Department or CAG: Cancer
E-mail: [email protected]
www.kcl.ac.uk/lsm/research/divisions/cancer/research/sections/cellbio/mtcd.aspx
Co-Supervisor 2: Prof Riki Eggert
Research Division/Department or CAG: Randall and Chemistry
Email: [email protected]
www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/motility/eggert/index.aspx
Project Description:
During division, cells undergo dramatic remodelling of their membranes and cytoskeleton.
Membrane-bound organelles, including the nuclear envelope, the endoplasmic reticulum, the Golgi
apparatus and mitochondria have to be equally partitioned between dividing daughter cells, which
requires extensive organelle rearrangement. Whilst we have varying amounts of information about the
proteins involved in different organelles’ remodelling, our understanding of the role of lipids in these
process remains severely underappreciated. Faithful cell division is essential for the maintenance of
genome integrity and failures in this process are thought to underlie a variety of human malignancies.
The goal of this project is to investigate the roles lipids and membrane associated proteins play in the
remodelling of organelles during cell division.
We will focus on a number of organelles, and by removing enzymes necessary for production of
various lipid species or proteins that can shape membranes, you will test whether these organelles are
remodelled and separated correctly during division and will analyse the consequences of perturbing
this remodelling on cell division. You will use genome-editing to introduce epitope tags into organelle
markers and will extract the tagged markers and will perform mass spectrometry and lipidomic
analysis to identify lipid species bound. Once candidate lipids have been identified, you will verify
interactions using liposome-based binding assays.
You will join laboratories examining organelle remodelling during cell division (Carlton laboratory –
ESCRTs; Eggert laboratory - lipids and the cytoskeleton) and will be trained in techniques including
molecular biology, advanced imaging, protein biochemistry, lipidomics and lipid biochemistry.
Two representative publications from supervisors:
ESCRT-III controls nuclear envelope reformation. Olmos Y, Hodgson L, Mantell J, Verkade P,
Carlton JG. Nature (2015) 522:236-9
Dividing cells regulate their lipid composition and localization. Atilla-Gokcumen GE, Muro E,
Relat-Goberna J, Sasse S, Bedigian A, Coughlin ML, Garcia-Manyes S, Eggert US. Cell (2014)
156:428-39.
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19.1 Identifying effective drugs to treat oral squamous cell carcinoma
Co-Supervisor 1: Fiona M. Watt
Research Division or CAG: GMM
E-mail: [email protected]
www.kcl.ac.uk/lsm/research/divisions/gmm/departments/stemcells/wattfiona.aspx
Co-Supervisor 2: Allessandra Vigilante
Research Division or CAG: GMM
Email:
Website:
Project Description:
Oral squamous cell carcinoma (OSCC) is a tumour of the multilayered epithelia lining the mouth. It
is the sixth most common cancer affecting men in the UK and the long-term survival rate is only 50%.
One of the challenges of treating OSCC is that it is highly heterogeneous at both the genetic and
cellular levels. To create an in vitro model that accurately reflects this heterogeneity, we have
generated a panel of human OSCC cell lines with a mutational spectrum that is representative of
primary OSCC in The Cancer Genome Atlas (Hayes et al., 2016). The goal of the proposed PhD
project is to collaborate with researchers at the Wellcome Trust Sanger Institute to use the cell lines
to identify drugs that prevent OSCC growth in culture (see Iorio et al (2016) Cell 166:740-754) and
in xenografts (Benaich et al., 2014).
The objective of the rotation project is to develop robust, quantitative assays for cell proliferation,
death and differentiation, based on high content imaging.
The goal of year 1 is to screen the available drug library for hits.
In year 2 the effects of the drugs will be confirmed using additional cell based assays (Hayes et al.,
2016) and growth of transplanted cells in NSG mice (see Benaich et al., 2014)
In the final year mechanistic experiments will be used to establish how certain drugs or combinations
of drugs target cells that are mutant for NOTCH1, CASP8 and FAT1 (see Hayes et al., 2006).
Two representative publications from supervisors:
Benaich, B., Woodhouse, S., Goldie, S.J., Mishra, A., Quist, S.R., and Watt, F.M. (2014) Rewiring
of an epithelial differentiation factor, miR-203, to inhibit human squamous cell carcinoma
metastasis. Cell Reports 9:104-117
Hayes, T.F., Benaich, N., Goldie, S.J., Sipilä, K., Ames-Draycott, A., Cai, W., Yin, G. and Watt,
F.M. (2016) Integrative genomic and functional analysis of human oral squamous cell carcinoma cell
lines reveals synergistic effects of FAT1 and CASP8 inactivation. Cancer Letters 383:106-114.
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20.1 Interventions to improve maternal metabolic profile in obese pregnancy and prevent cardio-
metabolic and behavioural deficits in future generations.
Co-Supervisor 1: Dr Paul Taylor
Research Division or CAG: Women’s Health Academic Centre, KHP
E-mail: [email protected]
Website: www.kcl.ac.uk/wh
Co-Supervisor 2:Prof Clive Coen
Research Division or CAG: Women’s Health Academic Centre, KHP
Email: [email protected]
Website: www.kcl.ac.uk/wh
Project Description:
Maternal obesity is now the single biggest obstetric risk factor, and it is now widely recognised that
maternal obesity is not only a risk factor for pregnancy outcomes (e.g. pre-eclampsia, gestational
diabetes and fetal macrosomia) but also for the long term health of the child, with increased risk of
obesity and related comorbidities. Diet and nutrition in pregnancy are modifiable risk factors for
offspring metabolic health and offer the opportunity for intervention to stem the growing tide of
childhood obesity and impact on the cardiovascular and mental health of the next generation.
We have identified two candidate compounds, resveratrol and polydextrose which we intend to test
for safety and efficacy (therapeutic potential) in a rat model of obesity in pregnancy. Resveratrol is a
polyphenolic compound with numerous biological activities and anti-oxidant properties, found in high
concentrations in the skins of red grapes. Polydextrose, on the other hand, is a soluble fibre with low
glycaemic index and pro-biotic properties. The study will employ rodent models to advance
understanding of the mechanism of action of these compounds in improving maternal metabolic
profiles in obese pregnancy and their disease-preventive potential for cardiovascular (blood pressure)
metabolic (obesity and diabetes) and behavioural deficits (cognitive function and ADHD) in future
generations. Interventions with these two promising compounds, conceivably acting through
divergent pathways, will also provide insight and mechanistic understanding of how obesity in
pregnancy can beget cardio-metabolic disorders in childhood.
The studentship focuses on in vivo physiological techniques and is supported by an MRC Project
grant.
Two representative publications from supervisors:
Poston L & Taylor PD. Obesity in Pregnancy and the Legacy for the Next Generation. What Can
we Learn from Animal Models? RCOG Obesity Study Group (2007).
Taylor PD. Samuelsson AM & Poston L. (2014) Maternal Obesity and the Developmental
Programming of Hypertension: A role for leptin. Acta Physiol 2014, 210, 508–523.
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21.1 Molecular dissection of epigenetic signals controlling muscle stem cell behaviour during
regeneration
Co-Supervisor 1: Robert Knight
Research Division or CAG: Craniofacial Development and Stem Cell Biology
E-mail: [email protected] www.kcl.ac.uk/dentistry/research/divisions/craniofac/ResearchGroups/KnightLab/KnightLab.aspx
Co-Supervisor 2: Fiona Wardle
Research Division or CAG: Randall Division of Cell and Molecular Biophysics
Email: [email protected]
www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/signalling/wardle/index.aspx
Project Description:
Muscle stem cells (muSCs) are critical for maintaining muscle strength in disease, injury and ageing.
They are highly migratory, yet almost nothing is known about their behaviour during regeneration in
vivo, as it has been problematic to visualise migration to injury sites in mouse or human. We have
recently described the use of transparent zebrafish for imaging muSC responses to injury and for
identifying regulators in vivo. Epigenetic signals control chromatin packaging and hence gene
expression and recent evidence suggests that these signals may influence the migratory ability of many
cell types. We find this includes muSCs. This project therefore aims to test the importance of an
epigenetic modifying protein, Ezh2, in controlling muSC responses in zebrafish models of muscle
injury.
This will be achieved by time-lapsed imaging of muSCs responses to small laser injuries using confocal
microscopy to measure cell responses. Ezh2 function in muSCs will be tested using a mutant, by
addition of small molecule inhibitors or over-expression of functionally altered Ezh2 genes; Ezh2-
dependent changes to gene expression and chromatin marks will be evaluated by sorting cells and
performing qPCR and ChIP-qPCR in combination with immunolabelling and in situ hybridisation.
Training will be given in all these techniques.
Objectives for the project are:
1. determine whether loss of Ezh2 function compromises muSC migration and ability to
regenerate muscle (year 1)
2. determine whether small molecule inhibitors of Ezh2 affect muSC responses to injury (year
2)
3. identify candidate targets of Ezh2 regulating muSCs during regeneration (year 3-4)
Two representative publications from supervisors:
Knappe, Stefanie; Zammit, Peter S.; Knight, Robert D. 'A population of Pax7- expressing muscle
progenitor cells show differential responses to muscle injury dependent on developmental stage and
injury extent'. Frontiers in aging neuroscience, Vol. 7, No. 161, 25.08.2015.
Nelson, A.C., Cutty, S.J., Niini, M., Stemple, D.L., Flicek, P., Corinne Houart, C., Bruce, A.E.E.,
Wardle, F.C. (2014). Global identification of Smad2 and Eomesodermin targets in zebrafish identifies
a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression
of ectodermal gene expression. BMC Biology, 12(1):81.
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22.1 A Bioengineering Approach To Polarise Glioma Tumour Initiating Cells and Induce
Asymmetric Cell Division In Order To Limit Their Tumorigenic Potential
Co-Supervisor 1: Dr Shukry James Habib
Research Division or CAG: Centre for Stem Cells and Regenerative Medicine
E-mail: [email protected]
www.kcl.ac.uk/lsm/research/divisions/gmm/departments/stemcells/people/dr-shukry-j-habib.aspx
Co-Supervisor 2: Prof Jeremy Green
Research Division or CAG: Craniofacial Development and Stem Cell Biology
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/jeremy.green.html
Project Description:
Adult gliomas are malignant human brain tumours with no curative therapy available. They can occur
via transformation of adult neural progenitor cells (NPCs) into glioma tumour-initiating cells
(GTICs). Several studies have shown that NPCs usually divide asymmetrically to produce one NPC
and another differentiated cell, however during gliomagenesis the cells mainly divide symmetrically,
promoting tumour growth.
This project will investigate these cell division processes, and engineer strategies to polarise GTICs in
order to direct them to divide asymmetrically. We hypothesise that the Wnt signaling pathway could
be employed for controlling the cellular polarity and division of GTICs, as the majority of gliomas do
not acquire mutations in the Wnt signalling components.
The Habib lab has engineered localised Wnt niches that can induce asymmetric cell division of
embryonic and adult stem cells. The combination of our bioengineering approaches with cell polarity
expertise (Green lab) provide grounds to explore the mechanistic regulation of GTIC division and
opportunities to limit their tumorigenic potential.
1st -2nd year: Culturing and characterising human NPCs and GTICs. Employing 3D microscopy to
study the division NPCs and GTICs by establishing a molecular segregation map for cell polarity
proteins, Wnt pathway components and cell fate markers. Purification of Wnt proteins will also be
done.
3nd- 4th year: Engineering localised Wnt niches and testing their effect on NPCs and GTIC division
mode. Flow cytometery to separate between the daughter cells of GTICs and investigating their
tumorigenic potential in in vitro and in vivo transplantation assays.
