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Theme 1
Molecules, Cells and the Basis
for Disease
2019/2020
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 & Dr Cynthia Andoniadou
When choosing a project from this catalogue in the funding section & research proposal
section of the online application form please enter MRCDTP2019_Theme1
Deadline for application: Sunday 25th November 2018
Shortlisted candidates will be contacted in early January.
Interviews: 30th & 31st January 2019
The 2019/20 studentships will commence in September 2019.
For further Information or queries relating to the application process please contact
Projects listed in this catalogue are subject to change, candidates
invited to interview will have the opportunity to discuss projects in
further detail.
Contents 1.1 Prostate and colo-rectal cancer - interrogating Wnt signalling expression and function for
biomarkers and therapy .......................................................................................................................... 5
3.1 A systems biology approach integrating multi-omic datasets to elucidate the role of smoking in
inflammatory bowel disease: implications for therapy ........................................................................... 6
4.1 Investigating the epigenetic regulation of autophagy during aging and its impact on
cardiovascular health ............................................................................................................................... 8
5.1 A study of IL-36 as a disease driver in psoriatic arthritis ................................................................... 9
6.1 Gene and environment interactions in obesity: the influence of early life nutrition .....................11
7.1 Generation of a bioartificial pituitary ..............................................................................................13
8.1 Investigating the role of aberrant Type I Interferon response in paradoxical psoriasis .................15
9.1 Development of monoclonal antibodies for treatment of emerging hantavirus infection ............17
10.1 How complex patterns of genetic variation within the large inversion on chromosome 8..........19
11.1 Development of in vivo traceable diagnostic and therapeutic IgE-like antibodies. ......................21
12.1 Dynamic control of the heartbeat by thick filament regulation ...................................................23
13.1 The effect of lipid composition on the mechanostransduction of individual live cells .................25
14.1 Clinical, biochemical and cellular phenotyping of titin gene mutations in paediatric patients ....27
16.1 Investigating the developmental basis for unique wound healing properties of facial skin ........29
17.1 Control of embryoid development by morphogens and matrix properties in 3D ........................31
18.1 Phagocyte development during cancer progression and immunotherapy. ..................................33
19.1 Dissecting the role of Follicular Dendritic Cells in the lymphoma tumour microenvironment ....35
20.1 Coordination of forebrain and sense organ development in vertebrates. ...................................37
21.1 Application of lightsheet functional imaging to identify regulators of regulators of inflammation
during tissue regeneration ....................................................................................................................39
22.1 Role of the Nance Horan Syndrome protein family in breast cancer invasion. ............................41
23.1 Disease in a dish: use of patient-derived human induced pluripotent stem cells (hiPSCs) to
model ciliopathic neural crest anomalies ..............................................................................................43
25.1 The role of NSA2 in renal and cardiovascular disease in diabetes. ...............................................45
26.1 Generation of tissue specific CAR-Tregs to modulate liver inflammatory and promote immune
tolerance ................................................................................................................................................47
27.1 Identification of host factors that promote assembly of Ebola virus ............................................49
28.1 Catching the unconventional epitopes that target the autoimmune response in Type 1 Diabetes
...............................................................................................................................................................51
29.1 Investigating driver gene mutations in T-cell signalling pathways to identify therapeutic targets
and genetic biomarkers for cutaneous T-cell lymphoma. .....................................................................53
30.1 Inborn error of immunity: characterisation of IL-10/PGE2 axis in regulation of inflammation
using a patient-derived induced pluripotent stem cell model ..............................................................55
31.1 Characterising the role of MAP3K8/COTK during mucosal infection. ...........................................57
32.1 HIV-1 modulation of chromatin architecture by targeting of the cohesin regulator ESCO2 ........59
33.1 Understanding epigenetic mechanisms in tissue-specific gene expression .................................61
34.1 Inhibition of Interferon signalling by Shigella sonnei ....................................................................62
35.1 Understanding chromatin remodelling at the nuclear periphery .................................................64
36.1 Biophysical regulation of EGFR signalling in tumour cells .............................................................66
37.1 Platelets and allergen sensitization: A critical interface between trained innate immunity and
the adaptive immune response. ............................................................................................................67
38.1 Investigating the role of the gut microbiome on the cardioprotective effect of polyphenol-rich
diets .......................................................................................................................................................69
39.1 Liver transplantation and immunogenicity ...................................................................................71
40.1 Microfluidics modelling of an adult stem cell niche ......................................................................72
41.1 Regulation of gene expression in fat tissue and its contributions to Type 2 Diabetes and Obesity
...............................................................................................................................................................73
42.1 Lineage reprogramming of hepatocytes into pancreatic beta-cells .............................................74
43.1 Dissecting the role and regulation of contact inhibition of locomotion in cancer........................76
44.1 Gene editing approaches for treating sickle cell disease ..............................................................77
45.1 Inhibition of human immunodeficiency virus (HIV) replication by CpG dinucleotides, the cellular
antiviral protein ZAP and its cofactors ..................................................................................................79
46.1 Predictive Immune Atlas of Cancer Resistance to Radiotherapy ..................................................81
47.1 Understanding and enhancing repair of the ear ...........................................................................83
48.1 Uncovering the properties of human Liver Stem Progenitor Cells (hLSPC) and surrounding
microenvironment during development, homeostasis and disease. ....................................................85
49.1 Transcriptional regulation of cardiac progenitor cell fate .............................................................87
51.1 Identification of novel immunomodulatory target checkpoints for Prostate Cancer therapeutics
...............................................................................................................................................................89
1.1 Prostate and colo-rectal cancer - interrogating Wnt signalling
expression and function for biomarkers and therapy
Co-Supervisor 1A: Dr Aamir Ahmed, Head of Prostate Cancer and Stem Cell Group, Centre for Stem
Cell and Regenerative Medicine
Research School/Division or CAG: School of Basic and Medical Biosciences
E-mail: [email protected]
Website: http://goo.gl/NsFAkV
Co-Supervisor 1B: Mr Amyn Haji MA MBBChir MSc MD FRCS
School/Division or CAG: Clinical Lead for Endoscopy and Colorectal Surgery, King's College Hospital
Email: [email protected]
Website: https://www.kch.nhs.uk/service/cancer/cancer-types/colorectal
Project description
We are interested in prostate and colo-rectal cancers, the two most common cancers in the UK (92,000 new cases and 26,000 deaths / year). Tissue biopsy remains a key diagnostic and prognostic modality. Early detection could save many lives. There is an urgent need for cancer specific, prognostic, minimally-invasive, biomarkers. Signaling molecules in the tumour microenvironment could be harvested as a rich source of such biomarkers. Wnts are secreted ligands that act as close-range cell-signaling proteins; Wnt activated ß-catenin transcription is a key step in carcinogenesis in prostate, colon and other carcinomas. Wnt ligands and transcription targets that are secreted proteins could act as early prognostication markers for prostate and colon cancers. This study will (i) investigate expression of single molecule RNA and proteins for secreted Wnt
targets in >400 archival, human tissue samples (normal, early, low and high-grade cancer) to validate
these as potential early biomarkers (ii) develop technologies to detect these in liquid biopsy
samples. We will investigate RNA and protein expression Wnt/beta catenin transcription (e.g. WISP-
1, TNC, COL1A1, HIG2) and Wnt ligands (e.g. Wnt 4, Wnt 5A and Wnt 10B) in the secretome of
prostate and colo-rectal (normal, low and high-grade cancers) tissue using immunohistochemical
analysis (see publication below for technical details). Other objectives will be to (iii) sequence
membrane associated polysome RNA from fresh cancer tissue for other secretome biomarkers (iv)
investigate the functional characteristics of Wnt signaling in prostate and colon cancer cell lines and
test novel inhibitors of Wnt signaling as therapeutic agents.
One representative publication from each co-supervisor:
Arthurs, C, Murtaza, BN, Thomson, C, Dickens, K, Henrique, R, Patel, HRH, Beltran, M, Millar, M, Thrasivoulou, C and Ahmed, A. Expression of ribosomal proteins in normal and cancerous human prostate tissue. PLoS ONE 12(10): e0186047. https://doi.org/10.1371/journal.pone.0186047, 2017.
Emmanuel, A, Gulati, S, Burt, M, Hayee, B and Haji, A. Colorectal endoscopic submucosal dissection:
patient selection and special considerations. Clin Exp Gastroenterol 10: 121-131, 2017.
3.1 A systems biology approach integrating multi-omic datasets to
elucidate the role of smoking in inflammatory bowel disease:
implications for therapy
Co-Supervisor 1A: Dr Jordana Bell
School/Division or CAG: School of Life Course Sciences
E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/schools/life-course-sciences/departments/twin-research-and-
genetic-epidemiology/research/bell/index.aspx
Co-Supervisor 1B: Dr Natalie Prescott
School/Division or CAG: School of Basic & Medical Biosciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/natalie.prescott.html
Project description
Inflammatory bowel disease (IBD) represents a group of autoimmune diseases that affect the
gastrointestinal tract, with two primary disease subtypes - Crohn’s Disease (CD) and Ulcerative
Colitis (UC). It is well established that smoking has a strong impact on IBD, but with striking divergent
risk effects between CD and UC: while smoking is a risk factor in CD with detrimental effects on its
clinical course, smoking has protective effects in UC with a beneficial influence on progression.
Despite the identification of differential smoking effects in IBD subtypes, the molecular mechanisms
involved are poorly understood. We aim to tackle this by studying the impact of smoking on human
gut biology, including impacts on the gut microbiota and host gene regulation. Our hypothesis is that
smoking effects in IBD are mediated through gut microbiota changes, which in turn either trigger or
mirror epigenetic alterations in the intestine. The project will investigate this using human gut
microbiome and intestinal biopsy DNA methylation data in smoker and non-smoker healthy controls
and IBD cases.
Aim 1. Identify methylation changes in the gut and blood that mediate the contrasting risk effects of
smoking on CD and UC.
Aim 2. Explore gene expression in gut from patients and controls to identify functional epigenetic
impacts.
Aim 3. Identify smoking-associated signals in the human gut microbiome in a large-scale control
dataset.
Aim 4. Systems biology approaches integrating microbiome, epigenetic , metabolomic, and
expression data at candidate molecular pathways of divergent smoking risk in IBD subtypes.
One representative publication from each co-supervisor:
Wahl S*, Drong A*, Lehne B*, Loh M*, Scott WR*, … 92 authors …, Bell JT*, Matullo G*, Gieger C*,
Kooner JS*, Grallert H*, Chambers JC*. 2017. Epigenome-wide association study of body mass index,
and the adverse outcomes of adiposity. Nature, 541(7635):81-86. *Joint first, and senior authors
Genome-wide association study implicates immune activation of multiple integrin genes in
inflammatory bowel disease. de Lange, K. M. , Moutsianas, L. , Lee, J. C. , Lamb, C. A. , Luo, Y. ,
Kennedy, N. A. , Jostins, L. , Rice, D. L. , Gutierrez-Achury, J. , Ji, S-G. , Heap, G. , Nimmo, E. R. ,
Edwards, C. , Henderson, P. , Mowat, C. , Sanderson, J. , Satsangi, J. , Simmons, A. , Wilson, D. C. ,
Tremelling, M. Hart, A., Mathew, C. G., Newman, W. G., Parkes, M., Lees, C. W., Uhlig, H., Hawkey,
C., Prescott, N. J., Ahmad, T., Mansfield, J. C., Anderson, C. A. & Barrett, J. C. 9 Jan 2017 In : Nature
Genetics.
4.1 Investigating the epigenetic regulation of autophagy during aging
and its impact on cardiovascular health
Co-Supervisor 1A: Dr Joseph Burgoyne
School/Division or CAG: School of Cardiovascular Medicine & Sciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/joseph.r.burgoyne.html
Co-Supervisor 1B: Professor Philip Eaton
School/Division or CAG: School of Cardiovascular Medicine & Sciences
Email: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/cardio/about/people/eatonp.aspx
Project description
Autophagy is a crucial process that maintains cellular homoeostasis by removing damaged and
dysfunctional proteins and organelles, as well as providing a source of fuel during nutrient
deprivation. As we age the process of autophagy declines, leading to accumulation of damaging
organelles and macromolecules that increase our risk of developing cardiovascular disease. The aim
of this study is to investigate how epigenetic changes during aging impact on the process of
autophagy and cardiovascular health. This is based on the novel observation that histone H3
lysine27 tri-methylation (H3K7me3) increases within the myocardium of aged compared to young
mice. Histone H3K27me3 is associated with impaired autophagy flux, as this catabolic process is
improved upon inhibition of the site-specific methyltransferase EZH2. Furthermore, drosophila with
an inactive mutated EZH2 homolog, have decreased histone H3K27me3 and significantly improved
life-span. In this study the candidate will use cell culture and animal models to investigate the impact
of histone H3K27me3 on autophagy and cardiovascular function during aging. This will be achieved
using echocardiography to measure cardiac function, and histone methylation and autophagy using
biochemical techniques, including western blotting, real-time PCR, ChIP-seq and confocal
microscopy. For this study the objective for year one will be to investigate how histone H3K27me3
impairs autophagy, and in year two and three to assess EZH2 inhibition on autophagy and cardiac
function in aged mice. We anticipate that this study will have translational relevance, as targeting
histone H3K27me3 within the aging population may provide a therapy to improve cardiovascular
health and extend life-span.