Two representative publications from supervisors:
Habib SJ et al A localized Wnt signal orients asymmetric stem cell division in vitro. Science 2013
Tabler JM, Yamanaka H, Green JB. PAR-1 promotes primary neurogenesis and asymmetric cell
divisions via control of spindle orientation. Development 2010
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23.1 Mesenchymal Stromal cells – a novel therapy for Crohn’s disease
Co-Supervisor 1: Dr. Nick Powell
Research Division or CAG: Division of Transplantation Immunology & Mucosal Biology
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/nicholas.1.powell.html
Co-Supervisor 2: Prof. Francesco Dazzi
Research Division or CAG: Division of Cancer Studies
Email: [email protected]
www.kcl.ac.uk/lsm/research/divisions/cancer/research/groups/haematooncology/research/Regene
rativeMedicine.aspx
Project Description:
Crohn’s disease is a severe intestinal disease caused by excessive activation of the mucosal immune
system. It causes disabling symptoms and is linked to excess mortality and severe complications,
including cancer. Many patients require disfiguring surgery and need to take powerful drugs lifelong
that are fraught with side effects. There is a pressing need to develop novel therapies.
Cell therapy is an exciting novel way of treating inflammatory diseases. Cells from individual patients
(autologous) or other individuals (allogeneic) can be purified, expanded and manipulated to possess
potent anti-inflammatory properties. This immunomodulatory cell product can then be infused back
into patients with immune-mediated diseases to target excessive inflammation. The time is now ripe
to determine whether cell therapies can be utilized to treat Crohn’s disease and to understand the
mechanisms of action of this novel treatment.
MSC) possess potent anti-inflammatory activity and are emerging as an exciting form of cell therapy.
In this project the student will evaluate how MSCs modulate key immune cells implicated in Crohn’s
disease pathogenesis, including T-cells, monocytes and innate lymphoid cells. Immune cells will be
purified directly from diseased tissue of Crohn’s disease patients.
This work is expected to provide crucial “proof of concept” data and will pave the way to guide a new
trial of MSC in Crohn’s disease. Key techniques will include cell culture, flow cytometry, gene
expression analyses (gene expression microarrays, RNA sequencing), etc. The candidate will fully
integrate within our extended inflammatory bowel disease team of clinicians and scientists.
Two representative publications from supervisors:
Krampera M, Glennie S, Dyson J, Scott D, Laylor R, Simpson E, and Dazzi F. Bone marrow
mesenchymal stem cells inhibit the response of naïve and memory antigen-specific T cells to their
cognate peptide. Blood 101:3722-9, 2003.
Powell N, Lo JW, Stolarczyk E, et al Interleukin 6 Increases Production of Cytokines by Innate
Lymphoid Cells in Colon Tissues from Mice with Colitis and Patients with Inflammatory Bowel
Disease. Gastroenterology 2015; 149:456-467
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24.1 HIV-1 mediated reprogramming of T cell gene expression networks
Co-Supervisor 1: Michael MALIM
Research Division or CAG: DIIID
E-mail: [email protected]
Website: http://www.kcl.ac.uk/malim
Co-Supervisor 2: Rebecca OAKEY
Research Division or CAG: GMM
Email: [email protected]
www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/OakeyLab/index.
aspx
Project Description:
Virus infection triggers two fundamental types of cellular response: those that inhibit infection (termed
immune responses) and those that promote virus production, persistence and/or dissemination (here
called reprogramming). The balance between these opposing forms of response dictates the overall
outcome of infection and, ultimately, contributes to the pathogenic consequences for the infected host.
To date, little is understood regarding the capacity of the pathogenic retrovirus, HIV-1, to
reprogramme infected T lymphocytes, or the consequences of such changes for altering cell function.
This project will build upon a substantial body of data where we have demonstrated that HIV-1
reorganises the transcriptional landscape of T lymphocytes within the first few hours of infection. We
will employ a multi-disciplinary approach including virology, molecular genetics, biochemistry, high-
throughput nucleic acid sequencing, single-cell analytics and bioinformatics to tackle the following
key questions. One, what are the virus determinants that drive these RNA expression changes and
through which signalling pathways do they operate? Two, what genome-wide alterations in
chromatin and epigenetic marks underpin changes in RNA levels, and which steps of RNA biogenesis
are regulated? Three, do all cells respond to infection equivalently or is there cell-to-cell variation;
and if the latter, what cell-specific signatures underpin the differences? Four, how does
reprogramming impact the fate of HIV-1 infection, perhaps by altering virus production or persistence
(a form of which is called latency)? Together, insight in these areas will yield new information on the
dynamic interplay between HIV-1 and its human host.
Two representative publications from supervisors:
Goujon, C., Moncorgé, O., Bauby, H., Doyle, T., Ward, C.C., Schaller, T., Hué, S., Barclay, W.S.,
Schulz, R. and Malim, M.H. (2013). Human MX2 is an interferon-induced post-entry inhibitor of
HIV-1 infection. Nature 502, 559-562. This paper employed comparative transcriptomics to
identify candidate innate immune inhibitors of HIV infection, that were subsequently functionally
screened and validated.
Prickett, A.R., Barkas, N., McCole, R.B., Hughes, S., Amante, S.M., Schulz, R., and Oakey, R.J.
Genome wide and parental allele specific analysis of CTCF and Cohesin binding sites in mouse brain
reveals a tissue-specific binding pattern and an association with differentially methylated regions.
Genome Research 2013. 23(10):1624-1635. This paper illustrates the use of genome wide sequencing
techniques in understanding gene regulation.
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25.1 The role of the pro-FLG Ca2+-binding domain in the formation of the skin barrier and
pathogenesis of atopic dermatitis
Co-Supervisor 1: Dusko ILIC
Research Division or CAG: Women’s Health
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/dusko.ilic.html
Co-Supervisor 2: Carsten FLOHR
Research Division or CAG: GMM
Email: [email protected]
Website:
www.kcl.ac.uk/lsm/research/divisions/gmm/departments/dermatology/Groups/flohr/index.aspx
Project Description:
Atopic dermatitis (AD) affects 20% of children and 5% of adults in the UK and has a profound effect
on patients’ quality of life. A genetic predisposition for skin barrier dysfunction, together with
environmental factors, such as exposure to hard water (high CaCO3 levels) and the use of protease
containing detergents, results in the typical immunological phenotype of AD.
Normal epidermis displays a marked Ca2+ gradient, which controls the expression of filaggrin (FLG)
and differentiation of the epidermis. Recent genetic studies have found that loss-of-function mutations
in the FLG gene are present in up to 50% of AD patients. Pro-FLG has a Ca2+-binding domain of
unknown function, which is cleaved off when pro-FLG is proteolytically processed into functional
FLG during the biogenesis of the stratum corneum.
We will use CRISPR/Cas9 gene-editing technology to delete the FLG Ca2+-binding domain in
healthy human embryonic stem cell (hESC) lines. We will then use these isogenic normal and mutated
hESC to differentiate various skin cell types and build 3D in vitro models of full thickness skin. The
developed model will be used to assess processes related to keratinocyte differentiation and skin
barrier integrity to determine the role of the pro-FLG Ca2+-binding domain in the formation of a
functional skin barrier and the pathogenesis of AD. We will also expose the outer surface our 3D in
vitro model to varying CaCO3 levels to assess the effect on skin barrier integrity. The project will
inform novel methods of treatment and disease prevention.
Two representative publications from supervisors:
Petrova A, Celli A, Jacquet L, Dafou D, Crumrine D, Hupe M, Arno M, Hobbs C, Cvoro A,
Karagiannis P, Devito L, Sun R, Adame LC, Vaughan R, McGrath JA, Mauro TM, Ilic D. 3D In
vitro model of a functional epidermal permeability barrier from human embryonic stem cells and
induced pluripotent stem cells. Stem Cell Reports 2014;2:675-689.
Perkin MR, Craven J, Logan K, Strachan D, Marrs T, Radulovic S, Campbell LE, MacCallum SF,
McLean WH, Lack G, Flohr C. Association between domestic water hardness, chlorine, and atopic
dermatitis risk in early life: A population-based cross-sectional study. J Allergy Clin Immunol
2016;138(2):509-516.atopic dermatitis risk in early life: A population-based cross-sectional study. J
Allergy Clin Immunol 2016;138(2):509-516.
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26.1 Exploring the general mechanisms of mammalian neural crest migration in vivo using live cell
imaging and how it is altered in neuroblastoma cancer cells
Co-Supervisor 1: Karen J. Liu
Research Division or CAG: Craniofacial Development and Stem Cell Biology
E-mail: [email protected]
www.kcl.ac.uk/dentistry/research/divisions/craniofac/ResearchGroups/Liu-Lab/index.aspx
Co-Supervisor 2: Matthias Krause
Research Division or CAG: Randall Division of Cell and Molecular Biophysics
Email: [email protected]
Project Description:
Neural crest cells are multipotent embryonic stem cells that give rise to diverse tissues such as
melanocytes, craniofacial skeleton and peripheral nervous system. During embryogenesis the neural
crest cells delaminate from the neural tube, undergo an epithelial to mesenchymal transition (EMT),
and migrate to populate distant organs. The highly migratory activity of these cells is critical to their
in vivo function—not only are their ultimate tissue descendants widespread in the organism, but
failures to regulate migration and differentiation in the correct locations leads to cancers such as
neuroblastoma. Despite the importance of the neural crest, the specific mechanisms underlying this
migratory activity and its control are poorly understood, especially in mammals.
In this project we propose a novel signal transduction pathway in which anaplastic lymphoma kinase
(ALK), a kinase mutated in neuroblastoma, phosphorylates glycogen synthase kinase (GSK3) to
regulate the actin cytoskeleton via Lamellipodin (Lpd), thereby controlling neural crest migration.
Overall goals:
1) Identify the cellular behaviours of mammalian neural crest cells as they migrate in their native
milieu. Approach: in vivo imaging of migrating neural crest cells. Techniques: in vivo live cell
microscopy, embryology, computational image analysis.
2) Pinpoint the requirements for GSK3 and Lpd during neural crest migration using genetic
mutants. Approach: Tissue culture, genetic analysis, molecular biology, biochemistry.
This project will have implications for understanding head patterning, human congenital anomalies,
and more broadly, processes that involve cell migration, such as wound healing and cancer cell
metastasis.
Two representative publications from supervisors:
Tabler et al., Fuz mutant mice reveal shared mechanisms between ciliopathies and FGF-related
syndromes. Dev Cell 2013 Jun 24; 25(6):623-35.
Liu et al., Chemical rescue of cleft palate and midline defects in conditional GSK3b mice. Nature
2007 Mar 1; 446(7131):79-82.
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27.1 Functional interrogation and therapeutic intervention of the molecular pathways driving
cutaneous T-cell lymphoma
Co-Supervisor 1: Dr Tracey Mitchell
Research Division or CAG: Genetics and Molecular Medicine/GRIDA
E-mail: [email protected]
Website:https://www.kcl.ac.uk/medicine/research/divisions/gmm/departments/dermatology/Gro
ups/WhittakerLab/index.aspx
Co-Supervisor 2: Professor Sean Whittaker
Research Division or CAG: Genetics and Molecular Medicine/GRIDA
Email: [email protected]
Website:https://www.kcl.ac.uk/medicine/research/divisions/gmm/departments/dermatology/Gro
ups/WhittakerLab/index.aspx
Project Description:
All cancers are characterised by the acquisition of gene mutations and structural aberrations that
initiate and drive the disease. Mapping the genomic landscape of tumour genomes is a powerful
approach to facilitate the identification of potential therapeutic targets. Primary cutaneous T-Cell
lymphoma (CTCL) is a heterogeneous malignancy of mature memory type, skin homing T-cells.
There are no effective treatments for CTCL patients with advanced stage disease and as a
consequence the survival rate is dismal (~3 years). Our research program aims to use the genomic
basis of CTCL to identify biomarkers for patient stratification and to design novel therapies. We have
recently performed a deep sequencing study that has identified >800 gene mutations and copy
number changes in CTCL tumours. Analysis of these data at the gene pathway level has identified
TCR signalling, cell survival, genome maintenance, DNA damage repair and epigenetic regulation as
the key pathways mediating the pathogenesis of CTCL. The aim of this PhD is to follow up this work
by functional validation of identified genes and involved pathways. The main objectives are to: (i)
examine the functional role of candidate driver mutations in the malignant transformation of T-cells
and will involve complementary experiments to examine gene function in healthy T-cells, cell lines
and tumour cells (years 1/2); and (ii) to screen identified mutations in specific pathways against small
molecule libraries to identify potential therapeutic targets (years 3/4). A range of cutting-edge
molecular genetic and immunological techniques will be used. Work will be undertaken in our state-
of-the-art laboratories in the Division of Genetics and Molecular Medicine.
Two representative publications from supervisors:
Woollard WJ, Pullabhatla V, Lorenc A, Patel VM, Butler RM, Bayega A, Begum N, Bakr F, Dedhia
K, Fisher J, Aguilar-Duran S, Flanagan C, Ghasemi AA, Hoffmann RM,Castillo-Mosquera N, Nuttall
EA, Paul A, Roberts CA, Solomonidis EG, Tarrant R,Yoxall A, Beyers CZ, Ferreira S, Tosi I,
Simpson MA, de Rinaldis E, Mitchell TJ, Whittaker SJ. Candidate driver genes involved in genome
maintenance and DNA repair in Sézary syndrome. Blood. 2016 Jun 30;127(26):3387-97.
doi:10.1182/blood-2016-02-699843. Epub 2016 Apr 27. PubMed PMID: 27121473.
Woollard WJ, Kalaivani NP, Jones CL, Roper C, Tung L, Lee JJ, Thomas BR, Tosi I, Ferreira S,
Beyers CZ, McKenzie RC, Butler RM, Lorenc A, Whittaker SJ, Mitchell TJ. Independent Loss of
Methylthioadenosine Phosphorylase (MTAP) inPrimary Cutaneous T-Cell Lymphoma. J Invest
Dermatol. 2016 Jun;136(6):1238-46.doi: 10.1016/j.jid.2016.01.028. Epub 2016 Feb 9. PubMed
PMID: 26872600.
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28.1 In-silico design and identification of novel antiviral drugs targeting vector borne viruses
(Zika, Dengue & Chikungunya)
Co-Supervisor 1: Dr Daniele Castagnolo, Lecturer
Research Division or CAG: Institute of Pharmaceutical Science
E-mail: [email protected]
Website: https://sites.google.com/site/danielecastagnoloresearchgroup/home
Co-Supervisor 2: Dr David Barlow, Lecturer
Research Division or CAG: Institute of Pharmaceutical Science
E-mail: [email protected]
Website: www.kcl.ac.uk/lsm/research/divisions/ips/research/pharmabio/Staff/Barlow/index.aspx
Project Description:
The project aims at developing urgently needed drug candidates targeting mosquito-borne viruses,
such as Zika, Dengue and Chikungunya, which are causing an increasing number of outbreaks in
humans worldwide and for which there are no current treatments available.
•In Year 1, two in-silico approaches will be undertaken in Dr Castagnolo’s Lab to design novel Zika,
Dengue and Chikungunya inhibitors. (1) A ligand-based virtual screening approach will be adopted
to identify structurally-innovative small molecules targeting vector borne viruses. New hit candidates
will be identified from chemical databases (e.g., ZINC) and synthesized at KCL. In parallel, (2) a
structure-based approach will be followed to design new inhibitors targeting specific viral proteins
(particularly protease and polymerase of Zika and Dengue).
• The newly identified hit compounds will then be tested for their antiviral activity. Enzymatic
screening on viral proteins will be carried out in the Dr Castagnolo's newly refurbished Lab for biology
at IPS. Phenothypic screening will be carried out in the BL3 lab of our collaborator Prof. Johan Neyts
at KU Leuven, Belgium (4 months placement). (Year 2/3).
•The SAR of the drugs will be evaluated and the hit compounds will be then optimised (Year 3)
leading to the identification of Drug Leads active againt Zika, Dengue and Chikungunya viruses (4
Year).
This project is highly multidisciplinary and it will offer a unique combination of expertise and skills
ranging from in-silico computational design, virtual screening on viral proteins, chemistry and biology,
virology up to commercial and industrial research.
Two representative publications from supervisors:
Magri, A.; Reilly, R. Scalacci, N.; Radi, M.; Hunter, M.; Ripoll, M.; Patel, A.; Castagnolo, D.*
“Rethinking the old antiviral drug moroxydine: discovery of novel analogues as potent anti-hepatitis
C virus (HCV) agents” Bioorg. Med. Chem. Lett. 2015, 25, 5372-5376.
Vincetti, P.; Caporuscio,F.; Gioiello,A.; Mancino,V.; Suzuki, Y.; Yamamoto, N.; Crespan, E.; Maga,
G.; Rastelli,G.; Castagnolo, D.; Kaptein, S.; Leyssen,P.; Neyts, J.; Costantino, G.; Radi, M.
“Discovery of multi-target antivirals acting on both the dengue virus NS5-NS3 interaction and the
host Src/Fyn kinases” J. Med. Chem.2015, 58, 4964-4975
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29.1 Defining the role of circulating fibrocytes in the pathogenesis of renal fibrosis; a study of cell-
signalling crosstalk
Co-Supervisor 1: Dr Claire Sharpe
Research Division or CAG: Division of Transplantation Immunology & Mucosal Biology
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/claire.sharpe.html
Co-Supervisor 2: Professor Antony Dorling
Research Division/Department or CAG: Division of Transplantation Immunology & Mucosal
Biology
E-mail: [email protected]
Website: www.kcl.ac.uk/lsm/research/divisions/timb/about/people/profiles/anthonydorling.aspx
Project Description:
Interstitial fibrosis is the process that leads to kidney failure, regardless of the initiating disease (e.g.
diabetes, high blood pressure, kidney transplant rejection), yet there is no drug available to stop this.
Understanding which cells are responsible for producing scar tissue and the signalling cascades that
control this process will help us to design drugs which can protect patients from the need for dialysis
or kidney transplantation. We have evidence that, following injury, circulating cells known as
fibrocytes are responsible for damage caused to blood vessels within the kidney. These cells may also
migrate into kidney tissue and be responsible for kidney scarring. These cells express a molecule called
tissue factor, which triggers the coagulation cascade but also signals through pro-fibrotic signalling
pathways such as Ras monomeric GTPases, via PAR-1. We have developed a transgenic strain of
mice that overexpress the naturally-occurring human tissue factor pathway inhibitor (TFPI) on
CD31+ fibrocytes.
This project aims to:
1) Discover what percentage of scar-forming cells are derived from circulating fibrocytes in a mouse
model of renal fibrosis (induced by aristolochic acid) (year 1)
2) Compare the degree of fibrosis that develops between the transgenic and wild-type mice to see
whether TFPI is anti-fibrotic (year 2)
3) To understand the cross-talk between Ras and PAR-1 signalling to highlight new potential targets
for drug discovery (year 3)
4) Test the impact of targeting those signalling molecules that have been newly identified as key in
the fibrotic pathway in in-vitro models using CRISPR technology. (year 4).
Two representative publications from supervisors:
Fibrocytes mediate intimal hyperplasia post-vascular injury and are regulated by two tissue factor-
dependent mechanisms. Chen D1, Ma L, Tham EL, Maresh S, Lechler RI, McVey JH, Dorling A. J
Thromb Haemost. 2013 May;11(5):963-74.
Antisense knockdown of KirstenRas inhibits fibrosis in a rat model of unilateral ureteric obstruction.
JiaHui Wang, Lucy J. Newbury, A.S. Knisely, Brett Monia, Bruce M. Hendry and Claire C. Sharpe.
Am J Pathol. 2012 Jan;180(1):82-90
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30.1 Structural characterisation of a novel cytolytic peptide toxin
Co-Supervisor 1: Julian Naglik
Research Division or CAG: Mucosal & Salivary Biology Division, Dental Institute
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/julian.naglik.html
Co-Supervisor 2: Antoni Borysik
Research Division or CAG: Department of Chemistry
Email: [email protected]
Website: http://www.kcl.ac.uk/nms/depts/chemistry/people/core/borysikantoni.aspx
Project Description:
We have recently identified the first cytolytic peptide toxin (Candidalysin) secreted by any human
fungal pathogen. Candidalysin is exclusively expressed by hyphal filaments of Candida albicans and
is essential for mucosal pathogenesis, epithelial activation and damage induction1. Candidalysin is an
amphipathic 31-mer peptide, and central to damage induction is its ability to intercalate and
permeabilise cell membranes. However, the mechanism of cell damage is currently unknown.
Therefore, the objectives are to understand how Candidalysin intercalates and causes membrane
destabilisation and cell damage.
We will investigate the structure, dynamics and assembly of Candidalysin using a broad range of
cutting edge techniques to understand how this peptide toxin intercalates and destabilises epithelial
membranes. In Year 1&2 the student will use molecular dynamics (MD) simulations to understand
the self-assembly properties of the peptide and generate candidate peptide assemblies. The MD
simulations will be complimented by native mass spectrometry (MS) and ion-mobility MS
experiments, which will be used to determine the respective stoichiometry and shape of the assembled
peptides2. In Year 2&3, the structure and dynamics of the peptide pores will be determined by
hydrogen-deuterium exchange MS. The student will also capitalise on recent advances in native MS
to understand the role of lipids in the structure and dynamics of the pore-forming properties of
Candidalysin.
This multidisciplinary project combines structural biology, infection, chemistry and biophysics to
determine how Candidalysin intercalates, destabilises and damages epithelial membranes, and will
identify key structural regions in Candidalysin that can be targeted for novel antifungal therapies.
Two representative publications from supervisors:
Moyes DL, Wilson D, Richardson JP, Tang SX, Wernecke J, Höfs S, Gratacap RL, Mogavero S,
Robbins J, Runglall M, Murciano C, Blagojevic M, Thavaraj S, Förster TM, Hebecker B, Kasper L,
Vizcay G, Iancu SI, Kichik N, Häder A, Kurzai O, Cota E, Bader O, Wheeler RT, Gutsmann T,
Hube B and Naglik JR (2016). Candidalysin: A fungal peptide toxin critical for mucosal infection.
Nature, 532, 64-68
Borysik AJ, Hewitt DJ, Robinson CV (2013). Detergent release prolongs the lifetime of native-like
membrane protein conformations in the gas-phase. J Am Chem Soc., 135, 6078-6083.
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31.1 MS1 - a cardiac regulator of development and stress
Co-Supervisor 1: Mark Pfuhl
Research Division or CAG: Cardiovascular & Randall Division
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/mark.pfuhl.html
Co-Supervisor 2: Alka Saxena
Research Division or CAG: NIHR Biomedical Research Center and Medical and Molecular Genetics
Email: [email protected]
www.guysandstthomasbrc.nihr.ac.uk/Professionals/Corefacilities/Genomicsfacility/Genomics-
core-facility.aspx
Project Description:
Ms1/STARS is a stress response protein of cardiac muscle. It was discovered as a protein
overexpressed in cardiomyocytes early in the hypertension model of rat aortic banding. It was shown
to be important for the maintenance of cardiac development in zebrafish and is upregulated in mouse
models of cardiac hypertrophy and in failing human hearts. We determined the structure of the only
folded part of the protein and discovered that it resembles the DNA binding domain of transcription
factors. Even though it was previously only ever reported to be present in a sarcomeric or cytosolic
location we were the first to identify it in the nucleus and to show that it can bind to DNA in a
sequence specific manner. We now want to find out what exactly Ms1 is doing in the nucleus by
ChIP-Seq and RNA-Seq experiments (year 1). We want to understand the upstream signalling that
decides about the subcellular localisation which we have shown to be dependent on its NLS -
intriguingly it is in the nucleus in neonatal but in the sarcomere in adult rat cardiomyocytes (see below,
year 2). Ultimately we want to understand how the role that Ms1 plays in the nucleus is related to the
onset of cardiac hypertrophy and ultimately heart failure by studying cardiomyocytes from mouse
models of hypertrophy as well as samples from patients with ventricular hypertrophy (year 3).