One representative publication from each co-supervisor:
Karen F, Burgoyne T, Burgoyne JR. Oxidation of Atg3 and Atg7 mediates inhibition of autophagy.
Nature Communications. 2018;9(1):95
Charles RL, Rudyk O, Prysyazhna O, Kamynina A, Yang J, Morisseau C, Hammock BD, Freeman BA,
Eaton P. Protection from hypertension in mice by the Mediterranean diet is mediated by nitro fatty
acid inhibition of soluble epoxide hydrolase. Proc Natl Acad Sci U S A. 2014; 111(22):8167-72
5.1 A study of IL-36 as a disease driver in psoriatic arthritis
Co-Supervisor 1A: Dr Francesca Capon
School/Division or CAG: School of Basic and Medical Biosciences
E-mail: [email protected]
Website: http://tinyurl.com/CaponLab
Co-Supervisor 1B: Professor Leonie Taams
School/Division or CAG: School of Immunology & Microbial Sciences
Email: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/diiid/centres/cibci/research/taams/index.aspx
Collaborating Clinician: Professor Bruce Kirkham
School/Division or CAG: School of Immunology & Microbial sciences (honorary); Rheumatology Dept,
GSTT
Email: [email protected]
Summary of role: Prof Kirkham will support patient recruitment and provide clinical advice and
insight into psoriatic arthritis.
Project description
In the UK alone, more than a million people suffer from psoriasis. This condition presents with
disfiguring skin plaques which, in severe cases, are accompanied by a disabling form of joint
inflammation, known as psoriatic arthritis (PsA).
We have shown that interleukin (IL)-36 is a key disease driver in psoriasis and propose here that this
cytokine also plays a pathogenic role in PsA.
During the rotation project, the student will explore this hypothesis by comparing the surface
expression of the IL-36 receptor (IL36R) in synovial cells (fibroblasts and leukocytes) of PsA cases and
controls (osteoarthritis, rheumatoid arthritis). They will then determine whether IL36R expression is
increased in PsA and whether this correlates with the accumulation of IFN-b and IL-1, two cytokines
that contribute to joint inflammation. These experiments will enable the student to master the
fundamentals of flow-cytometry, while also providing a solid foundation for the PhD project outlined
below.
Year 1: The student will undertake single-cell RNA-seq of case and control synovial leukocytes, to
further characterise the immune phenotype of IL-36R expressing cells. Training in the relevant
analytical methods will be provided.
Year 2: The student will focus on the populations identified in year 1 and will investigate the effects
of IL-36, IFN-b and IL-1 on cell activation and cytokine production.
Year 3: The student will determine whether the immune phenotype of PsA synovial cells can be
reversed by IL-36 blockade. Given that IL-36 antagonists are currently being tested in clinical trials,
these experiments have important translational implications.
One representative publication from each co-supervisor:
Mahil SK, Catapano M, Di Meglio P, Dand N, Ahlfors H, Carr IM, Smith CH, Trembath RC, Peakman M,
Wright J, Ciccarelli F, Barker JN, Capon F. An analysis of IL-36 signature genes and individuals with
IL1RL2 knockout mutations validates IL-36 as a psoriasis therapeutic target. Science Translational
Medicine, 2017 9:eaan2514
Taams LS, Steel KJA, Srenathan U, Burns LA, Kirkham BW. IL-17 in the immunopathogenesis of
spondyloarthritis. Nat Rev Rheumatol. 2018 Jul 13. doi: 10.1038/s41584-018-0044-2. [Epub ahead of
print]
6.1 Gene and environment interactions in obesity: the influence of
early life nutrition
Co-Supervisor 1A: Dr Marika Charalambous
School/Division or CAG: School of Basic and Medical Biosciences
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/Charalamb
ousLab/Index.aspx
Co-Supervisor 1B: Dr Michelle Holland
School/Division or CAG: School of Basic and Medical Biosciences
Email: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/hollandgro
up/index.aspx
Project description
The global epidemic of obesity poses a serious public health threat as increased fat mass is a major
risk factor for serious diseases such as Type 2 diabetes, cardiovascular disease and cancer. It is
known that both genetics and environmental factors contribute to obesity. One such factor that
influences obesity and related disease risk is poor nutrition in early life, although the mechanistic
basis for this effect is not known. One possibility is that the availability of nutrients during embryonic
and early postnatal life influences the development of key tissues that are involved in regulating
metabolism and energy storage.
In this project, the effect of maternal nutrition on the development of fat tissue in offspring will be
determined using a mouse model that allows for the isolation of fat cells originating from specific
stages of development. The number and function of these cells will be determined and gene
expression and epigenetic modifications of RNA will be profiled on a genome-scale to determine
how poor nutrition in early life determines fat cell development and behaviour. This will provide
better understanding of gene-environment interactions in obesity.
Aim 1 (Years 1-2): To determine if poor maternal nutrition alters fat tissue amount and function in
neonatal mice (animal models, microdissection, FACS, cell culture).
Aim 2 (Years 1-2): To examine if poor maternal nutrition alters gene expression and the
epitranscriptome in fat cells (molecular biology, high throughput sequencing, bioinformatics).
Aim 3: (Years 2-3): To examine how poor maternal nutrition influences the fat cell behaviour in adult
offspring fed a high calorie diet (microscopy, metabolic physiology).
One representative publication from each co-supervisor:
Cleaton MAM, Corish JA, Howard M, Gutteridge I, Takahashi N, Bauer SR, Powell TL, Ferguson-Smith AC, Charalambous M. (2016). Conceptus-derived Delta-like homologue-1 (DLK1) is required for maternal metabolic adaptations to pregnancy and predicts birthweight. Nat Genet 48(12):1473-1480. Holland ML, Lowe R, Caton PW, Gemma C, Carbajosa G, Danson AF,Carpenter AAM, Loche E, Ozanne
SE, Rakyan VK. Early life nutritionmodulates the epigenetic state of specific rDNA genetic variants in
mice. Science 2016; 353: 495-8.
7.1 Generation of a bioartificial pituitary
Co-Supervisor 1A: Dr Ricardo Mendes Pereira da Silva
School/Division or CAG: Dental Institute
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/en/persons/ricardo-m-p-da-silva(f9796d33-f6dc-4c13-
a61f-544054434c18).html
Co-Supervisor 1B: Dr Cynthia Lilian Andoniadou
School/Division or CAG: Dental Institute
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/cynthia.andoniadou.html
Project description
Background
Hypopituitarism, is a devastating chronic disorder of varied causes, where there is a diminished
production or section of one or more pituitary gland hormones. It is associated with increased
mortality and morbidity and treatment relies on lifelong hormone replacement which do not mimic
the complex homeostatic secretion patterns of the body. Cell replacement therapies with
appropriate integration of new endocrine cells can offer more permanent therapeutic options.
The overarching goal of this project is to engineer a bioartificial pituitary gland tailored for optimal
cell delivery and secretion. We have developed self-healing hydrogels built of reversible bonds that
continuously break and reform, therefore able to autonomously restore its integrity after
mechanical damage. These properties allow cells to remodel their 3D microenvironment by cell-
induced stress, supporting cell spreading and migration without degradation. These properties will
be harnessed to allow the in vivo delivery and optimal reorganisation and networking of pituitary
cells to restore normal endocrine function.
The student will create hydrogels with biophysical and biochemical properties tuned to mimic
pituitary gland extracellular matrix (ECM) and hypothalamic factor delivery and will study the
remodelling and function of pituitary cells within them in vitro, before moving into their delivery and
functional assessment in vivo.
Objectives for 3mo rotation
1. Tuning existing platform of self-healing hydrogels using peptide self-assembling motifs we have
previously developed to resemble pituitary gland ECM.
2. Culture anterior pituitary cells within the hydrogels and study their reorganisation, differentiation
and network integration in vitro.
Objectives for 3y PhD
1. Engineering the diffusion of hypothalamic and developmental factors through hydrogels to mimic
the in vivo pituitary microenvironment. Diffusion properties will be tuned by changing the hydrogel
network size, bond dynamics and incorporation of peptides with binding affinity to the targeted
proteins and studied both in the absence and presence of relevant cell populations.
2. In vitro evaluation and optimisation of the bioartificial pituitary unit functionality by long-term
studies of cell behaviour and secretion patterns.
3. In vivo evaluation of the bioartificial pituitary unit functionality in mouse models of
hypopituitarism.
Laboratory skills training provided
Solid phase peptide synthesis (SPPS), molecular self-assembly, rheology, biophysics of protein
diffusion, confocal fluorescence recovery after photobleaching (cFRAP), fluorescence correlation
spectroscopy (FCS), pituitary dissection, cell culture, immunostaining, confocal fluorescence
microscopy, mouse genetics.
One representative publication from each co-supervisor:
da Silva, R. M. P. et al. Super-resolution microscopy reveals structural diversity in molecular exchange among peptide amphiphile nanofibres. Nat. Commun. 7, 11561 (2016).
Andoniadou, C.L. et al. Sox2(+) stem/progenitor cells in the adult mouse pituitary support organ
homeostasis and have tumor-inducing potential. Cell Stem Cell. (2013) Oct 3;13(4):433-45.
8.1 Investigating the role of aberrant Type I Interferon response in
paradoxical psoriasis
Co-Supervisor 1A: Dr Paola Di Meglio
School/Division or CAG: School of Basic and Medical Bioscience
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/dermatology/Groups/DiMeglio/in
dex.aspx
Co-Supervisor 1B: Dr Catherine Smith
School/Division or CAG: School of Basic and Medical Bioscience
Email: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/dermatology/Research/stru/abou
t/people/smith-catherine.aspx
Third Supervisor: Jonathan Barker
School/Division & CAG: St John’s Institute of Dermatology, School of Basic and Medical Bioscience
Email: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/dermatology/groups/barker/inde
x.aspx
Project description
Psoriasis is a chronic inflammatory skin disease resulting from the interplay of genetic and
environmental factors, leading to aberrant immune responses. A number of environmental factors
are known to trigger or exacerbate psoriasis, including certain drugs, e.g. TNF-inhibitors (TNF-i);
however, triggers are still ill-defined on a mechanistic basis. TNF-i are effective in controlling several
immune-mediated diseases, including psoriasis, but in 2-5% of patients induce a paradoxical reaction
consisting of exacerbated or de novo psoriasis, named paradoxical psoriasis (PXP), which has been
recently linked to unabated production of Type I interferon in the skin. Aim of this project is to
dissect the cellular and molecular determinants of the dysregulated Type I interferon response
induced by TNF-i. Specific objectives are: rotation & Year 1) to derive a peripheral signature of PXP
by measuring Type I IFN in peripheral blood and serum of PXP, healthy controls and psoriasis
patients receiving TNF-inhibitors without developing PXP (Ps-TNFi), and to identify blood immune
cells responsive to Type I IFN; Year2) to measure Type 1 IFN production in relevant cell types
obtained from PXP, healthy controls and Ps-TNFi; Year3) to evaluate responsiveness to Type 1 IFN
production in previously identified immune cells of PXP, healthy controls and Ps-TNFi. The student
will benefit from the co-supervision model with clinical inputs from two academic dermatologists.
He/she will receive extensive training in a range of immunological and biological techniques such as
flow cytometer, Imaging flow-cytometer, multi-analyte bead assay, gene expression, as well as,
analysis of clinical data and statistics.
One representative publication from each co-supervisor:
1A) Di Meglio P, Villanova F, Navarini AA, Mylonas A, Tosi I, Nestle FO, Conrad C. Targeting CD8(+) T
cells prevents psoriasis development. J Allergy Clin Immunol. 2016 Jul;138(1):274-276.e6..
1B) Dand N, Mucha S, Tsoi LC, Mahil SK, Stuart PE, Arnold A, Baurecht H, Burden AD, Callis Duffin K,
Chandran V, Curtis CJ, Das S, Ellinghaus D, Ellinghaus E, Enerback C, Esko T, Gladman DD, Griffiths
CEM, Gudjonsson JE, Hoffman P, Homuth G, Hüffmeier U, Krueger GG, Laudes M, Lee SH, Lieb W,
Lim HW, Löhr S, Mrowietz U, Müller-Nurayid M, Nöthen M, Peters A, Rahman P, Reis A, Reynolds NJ,
Rodriguez E, Schmidt CO, Spain SL, Strauch K, Tejasvi T, Voorhees JJ, Warren RB, Weichenthal M,
Weidinger S, Zawistowski M, Nair RP, Capon F, Smith CH, Trembath RC, Abecasis GR, Elder JT, Franke
A, Simpson MA, Barker JN. Exome-wide association study reveals novel psoriasis susceptibility locus
at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. Hum Mol Genet.