Training in: cell culture, immunofluorescence, confocal microscopy, ChIP-Seq & RNA-Seq, DNA
binding assays, molecular biology, protein chemistry.
Two representative publications from supervisors:
M. Zaleska, C. Fogl, A. L. Kho, A. Ababou, E. Ehler, M. Pfuhl, “The Cardiac Stress Response Factor
Ms1 Can Bind to DNA and Has a Function in the Nucleus”, PLoSONE DOI:
10.1371/journal.pone.014461410, 2015
C. Fogl, L. Puckey, U. Hinssen, M. Zaleska, M. El-Mezgueldi, R. Croasdale, A. Bowman, A.
Matsukawa, N. J. Samani, R. Savva, M. Pfuhl, "A structural and functional dissection of the cardiac
stress response factor MS1", Proteins 80, 398-409, 2012
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32.1 Identifying novel molecular mechanisms involved in the generation of new insulin-
producing beta cells from adult stem/progenitor cells.
Co-Supervisor 1: Rocio Sancho
Research Division or CAG: GMM
E-mail: [email protected]
Co-Supervisor 2: Ivo Lieberam
Research Division or CAG: GMM
Email: mailto:[email protected]
Website: http://www.kcl.ac.uk/ioppn/depts/devneuro/Research/groups/lieberam.aspx
Project Description:
Diabetes is caused by the irreversible loss of insulin-producing beta cells in the pancreas. Recent
research has revealed that the adult pancreas is capable of surprising cellular plasticity, opening new
possibilities to reprogram adult stem/progenitor cells into insulin-producing cells (Puri et al. 2015;
Sancho et al. 2014). Three key transcription factors are sufficient to initiate a beta cell fate program
when artificially introduced into adult stem/progenitor cells: Ngn3, Pdx1 and MafA. However, the
tight regulation of these factors makes the process inefficient, and the beta cells generated are often
not fully functional.
The goal of the proposed PhD project is to understand how the pro-endocrine factors Ngn3, Pdx1
and MafA are regulated in adult stem cells, to enable us to optimise the regulating pathways to improve
the efficiency of beta cell generation and achieve fully functional beta cells.
During the rotation project the PhD student will set up pilot screens for novel regulators and
interactors of Ngn3/Pdx1/MafA. 0+4 students will also familiarise with all the techniques required
for screen validation by characterising a protein already identified as a regulator of Ngn3.
The goal of year 1/2 is to perform Crispr/Cas9 screening for Ngn3/Pdx1/MafA-regulators using flow
cytometry, and identify Ngn3/Pdx1/MafA-interacting proteins using immunoprecipitation and mass
spectrometry.
In year 2/3 biochemical and functional validation of the top screen hits will be performed.
In the final year functional (insulin release, calcium measuring, in vivo mouse kidney transplantation)
and translational assays (human primary cells) will be performed to assess the physiological function
of the newly generated beta cells.
Two representative publications from supervisors:
1: Sancho R, Gruber R, Gu G, Behrens A. Loss of Fbw7 reprograms adult pancreatic ductal cells
into α, δ, and β cells. Cell Stem Cell. 2014 Aug 7;15(2):139-53. doi: 10.1016/j.stem.2014.06.019.
PubMed PMID: 25105579; PubMed Central PMCID: PMC4136739.
2: Sancho R, Blake SM, Tendeng C, Clurman BE, Lewis J, Behrens A. Fbw7 repression by hes5
creates a feedback loop that modulates Notch-mediated intestinal and neural stem cell fate
decisions. PLoS Biol. 2013;11(6):e1001586. doi: 10.1371/journal.pbio.1001586. PubMed PMID:
23776410; PubMed Central PMCID: PMC3679002
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33.1 Therapeutic use of regulatory T cells in liver disease: Immunoregulation and tissue
regeneration
Co-Supervisor 1: Dr Marc Martinez-Llordella
Research Division/Department or CAG: Liver Sciences Department, Division of Transplantation and
Mucosal Biology
E-mail: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/timb/research/liver.aspx
Co-Supervisor 2: Prof Alberto Sanchez-Fueyo
Research Division/Department or CAG: Liver Sciences Department, Division of Transplantation and
Mucosal Biology – King’s College Hospital, Institute of Liver Studies
Email: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/timb/research/liver.aspx
Project Description:
Hepatic inflammation of any aetiology is characterized by lymphocyte infiltration. If the inflammation
is not controlled it could lead to fibrosis, resulting in cirrhosis or liver failure. The balance of effector
and regulatory T cells (Tregs) generally determines the outcome of hepatitis. Tregs are a
heterogeneous population with specific properties depending on the homing tissue, including
immunoregulation and tissue repair. However, the factors that modulate Treg homeostasis and
function in the liver remain unclear. Our previous studies have demonstrated that IL-2 administration
preferentially expand Tregs in the liver and increases their suppressive functions. Therefore, we
believe that IL-2 therapy can modulate Treg immunoregulation during hepatic inflammation and
enhance tissue regeneration.
The objectives of this study are: i) to characterise the phenotype and features of intrahepatic Tregs in
humans and mice (Year 1); ii) to determine the Treg homeostasis and cell-to-cell interactions during
chronic liver inflammation (Years 1-2); iii) to assess the role of Tregs in the tissue regeneration after
hepatic injury (Year 2); and iv) to evaluate the benefits of combining IL-2 therapy with hepatocyte
transplantation to improve regeneration of end-stage liver damage (Years 2-3).
In order to achieve our aims, we will employ animal models of acute hepatitis and liver fibrosis (wild-
type and Treg-depleted mice). We will perform isolation and cell culture methodologies from human
and mouse (MLR, Treg suppression assays…), cell biology assays (flow cytometry, ELISA…) and
molecular analysis (qPCR, microarray, DNA sequencing…).
Two representative publications from supervisors:
Bailey-Bucktrout SL, Martinez-Llordella M, Zhou X, Anthony B, Rosenthal W, Luche H, Fehling
HJ, Bluestone JA. Self-antigen-driven activation induces instability of regulatory T cells during an
inflammatory autoimmune response. Immunity. 2013 Nov 14;39(5):949-62.
Bohne F, Martínez-Llordella M, Lozano JJ, Miquel R, Benítez C, Londoño MC, Manzia TM,
Angelico R, Swinkels DW, Tjalsma H, López M, Abraldes JG, Bonaccorsi-Riani E, Jaeckel E,
Taubert R, Pirenne J, Rimola A, Tisone G, Sánchez-Fueyo A. Intra-graft expression of genes involved
in iron homeostasis predicts the development of operational tolerance in human liver transplantation.
J Clin Invest. 2012 Jan;122(1):368-82.
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34.1 Understanding regulation of cellular energy metabolism
Co-Supervisor 1: Snezhana Oliferenko
Research Division or CAG: Randall Division of Cell and Molecular Biophysics
E-mail: [email protected] OR [email protected]
Website: https://www.crick.ac.uk/research/a-z-researchers/researchers-k-o/snezhana-oliferenko/
Co-Supervisor 2: Simon Ameer-Beg
Research Division/Department or CAG: Randall Division of Cell and Molecular Biophysics
Email: [email protected]
http://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/cell/ameer-beg/index.aspx
Project Description:
Cellular energy metabolism occurs through oxidative phosphorylation in mitochondria and glycolysis
in the cytoplasm. In humans, differentiated cells tend to rely on oxidative phosphorylation but
dividing cells or abnormally proliferating cancers often adopt aerobic glycolysis that favours increased
macromolecular synthesis, a phenomenon known as Warburg effect. How is energy production
regulated? How do cells choose a particular energy generation route, and how do they switch between
alternative strategies? How do these metabolic choices affect the rates of cellular growth? We want
to answer these fundamental, yet surprisingly poorly understood questions by combining precise
spatiotemporal imaging of cellular energy metabolic pathways with the awesome power of genetic
engineering. We will visualize energy metabolites such as glucose, ATP, glutamate and others in real
time using Förster Resonance Energy Transfer (FRET)-based sensors and probe how fluctuations in
nutrient availability, cellular differentiation, chronological aging and genetic perturbations of
metabolic regulation affect their intracellular flux. To speed up our research by straightforward
genome editing, we will initially use two yeast species that exhibit divergent energy production
pathways. We will eventually translate our research to human cells with a view of understanding how
altered energy metabolism contributes to disease.
Year 1. Development of genetically encoded FRET-based biosensors to report metabolic activity (SO
and SAB).
Year 2. Understanding spatiotemporal regulation of metabolic sensors at a single-cell level in response
to environmental and genetic perturbations (SO and SAB).
Years 3-4. Studying the mechanisms underlying regulation of energy metabolism and preparing
experimental results for publication (SO and SAB).
Two representative publications from supervisors:
Makarova, M., Gu, Y., Chen, J-S., Beckley, J., Gould, K. and S. Oliferenko. 2016. Temporal
regulation of Lipin activity diverged to account for differences in mitotic programs. Current Biology.
26: 237-243.*Highlighted in Prasad, R. and Y. Barral. 2016. Posttranslational Regulation: A Way to
Evolve. Current Biology. 26: R102-124, and Editor’s Choice in Science: 351:828-829
A high speed multifocal multiphoton fluorescence lifetime imaging microscope for live-cell FRET
imaging. Poland, S. P., Krstajić, N., Monypenny, J., Coelho, S., Tyndall, D., Walker, R. J., Devauges,
V., Richardson, J., Dutton, N., Barber, P., Day-Uei Li, D., Suhling, K., Ng, T., Henderson, R. K. &
Ameer-Beg, S. M. 2015. Biomedical optics express. 6: 277-296
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35.1 Mechanism of action of a cancer-selective protein toxin
Co-Supervisor 1: Prof Mahvash Tavassoli
Research Division or CAG: Mucosal Biology/Cancer
E-mail:[email protected]
Website: https://kclpure.kcl.ac.uk/portal/mahvash.tavassoli.html
Co-Supervisor 2: Dr Manuel Muller
Research Division or CAG: Natural and Mathematical Sciences – Department of Chemistry
Email: [email protected]
Website: http://www.kcl.ac.uk/nms/depts/chemistry/people/core/MullerManuel.aspx
Apoptin, a small viral protein, can selectively induce cell death in cancer cells while sparing healthy
cell lines. Previous research suggests that selective phosphorylation of apoptin in cancer cells
contributes to this fascinating tumour selective cytotoxic property. A number of protein kinases have
been implicated in apoptin phosphorylation including protein kinase C and Akt. However, little is
known about the functional consequences of apoptin phosphorylation.
This projects aims to apply synthetic protein chemistry to address the mechanism of cancer-selective
toxicity of apoptin. The student will develop a protein semi-synthesis strategy to access site-
specifically phosphorylated apoptin derivatives (Mueller lab). Using state-of-the-art protein
transduction methodologies, semi-synthetic apoptin derivatives will be introduced into cancerous and
normal cell lines, allowing the student to directly test the effect of phosphorylation on pro-apoptotic
activity in a range of primary and metastatic cell lines as well as normal cells from various tissue type
(Tavassoli lab). The incorporation of photo-crosslinkers into apoptin variants will enable the
identification of phosphorylation-specific down-stream targets, potentially allowing the student to
establish a model for the mechanism of action of cancer-specific toxic. The information obtained can
also help future design of post-translationally modified proteins with therapeutic potential.