2017 Nov 1;26(21):4301-4313.
9.1 Development of monoclonal antibodies for treatment of
emerging hantavirus infection
Co-Supervisor 1A: Dr Katie Doores
School/Division or CAG: School of Immunology & Microbial Sciences
E-mail: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/doores/index.a
spx
Co-Supervisor 1B: Professor Jo Spencer
School/Division or CAG: School of Immunology & Microbial Sciences
Email: [email protected]
Website:
www.kcl.ac.uk/lsm/research/divisions/diiid/departments/immunobiology/research/JoSpencer/index
.aspx
Project description
Highly pathogenic animal and arthropod viruses capable of jumping the species barrier pose a
significant and continued threat to human health. The recent outbreak of Ebola virus in Western Africa
is a topical example and highlights the pressing need to develop therapeutic strategies to protect
against the spread or intentional dissemination of such deadly pathogens. Monoclonal antibodies
(mAbs), which target viral glycoproteins displayed on the virion envelope, have become some of the
most effective reagents for prevention or treatment of infected individuals, e.g. Palivizumab
(SynagisTM) for prevention of respiratory syncytial virus (RSV) infection and ZMappTM (a mAb cocktail)
for treatment of Ebola virus infection. Here, we will study hantaviruses, a geographically diverse group
of zoonotic pathogens, that cause hantavirus pulmonary syndrome (HPS) or hemorrhagic fever with
renal syndrome (HFRS) with morality rates up to 40%.
The aim of this project is to develop mAbs that cross-react between different hantaviral strains for
use in treatment during disease outbreaks. Cross-binding mAbs will be isolated using antigen-specific
B cell sorting of PBMCs from i) rabbits immunized with a prime-boost strategy using recombinant
glycoproteins from several hantavirus strains and ii) from individuals who have previously been
exposed to a hantavirus infection. Neutralizing activity of cloned antibodies and their cross-reactive
potential will be determined using a Cat2 pseudovirion system and the mechanism of cross-
neutralization determined through biochemical assays and structural studies. These studies will
reveal sites of antibody vulnerability conserved across distant hanta-viral species that could be
exploited for vaccine design.
One representative publication from each co-supervisor:
1. A. Zeltina, S. A. Krumm, M. Sahin, W. B. Struwe, K. Harlos, J. H. Nunberg, M Crispin, D. D.
Pinschewer, K. J. Doores*, T. A. Bowden*, Convergent immunological solutions to New World
Argentine hemorrhagic fever virus neutralization, PNAS, 2017, 114 (27), 7031-7036.
2. Y. Zhao, M. Uduman, J.HK. Siu, T.D. Tull, ….Spencer J. Spatiotemporal segregation of human
marginal zone and memory B cell populations in lymphoid tissue. Nature Communications, in press
10.1 How complex patterns of genetic variation within the large
inversion on chromosome 8
Co-Supervisor 1A: Dr Anders Eriksson
School/Division or CAG: School of Basic & Medical Biosciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/anders.eriksson.html
Co-Supervisor 1B: Professor Michael Simpson
School/Division or CAG: School of Basic & Medical Biosciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/michael.simpson.html
Project description
On the short arm of chromosome 8 in the human genome resides a large inversion that arose in the
lineage leading to anatomically modern humans, probably around 400-500 thousand years ago,
leading to a largely parallel evolution of the inverted and non-inverted versions due to lack of
homologous recombination in this region. The inversion and other genetic variants within this region
have been associated with a range of human diseases including several inflammatory diseases such
as severe acne, psoriasis, lupus as well as neurological conditions including depression.
The beta defensin gene cluster, located within the inverted region, encode critical components of
the innate immune system is. This cluster of genes is also is duplicated, commonly leading to a wide
array of copies of beta defensin genes and variable orientation of these genes within the population.
This project aims to understand the interaction of the orientation of the common inversion and the
number of copies of the beta defensin cluster contribute to the level of expression of beta defensins
and risk of disease.
In order to achieve the aims of this project the student will develop a range of skills relating to
- Bioinformatics analysis of genome and transcriptome next-generation sequencing datasets.
- Genetic annotation and functional analysis of genetic variants.
- Population genetic statistical analysis.
Project outline
Year 1: Integration of population scale genotype data with whole genome sequence data
Year 2: Evaluation of an association between changes in the regulatory network of beta defensins
and expression levels of these genes in multiple tissues.
Years 3 and 4: Integration of the association of molecular consequences of genetic variation in this
region with the disease specific datasets
One representative publication from each co-supervisor:
Navarini et al. Genome-wide association study identifies three novel susceptibility loci for severe
Acne vulgaris. Nature Communications. 2014. 5:4020
Clemente et al. A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations. Am J
Hum Genet. 2014 95:584
11.1 Development of in vivo traceable diagnostic and therapeutic
IgE-like antibodies.
Co-Supervisor 1A: Dr Gilbert Fruhwirth, Senior Lecturer in Imaging Biology
School/Division or CAG: School of Biomedical Engineering & Imaging Sciences E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/en/persons/gilbert-fruhwirth(e089cca1-3041-4cae-92ed-
c401bc7a2ba5)/biography.html
Co-Supervisor 1B:Dr Sophia Karagiannis, Reader in Translational Cancer Immunology, Head of Cancer Antibody Discovery and Immunotherapy School/Division or CAG: School of Basic & Medical Biosciences Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/en/persons/sophia-karagiannis(3d3bd60b-872b-4547-
b024-530ebfbec177)/biography.html
Collaborating Clinician: Prof. James F Spicer
School/Division & CAG: Cancer and Pharmaceutical Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/james.spicer.html
Summary of role: Prof. Spicer will provide expertise in translation of antibody therapeutics for
clinical oncology as this study is expected to inform the pathway of the novel experimental
antibodies towards clinical trials.
Project description
Human immunity produces several antibody classes. IgE class antibodies are the least abundant with
very short serum half-lives, but the longest residence times in target tissues. Specific glycosylation
patterns on their Fc domains may be responsible for their serum properties and this has hampered
their diagnostic and therapeutic use [1].
Combining our expertise in IgE biology/immunology and in vivo tumour imaging/radiochemistry, we
will develop optimised in vivo-traceable diagnostic and therapeutic IgE-like molecules with
favourable serum half-lives. We will employ molecular biology to modify: (i) glycosylation sites on
antibodies and (ii) glycosylation enzymes in the corresponding expression systems. We will also
reconstitute separately synthesised antibody fragments to generate chimeric molecules for
diagnostic imaging.
Objective rotation+Yr1/2: Alter IgE Fc glycosylation using genetic approaches; determine resultant
glycosylation patterns by immunoblotting and carbohydrate analysis (detection, digestion, mass
spectrometry, fluorimetry).
Objective Yr2/3: Radiolabel IgE glycovariants/chimeras, determine their in vivo distribution,
pharmacokinetics/dynamics in existing in vivo-traceable melanoma models (radionuclide/CT-
fluorescence multi-scale imaging). Combining traceable tumour cells and IgE-antibodies will allow
full preclinical cross-validation (distribution, redistribution, efficacy).
Objective Yr3: Determine optimised IgE glycovariant functions by characterizing antigen and receptor
binding properties (e.g. ELISA, Biacore, flow cytometry), IgE-mediated signalling (diagnostics and
safety) and tumour cell killing (therapeutic aspect).
These will form the basis for developing IgE immunodiagnostics and immunotherapeutics.
This studentship covers basic and translational research through close interactions with the
Comprehensive Cancer Imaging Centre (KCL&UCL) and St. John’s Institute of Dermatology and
benefits from multi-disciplinary experience in molecular biology, cancer immunology, and multi-
modal whole-body in vivo imaging.
One representative publication from each co-supervisor:
[1] Josephs, Spicer, Karagiannis et al mAbs (2014) 6:1, 54-72. [2] Diocou, …, Fruhwirth (2017) Scientific Reports, 7(1):946; doi: 10.1038/s41598-017-01044-4.
12.1 Dynamic control of the heartbeat by thick filament regulation
Co-Supervisor 1A: Dr Luca Fusi
School/Division or CAG: School of Basic & Medical Biosciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/luca.fusi.html
Co-Supervisor 1B: Malcolm Irving
School/Division or CAG: School of Basic & Medical Biosciences
Email: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/signalling/irving/index.aspx
Project description
Precise dynamic regulation of contraction and relaxation of cardiac muscle is essential for the
normal function of the heart. Defects in this dynamic regulation lead to reduced cardiac output and,
ultimately, to heart failure. Our limited understanding of the basic molecular mechanisms
responsible for heart failure currently limits the development of new therapies for heart diseases.
Recently it has been hypothesised that the contractility of cardiac muscle is largely controlled by
regulatory structural changes in the myosin-containing thick filaments, in addition to the well-known
calcium-induced structural changes in the actin-containing thin filaments.
The aim of this project is to investigate the role of thick filament-based regulation in the control of
the the speed of contraction and relaxation in the heart.
Project plan
Year 1: The student will be trained in in a broad set of skills in cardiovascular physiology, including
isolation of cardiac trabeculae from rat hearts and force measurements on isolated trabeculae in the
laboratory of Prof Irving and in the fluorescence-based approach developed in the lab of Dr Fusi to
measure protein orientation in cardiac muscle cells.
Year 2: Optical and biochemical methods for the control of contractility in heart muscle cells by
photolysis of caged calcium will be used in combination with fluorescent probes on troponin and
myosin to measure the speed of thin and thick filament activation during contraction of cardiac
trabeculae.
Year 3: Novel mechanical protocols will be used to mimic the contraction and relaxation of the
cardiac muscle cells during the heartbeat and investigate the dynamics of the structural changes in
thin and thick filament regulatory proteins under physiological conditions.
One representative publication from each co-supervisor:
Fusi, L., Brunello, E., Yan, Z., Irving, M. Thick filament mechano-sensing is a calcium-independent
regulatory mechanism in skeletal muscle. Nat Commun 7, 13281 (2016).
Kampourakis, T., Y. B. Sun, and M. Irving. (2016). Myosin light chain phosphorylation enhances
contraction of heart muscle via structural changes in both thick and thin filaments. Proc Natl Acad
Sci (USA) 113:E3039-E3047.
13.1 The effect of lipid composition on the mechanostransduction of
individual live cells
Co-Supervisor 1A: Professor Sergi Garcia-Manyes
Research School/Division or CAG: School of Basic & Medical Biosciences
E-mail: [email protected]
Website: http://garcia-manyeslab.org/
Co-Supervisor 1B: Professor Ulrike Eggert
Research School/Division or CAG: School of Basic & Medical Biosciences
Email: [email protected]
Website:
http://www.kcl.ac.uk/biohealth/research/divisions/randall/research/sections/motility/eggert/index.
aspx
Project description
Are the lipids forming the plasma membrane and nuclear envelope (NE) dynamically modified under
mechanical stress? Lipids and proteins are key components of membranes, yet most of the effort to
understand mechanotransduction has focused on proteins alone. We will explore whether the
lipidome changes in the plasma membranes and NE of cells exposed to mechanical stress. We will
subject cultured cells to substrates of different stiffness, and extract their nuclei. Plasma membrane
and nuclear lipids will be extracted and analysed by MS to determine their lipidomic profiles. In
parallel, we will use Atomic Force Microscopy (AFM) in combination with magnetic tweezers cell
stretching experiments to probe the mechanical properties of plasma and nuclear membranes.
We will investigate the effect of mechanical forces on the lipid composition of cells and isolated
nuclei. The student will gain expertise in single cell AFM and magnetic tweezers characterisation,
combined with cell and molecular biology techniques. S/he will also gain deep knowledge in mass
spectrometry. In Year 1, cell biology experiments will be performed at UE lab and the student will
learn how to prepare substrates of different stiffness in SGM lab. Year 2 will be devoted to conduct
single cell mechanical experiments using AFM and Magnetic Tweezers (SGM). During Year 3 the
student will concentrate on lidiomics (UE). Experiments, analysis and paper writing will continue in
Year 3-4.
This is a unique opportunity to explore fundamental biophysical questions of lipids during
mechanotransduction at the single cell level, combining cutting-edge nanomechanical biophysical
techniques (Garcia-Manyes) and modern cell biology and mass spectrometry (Eggert).
One representative publication from each co-supervisor:
Atilla-Gokcumen, Muro, E.; Relat-Goberna, J.; Sasse, S.; Bedigian, S.; Coughlin, M.L.; Garcia-Manyes,
S.; Eggert, U.S.; «Dividing cells regulate their lipid composition and localization» Cell (2014), 156 (3),
428
Beedle, A. E., Mora, M., Lynham, S., Stirnemann, G., Garcia-Manyes, S. «Tailoring protein
nanomechanics with chemical reactivity» Nature Communications (2017).