Collectively, this interdisciplinary project will provide in-depth training in cancer biology and protein
chemistry, and provides training in a range of cellular, molecular, imaging, biochemical and
bioinformatics methods. This study is expected to yield crucial mechanistic insight into the function
of apoptin with important implications for its potential use as selective cancer therapy therapeutics.
Two representative publications from supervisors:
Apoptin interacts with and regulates the activity of protein kinase C beta in cancer cells.
Bullenkamp J, Gäken J, Festy F, Chong EZ, Ng T, Tavassoli M.
Apoptosis. 2015 Jun;20(6):831-42. doi: 10.1007/s10495-015-1120-6.
Activation of the Chicken Anemia Virus Apoptin Protein by Chk1/2 Phosphorylation Is Required
for Apoptotic Activity and Efficient Viral Replication.
Kucharski TJ, Ng TF, Sharon DM, Navid-Azarbaijani P, Tavassoli M, Teodoro JG.
J Virol. 2016 Sep 29;90(20):9433-45. doi: 10.1128/JVI.00936-16. Print 2016 Oct 15.
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36.1 Mitochondrial microRNA (MitomiRs) and their relationship to mitochondrial bioenergetics
Co-Supervisor 1: Shirin Elizabeth Khorsandi
Research Division or CAG: Liver, Renal, Urology, Transplant, Gastro/Gastro Intestinal Surgery
CAG
E-mail: [email protected]
http://www.kingshealthpartners.org/clinical-excellence/40-liver-renal-urology-transplant-
gastrogastro-intestinal-surgery
Co-Supervisor 2: Celine Filippi
Research Division or CAG: Child Health CAG
Email: [email protected]
Project Description:
How a cell generates energy is fundamental in determining cell phenotype and survival. This aspect
is of importance both in cancer and liver transplantation. The cancer cell needs to generate energy in
a manner that will support its survival, irrespective of the prevailing oxygen and nutrient availability,
to drive cancer cell division, invasion and the fatality of metastasis. While in liver transplantation, the
behaviour and resilience of liver mitochondria on reperfusion, determines graft and ultimately,
recipient survival. The aim of this work is to look at how mitochondrial microRNA (MitomiRs) define
cancer cell behaviour and whether MitomiR species, can be used to assess the transplantability of the
human liver.
Y1 Establish experience in lab techniques (mitochondrial isolation, MitomiR extraction,
mitochondrial bioenergetic measurements, EM architecture). Y2 Analyze tissue samples and interpret
data from clinical models of cancer and transplantation Y3/Y4 In vitro validate clinical MitomiR
observations. Y4 Computationally explore putative MitomiR clinical applications and write up.
Techniques to be utilised will range from basic molecular biology techniques, to functional
mitochondrial measurements, microRNA arrays, NGS, transient transfection of microRNA mimics,
design and construction of Lentiviral/Adenoviral vectors for RNAi with siRNA or shRNA, and
primary human hepatocyte isolation and culture. The Institute of Liver Studies is a unique
environment where clinicians and scientists coexist facilitating translational projects. The clinical
material available for analysis will extend from the human neonate to adult liver in a variety of cancers
and the transplant liver. There will also be the opportunity to visit the microRNA labs at John
Hopkins, USA.
Two representative publications from supervisors:
The microRNA Expression Profile in Donation after Cardiac Death (DCD) Livers and Its Ability to
Identify Primary Non Function. Khorsandi SE, Quaglia A, Salehi S, Jassem W, Vilca-Melendez H,
Prachalias A, Srinivasan P, Heaton N. PLoS One. 2015 May 15;10(5):e0127073. doi:
10.1371/journal.pone.0127073.
Alginate microencapsulated hepatocytes optimised for transplantation in acute liver failure.
Jitraruch S, Dhawan A, Hughes RD, Filippi C, Soong D, Philippeos C, Lehec SC, Heaton ND,
Longhi MS, Mitry RR. PLoS One. 2014 Dec 1;9(12):e113609. doi: 10.1371/journal.pone.0113609.
eCollection 2014
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37.1 Using chemical modification of anticancer drug scaffolds to study efflux mediated
chemoresistance in cancer stem cells
Co-Supervisor 1: Dr Khondaker Miraz Rahman
Research Division or CAG: Institute of Pharmaceutical Science
E-mail: [email protected]
http://www.kcl.ac.uk/lsm/research/divisions/ips/about/people/Rahman/index.aspx
Co-Supervisor 2: Professor Ben Forbes
Research Division or CAG: Institute of Pharmaceutical Science
Email: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/ips/about/people/Forbes/index.aspx
Project Description:
Cancer stem cells (CSCs) are key tumor-initiating cells that may play an integral role in disease
recurrence following chemotherapy. To improve clinical outcomes for cancer patients, treatments
must have the ability to kill the entirety of cancer cells, including CSCs. One of the key mechanisms
of chemoresistance in CSCs is the overexpression of ABC transporters such as P-glycoprotein (P-gp).
Although a relationship between P-gp expression and drug resistance is widely accepted in cancer
cells, the situation is less well defined for CSCs. We have recently identified a number of putative P-
gp inhibitors with the help of advanced computational modelling. Some of these molecules are
regulatory agency approved molecules with known safety profiles. The PhD project aims to use these
molecules as chemical tools to understand the role of efflux modulation in reversing chemoresistance
in CSCs. We aim to identify specific pharmacophores that can be chemically linked to existing
chemotherapeutic agents and alter their propensity to be substrates for the P-gp efflux pumps. The
student will explore the phenomenon of efflux transporter associated resistance, and the findings from
the study could help the researchers to understand the role of P-gp in conferring multi-drug resistance
in CSCs and develop targeted therapies to overcome efflux mediated chemoresistance.
Specific deliverables and work plan of the project includes -
Year1: In silico validation of the identified lead structures and medicinal-chemical modification to
develop suitable chemical tools.
Year 2: Use the identified and synthesised compounds as chemical tools to study the role of P-gp
modulation on chemoresistance in CSCs using biochemical and cellular assays.
Year 3 & 4: Develop pharmacophore-drug hybrids and evaluate their ability to overcome efflux-
mediated resistance in CSCs.
Two representative publications from supervisors:
Jamshidi, Shirin, J. Mark Sutton, and Khondaker M. Rahman. "An overview of bacterial efflux pumps
and computational approaches to study efflux pump inhibitors." Future Medicinal Chemistry 8.2
(2016): 195-210.
Madlova M, Bosquillon C, Asker D, Dolezal P, Forbes B. In vitro respiratory drug delivery models
possess nominal functional P-glycoprotein activity. Journal of Pharmacy and Pharmacology 61
(2009): 293-301
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38.1 Role of sphingosine-1-phosphate (S1P) signalling in cochlear homeostasis and progressive
hearing loss
Co-Supervisor 1: Professor Karen P Steel
Research Division or CAG: Wolfson Centre for Age-Related Diseases
E-mail: [email protected]
http://www.kcl.ac.uk/ioppn/depts/wolfson/research/Deafness/Index.aspx
Co-Supervisor 2: Professor Andrea Streit
Research Division or CAG: Department of Craniofacial Development and Stem Cell Biology
Email: [email protected]
http://www.kcl.ac.uk/dentistry/research/divisions/craniofac/ResearchGroups/StreitLab/StreitLa
b.aspx
Project Description:
Progressive hearing loss is very common with a major impact on quality of life. One form of pathology
involves loss of cochlear homeostasis. The fluid bathing sensory hair cells is maintained at 100mV
(endocochlear potential, EP) by the stria vascularis, and this is critically dependent on its blood supply.
EP provides a voltage gradient across hair cell transduction channels, facilitating synaptic activation.
S1P signalling is required for cochlear homeostasis. In mouse, mutations in genes involved in S1P
signalling (S1pr2 and Spns2) cause rapid loss of EP and worsening hearing. Spns2 transports S1P out
of cells that generate it and S1pr2 is the major S1P receptor required for normal hearing. S1PR2 and
SPNS2 are involved in human hearing.
The project asks if strial dysfunction in mice with abnormal S1P signalling is mediated by abnormal
capillary function, and involves:
• Analysis of the capillaries of the stria vascularis in S1P-mutant and control mouse cochleas
using gene expression, confocal and 3D ultrastructural methods to identify pathological changes (Y1);
• Isolation of fresh strial explants and exposure in vitro to a series of pharmacological agents
known to affect S1P signalling to investigate their effects on capillary constriction/dilation (Y2);
• Using intravenous tagged markers to determine the permeability of mutant and control strial
capillaries combined with exposure to vasoactive agents to ask if normal capillary permeability can be
restored to mutants (Y3).
• Testing effects of suitable pharmacological agents on hearing in mutants (Y4).
The findings will have obvious translational potential in cases of deafness due to strial dysfunction.
Two representative publications from supervisors:
Ingham NJ, Carlisle F, Pearson S, Lewis MA, Buniello A, Chen J, Isaacson RL, Pass J, White JK,
Dawson SJ and Steel KP. (2016) S1PR2 variants associated with auditory function in humans and
endocochlear potential decline in mouse. Scientific Reports, 6:28964.
Steventon B, Mayor R, Streit A. (2016) Directional cell movements downstream of Gbx2 and Otx2
control the assembly of sensory placodes. Biol Open. bio.020966.
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39.1 Characterising the epigenome in mice after exposure to environmental carcinogens
Co-Supervisor 1: Dr. Volker M. Arlt
Research Division or CAG: Analytical and Environmental Sciences Division/ MRC-PHE Centre for
Environment & Health/ NIHR Health Protection Research Unit in Health Impact of Environmental
Hazards
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/volker.arlt.html
Co-Supervisor 2: Prof. David H. Phillips
Research Division or CAG: Analytical and Environmental Sciences Division/ MRC-PHE Centre for
Environment & Health/ NIHR Health Protection Research Unit in Health Impact of Environmental
Hazards
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/david.phillips.html
Project Description:
Modern life involves unavoidable exposure to environmental carcinogens. These can damage
cellular DNA, which can lead to mutations, and mutations in critical genes are characteristic features
of tumours. Despite linear relationships between dose, DNA damage in target tissues and tumour
incidence, identifying which tissues are targets for carcinogenicity by an agent is problematic. This
suggests the importance of events subsequent to DNA damage and mutation in determining
organotropism, which may include epigenetic alterations (e.g. DNA methylation). The methylation
status in DNA can regulate the expression of genes, i.e. if they are switched on or off within the body
and this regulation is impacted by the exposure to environmental carcinogens. For example, it has
been suggested that epigenetic changes induced by combustion-derived polycyclic aromatic
hydrocarbons (PAHs) may contribute to carcinogenesis, although a direct cause and effect
relationship has yet to be established.
Aims: to investigate:
• whether epigenetic changes occur in mice in response to exposure to environmental carcinogens
(e.g. PAHs) (YEAR 1+2).
• if changes to the epigenetic (methylation) marks on DNA can act as biomarkers of carcinogen
exposure (YEAR 1+2).
• if such epigenetic effects distinguish target and non-target organs for tumour formation (YEAR
3+4).
Genome-wide analysis of various tissues from mice exposed to different environmental
carcinogens will identify changes in DNA methylation status in all genes by reduced representation
bisulphite sequencing. Results will be validated by pyrosequencing measuring methylation at specific
genes. Bioinformatics analysis will identify preferential targets of hypo- or hypermethylation and
concomitant gene dysregulation related to carcinogenesis.
Two representative publications from supervisors:
Krais AM, Speksnijder EN, Melis JP, Indra R, Moserova M, Godschalk RW, van Schooten FJ, Seidel
A, Kopka K, Schmeiser HH, Stiborova M, Phillips DH, Luijten M & Arlt VM (2016) The impact of
p53 on DNA damage and metabolic activation of the environmental carcinogen benzo[a]pyrene:
effects in Trp53(+/+), Trp53(+/-) and Trp53(-/-) mice. In: Archives of Toxicology, 90, 839-851.
Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I, Nik-Zainal S, Totoki Y, Fujimoto A,
Nakagawa H, Shibata T, Campbell PJ, Vineis P, Phillips DH, Stratton MR (2016) Mutational
signatures associated with tobacco smoking in human cancer. In: Science, in press.
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40.1 Understanding immune responses in intestinal homeostasis and disease
Co-Supervisor 1: Patricia Barral
Research Division or CAG: Division of Immunology, Infection and Inflammatory Diseases
E-mail: [email protected]
http://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/immunobiology/research/Patricia
-Barral/index1.aspx
Co-Supervisor 2: Jo Spencer
Research Division or CAG: Division of Immunology, Infection and Inflammatory Diseases
Email: [email protected]
http://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/immunobiology/research/JoSpenc
er/index.aspx
Project Description:
Humans carry 10 times more bacteria in the intestine than total cells constituting the body. These
commensal bacteria influence health and disease through complex interactions with the immune
system. Alterations in the crosstalk between commensals and immune cells can lead to the
development of inflammatory and autoimmune diseases including asthma, multiple sclerosis and
inflammatory bowel disease (IBD).
This project seeks to understand the mechanisms that control the crosstalk between commensals and
immune cells and how those modulate health and disease. We will focus in a population of intestinal
T cells (called NKT cells) that recognise lipids from commensal bacteria. NKT cells collaborate to
control commensals in the healthy intestine, but they also accumulate in the intestine of IBD patients,
which suggests that they are important for the onset and/or progression of the disease. In this project
we will investigate the mechanisms that control the function of intestinal NKT cells in health and IBD.
We will isolate NKT cells from the intestine of mice and humans and perform functional assays to
define their features, distribution and functions (year 1). Using mouse models and samples from IBD
patients we will study how NKT cell features are altered during inflammation (year 2). Finally, we
will explore the cellular and molecular mechanisms that lead to NKT cell activation in IBD and how
these are regulated by commensals (years 3 and 4). These experiments will provide insight into the
mechanisms of inflammatory diseases and guide the search for new therapies.
Training: cell isolation and culture, flow-cytometry, imaging techniques, qPCR, mouse genetics,
models of disease.
Two representative publications from supervisors:
Saez de Guinoa J, Jimeno R, Farhadi N, Jervis PJ, Cox LR, Besra GS & Barral P. CD1d-mediated
activation of group 3 Innate Lymphoid Cells drives IL-22 production. EMBO Reports (2016) in press
Vossenkämper A, Blair PA, Safinia N, Fraser LD, Das L, Sanders TJ, Stagg AJ, Sanderson JD, Taylor
K, Chang F, Choong LM, D'Cruz DP, Macdonald TT, Lombardi G, Spencer J. A role for gut-
associated lymphoid tissue in shaping the human B cell repertoire. J Exp Med. (2013) 210:1665-74
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41.1 Broadly neutralizing antibody responses against HIV
Co-Supervisor 1: Dr Katie Doores
Research Division or CAG: Immunology, Infection and Inflammatory Diseases
E-mail: [email protected]
http://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/doores/index.
aspx
Co-Supervisor 2: Dr Julie Fox
Research Division or CAG: GRIDA, Guy’s and St Thomas’ NHS Foundation Trust
Email: [email protected]; [email protected]
http://www.kcl.ac.uk/medicine/research/divisions/diiid/departments/infectious/research/juliefox.
aspx
Project Description:
Approximately 10-30% of HIV infected individuals generate antibodies that are capable of
neutralizing a broad range of HIV isolates and these antibodies have been shown to protect against
SHIV challenge in Macaque models. Isolation and characterisation of these antibodies has revealed
regions of the HIV envelope glycoprotein, gp120/gp41, that are susceptible to antibody binding and
re-eliciting these antibodies may be a key step for a successful HIV vaccine. Gp120 is heavily
glycosylated with host-derived N-linked glycans and it was previously thought that these glycans
shield conserved protein regions from the immune system. However, we have recently shown that a
number of the HIV broadly neutralizing antiodies (bnAbs) bind directly to these glycans highlighting
them as potential targets for HIV vaccine design. Using unique longitudinal samples from acutely HIV
infected patients in the SPARTAC study (N Engl J Med 2013;368:207-17) we will investigate the
development of glycan-binding bnAbs in vivo using in vitro neutralization assays, antigen-specific B
cell sorting and single genome amplification. We will determine how the evolving glycan shield
impacts and directs bnAb development. Ultimately these studies will be used to design immunogens
and immunization strategies aimed at re-eliciting these bnAbs through vaccination.
Two representative publications from supervisors:
L. M. Walker,* M. Huber,* K. J. Doores,* E. Falkowska, R. Pejchal, J.-P. Julien, S.-K. Wang, A.
Ramos, P. Y. Chan-Hui, M. Moyle, J. L. Mitcham, P. W. Hammond, O. A. Olsen, P. Phung, S. Fling,
C.-H. Wong, S. Phogat, T. Wrin, M. D. Simek, Protocol G Principal Investigators, W. C. Koff, I. A.
Wilson, D. R. Burton, P. Poignard, Broad neutralization coverage of HIV by multiple highly potent
antibodies, Nature, 2011, 477, 466-470.
S. A. Krumm, H. Mohammed, K. M. Le, M. Crispin, T. Wrin, P. Poignard, D. R. Burton, K. J.
Doores, Mechanisms of escape from the PGT128 family of anti-HIV broadly neutralizing antibodies,
Retrovirology, 2016, 13(1), 8.
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42.1 The CXCL8-producing T cell: function in health and carcinogenesis
Co-Supervisor 1: Dr Deena Gibbons
Research Division or CAG: DIIID
E-mail: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/immunobiology/research/gibbons
/index.aspx
Co-Supervisor 2: Dr Susan John
Research Division or CAG: DIIID
Email: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/immunobiology/research/SusanJo
hn/index.aspx
Project Description:
The human neonatal immune system is not just an immature version of that of the adult but is
qualitatively and quantitatively different. Our research focuses on understanding immune cell
development and function in the human neonate and how this impacts on disease. We have identified
a novel T cell effector function in neonates that contrasts with T cell biology in adults. Furthermore,
this discovery dispels the long held belief that the newborn immune system is anti-inflammatory. This
effector function, the ability to produce CXCL8 (aka interleukin-8, IL8), is imprinted in the thymus
during T cell development and represents an intermediate function en route to classic adaptive
uestions that form
the basis of this PhD project:
1. What is the function of CXCL8 during T cell development in the thymus and does this play
a role in the transformation of progenitors to T cell acute lymphocytic leukaemia (T-ALL) or in its
maintenance?
2. What is the fate of these cells as the human immune system develops post-natally and do these
cells determine how infants respond to infection?
3. What are the signals and signalling pathways that allow conversion of CXCL8-producing T
-producing cells and other T cell lineages?
Methods will involve multiple cellular and molecular techniques as well as work both in vitro and in
vivo mouse models.
Two representative publications from supervisors:
Deena Gibbons, Paul Fleming, Alex Virasami, Marie-Laure Michel, Neil Sebire, Kate Costeloe,
Robert Carr, Nigel Klein, Adrian Hayday. Interleukin-8 (CXCL8) Production is the signatory T cell
effector function of human newborn infants. Nature Medicine 20, 1206-10 (2014)
Rani A, Afzali B, Kelly A, Tewolde-Berhan L, Hackett M, Kanhere A.S, Pedroza-Pacheco I, Bowen
H, Jurcevic S, Jenner R.G., Cousins, D., Ragheb J.A., Lavender Pand John S. IL-2 regulates
expression of c-maf in human CD4 T cells. 2011. J. Immunol. 187(7): 3721-9.
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43.1 Elucidating the crosstalk between lymphocytes and intestinal epithelial cells using human
mini-guts
Co-Supervisor 1: Graham Lord
Research Division or CAG: Division of Transplantation Immunology and Mucosal Biology
E-mail: [email protected]
www.kcl.ac.uk/lsm/research/divisions/timb/about/people/profiles/grahamlord.aspx
Co-Supervisor 2: Joana F Neves
Research Division or CAG: Division of Transplantation Immunology and Mucosal Biology
Email: [email protected]
Project Description:
Studies, by us and others, have found that maintaining intestinal homeostasis depends on the
interactions between the gut epithelium, the intestinal microbiota and the gut-associated immune
system. Disrupting this delicate balance usually results in intestinal inflammation, which is associated
with several diseases such as Inflammatory Bowel Disease (IBD) and cancer.
We recently developed a novel in vitro system of lymphocyte culture in intestinal organoids (“mini-
guts”) that mimics the intestinal environment. This pioneer system allows us to identify and dissect
the mechanisms that govern the crosstalk between lymphocytes and epithelial cells at the intestinal
barrier. Certain populations of a recently discovered group of lymphocytes, called Innate Lymphoid
Cells (ILC) are increased in IBD patients. Thus, we are particularly interested in studying the
interaction of ILC with intestinal epithelial cells.
Aim-1) Ascertain the differences between intestinal organoids established from inflamed and non-
inflamed tissue of IBD patients and their effect on the function and differentiation of ILC (Years 1-2).
Aim-2) Understand the effect of ILC on the biology of intestinal epithelial cells (Years 2-3).
Aim-3) Identify the molecular pathways that regulate the crosstalk between ILC and intestinal
epithelial cells (Years 3-4).
This study can lead to the identification of novel targets to modulate ILC and intestinal epithelial cells
in order to promote intestinal homeostasis. During this project the student will acquire a wide range
techniques such as flow cytometry, imaging, molecular biology (including CRISPR), transcriptomic,
bioinformatics and lymphocyte biology and mucosal immunology techniques (mouse/human). The
supervisors and their established collaborations have vast expertise these areas.
Two representative publications from supervisors:
Powell N, Lo JW, Biancheri P, Vossenkämper A, Pantazi E, Walker, AW, Stolarczyk E, Ammoscato
F, Goldberg R, Scott P, Canavan JB, Perucha E, Garrido-Mesa N, Irving PM, Sanderson JD, Hayee
B, Howard JK, Parkhill J, MacDonald TT, Lord GM. Interleukin 6 Increases Production of
Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal
Inflammation. Gastroenterology. 2015 149(2):456-67.
Olszak T*, Neves JF*, Dowds CM*, Baker K, Glickman J, Davidson NO, Lin CS, Jobin C, Brand S,
Sotlar K, Wada K, Katayama K, Nakajima A, Mizuguchi H, Kawasaki K, Nagata K, Müller W,
Snapper SB, Schreiber S, Kaser A, Zeissig S*, Blumberg RS*. Protective mucosal immunity mediated
by epithelial CD1d and IL-10. Nature, 2014; 509 (7501): 497-502.
*These authors contributed equally to this work
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44.1 Elucidating the molecular mechanisms of peanut allergies
Co-Supervisor 1: James McDonnell
Research Division or CAG: Randall Division
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/james.mcdonnell.html
Co-Supervisor 2: Alexandra Santos
Research Division or CAG: Allergy, Asthma and Lung Biology
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/alexandra.santos.html
Project Description:
The incidence of allergic disorders is increasing worldwide and now affects more than a quarter of the
population in industrialised countries and there is an urgent need for better treatments.
Immunoglobulin E (IgE) is the central player in allergic reactions, recognising allergens both as a B
cell receptor (BCR) and bound to high-affinity receptor FcεRI on effector cells and antigen presenting
cells (APCs). Allergic reactions are rapidly generated when allergens bind and crosslink IgE-FcεRI
complexes on mast cells and basophils, resulting in cell degranulation and release of inflammatory
mediators.