14.1 Clinical, biochemical and cellular phenotyping of titin gene
mutations in paediatric patients
Co-Supervisor 1A: Professor Mathias Gautel
School/Division or CAG: School of Basic and Medical Biosciences
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/signalling/gautel/g
autelmathias.aspx
Co-Supervisor 1B: Professor Heinz Jungbluth
School/Division or CAG: IoPPN/ Evelina Children’s Hospital/ School of Basic & Medical Biosciences
Email: [email protected], [email protected]
Website: https://www.kcl.ac.uk/ioppn/depts/bcn/newsevents/records/Professor-
Heinz-Jungbluth-and-collaborators-win-European-Marie-Sklodowska-Curie-Actionaward.
aspx
https://www.evelinalondon.nhs.uk/our-services/hospital/consultants/jungbluth-heinz.aspx
Project description
Mutations in the TTN gene, encoding the giant muscle protein titin, are increasingly being
identified by next-generation sequencing projects as a major cause of cardiomyopathies and
skeletal or combined myopathies with early (paediatric) and late onset. Our interdisciplinary team
has collected a cohort of currently over 30 paediatric patients with titin-linked myopathy with and
without accompanying cardiomyopathy that is growing steadily. All paediatric patients carry
compound-heterozygous recessive TTN mutations, of which one is generally a predicted destabilising
missense mutation, the other truncating or missense. In this project, we will combine
comprehensive clinical phenotyping including advanced cardiac & skeletal imaging with biochemical
and biophysical analysis of titin missense mutations in the cohort of paediatric patients. The
functional impact of TTN variations will be assessed in an integrated programme combining protein
characterization of the direct impact of the mutations, analysis of genome edited iPSC-derived
cardiomyocyte cultures for cellular contractile phenotyping, stress responses and protein turnover.
Classifying TTN variants based on biocomputational criteria (sequence based homology modelling by
our unique TITINdb database http://fraternalilab.kcl.ac.uk/TITINdb/#), will be correlated with
biochemical/biophysical characterisation of protein stability (CD spectroscopy (CD), differential
scanning fluorimetry (DSF) and single-molecule atomic force spectroscopy) and structural biology (X-
ray crystallography) data. Exploratory screens using small-molecule libraries will be performed on
proven destabilising mutants to identify possible stabilising compounds that could be developed
towards potential therapy. These data will feed back into databases integrating experimental
structural and stability data to improve the accuracy of variant classification.
One representative publication from each co-supervisor:
1. Chauveau, C., C. Bonnemann, C. Julien, A.L. Kho, H. Marks, B. Talim, P. Maury, M.C. Arne-
Bes, E. Uro-Coste, A. Alexandrovich, A. Vihola, S. Schafer, B. Kaufmann, L. Medne, N.
Hübner, R.A. Foley, M. Santi, B. Udd, H. Topaloglu, S.A. Moore, M. Gotthardt, M.E.
Samuels, M. Gautel, and A. Ferreiro, Recessive TTN truncating mutations define novel
forms of core myopathy with heart disease. Hum Mol Genet, 2014. 23(4): p. 980-991. PMID:
24105469
2. Byrne, S., L. Jansen, J.-M. U-King-Im, A. Siddiqui, H. Lidov, I. Bodi, L. Smith, R. Mein, T.
Cullup, C. Dionisi-Vici, L. Al-Gazali, M. Al-Owain, Z. Bruwer, R. El-Garhi, K. Flanigan, K.
Manickam, R. Gershoni-Baruch, H. Mandel, E. Dagan, A. Raas-Rothschild, F. Filloux, D.
Creel, M. Harris, A. Hamtosh, S. Koelker, D. Manchester, P. Boyer, O. Magli, A. Manzur, C.
Marques Lourenco, R. Miyata, D. Pilz, A. Kamath, P. Prabhakar, V. Rao, C.C. Rogers, M.
Ryan, N.J. Brown, E. Said, U. Schara, L. Travan, F.A. Wijburg, M. Zenker, S. Mohammed,
M. Fanto, M. Gautel, and H. Jungbluth, EPG5-related Vici syndrome: a paradigm for
neurodevelopmental disorders with defective autophagy. Brain, 2016. 116: p. 765-781.
PMID: 26917586
16.1 Investigating the developmental basis for unique wound healing
properties of facial skin
Co-Supervisor 1A: Prof Anthony Graham
School/Division or CAG: Academic Neuroscience
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/en/persons/anthony-graham(e5e59e9f-4b4c-49e7-bc68-
26590f6822b3).html
Co-Supervisor 1B: Dr Tanya Shaw
School/Division or CAG: School of Immunology & Microbial Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/tanya.shaw.html
Project description
The skin exhibits anatomical diversity, with different regions fulfilling different functions. These
regional differences in the skin emerge during development and are imparted by the dermis.
Importantly, the dermis of the face has a distinct developmental origin from that of the rest of the
body in that it is derived from the neural crest, rather than the mesoderm. We hypothesize that the
distinct dermal features of the face (including repair and regeneration potential, and susceptibility to
site-specific skin diseases) reflect its different developmental origin. However, there is scant
information of how the facial dermis is generated and how it is functionally distinct. This project will
use in vivo models and human tissue samples. 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.
The objectives are:
1. Characterise the emergence of the facial dermis and to contrast that with mesodermally-derived
dermis, such as that of the limbs.
2. Determine if the facial dermis has different wound healing properties from mesodermally-derived
dermis.
3. Investigate whether skin diseases that are more prevalent in the facial skin, such as keloid scars,
betray signs of their neural crest origin.
Year1: Cellular/molecular analysis of dermis development, learn wounding protocol, collect keloid
material; Year2: Continue analysis of dermal development, conduct wounding experiments and
evaluate many parameters of healing, RNAseq analysis of keloids; Year3: Complete development
analysis, investigate site-specific cellular and molecular aspects of wound healing, analyse keloid
cells in vitro.
One representative publication from each co-supervisor:
Shone, V. and Graham, A. (2014). Endodermal/ectodermal interfaces during pharyngeal
segmentation in vertebrates. Journal of Anatomy 225, 479-491.
Shaw, T.J. and Martin, P. (2016).Wound repair: a showcase for cell plasticity and migration. Curr
Opin Cell Biol 42, 29-37.
17.1 Control of embryoid development by morphogens and matrix
properties in 3D
Co-Supervisor 1A: Professor Jeremy Green
School/Division or CAG: Dental Institute
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/dentistry/research/divisions/craniofac/researchgroups/greenlab/groupmem
bers.aspx
Co-Supervisor 1B: Dr Lorenzo Veschini
School/Division or CAG: Dental Institute
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/lorenzo.1.veschini.html
Collaborator: Dr Davide Danovi
School/Division or CAG: School of Basic and Medical Bioscience
Email: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/stemcells/people/dr-
davide-danovi.aspx
Project description
In recent years a number of groups have been able to apply morphogen gradients to embryonic cells
cultured on adherent spots and observe both radial patterning and cell behaviours resembling
gastrulation. However, these cultures have some peculiarities in that they are essentially flat (“2.5D”)
rather than 3D and the cells are polarised by the underlying substrate. This project is to examine the
influence of culture geometry (full 3D rather than 2.5D) as well as the effects of changing the physical
properties of the 3D embedding medium on responses to applied diffusible morphogens (BMP, FGF,
etc.). A systematic analysis of morphogen concentrations and combinations together with controlled
variation of medium stiffness will be performed. The project will build on our existing exhaustively
characterised panel of human iPS cell lines (Danovi group), our expertise in imaging and image analysis
to extract cell features (Danovi, Green labs) and our understanding of gastrulation (Green lab). The
embedding materials will be PEG-based hydrogels focused on by the Gentleman lab. The study will
provide a workflor for analysis and a baseline understanding of parameters that can be used to shape
and influence organoid culture. Moreover, this approach will enable improved models of organ
function for drugs screening and regenerative medicine.
One representative publication from each co-supervisor:
1. Lengerke C, Schmitt S, Bowman TV, Jang IH, Maouche-Chretien L,
McKinney-Freeman S, Davidson AJ, Hammerschmidt M, Rentzsch F, Green JB, Zon LI,
Daley GQ. BMP and Wnt specify hematopoietic fate by activation of the Cdx-Hox
pathway. Cell Stem Cell. 2008 Jan 10;2(1):72-82. doi: 10.1016/j.stem.2007.10.022.
PubMed PMID: 18371423.
2. Leha A, Moens N, Meleckyte R, Culley OJ, Gervasio MK, Kerz M, Reimer A, Cain
SA, Streeter I, Folarin A, Stegle O, Kielty CM; HipSci Consortium, Durbin R, Watt
FM, Danovi D. A high-content platform to characterise human induced pluripotent
stem cell lines. Methods. 2016 Mar 1;96:85-96. doi: 10.1016/j.ymeth.2015.11.012.
Epub 2015 Nov 25. PubMed PMID: 26608109; PubMed Central PMCID: PMC4773406.
18.1 Phagocyte development during cancer progression and
immunotherapy.
Co-Supervisor 1A: Dr Pierre Guermonprez
School/Division or CAG: School of Immunology & Microbial sciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/pierre.guermonprez.html
Co-Supervisor 1B: Dr Annika Warnatsch
School/Division or CAG: School of Immunology & Microbial sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/annika.warnatsch.html
Project description
BACKGROUND:
Tumour-infiltrating phagocytes (TIPs) are important components of host-tumour interactions. TIPs are composed of neutrophil-like and monocyte-like phagocytes displaying an altered phenotype. Tumours secrete factors actively instructing TIP recruitment from bone marrow hematopoietic stem cells. For example, oncogenic variants of Kras-driven lung cancer induce GMCSF or GCSF secretion that promotes recruitment and differentiation. TIPs release a variety of immunosuppressive factors dampening the adaptive immune response to tumours and further prime recipient organs for metastatic seeding. In contrast, immunotherapies by immune checkpoint blockade restore T cell function but also promote inflammation.
AIMS:
1) Understand the mechanisms leading to pro-tumoural TIP activity and metastasis. 2) Identify key factors released by tumours instructing the development of pro-tumoural TIPs. 3) Address if checkpoint blockade immunotherapy (aPD1/PDL1) alters the development of pro-
tumoural TIPs.
EXPERIMENTAL APPROACH:
This investigation will be performed in the context of lung adenocarcinoma and a lung model of melanoma metastasis. Using a combination of inducible oncogenes in mouse models as well as transplanted human tumour lines in immune-deficient mice, we aim to:
1) Define and characterise the heterogeneity of TIPs in relationship to tumour-derived hematopoietic growth factors using unbiased high dimensional flow cytometry and single cell transcriptome analysis.
2) Decipher the molecular mechanisms by which diverse TIPs promote metastatic seeding. 3) Assess how inflammation driven by immunotherapy re-purposes the development of TIPs.
The student will be trained in the area of cancer immunology, will use in vitro and in vivo models, and learn techniques associated with transcriptional profiling, bioinformatics, flow cytometry and microscopy.
One representative publication from each co-supervisor:
Warnatsch, A. et al. Neutrophil extracellular traps license macrophages for cytokine production in
atherosclerosis. Science 2015; 349(6245): 316-20.
Menezes, S., …, Guermonprez P. The Heterogeneity of Ly6Chi Monocytes Controls Their Differentiation into iNOS+Macrophages or Monocyte-Derived Dendritic Cells. Immunity. 2016 Dec 20;45(6):1205-1218.
19.1 Dissecting the role of Follicular Dendritic Cells in the lymphoma
tumour microenvironment
Co-Supervisor 1A: Dr. Robbert Hoogeboom
School/Division or CAG: School of Cancer and Pharmaceutical Science
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/robbert.hoogeboom.html
Co-Supervisor 1B: Dr. Alan Ramsay
School/Division or CAG: School of Cancer and Pharmaceutical Science
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/en/persons/alan-ramsay(63b24881-b9c0-4bf6-ac09-
39cd7280f291).html
Collaborating Clinician: Dr. Piers Patten
School/Division & CAG: School of Cancer and Pharmaceutical Science
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/piers.patten.html
Summary of role: Dr. Patten will aid in acquiring adequate patient material as well as provide
intellectual input on Lymphoma Biology and the use of Xenograft mouse models.
Project description
The lymph node microenvironment provides a supportive and protective niche for B cell leukaemia
and lymphoma cells, but it is not well understood how. Within healthy lymph nodes, B cells are
usually in close contact with Follicular Dendritic Cells (FDCs) and these cells are also present in the
lymph nodes of B cell Chronic Lymphocytic Leukemia (CLL) and Mantle Cell Lymphoma (MCL)
patients. Interestingly, mouse models suggest that CLL cells induce the FDC network and in vitro
experiments suggest FDCs induce survival and proliferation of CLL cells. However, how FDCs support
malignant B cells is unclear.
In this project we aim to elucidate the role of FDCs in lymphomagenesis. Our specific objectives are:
1. To examine if the organisation and size of the FDC networks correlate with disease aggressiveness
and response to therapy of CLL and MCL patients using immuno(fluorescent) staining of patient
lymph node biopsies and (xeno-transplantation-)mouse models (Years 1-2).
2. To investigate how FDCs contribute to the activation, survival and proliferation of primary
malignant B cells and vice versa how malignant B cells activate and induce FDCs using co-cultures
and transcriptomic analysis (Years 1-2).
3. To explore the therapeutic potential of targeting FDCs by disrupting key ligand-receptor
interactions using CRISP-Cas9 technology (Years 2-3).
4. To determine the role of FDCs in vivo by blocking or over-stimulating key interactions in xeno-
transplantation and transgenic mouse models (Years 3-4).
This project will provide training in immuno(fluorescent)-microscopy, cell culture, Next-Generation
Sequencing, Crispr-Cas9 gene editing, in vivo mouse models and flow cytometry.
One representative publication from each co-supervisor:
Myosin IIa promotes antibody responses by regulating B cell activation, acquisition of antigen, and
proliferation. Hoogeboom R, Natkanski EM, Nowosad CR, Malinova D, Menon RP, Casal A, Tolar P.