This project seeks to understand the mechanisms of allergic reactions against peanut allergens, one of
the most common and most dangerous types of food allergies. Recent work by Dr. Santos has
demonstrated that not all anti-peanut IgE antibodies found in patients are pathogenic. Using a set of
patient derived anti-peanut IgE antibodies, this project will test the hypothesis that a number of factors
- including allergen epitope, epitope number (valency), spatial arrangement and IgE affinity -
contribute to triggering of allergic responses and thus determine IgE pathogenicity.
The project will offer training in methods of antibody discovery/expression/characterisation, cellular
immunology, bioinformatics, molecular interaction analysis, and molecular structure determination.
Early priorities in the project will be to produce a representative set of patient-derived pathogenic and
non-pathogenic IgE antibodies, using in-house protocols for highly efficient single B cell cloning and
antibody production, which will then be used to test hypotheses on the molecular mechanisms that
determine the allergy triggering properties of IgE antibodies.
Two representative publications from supervisors:
Santos et al. (2014) Basophil activation test discriminates between allergy and tolerance in peanut
sensitized children. J. Allergy Clin. Immunol. 134:645-652.
Drinkwater et al. (2014) Human immunoglobulin E flexes between acutely bent and extended
conformations. Nature Struct. Mol. Biol. 21:397-404
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45.1 Targeting PSK kinases for breast cancer therapy
Co-Supervisor 1: Dr Jonathan Morris
Research Division or CAG: Cancer Studies
E-mail: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/cancer/research/groups/cspcc.aspx
Co-Supervisor 2: Dr John Maher
Research Division or CAG: Cancer Studies
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/john.maher.html
Project Description:
Drugs that target and inhibit microtubule dynamics (eg. taxanes) provide one of the most effective
classes of therapeutics for the front-line treatment of metastatic breast cancer, but these compounds
also produce debilitating side effects and patients relapse and become resistant within 3-8 months.
Microtubules are therefore proven targets for chemotherapy and their disruption works well in the
clinic, but additional and better strategies are now needed to target these structures in dividing breast
cancer cells to provide more effective and longer lasting treatment.
In seeking candidates for intervention we have identified an unusual family of proteins called prostate-
derived sterile 20-like kinases (PSKs), which bind microtubules and regulate their stability and
organisation. PSKs are activated catalytically in dividing breast cancer cells and this activity is
required for their proliferation.
The initial project will use novel small molecule inhibitors for PSKs to assess the requirements for
these proteins during mitosis and for cell proliferation
The PhD objectives will be to:
• Identify biological functions for PSKs and their mechanisms of action in breast cancer cells
• Inhibit PSK activity and downstream substrates in breast cancer cell models in order to alter
cell proliferation
• Characterise novel chemical inhibitors for PSKs and establish their biological effects on
malignant cells
• Use breast cancer tissue arrays to identify patient subtypes suitable for kinase inhibition and
therapy
The results will establish whether PSKs offer suitable targets for breast cancer therapy.
Skills:
• Expertise in cellular and molecular biology techniques (Morris)
• Knowledge of cancer cell biology and treatment (Maher)
Two representative publications from supervisors:
Wojtala RL, Tavares IA, Morton PE, Valderrama F, Thomas NS, Morris JD. Prostate-derived sterile
20-like kinases (PSKs/TAOKs) are activated in mitosis and contribute to mitotic cell rounding and
spindle positioning. 2011. J. Biol. Chem. 286. 30161-70.
Tavares IA, Touma D, Lynham S, Troakes C, Schober M, Causevic M, Garg R, Noble W, Killick
R, Bodi I, Hanger DP, Morris JD. Prostate-derived sterile 20-like kinases (PSKs/TAOKs)
phosphorylate tau protein and are activated in tangle-bearing neurons in Alzheimer Disease. 2013. J.
Biol. Chem. 288. 15418-29.
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46.1 How do mutations in MYO18B lead to muscle diseases?
Co-Supervisor 1: Dr. Julien Ochala (basic scientist)
Research Division or CAG: Centre of Human and Aerospace Physiological Sciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/julien.ochala.html
Co-Supervisor 2: Dr. Heinz Jungbluth (clinician/clinician scientist)
Research Division or CAG: Randall Division of Cell and Molecular Biophysics
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/heinz.1.jungbluth.html
Project Description:
Myopathies are life-threatening diseases characterized by devastating muscle weakness. The
understanding of this group of disorders has advanced in recent years through the identification of the
causative gene mutations such as MYO18B. The aim of the present project is to underpin the hitherto
pathophysiological mechanisms by which MYO18B mutations lead to muscle weakness. MYO18B
encodes a member of the myosin superfamily, Myo18b. As this protein is involved in muscle
trafficking, the overall hypothesis of the present project is that MYO18B mutations alter the
organisation and function of myosin molecules in muscle, disrupting the force production mechansims.
To prove this, the present project will be divided into three sub-objectives:
Sub-objective 1 (year 1, with Dr. Jungbluth): Determining how MYO18B mutations affect myosin
arrangement using muscle samples from human patients and advanced microscopy.
Sub-objective 2 (years 2, with Dr. Ochala): Characterising how MYO18B mutations modify myosin
motor function and force production using muscle tissue from human patients and motility assays.
Sub-objective 3 (years 3 and 4, with Dr. Ochala and Jungbluth): Identifying the time course of above
changes using muscles from mice with a specific Myo18b deficiency. This will allow a clear genotype-
phenotype correlation, potentially helping the design of efficient therapeutic interventions.
At the end of this project, the student should be able to:
- Master biophysical techniques and advanced microscopy,
- Apply his newly developed skills to normal and diseased cells/molecules,
- Generate and analyse large sets of data,
- Synthetize the findings by writing scientific papers
Two representative publications from supervisors:
Cullup T, Kho AL, Dionisi-Vici C, Brandmeier B, Smith F, Urry Z, Simpson MA, Yau S, Bertini E,
McClelland V, Al-Owain M, Koelker S, Koerner C, Hoffmann GF, Wijburg FA, ten Hoedt AE,
Rogers RC, Manchester D, Miyata R, Hayashi M, Said E, Soler D, Kroisel PM, Windpassinger C,
Filloux FM, Al-Kaabi S, Hertecant J, Del Campo M, Buk S, Bodi I, Goebel HH, Sewry CA, Abbs
S, Mohammed S, Josifova D, Gautel M, Jungbluth H. (2013) Recessive mutations in EPG5 cause
Vici syndrome, a multisystem disorder with defective autophagy. Nat Genet. 45: 83-87.
Ochala J, Gokhin DS, Penisson-Besnier I, Quijano-Roy S, Monnier N, Lunardi J, Romero NB,
Fowler VM. (2012) Congenital myopathy-causing tropomyosin mutations induce thin filament
dysfunction via distinct physiological mechanisms. Hum Mol Genet. 21: 4473-4485.
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47.1 Developmental basis of skin diversity
Co-Supervisor 1: Tanya Shaw
Research Division or CAG: Immunology, Infection & Inflammatory Disease
E-mail: [email protected]
www.kcl.ac.uk/lsm/research/divisions/diiid/centres/cmcbi/research/shaw/DrTanyaShaw.aspx
Co-Supervisor 2: Anthony Graham
Research Division or CAG: Centre for Developmental Neurobiology
Email: [email protected]
Website: http://www.kcl.ac.uk/ioppn/depts/devneuro/Research/groups/graham.aspx
Project Description:
The skin exhibits anatomical diversity, with different regions fulfilling different functions; the skin
over our heads is covered in hair, the skin of our hands and feet is quite different that of our abdomen.
Regional differences in the skin emerge during development and these are imparted by the dermis,
which has a complex developmental history. Specifically, the dermis of the back is derived from
somites, derivatives of the paraxial mesoderm, the dermis of the limbs is derived from lateral plate
mesoderm and the dermis of the face from neural crest cells. We hypothesize that the positionally
distinct dermal features (including repair and regeneration potential, and susceptibility to site-specific
skin diseases) reflect the developmental origin of the tissue. Having discovered significantly different
gene expression profiles of dermis from various anatomical sites in homeostasis, the objectives of this
project are to:
1. Determine if dermis of different embryonic origins has different properties during wound healing.
2. Investigate whether the anatomical distribution of site-specific skin diseases reflects the distinct
histories of the tissue.
This project will use a combination of human samples and in vivo models; the student will be trained
in many cellular and molecular biology techniques, including primary tissue culture, gene expression
profiling (e.g. RNA-seq), western blotting, immunohistochemistry, and microscopy.
Two representative publications from supervisors:
EJ Fitzgerald O'Connor, II Badshah, LY Addae, P Kundasamy, S Thanabalasingam, D Abioye, TJ
Shaw. Histone deacetylase 2 is upregulated in normal and keloid scars. J Invest Dermatol 2012, 132,
1293-6.
Shone, V. and Graham, A. Endodermal/ectodermal interfaces during pharyngeal segmentation in
vertebrates. Journal of Anatomy 2014, 225, 479-491.
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48.1 Molecular mechanisms underlying the contractile dysfunction in ageing-related muscle
weakness
Co-Supervisor 1: Dr. Yin Biao Sun (basic scientist)
Research Division or CAG: Randall Division of Cell and Molecular Biophysics
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/yin-biao.sun.html
Co-Supervisor 2: Prof. Steve Harridge (basic scientist)
Research Division or CAG: Centre of Human and Aerospace Physiological Sciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/stephen.harridge.html
Project Description:
Ageing-related muscle weakness represents a major, and growing, healthcare burden, which leads to
declines in physical function, independency and quality of life. The molecular mechanisms underlying
such phenomena remain unclear but potentially include a dysfunction of the molecular motor, myosin,
that can only partly explain the decline in the force-generating capacity. In the present project, we
aim to precisely characterise such myosin dysfunction. Understanding the mechanisms underpinning
such contractile dysfunction is essential in the development of effective ‘preventative’ or ‘therapeutic’
interventions.
We are going to apply two of the state-of-the-art techniques, the Fluorescence for In Situ Structure
(FISS) and the Small-angle X-ray scattering, to study both structural and functional effect of aging
on myosin in human skeletal muscle cells. We will use muscle biopsy specimens that we have already
obtained from healthy young adults, and three groups of older individuals aged over 75 years who
represent the health and activity span.
Performing FISS and X-ray experiment requires a unique combination of expertise, ranging from
molecular biology, protein biochemistry, muscle physiology to biophysics of data interpretation.
Depends on the student’s background and previous experience, he/she will have opportunities to be
trained in all these skills.
- Years 1 and 2 (with Dr. Sun): trainings in basic skills required for the experiment and
performing FISS to complete the control experiments using myosin probes.
- Years 3 and 4 (with Dr. Ochala and Dr. Sun): specifically characterise the alterations in
myosin function in aging muscle cells using both X-ray and FFSS techniques.
Two representative publications from supervisors:
Kampourakis T, Sun YB, Irving M. (2013) Myosin light chain phosphorylation enhances contraction
of heart muscle via structural changes in both thick and thin filaments. PNAS. 113: E3039-3047.
Li M, Ogilvie H, Ochala J, Artemenko K, Iwamoto H, Yagi N, Bergquist J, Larsson L. (2015)
Aberrant post-translational modifications compromise human myosin motor function in old age.
Aging Cell. 14: 228-235.