Cell Reports. 2018;23(8): 2342-2353
Chronic lymphocytic leukemia T cells show impaired immunological synapse formation that can be reversed with an immunomodulating drug. Ramsay AG, Johnson AJ, Lee AM, Gorgün G, Le Dieu R, Blum W, Byrd JC, Gribben JG. J Clin Invest. 2008 Jul;118(7):2427-37. doi: 10.1172/JCI35017.
20.1 Coordination of forebrain and sense organ development in
vertebrates.
Co-Supervisor 1A: Professor Corinne Houart
School/Division or CAG: Neuroscience CAG
E-mail: [email protected]
Website: https//:devneuro.org/cnd/
Co-Supervisor 1B: Professor Andrea Streit
School/Division or CAG: Dental Institute
Email: [email protected]
Website:
http://www.kcl.ac.uk/dentistry/research/divisions/craniofac/ResearchGroups/StreitLab/StreitLab.as
px
Project description
Our complex behaviours depend on our ability to perceive our environment and respond to it. This
ability requires sophisticated neuronal circuits between senses and central nervous system that arise
from coordinated development of the sense organs and their corresponding central neuronal
populations. Failure of this coordination leads to debilitating impairments, yet very little is known of
the cellular and molecular mechanisms controlling this process.
This project will fill this gap of understanding, focussing on the olfactory and visual senses, addressing
the problem as it arises in development, during interaction between the anterior neural plate (future
olfactory bulbs, telencephalon and retina) and the surrounding sensory non-neural epithelium
(precursors of nose and lens). These cell populations are initially intermingled at the anterior neural
plate border, and segregate over-time, while acquiring their various identities.
Taking a multi-species approach using zebrafish, chick and mouse, we aim to identify conserved and
divergent signalling and regulatory mechanisms controlling the integration of forebrain and sense
organ formation. The student will take advantage of the complementary expertise from the Houart
and Streit labs in induction and patterning of the forebrain and sensory progenitors, respectively. The
student will investigate:
How do signalling events at the neural plate border drive cell behaviour?
How do signals driving forebrain organisation influence sensory progenitor identity and vice versa?
How are cell fate decisions at the anterior neural/non-neural border integrated transcriptionally?
The student will receive multidisciplinary training including high-resolution live imaging, genetics,
bioinformatics & computational modelling, transcriptomics and cell biology. S/he will benefit from a
broad-range of training courses, and an international interactive environment.
One representative publication from each co-supervisor:
Hintze, M., Prajapati, R.S., Tambalo, M., Christophorou, N., Grocott, T. and Streit, A. 2017. Cell interactions, signals and transcriptional hierarchy governing placode progenitor induction. Development 144, 2810-2823. Bielen H. and Houart C. 2012. BMP signaling protects telencephalic fate by repressing eye identity
and its Cxcr4-dependent morphogenesis. Dev Cell. 2012 Oct 16;23(4):812-22.
21.1 Application of lightsheet functional imaging to identify
regulators of regulators of inflammation during tissue regeneration
Co-Supervisor 1A: Dr Robert Knight
School/Division or CAG: Dental Institute
E-mail: [email protected]
Website:
http://www.kcl.ac.uk/dentistry/research/divisions/craniofac/ResearchGroups/KnightLab/KnightLab.
aspx
Co-Supervisor 1B: Dr Simon Ameer-Beg
School/Division or CAG: School of Basic & Medical Biosciences
Email: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/cell/ameer-
beg/index.aspx
Project description
A failure to resolve inflammation is the fundamental basis for many chronic diseases including
rheumatoid arthritis, inflammatory bowel disease and diabetes. This project aims to identify
molecules that can enhance resolution of inflammation in an animal model then validate their
activity in human immune cells.
Zebrafish are a powerful tool for dissecting the molecular regulation of cell behaviour: larvae can
easily be exposed to drugs, are transparent and so are amenable to live cell imaging. Measurement
of FRET reporters expressed in macrophages of injured animals will to be used to determine whether
specific clinically approved drugs can promote resolution and regeneration. Promising candidate
drugs will then be assayed on human macrophages to demonstrate if they could be candidates for
promoting resolution in chronic human disease.
The project will involve optimising use of a bespoke lightsheet microscope for measuring of lifetime
fluorescence that we have developed for fast in vivo functional imaging (Mitchell et al, 2017). A
combined functional imaging and microfluidics platform will be developed for this purpose, exposing
the student to engineering and software design in addition to microscopy and in vivo cell biology
techniques.
Training and supervision will be from Dr. Knight (use of zebrafish and live cell imaging) and Dr.
Ameer-Beg (FRET, software design and microscopy).
Objectives are:
Year 1:
optimise drug delivery and imaging on lightsheet system
Year 2:
screen candidate pro-resolution drugs on zebrafish larvae
Year 3:
Validate target drugs in human macrophages
Year 4:
Follow up on potential mechanisms for drug action
One representative publication from each co-supervisor:
Functional in vivo imaging using fluorescence lifetime light-sheet microscopy
Mitchell, C A., Poland, S. P., Seyforth, J., Nedbal, J., Gelot, T., Huq, T., Holst, G., Knight, R.
D. & Ameer-Beg, S. M. 23 Mar 2017 In : Optics Letters. 42, 7, p. 1269-1272
Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral
muscular dystrophy
Moyle, L. A., Blanc, E., Jaka Irizar, O., Prueller, J., Banerji, C. R., Tedesco, F. S., Harridge, S. D.
R., Knight, R.* D. & Zammit, P. S.* 14 Nov 2016 In : eLife. 5, p. 1-35 , e11405
* joint corresponding author
22.1 Role of the Nance Horan Syndrome protein family in breast
cancer invasion.
Co-Supervisor 1A: Dr Matthias Krause
School/Division or CAG: School of Basic & Medical Biosciences
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/motility/krause/krausemat
thias.aspx
Co-Supervisor 1B:Dr Cheryl Gillett
School/Division or CAG: School of Cancer Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/cheryl.gillett.html
Project description
Breast cancer metastasis is the most frequent cause of cancer-associated mortality in women. There
is an urgent need to identify driver mutations in oncogenes and tumour suppressors, specific for
breast cancer subtypes and their metastasis, which is one of the top 10 critical research gaps
identified in a study initiated by the Breast Cancer Campaign.
A classification of breast cancer into 10 subtypes with distinct clinical outcomes found that
subtype 2 has the second worst prognosis. In this subtype Nance-Horan-Syndrome-like 2 (NHSL2) is
the 5th most highly mutated gene and the only gene where the mutational frequency shows a
significant subtype-specific association suggesting that NHSL2 might be a key genomic driver for this
subtype. However, the molecular function of NHSL2 is unknown. NHSL2 is part of a gene family,
which includes the brain specific Nance-Horan-Syndrome protein and the ubiquitously expressed
NHSL1 and NHSL2.
You will generate NHSL2 specific antibodies and quantify expression levels of NHSL2 in breast
cancer tissue microarrays and breast cancer cell lines of increasing invasive and metastatic potential.
We have evidence that NHSL1 functions to negatively regulate cell proliferation and migration and
binds to two important regulators of cell migration, Ena/VASP and Scar/WAVE. You will explore
whether NHSL2 binds to Ena/VASP and Scar/WAVE as well and generate NHSL2 KO cell lines by
CRISPR-Cas9. You will use these to test how NHSL2 controls breast cancer cell migration and invasion
via these effectors. Finally, you will investigate how NHSL2 mutations found in breast cancer patients
affects breast cancer invasion.
One representative publication from each co-supervisor:
Lamellipodin promotes invasive 3D cancer cell migration via regulated interactions with Ena/VASP
and SCAR/WAVE. Carmona, G., Perera U., Gillett C., Naba A., Law A., Sharma V.P., Wang J., Wyckoff
J., Balsamo M., Fuad Mosis F., De Piano, M., Monypenny, J., Woodman, N., McConnell, R.E.,
Mouneimne, G., Van Hemelrijck, M., Cao, Y., Condeelis, J., Hynes, R.O., Gertler, F.B., and Krause M.
(2016) Oncogene, doi: 10.1038/onc.2016.47
Lamellipodin and the Scar/WAVE complex cooperate to regulate cell migration. Law, A., Vehlow,
A., Kotini, M., Dodgson, L., Soong, D., Theveneau, E., Bodo, C., Taylor, E., Navarro, C., Perera, U.,
Michael, M., Dunn, G.A., Bennett, D., Mayor, R., and Krause M. (2013) Journal of Cell Biology, 203(4),
673-689.
23.1 Disease in a dish: use of patient-derived human induced
pluripotent stem cells (hiPSCs) to model ciliopathic neural crest
anomalies
Co-Supervisor 1A: Dr Karen J. Liu
School/Division or CAG: Dental Institute
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/karen.liu.html
Co-Supervisor 1B: Dr Rocio Sancho
School/Division or CAG: School of Basic & Medical Biosciences
Email: [email protected]
Website: Rocio Sancho
Collaborating Clinician: Professor Philip Beales, ICH/UCL
Project description
Neural crest cells are multipotent stem cells that give rise to diverse tissues such as melanocytes, craniofacial skeleton and peripheral nervous system. During embryogenesis, neural crest cells delaminate from the neural tube and migrate to integrate into distant organs. Birth defects arising from neural crest dysfunction can lead to very diverse phenotypes such as craniofacial anomalies to pigment defects and problems with innervation of the gut.
Our hypothesis is that loss of cilia in the neural crest lineage leads to changes in cell migration and differentiation. Furthermore, we hypothesise that genetic variations between patients may modify the severity of their phenotypes, which would explain why some patients with similar gene mutations have a different range of symptoms.
Approach: In order to test this hypothesis in humans, we use human induced pluripotent stem cells (hiPSCs) from ciliopathic patients, allowing us to model differentiation to neural crest and other lineages.
Overall goals:
1) Identify the cellular behaviours of normal and diseased neural crest cells. Approach: Live imaging of migrating neural crest cells, analysis of cellular and molecular markers. Techniques: tissue culture, live microscopy, computational image analysis, immunofluorescent labelling, western blotting.
2) Pinpoint the requirements for ciliopathic (Bardet Biedl Syndrome) genes during induction, migration and differentiation of the neural crest lineage. Approach: Tissue culture, genetic analysis, molecular biology, biochemistry.
This project will have implications for understanding stem cells, human congenital anomalies, and
more broadly, processes that involve cell migration and differentiation.
One representative publication from each co-supervisor:
Gonzalez Malagon SG, Lopez Muñoz AM, Doro D, Bolger TG, Poon E, Tucker ER, Adel Al-Lami H, Krause M, Phiel CJ, Chesler L, Liu KJ. Glycogen synthase kinase 3 controls migration of the neural crest lineage in mouse and Xenopus. Nat Commun. 2018 Mar 19;9(1):1126. 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.
25.1 The role of NSA2 in renal and cardiovascular disease in diabetes.
Co-Supervisor 1A: Dr Afshan Malik
School/Division or CAG: School of Life Course Sciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/afshan.malik.html
www.maliklab.com
Co-Supervisor 1B: Professor Christer Hogstrand
School/Division or CAG: School of Life Course Sciences
Email: [email protected]
Website: https://www.kcl.ac.uk/lsm/Schools/life-course-
sciences/departments/diabetes/about/people/Profiles/christerhogstrand.aspx
Project description
Diabetic kidney/cardiovascular disease affect >30% of the >450 million people with diabetes
worldwide and are major contributors to morbidity and mortality. Transforming growth factor (TGF)-
β1 is a well-known mediator of damage in the heart and kidney in diabetes but therapies to inhibit
over expression of TGF-β1 have failed due to off target effects. In a screen for glucose regulated genes,
we cloned nop-7-associated-2 (NSA2), a glucose regulated gene which is regulated by glucose,
abnormally elevated in diabetic kidney, and is upstream of the TGF-β1 pathway. In a genetic study
(ACCORD trial) of >5000 subjects, NSA2 showed strong linkage to cardiovascular disease.
Hypothesis: Aberrant expression of NSA2 is involved in TGF-β1 mediated disease progression in
diabetic kidney and cardiovascular disease.
Year 1. Identify kidney/heart specific NSA2 transcripts/variants. Develop an ELISA based assay for the
detection of circulating NSA2 as an evaluator of treatment efficacy in patients.
Year 2. Identify upstream/downstream pathways (will over-express and knock down NSA2 in-vitro to
examine the effect of on whole transcriptome microarrays).
Year 3. Screen libraries of potential therapeutic compounds (seeking inhibition of glucose- induced
NSA2 or its pathways. ELISA based assay to undertake clinical study of NSA2 expression in patients.
The work will utilise in-vitro cell and diabetic mouse models, and human clinical samples, techniques include molecular/cell/translational biology and will provide an excellent and thorough training in experimental medicine. The student will join a vibrant research group comprising of PhD students, postdocs and PIs within the Diabetes Department at the Guy’s campus. One representative publication from each co-supervisor:
Nop-7-associated 2 (NSA2), a candidate gene for diabetic nephropathy, is involved in the TGFβ1
pathway. Shahni, Czajka, Mankoo, Guvenel, King, . & Malik, International Journal of Biochemistry
and Cell Biology. 45, 3, p. 626-635 PMID: 23220173
Differential cytolocation and functional assays of the two major SLC30A8 (ZnT8) isoforms
Carvalho, S., Molina-López, J., Parsons, D., Corpe, C., Maret, W. & Hogstrand, C. Dec 2017 In : Journal
of Trace Elements in Medicine and Biology. 44, p. 116-124`.
26.1 Generation of tissue specific CAR-Tregs to modulate liver
inflammatory and promote immune tolerance
Co-Supervisor 1A: Dr Marc Martinez-Llordella
School/Division or CAG: School of Immunology and Microbial Sciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/marc.martinez-llordella.html Co-Supervisor 1B: Professor Giovanna Lombardi
School/Division or CAG: School of Immunology and Microbial Sciences
Email: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/timb/about/people/profiles/giovannalombardi.aspx Project description
The burden of liver disease is increasing in the UK, becoming the third most common cause of
premature death and continuing to rise. This emphasises the need for novel strategies to treat
persistent liver inflammation. Regulatory T cells (Tregs) play a key role in the control of most
inflammatory diseases. In addition, recent studies have shown that antigen-specific Tregs are more
efficient than polyclonal Tregs for the modulation of immune responses. Therefore, the use of Treg-
directed therapies with tissue specific properties brings the promise of a breakthrough strategy for
the treatment of patients with severe chronic inflammatory and autoimmune diseases.
Cellular therapy with chimeric antigen receptor (CAR)-redirected cytotoxic T cells has shown
impressive efficacy in the treatment of hematologic malignancies. Increasing efforts are currently
focus on developing a similar CAR-strategy employing Tregs to enhance immune tolerance. Indeed,
we and others have recently reported that CAR-Tregs can be used to improve graft survival in animal
models of transplantation. We believe that adoptive transfer of Tregs directed by a CAR toward liver
antigens will restore the intrahepatic immune balance during chronic inflammation and will
additionally enhance tissue regeneration. Considering our experience in the performance of early
phase Treg-directed clinical trials, we are confident in being able to successfully translate our results
into a pilot human study.
Year 1: Identification and selection of human liver-specific biomarkers. Design and construction of
CAR-Tregs.
Year 2: In vitro and preclinical in vivo validation on humanised mouse models of liver disease.
Years 3-4: Studying the mechanisms underlying intrahepatic immunoregulation and tissue repair
mediated by CAR-Tregs.
One representative publication from each co-supervisor:
- Whitehouse G, Gray E, Mastoridis S, Merritt E, Kodela E, Yang JHM, Danger R, Mairal M,
Christakoudi S, Lozano JJ, Macdougall IC, Tree T, Sanchez-Fueyo A, Martinez-Llordella M.
IL-2 therapy restores regulatory T-cell dysfunction induced by calcineurin inhibitors PNAS. 2017; 114(27):7083-7088 - Boardman DA, Philippeos C, Fruhwirth GO, Ibrahim MA, Hannen RF, Cooper D, Marelli-Berg FM,
Watt FM, Lechler RI, Maher J, Smyth LA, Lombardi G.
Expression of a Chimeric Antigen Receptor Specific for Donor HLA Class I Enhances the Potency of
Human Regulatory T Cells in Preventing Human Skin Transplant Rejection
Am J Transplant. 2017 Apr;17(4):931-943
27.1 Identification of host factors that promote assembly of Ebola
virus Co-Supervisor 1A: Professor Juan Martin-Serrano
School/Division or CAG: School of Immunology & Microbial Sciences
E-mail: : [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/Martin-Serrano/indexJD.aspx
Co-Supervisor 1B: Dr Monica Agromayor
School/Division or CAG: School of Immunology & Microbial Sciences
Email: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/agromayor/index.aspx Project description
Ebola virus (EBOV) is a filovirus that causes severe haemorrhagic fever. The major EBOV structural
component is VP40, the matrix protein that plays a central role in the assembly of infectious viral
particles. VP40 expression is sufficient to form viral-like particles that share the filamentous
morphology with infectious Ebola virions. Therefore, VP40 is the minimal unit required for assembly
that recruits the host factors required for this process, as shown by our observations that VP40
recruits the Endosomal Sorting Required for Transport (ESCRT) machinery to promote viral egress.
VP40 promotes assembly by adopting multiple conformations. VP40 dimers change membrane
curvature and subsequently assemble into hexamers that form the filaments that shape EBOV
virions. The octameric ring conformation of VP40 binds RNA and plays a poorly defined role in EBOV
replication.
The aim of this project is the identification of VP40-binding host proteins that are involved in EBOV
replication. We have performed a genome-wide screen to identify human proteins that bind either
WT or the octamer-locked form of VP40. The student will determine the role of the candidate hits in
EBOV replication. The selected open reading frames will be cloned into yeast two-hybrid and co-
precipitation plasmids to further validate the interaction with VP40. Co-localization by super-
resolution and live-cell microscopy will further confirm the interaction of candidate host proteins
with VP40. Expression of the short-listed genes will be disrupted by siRNA and CRISPR-based gene
editing to assess their contribution to EBOV assembly and replication, taking advantage of a
transcription/replication-competent virus-like particle (trVLP) system.
One representative publication from each co-supervisor:
HECT ubiquitin ligases link viral and cellular PPXY motifs to the vacuolar protein-sorting pathway.
Martin-Serrano J, Eastman SW, Chung W, Bieniasz PD. J Cell Biol. 2005 Jan 3;168(1):89-101.
The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a SOUBA domain. Agromayor M, Soler N, Caballe A, Kueck T, Freund SM, Allen MD, Bycroft M, Perisic O, Ye Y, McDonald B, Scheel H, Hofmann K, Neil SJ, Martin-Serrano J, Williams RL. Structure. 2012 Mar 7;20(3):414-28.
28.1 Catching the unconventional epitopes that target the
autoimmune response in Type 1 Diabetes Co-Supervisor 1A: Dr Michele Mishto School/Division or CAG: School of Immunology & Microbial Sciences E-mail: [email protected] Website: https://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/immunobiology/research/mishto/Michele-Mishto.aspx Co-Supervisor 1B: Professor Mark Peakman School/Division or CAG: School of Immunology & Microbial Sciences Email: [email protected] Website: www.kcl.ac.uk/lsm/research/divisions/diiid/.../peakman/index.aspx Project description
One of the most challenging questions in immunology is how the immune system discriminates “self” from “non-self”. In two areas – cancer and autoimmunity – this question is very fundamental to our understanding of the basis of disease and our ability to design new therapies. In cancer we want to harness the power of the immune system to recognize tumours (“self”) and in autoimmunity we want to switch this off.
This project aims to examine a very new area of self-recognition: namely the generation of new antigens by peptide splicing.
Conventionally it has been thought that within target cells a catalytic cascade called the proteasome cleaves polypeptide sequences into short linear epitopes for presentation to cytotoxic T cells. However, we recently showed that this is only part of the story: in fact, around 30% of self-peptides that the proteasome generates are actually spliced: they are 2 separate polypeptide regions fused together (Liepe et al., Science 2016). Spliced epitopes can trigger a cytotoxic T cell response against cancer (Mishto and Liepe, Trends Imm. 2017) and could be important in triggering autoimmunity, for example in the autoimmune disease Type 1 diabetes.
Our ground-breaking discovery of the unexpectedly high frequency of spliced self-antigenic peptides opens a window onto a large, and so far unforeseen, pool of epitopes of potentially great importance in cytotoxic T cell responses. Since the systematic identification of spliced peptides is now feasible (Liepe et al., Science 2016) through a combination of cellular biology, mass spectrometry and bioinformatics approaches, we aim to apply this new thinking to a project of considerable relevance to human disease. The PhD student will work in tight collaboration with the two co-supervisors and a selected group of international collaborators. Upon identification of diabetes-associated spliced antigenic peptides, the PhD student will test patient samples using peptide-HLA tetramer reagents and deep immunophenotyping by flow cytometry, and will further characterise the cellular processing and presentation pathways involved in splicing using biochemical and molecular biology methods, which are well established in the groups of the two co-supervisors. The translational application of the outcome of the research will be evaluated, and eventually private companies will be involved through the co-supervisor collaboration network. One representative publication from each co-supervisor:
Liepe J, Marino F, Sidney J, Jeko A, Bunting DE, Sette A, Kloetzel PM, Stumpf MP, Heck AJ, Mishto M. A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science 2016 Oct; 354(6310): 354-358. DOI: 10.1126/science.aaf4384. Epub 2016 Oct 20. PubMed PMID: 27846572. Yeo L, Woodwyk A, Sood S, Lorenc A, Eichmann M, Pujol-Autonell I, Melchiotti R, Skowera A, Fidanis E, Dolton GM, Tungatt K, Sewell AK, Heck S, Saxena A, Beam CA, Peakman M. Autoreactive T effector memory differentiation mirrors β cell function in type 1 diabetes. J Clin Invest. 2018 Jul 16. pii: 120555. doi: 10.1172/JCI120555. [Epub ahead of print] PubMed PMID: 29851415.
29.1 Investigating driver gene mutations in T-cell signalling pathways
to identify therapeutic targets and genetic biomarkers for cutaneous
T-cell lymphoma. Co-Supervisor 1A: Dr Tracey Mitchell
School/Division or CAG: School of Basic & Medical Biosciences
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/medicine/research/divisions/gmm/departments/dermatology/Groups/Whitt
akerLab/index.aspx
http://www.viapath.co.uk/our-people/dr-tracey-mitchell
Co-Supervisor 1B: Professor Sean Whittaker Research Division or CAG: Genetics and Molecular Medicine/GRIDA Email: [email protected] KCL/KHP Website: https://www.kcl.ac.uk/medicine/research/divisions/gmm/departments/dermatology/Groups/WhittakerLab/index.aspx Project description
Background: All cancers are characterised by the acquisition of gene mutations and consequent changes in gene expression that initiate and drive malignancy. Primary cutaneous T-Cell lymphoma (CTCL) is a heterogeneous malignancy of mature memory type, skin homing T-cells with limited treatment options. The commonest subtypes of CTCL are mycosis fungoides (MF) accounting for over 50% of cases and the rare leukemic variant Sézary syndrome (SS). We have recently performed a deep sequencing study of tumour cells derived from SS patients that has identified >500 gene mutations affecting genes involved in TCR signalling, cell survival, genome maintenance, DNA damage repair and epigenetic regulation. The aim of this PhD is to extend this work to early stage MF, which will facilitate the identification of gene mutations likely to be of critical significance in early stages of T-cell transformation and clonal evolution of the disease.
Objectives:
Years 1-2: Isolation of malignant and reactive (control) T-cells from MF skin biopsies using cell migration assays, preparation of DNA and RNA libraries for whole exome/transcriptome sequencing
Years 2: Analysis of whole exome and RNAseq data, identification of the driver genes and dysfunctional pathways, gene set enrichment analysis to identify differentially expressed biological processes.
Year 3: Functional validation of candidate driver gene mutations in T-cells to define potential therapeutic targets
Skills training:
‘Wet lab’ techniques: advanced cell culture techniques; flow cytometry cell sorting; next generation sequencing; functional assays (including transformation, proliferation, apoptosis)
Bioinformatics: NGS data analysis (alignment, filtering, variant calling); identification of driver genes; RNAseq data analysis and GSEA One representative publication from each co-supervisor:
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.
Patel VM, Flanagan CE, Martins M, Jones CL, Butler RM, Woollard WJ, Bakr FS, Yoxall A, Begum N,
Katan M, Whittaker SJ, Mitchell TJ. Frequent and persistent PLCG1 mutations in Sézary cells directly
enhance PLCγ1 activity and stimulate NFκB, AP-1 and NFAT signalling. J Invest Dermatol. 2019 Jul 31.
pii: S0022-202X(19)32679-X. doi: 10.1016/j.jid.2019.07.693. [Epub ahead of print] PubMed PMID:
31376383.
30.1 Inborn error of immunity: characterisation of IL-10/PGE2 axis in
regulation of inflammation using a patient-derived induced
pluripotent stem cell model
Co-Supervisor 1A: Dr Subhankar Mukhopadhyay
School/Division or CAG: School of Immunology and Microbial Sciences
E-mail: [email protected]
Co-Supervisor 1B: Professor Steven Sacks
School/Division or CAG: School of Immunology and Microbial Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/steven.sacks.html Project description
Background:
We aim to understand how natural genetic variations influence innate immune responses in rare patients with specific genetic immunodeficiency/inflammatory pathologies. The induced pluripotent stem cell (iPSC) technology provides an attractive experimental system to study disease mechanisms.
Previously we generated iPSCs from an early-onset Inflammatory Bowel Disease (IBD) patient carrying a loss of function mutation in the IL10RB gene. Patient iPSC-derived macrophages are unresponsive to inhibitory cytokine IL-10 and show hyperactive phenotype. Despite their activated phenotype, patient iPSC-derived macrophages showed a striking defect in bacterial killing, linked to overproduction of the immuno-regulatory lipid mediator PGE2, in the absence of IL-10 signalling.