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49.1 Linking Genotype to Phenotype in Psoriatic Arthritis: determining the role of disease-
associated genes in Tc17 cell function and development
Co-Supervisor 1: Prof Leonie Taams
Research Division or CAG: DIIID / GRIID
E-mail: [email protected]
www.kcl.ac.uk/lsm/research/divisions/diiid/centres/cmcbi/research/taams/index.aspx
Co-Supervisor 2: Dr Francesca Capon
Research Division or CAG: GMM/GRIID
Email: [email protected]
Website: http://tinyurl.com/CaponLab
Project Description:
Psoriatic arthritis (PsA) is an inflammatory disease of the joints, with frequent skin involvement. The
disease is typically associated with HLA class I, suggesting a role for CD8+ T cells. We previously
demonstrated that the inflamed joints of patients with PsA contain higher frequencies of CD8+ T cells
expressing the pro-inflammatory cytokine IL-17. These IL-17+ CD8+ T cells (Tc17 cells) correlate
with clinical parameters of disease activity. Tc17 cells are also found in the skin of patients with
psoriasis. In addition to particular HLA class I associations, a number of other genetic variants have
been associated with PsA and psoriasis. Interestingly, some of these genetic variants relate to the IL-
17 pathway (e.g. IL23R, TRAF3IP2). Together, this leads us to hypothesize that (i) the presence of
Tc17 cells in the inflamed joint is driven by particular HLA class I associations, and (ii) IL-17
production by CD8+ T cells can be influenced by particular non-HLA genetic variants.
Overarching objectives:
Year 1: determine HLA genotypes and other genetic variants in existing samples from patients with
PsA, and link this information to Tc17 frequency.
Year 2/3: assess gene/protein expression of PsA-associated genetic variants that are associated with
the IL-17 pathway in relevant immune cells.
Year 3/4: determine the functional effects of these genetic variants on the expression of IL-17 by
CD8+ (and CD4+) T cells, and Tc17 development and function.
Skills training: mononuclear cell isolation, cell culture, intracellular cytokine staining, multi-colour
flow cytometry, ELISA, Western blotting, DNA/RNA extraction, qPCR, genotyping,
overexpression/knockdown, bioinformatics.
Two representative publications from supervisors:
Menon B, Gullick NJ, Walter GJ, Rajasekhar M, Garrood T, Evans HG, Taams LS*, Kirkham BW*
(*joint senior authors). Interleukin-17+CD8+ T Cells Are Enriched in the Joints of Patients With
Psoriatic Arthritis and Correlate With Disease Activity and Joint Damage Progression. Arthritis
Rheumatol. 66 (5): 1272–1281 (2014)
Mahil SK, Twelves S, Farkas K, Setta-Kaffetzi N, Burden AD, Gach JE, Irvine AD, Képíró L,
Mockenhaupt M, Oon HH, Pinner J, Ranki A, Seyger MM, Soler-Palacin P, Storan ER, Tan ES,
Valeyrie-Allanore L, Young HS, Trembath RC, Choon SE, Szell M, Bata-Csorgo Z, Smith CH, Di
Meglio P, Barker JN, Capon F. AP1S3 mutations cause skin autoinflammation by disrupting
keratinocyte autophagy and up-regulating IL-36 production. J Invest Dermatol Epub ahead of print
4th July 2016; doi: 10.1016/j.jid.2016.06.618
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50.1 TRPV1 and TRPA1 ligands as P-gp substrates: a wide-reaching investigation from basic
molecule through to animal models of disease
Co-Supervisor 1: Sarah A. Thomas BSc, PhD (Reader in Physiology)
Research Division or CAG: Institute of Pharmaceutical Science
E-mail: [email protected]
http://www.kcl.ac.uk/lsm/research/divisions/ips/about/people/Thomas/index.aspx
Co-Supervisor 2: Julie Keeble BSc, PhD (Lecturer in Pharmacology and Named training and
competency officer)
Research Division or CAG: Institute of Pharmaceutical Science
Email: [email protected]
http://www.kcl.ac.uk/lsm/research/divisions/ips/research/pharmathera/Staff/Keeble.aspx
Project Description:
Transient Receptor Potential Vanilloid 1 (TRPV1) receptors are intrinsically involved in pain
and inflammation (Keeble et al., 2005). TRPV1 ligands appear to act on the intracellular side of the
channel, in contrast to ligands of other ligand-gated ion channels. This suggests that ligands need to
pass through the cell membrane in order to access their binding site and for metabolism/excretion
from cells, perhaps via passive diffusion due to their lipid solubility. However, it is also possible that
TRPV1 ligands are transported by an efficient biological system. Indeed, a recent article in Nature
Neuroscience identified a FAAH-1 variant as a driver for anandamide transport into neuronal cells
(Fu et al., 2012). Preliminary experiments in our laboratory show for the first time that anandamide,
an endogenous TRPV1 agonist, is a P-glycoprotein (P-gp) efflux transporter substrate (Brown et al.,
2015).
The aims of this multi-disciplinary PhD project will therefore be to (1) characterise the
transport of various TRPV1 and TRPA1 agonists via P-gp and other ABC transporters through the
use of cell culture and assay studies, (2) carry out a study of co-expression of TRPV1 with the various
transporters in different tissues, e.g. blood-brain barrier, neurons and inflammatory cells, using
immunohistochemical, PCR and Western blot techniques and (3) perform an in vivo investigation
into the physiological/pathophysiological implications of TRPV1/TRPA1 ligand transport by P-
gp/other transporters, e.g. effects of transporter inhibitors in murine models of pain, inflammation and
thermoregulation.
Gannt chart 0-6
months
6-12
months
12-18
months
18-24
months
24-30
months
30-36
months
36-42
months
42-48
months
Cell culture and
assay studies
x x x
Transporter and
TRPV1/TRPA1
co-expression
x x x
In vivo studies x x x
Writing up x
SAT will supervise the in vitro component and JEK will supervise the in vivo component.
Brown et al. (2015) E-journal of the British Pharmacological Society 279P.
Fu et al. (2012). Nat Neurosci, 15(1):64-69.
Keeble et al. (2005). Arthritis Rheumatism, 52(10):3248-56.
Thomas (2012) Brain Res1436:111
Thomas (2011) J.Pharm.Exp.Ther336:506.
P a g e 55 | 58
Two representative publications from supervisors:
Watson, CP, Pazarentzos, E., Fidanboylu, M., Padilla, B., Brown, R and Thomas S.A. The transporter
and permeability interactions of asymmetric ADMA and L-arginine with the human blood-brain
barrier in vitro. Brain Research 1648 (2016) 232-242.
Alawi, KM, Aubdool, AA, Liang ,L, Wilde, E, Vepa, A, Psefteli, MP, Brain, SD and Keeble JE (2015).
The sympathetic nervous system is controlled by transient receptor potential vanilloid 1 in the
regulation of body temperature. FASEB J. 29(10):4285-98.
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51.1 Role of Genetic Regulation of Gene Expression in Type 2 Diabetes and Obesity.
Co-Supervisor 1: Kerrin Small
Research Division or CAG: Genetics and Molecular Medicine
E-mail: [email protected]
http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/twin/research/small/index.aspx
Co-Supervisor 2: Dr Alan Hodgkinson
Research Division or CAG: Genetics and Molecular Medicine
Email: [email protected]
http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/Hodgkinso
nGroup.aspx
Project Description:
Genome-wide association studies (GWAS) have identified thousands of regions of the genome that
are associated with disease, including Type 2 Diabetes and other obesity-related traits. However,
GWAS studies only identify a region of the genome, not the casual gene or underlying molecular
mechanism. An important tool for interpreting GWAS loci are eQTL studies, which identify
genetic variants that regulate gene expression. We have previously shown that eQTLs in adipose
(fat) tissue mediate a subset of Type 2 Diabetes loci, including a master trans-regulator at the KLF14
locus. This project will seek to identify novel regulatory variants and use them to further interpret
disease associations, with a particular focus on Type 2 Diabetes and obesity-related traits. In
particular this project will focus on two under-explored classes of regulatory variants, rare variants
and trans-eQTLs. The student will utilize a unique multi-tissue RNAseq data set from deeply-
phenotyped twins from the TwinsUK cohort, and integrate this newly generated matched whole
genome sequence data. The student will be taught how to analyze high-throughput sequencing data
to answer important biological questions. More broadly the student will undergo training in genomic
analysis, bioinformatics (including programming) and scientific writing.
Objectives:
Year 1: Identify regulatory variants (eQTLs, rare variants and splicing) utilizing RNAseq data from
multiple tissues and matched whole genome sequence.
Year 2: Identify trans-eQTLs in adipose tissue in a large multi-center dataset.
Year 3: Integrate identified regulatory variants with Type 2 Diabetes and obesity-related traits to
elucidate underlying regulatory mechanisms mediating disease risk and response.
Two representative publications from supervisors:
Glastonbury C, Vinuela A, Buil A, Halldorsson, G, Thorleifsson, G, Helgason. H, Thorsteinsdottir
U, Stefansson K, Dermitzakis ET, Spector TD, Small KS Adiposity-dependent regulatory effects
on multi-tissue transcriptomes. Am J Hum Genet. 2016 Sept 1;99(5):567-79. doi:
10.1016/j.ajhg.2016.07.001
Hodgkinson, A., Idaghdour, Y., Gbeha, E., Grenier, J.C., Hip-Ki, E., Bruat, V., Goulet, J.P., de
Malliard, T. and Awadalla, P. 2014. High-Resolution Genomic Analysis of Human Mitochondrial
RNA Sequence Variation. Science 344: 413-415.
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52.1 Identifying novel therapeutics to target pancreatic cancer metastasis
Co-Supervisor 1: Dr. Claire Wells (basic scientist)
Research Division or CAG: Cancer Studies
E-mail: mailto:[email protected]
Website: https://kclpure.kcl.ac.uk/portal/claire.wells.html or
http://wellslaboratory.blogspot.co.uk/
Co-Supervisor 2: Dr. Debashis Sarker (clinical)
Research Division or CAG: Cancer Studies
Email: mailto:[email protected]
Website: https://kclpure.kcl.ac.uk/portal/debashis.sarker.html
Project Description:
Pancreatic cancer (PC) survival is devastatingly low with few patients surviving more than 5 years
post diagnosis due to the prevalence of metastatic disease. Currently there are no treatment options
that target metastasis and thus novel therapeutic approaches are urgently required. We have recently
completed a screen of existing drugs to identify novel therapeutic compounds that can block PC
invasion. We now need to validate these hits and elucidate the molecular mechanism that underpins
suppression of invasion.
One of our top screen hits was a p-21 activated kinase inhibitor. The PAK family are associated with
cancer cell invasion and PAK is amplified in PC. Interestingly we have recently published that PAK
activity is linked to cancer cell invasion via promotion of a cellular process called invadopodia.
However, there is much we still don’t understand about PAK in invadopodia and how this process is
regulated. This project aims to bring together our screen discoveries with our existing expertise in
PAK biology to develop novel therapeutics to target pancreatic cancer invasion.
Project Outline
Rotation: Identify PC cell lines that form invadopodia and correlate with PAK activity
Year 1: Follow up top 5 hits (including PAK) – expand screen to include invadopodia studies. Identify
most promising lead to take into year 2
Year 2: dose responses , invadopodia life cycle analysis, organotypic validation
Year 3: Define the biochemical signalling nexus that underpins suppression of invasion. Test findings
in clinical material.
Training: high resolution live/fixed cell imaging, cell biology, biochemistry, translational medicine
techniques.
Two representative publications from supervisors:
Nicole S. Nicholas, Aikaterini Pipili, Simon M. Ameer-Beg, Jenny L. C. Geh, Ciaran Healy,
Alistair D. MacKenzie Ross, Maddy Parsons, Frank O. Nestle, Katie E. Lacy and Claire M. Wells
(2016) PAK4 suppresses PDZ-RhoGEF activity to drive invadopodia maturation in melanoma cells
Oncotarget DOI: 10.18632/oncotarget.12282
Anna Dart, Gary Box , William Court , Madeline Gale, John Brown, Sarah Pinder, Sue Eccles and
Claire M Wells (2015) PAK4 promotes kinase-independent stabilization of RhoU to modulate cell
adhesion. J Cell
Biol. 211:863
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