In this PhD project, we aim to understand how the IL-10/PGE2 axis regulates macrophage activation to promote resolution of inflammation. We have generated additional iPSCs lacking specific components downstream of IL-10 receptors; as well as components of PGE2/PGE2 receptors pathway. These iPSCs will be differentiated into macrophage/relevant cell types to answer functional questions.
Objectives for rotation project (3 mo):
• The student will learn specific techniques related to iPSCs culture, genetic manipulation and differentiation into macrophages
Objectives for main PhD project (3.5 Yrs):
• To characterise the molecules involved in feedback regulation of IL-10 and PGE2.(Year 1-2)
• How IL-10 and PGE2 regulate excessive macrophage activation. (Year 2)
• How the IL-10/PGE2 axis promotes resolution of inflammation. (Year 2-3)
The student will receive training in wet lab techniques, bioinformatics; and there will be ample scope
for collaborating with leading laboratories in Oxford, Cambridge and internationally.
One representative publication from each co-supervisor:
Alasoo K, Rodrigues J, Mukhopadhyay S, Knights AJ, Mann AL, Kundu K; HIPSCI Consortium, Hale C, Dougan G, Gaffney DJ. Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response. Nat Genetics. 2018 Jan 29. Human stem cell-derived retinal epithelial cells activate complement via collectin 11 in response to stress. Fanelli G, Gonzalez-Cordero A, Gardner PJ, Peng Q, Fernando M, Kloc M, Farrar CA, Naeem A, Garred P, Ali RR, Sacks SH. Sci Rep. 2017 Nov 7;7(1):14625
31.1 Characterising the role of MAP3K8/COTK during mucosal
infection. Co-Supervisor 1A: Professor Julian Naglik
School/Division or CAG: Dental Institute
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/julian.naglik.html
Co-Supervisor 1B: Dr David Moyes
School/Division or CAG: Dental Institute
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/david.moyes.html
Co-Supervisor 1B: Dr Jonathan Richardson
School/Division or CAG: Dental Institute
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/jonathan.richardson.html Project description
Human epithelial cells are often the first point of contact between the host and pathogenic
microbes. Epithelial barriers have evolved to initiate a range of intracellular signalling pathways and
immune responses designed to combat infecting microbes. During infection, the fungal pathogen
Candida albicans secretes a peptide toxin (candidalysin) that drives MAPK signalling in epithelial
cells, identifying this pathway as an important component of the host response to fungal infection.
Recently, our laboratory has identified MAP3K8/COTK (mitogen-activated protein kinase kinase
kinase 8/Cancer Osaka thyroid kinase); a serine/threonine kinase and proto-oncogene as a novel
component of the host epithelial response to Candida infection. RNA Seq analysis reveals that
MAP3K8 is upregulated in epithelial cells exposed to candidalysin while MAP3K8 inhibition causes
altered immune responses, suggesting that MAP3K8 activity contributes to candidalysin-induced
intracellular signalling.
This project will characterise the role of MAP3K8 during fungal infection in vitro and in vivo.
Year 1 will characterise the MAP3K8 epithelial response to candidalysin and wild type/mutant fungal
strains and will identify critical phosphorylation sites in MAP3K8 required for activity. Year 2 will use
small molecular inhibitors of known cell surface receptors and signalling pathways to establish the
contribution of MAP3K8 to signalling responses. Year 3 will characterise the role of MAP3K8 in
driving epithelial immune responses and cellular oncogenesis in response to infection.
This project will combine microbiology, immunology, tissue culture, molecular biology and a range of in vitro and in vivo analyses to elucidate the role of MAP3K8/COTK in the host response to fungal infection. One representative publication from each co-supervisor:
Moyes DL, Wilson D, Richardson JP, Mogavero S, Tang SX, Wernecke J, Höfs S, Gratacap RL, 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, Luo T, Krüger T, Kniemeyer O, Cota E, Bader O, Wheeler RT,
Gutsmann T, Hube B and Naglik JR (2016). Candidalysin is a fungal peptide toxin critical for mucosal
infection. Nature. 532, 64-68.
Richardson JP, Mogavero S, Moyes DL, Blagojevic M, Krüger T, Verma AH, Coleman BM, De La Cruz
Diaz J, Schulz D, Ponde NO, Carrano G, Kniemeyer O, Wilson D, Bader O, Enoiu SI, Ho J, Kichik N,
Gaffen SL, Hube B and Naglik JR (2018). Processing of Candida albicans Ece1p is critical for
Candidalysin maturation and fungal virulence. mBIO. DOI: 10.1128/mBio.02178-17.
32.1 HIV-1 modulation of chromatin architecture by targeting of the
cohesin regulator ESCO2 Co-Supervisor 1A: Professor Stuart Neil
School/Division or CAG: School of Immunology & Microbial Sciences
E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/neil/index.aspx Co-Supervisor 1B: Dr Cameron Osborne
School/Division or CAG: School of Basic & Medical Biosciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/cameron.osborne.html Collaborator: Dr Vlad Seitan
School/Division or CAG: School of Basic & Medical Biosciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/vlad.seitan.html
Project description
Overview: Vpr is a primate lentivirius-encoded accessory protein that is incorporated into HIV-1
particles and induces widespread changes in the host cell proteome within the first hours of infection
through hijacking the DCAF1-Cullin4 E3 Ubiquitin ligase complex. One consequence is the
dysregulation of DNA-damage responses to a cell cycle arrest at G2/M in CD4+ T cells; another is the
suppression of the induction of proinflammatory gene expression after pattern recognition in infected
macrophages to facilitate viral replication. However, understanding of how Vpr effects these changes
is lacking. Recent large-scale proteomic analyses have revealed a number of novel Vpr targets that are
degraded within the first few hours of infection. One of these is ESCO2, an acetyltransferase for the
Smc3 subunit of cohesin, a ring-like multiprotein complex that plays an essential role in regulating
sister chromatid segregation during mitosis. Accumulating evidence shows cohesin also plays a role in
gene expression and chromosomal architecture during interphase by linking distant DNA regulatory
sequences, and recent studies implicate cohesin as important for inducible proinflammatory gene
expression in macrophages and haematopoetic precursor stem cells.
Aims. This project will test the hypothesis that through the targeted degradation of ESCO2, Vpr rapidly
dysregulates cohesin to prevent the infected cell responding to the virus during the early phases of
replication.
Yr1: map the determinants of Vpr interaction and degradation in ESCO2, and whether HIV-1 infection
affects Smc3 acetylation.
Yr 1-2: perform Capture Hi-C, cut-and-run seq for cohesin/chromatin interactions, and parallel RNAseq
on infected THP-1 and primary CD4+ T cells infected with HIV-1 and Vpr mutants.
Yr3: determine whether ESCO2 degradation contributes to viral integration and the establishment of
viral latency; extend observations to primary macrophages
Skills – molecular biology, primary cell culture, HIV-1 culture and propagation, Capture Hi-C, cut-
and-run seq, RNAseq, bioinformatic analyses
One representative publication from each co-supervisor:
Foster TL, Wilson H, Iyer SS, Coss K, Doores KJ, Smith S, Kellam P, Finzi A, Borrow P, Hahn BH and Neil SJD (2016) Resistance of Transmitted Founder HIV-1 to IFITM-mediated restriction. Cell Host and Microbe 20(4):429-442. doi: 10.1016/j.chom.2016.08.006.
Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Giorgetti L, Fisher AG, Heard E, Flicek P, Dekker J, Merkenschlager M, (2013) Cohesinbased chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Research, 23(12), 206677
B Mifsud, F Tavares-Cadete, AN Young, R Sugar, S Schoenfelder, L Ferreira, SW Wingett, S Andrews, W Grey, PA Ewels, B Herman, S Happe, A Higgs, E LeProust, GA Follows, P Fraser, NM Luscombe and CS Osborne. (2015). Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nature Genetics. DOI: 10.1038/ng.3286.
33.1 Understanding epigenetic mechanisms in tissue-specific gene
expression Co-Supervisor 1A: Professor Rebecca Oakey
School/Division or CAG: School of Basic & Medical Biosciences
E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/OakeyLab/index.aspx Co-Supervisor 1B: Dr Rocio Martinez-Nunez
School/Division or CAG: School of Immunology & Microbial Sciences
Email: [email protected]
Website: https://www.kcl.ac.uk/research/martinez-nunez-lab Third Supervisor: Dr Bertille Montibus School/Division or CAG: School of Basic & Medical Biosciences Email: [email protected]
Website: https://www.kcl.ac.uk/people/bertille-montibus Project description
The transcriptome of a cell is tightly regulated by epigenetic mechanisms including DNA methylation
and histone modifications. We previously found that epigenetic modifications can influence the
utilization of alternative polyadenylation sites and induce intron retention. Others have shown that
epigenetic factors influence alternative splicing. Tissue-specific gene expression requires tight
control mechanisms during development and evidence shows that differential epigenetic marking of
CpG rich regions, or islands, residing in intragenic locations play a pivotal role in this process. Here
we will use imprinted genes as model systems for exploring epigenetic mechanisms and exploit
genome-wide data to find out how tissue-specific gene expression is modulated during
development. This project will combine molecular biology, genetics, epigenetics and bioinformatic
analyses of big data sets to interrogate biological mechanisms principally in the brain.
One representative publication from each co-supervisor:
Prickett, A., Barkas, N., McCole, R.B., Hughes, S., Amante, S.M., Schulz, R., and Oakey, R.J.
Genomewide 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. PMID:23804403.
34.1 Inhibition of Interferon signalling by Shigella sonnei Co-Supervisor 1A: Dr Charlotte Odendall
School/Division or CAG: School of Immunology & Microbial Sciences
E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/odendall/index.aspx Co-Supervisor 1B: Dr Nick Powell
School/Division or CAG: School of Immunology & Microbial Sciences
Email: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/diiid/centres/cibci/research/Nick-Powell/Dr-Nick-Powell.aspx Project description
Shigella species are the causative agents of bacillary dysentery. Shigellae colonise the intestine and
cause virulence using a type III secretion system (T3SS): a molecular syringe that injects toxins into
host cells. These weapons enable Shigella to invade the epithelium, replicate within host cells and
manipulate innate and adaptive immunities. We found that several Shigella toxins termed Osps
block signalling downstream of interferons (IFNs), cytokines that have known antiviral and
antibacterial functions. Mutant Shigella strains lacking Osps were defective in their ability to
replicate within host cells. Importantly, we also found that recombinant IFNs block intracellular
Shigella replication. Therefore, it appears that IFNs affect bacterial virulence, and that Shigella has
evolved virulence mechanisms (Osps) to circumvent this aspect of host defence.
The aims of this project are to
1- Further characterise the molecular mechanisms that enable Osps to block IFN signalling (Year 1)
2- Identify how IFN inhibition affects intracellular bacterial replication in vitro (Year 1 and 2)
2- Determine how IFN inhibition affects bacterial pathogenesis in vivo (Year 2 and 3)
Mechanistic studies will be carried out in vitro using a combination of overexpression and infection
assays, basic biochemical studies and microscopy. For example, we will express tagged Shigella Osps
and perform a pulldown followed by mass spectrometry to identify host targets of these Shigella
effectors.
Functional studies will be performed in vitro and in vivo. Cells will be infected with Shigella strains
and treated with IFNs. Bacterial replication and survival will be assessed via plating of live colony
forming units (CFUs) or flow cytometry. In vivo studies will be carried out in a mouse model of
Shigella infection. Mice will be orally infected with different Shigella strains including the Osp
knockouts (that are unable to block IFN signalling). Animals lacking IFN receptors will be used to
examine the roles of IFNs in the defence against Shigella infection. Bacterial growth in different
organs will be quantified by CFU plating, and Shigella pathogenesis and inflammation will be
assessed using RT-qPCR, ELISA and imaging of stained tissue sections.
Techniques involved will be :
- Molecular Biology and Microbiology
- Biochemistry
- Tissue culture
- Flow cytometry
- In vitro replication and survival assays
- Mouse model of Shigella infection
One representative publication from each co-supervisor:
1a- Odendall C, Voak AA, Kagan JC. Type III IFNs Are Commonly Induced by Bacteria-Sensing TLRs
and Reinforce Epithelial Barriers during Infection. J Immunol. 2017 Nov 1;199(9):3270-3279
1b- Powell N, et al,. The mucosal immune system is the master regulator of bidirectional gut-brain
communications. Nature Reviews in Gastroenterology and Hepatology(2017); 14:143-159.
35.1 Understanding chromatin remodelling at the nuclear periphery Co-Supervisor 1A: Professor Snezhana Oliferenko
School/Division or CAG: School of Basic & Medical Biosciences E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/randall/people/profiles/oliferenkosnezhana.aspx Co-Supervisor 1B: Dr Jeremy Carlton
School/Division or CAG: School of Cancer and Pharmaceutical Sciences
Email: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/cancer/research/groups/mtcd.aspx Project description
Eukaryotic genomes are highly organized within membrane-bound nuclei. Most cell types tether
heterochromatin – a complex set of transcriptionally repressed chromatin domains – to a protein
meshwork occupying the inner nuclear membrane (INM). This tethering establishes proper spatial
organization of chromosomes within the nucleus and can promote silencing of tethered chromatin,
allowing high-level regulation of gene expression. Mutations in INM heterochromatin-interacting
proteins (e.g., MAN1, LBR) can manifest in human diseases known as nuclear envelopathies, and
heterochromatin dysfunction can increase cancer susceptibility. In spite of profound fundamental and
clinical interest, we know little about the molecular mechanisms underlying this sub-nuclear
chromatin domain organisation and the extent of its functional significance. Importantly, we do not
understand how patterns of chromatin organisation can be maintained throughout many cell
divisions, or how cells reorganize their chromatin-NE interactions during cell fate change. Working in
mammalian and yeast cell biology labs, you will answer these questions by building on our preliminary
observations in fission yeast, indicating that the membrane remodeller ESCRT-III/Vps4 may promote
the dynamic turnover of heterochromatin-NE attachments, through its interactions with the
evolutionarily conserved INM protein Lem2.
Y1. Developing tools to assess chromatin dynamics at the NE and to allow acute manipulation of
ESCRT-III/Vps4 function in human cells (molecular biology, biochemistry).
Y2. Probing the roles of INM proteins (including Lem2) and ESCRT-III/Vps4 in chromatin restructuring
at the nuclear periphery during cell division and differentiation (RNAi, CRISPR, advanced microscopy).
Y3-Y4. Obtaining mechanistic insights into the observed phenotypes (stable/knock-in cell line
generation, yeast genetics, cell fate studies).
One representative publication from each co-supervisor:
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.
Olmos Y, Hodgson L, Mantell J, Verkade P and Carlton JG. ESCRT-III controls nuclear
envelope reformation. Nature (2015) 522:236-9.
36.1 Biophysical regulation of EGFR signalling in tumour cells Co-Supervisor 1A: Professor Maddy Parsons
School/Division or CAG: School of Basic & Medical Biosciences
E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/motility/parsons/parsonsmaddy.aspx Co-Supervisor 1B: Professor George Santis
School/Division or CAG: School of Immunology & Microbial Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/en/persons/george-santis(bd17b6b8-29b6-48fb-b710-0037e5784697)/biography.html Project description
Cancer cells respond to the changes in rigidity of the extracellular matrix (ECM) to induce signalling changes that promote tumourigenesis. Cell surface adhesion receptors provide a direct link to the ECM to mediate this mechano-sensing. However, emerging evidence suggests that epidermal growth factor receptor (EGFR), a receptor tyrosine kinase that is upregulated or mutated in cancers and drives tumour growth, is a mechano-responsive protein despite being incapable of binding ECM proteins. This suggests EGF-independent signalling occurs within different tumour microenvironments. This project aims to investigate this novel rigidity sensing to understand the co-ordination of the spatiotemporal EGFR mechano-signalling events that promote proliferation and invasion. This will be analysed using human cancer cells cultured in physiologically-relevant 3D ECM scaffolds of differing stiffness, controlled through ECM concentration and crosslinking. The aims are to:
1. Define EGFR contributions to mechano-sensing: using gene-edited cells to define how loss of or the oncogenic L858R and T870M activating mutations in EGFR alters cell-ECM interactions and invasive signalling in differing mechanical environments. Quantify co-ordination of cell proliferation, protrusion and invasion.
2. Analyse spatiotemporal EGFR signalling controlling invasion in different ECM environments: use advanced live cell imaging to study activation and traffic of EGFR in response to altered ECM rigidity and effects of oncogenic mutations in this process.
3. Determine whether cell-cell adhesion alters EGFR mechano-signalling: analyse differential signalling across spheroids and organoids, and resulting invasion, within differing ECM densities.
Data arising from this study will shed light on a novel paradigm in cancer cell signalling with potential therapeutic consequences. One representative publication from each co-supervisor:
- Pike R et al. KIF22 co-ordinates CAR and EGFR dynamics to promote cancer cell proliferation. Science Signaling. 2018. 11, eaaq1060. - 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.
37.1 Platelets and allergen sensitization: A critical interface between
trained innate immunity and the adaptive immune response. Co-Supervisor 1A: Dr Simon Pitchford
School/Division or CAG: School of Cancer and Pharmaceutical Sciences
E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/ips/about/people/pitchford/index.aspx
https://kclpure.kcl.ac.uk/portal/en/persons/simon-pitchford(8020a084-83b7-4400-9676-
1cca1178cdcc).html
Co-Supervisor 1B: Prof. Clive Page
School/Division or CAG: School of Cancer and Pharmaceutical Science
E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/ips/about/people/Page/index.aspx
Project description
Background. Platelets have been recognized for some time to act as inflammatory cells in the defence of the body against infection, performing many functions normally associated with leukocytes. These roles are distinct from platelet function during haemostasis. Interestingly, platelets act as a ‘bridge’ between the innate and adaptive immune response. In particular, platelets are activated in patients with asthma, and are responsible for the misdirected inflammatory response. Recently, we reported that platelets migrate into lung tissue upon allergen sensitization and challenge and associate with lung dendritic cells, and that temporary platelet depletion at the time of initial allergen sensitization resulted in reduced inflammatory responses upon subsequent, secondary allergen exposure. We outline a PhD programme to investigate how the process of antigen sensitization affects platelet activity and the development of immune memory. Future impact might lead to alternative strategies for ‘disease modifying’ therapies of allergic disease or infections.
Details of Techniques: In vivo skills pertinent to murine models of allergic lung inflammation: allergen sensitization and exposure procedures, cell and tissue harvesting and purification, immunohistochemistry. An exciting research avenue is advanced real time imaging techniques to record, for example, antigen presenting cell and platelet localization in mice. In vitro functional assays to elucidate platelet activation, function, and interactions with innate immune cells (e.g. flow cytometry, chemotaxis).
Objectives: Year 1. How does antigen exposure modulate platelet production and phenotype?
Year 2. How do platelets stimulate innate immune cells, their tissue recruitment and transit?
Year 3-4. How do platelets modulate antigen sensitization and recognition? One representative publication from each co-supervisor:
Pitchford: Amison RT et al. Platelets play a central role in sensitisation to allergen. Am J Respir Cell Mol Biol. 2018. 59: 96-103.
Page: Idzko M, Pitchford S, Page C. Role of Platelets in allergic airway inflammation. J Allergy Clin Immunol. 2015;135:1416-1423.
38.1 Investigating the role of the gut microbiome on the
cardioprotective effect of polyphenol-rich diets Co-Supervisor 1A: Dr Ana Rodriguez-Mateos
School/Division or CAG: School of Life Course Sciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/ana.rodriguez-mateos.html Co-Supervisor 1B: Professor Tim Spector
School/Division or CAG: School of Life Course Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/tim.spector.html Third Supervisor: Dr Cristina Menni
School/Division or CAG: School of Life Course Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/cristina.menni.html Project description
Dietary polyphenols are natural compounds occurring in plants, including foods such as fruits,
vegetables, cocoa, tea, coffee and wine. Epidemiological and clinical evidence indicates that they
may have a role in the prevention of cardiovascular diseases (CVD). Polyphenols are extensive
metabolized by the gut microbiota, and recent evidence suggests that polyphenol consumption can
stimulate the production of beneficial bacteria and increase gut microbiome diversity.
The main aim of this project is to investigate the relationships between polyphenol intake, CVD risk
and changes in the gut microbiome using the TwinsUK cohort (one of the most detailed omics and
phenotypic resource in the world) and a number of randomized controlled trials. which have
detailed longitudinal CVD phenotyping, 16s gut microbiome and metabolomics.
Specific objectives are:
1) To analyse urinary gut microbial polyphenol metabolites of 1200 individuals from the
TwinsUK, using liquid chromatography-mass spectrometry, and to investigate correlations
with CVD risk and the gut microbiome (YEAR 1)
2) To integrate the findings with other OMICS and dietary data including genomics, blood and
faecal metabolomics and 16s gut microbiome using bioinformatics tools (YEAR 2)
3) To compare and validate results with data from around 250 individuals from the CHARM,
CONCARD and ABP randomized controlled studies (PI Ana Rodriguez-Mateos) (YEAR 3)
The student will learn a wide range of techniques in the areas of analytical chemistry (in particular
mass spectrometry and chromatography), bioinformatics, statistical epidemiology, big data
management, and multi-omics data analysis.
One representative publication from each co-supervisor:
Rodriguez-Mateos A, Rendeiro C, Bergillos-Meca T, Tabatabaee S, George TW, Heiss C, Spencer JP.
Intake and time dependence of blueberry flavonoid-induced improvements in vascular function: a
randomized, controlled, double-blind, crossover intervention study with mechanistic insights into
biological activity.Am J Clin Nutr. 2013 Nov;98(5):1179-91.
Menni C, Lin C, Cecelja M, Mangino M, Matey-Hernandez ML, Keehn L, Mohney RP, Steves CJ, Spector TD, Kuo CF, Chowienczyk P, Valdes AM. Gut microbial diversity is associated with lower arterial stiffness in women. Eur Heart J. 2018 May 9.
39.1 Liver transplantation and immunogenicity Co-Supervisor 1A: Professor Alberto Sanchez-Fueyo
School/Division or CAG: School of Immunology & Microbial Sciences
E-mail: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/timb/research/liver.aspx Co-Supervisor 1B: Miriam Cortes
School/Division or CAG: King's College Hospital
Email: [email protected]
Website: https://www.kch.nhs.uk/service/a-z/liver-transplant Project description
The ex vivo machine perfusion of organs is an emerging strategy to improve/recondition grafts prior to transplantation. Recent evidences indicate that this strategy can also significantly modify the immunogenicity of the transplant and reduce the risk of rejection. This could have a substantial clinical impact by reducing the need for immunosuppressive medications and in the setting of liver transplantation promoting the establishment of immunological tolerance. The objective of this project is to investigate the mechanisms through which the 2 main modalities of ex vivo machine perfusion currently employed in clinical liver transplantation, namely ‘End Hypothermic Oxygenated Perfusion’ and ‘Normothermic Machine Perfusion’, influence the immune responses directed against the allogeneic liver after transplantation in humans. A particular emphasis will be put in analysing the effects on lymphocyte activation and costimulation pathways. The student will work in a transplant immunology laboratory and acquire expertise in advanced immunology techniques including lymphocyte isolation and flow cytometric phenotyping, transcriptional profiling, and cell culture, as well as knowledge in study design, data analysis, reporting and dissemination.
1st year: collection of relevant biological specimens; development of library of single-HLA expressing cell lines and optimisation of an alloreactivity assay; acquiring expertise in flow cytometry, cell culture and molecular profiling.
2nd year: performance of immunological assays comparing different machine perfusion techniques.
3rd year: completion of the experimental plan, data analysis and write-up. One representative publication from each co-supervisor:
-Londoño MC, Souza LN, Lozano JJ, Miquel R, Abraldes JG, Llovet LP, Quaglia A, Rimola A, Navasa M, Sánchez-Fueyo A. Molecular profiling of subclinical inflammatory lesions in long-term surviving adult liver transplant recipients. J Hepatol. 2018 Sep;69(3):626-634.
- Cortes-Cerisuelo M, Laurie SJ, Mathews DA, Winterberg PD, Larsen CP, Adams AB, Ford ML. Increased pre-transplant frequency of cd28+ cd4+ tem predicts belatacept-resistant rejection in human renal transplant recipients. Am J Transplant 2017; 17: 2350-2362.
40.1 Microfluidics modelling of an adult stem cell niche Co-Supervisor 1A: Professor Paul Sharpe
School/Division or CAG: Dental Institute
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/paul.sharpe.html Co-Supervisor 1B: Dr Ciro Chiappini
School/Division or CAG: Dental Institute
Email: [email protected]
Website: https://chiappinilab.com Project description
The proposed study will make use of recent advances in the identification of the cell populations that constitute an adult stem cell microenvironment and aims to investigate how cell transitions are regulated by intrinsic and extrinsic cues to maintain a constant rate of cell differentiation and growth. Microfluidics devices will be constructed to recapitulate key functional aspects of the microenvironments that permit conversion of stem cells to progenitors and progenitor differentiation. Four connected microenvironments will be created to recapitulate the niche. In the first environment conditions will maintain stem cell self-renewal through Shh signalling and the appropriate ECM and stiffness. In the second environment, adjacent to the first, formation and maintenance of progenitors through tethered (immobilised) Wnts and accordingly modulating ECM and stiffness will be created. The third and fourth environments, placed side by side and both adjacent to the second will introduce cell differentiation by presenting the necessary ECM, stiffness and signalling factors. Hydrogel stiffness that match those of the native tissue (we expect ~200 to 5000 Pa) will be generated using polyacrylamide hydrogels as a substrate.
Sequential photopatterning will be used to immobilise ECM and signalling factors. Gradients of two soluble factors will be provided by the microfluidic system and will be overlaid to the patterned hydrogel substrate to combine the mechanical, ECM and soluble signals. All these devices will be seeded with FACs-isolated stem cells and their subsequent growth and transition into progenitors followed in real time by high-content imaging and combined with molecular analysis by RTPCR, flow cytometry and RNAseq. One representative publication from each co-supervisor:
C. Chiappini et al. Biodegradable silicon nanoneedles delivering nucleic acids intracellularly induce localized in vivo neovascularization, Nat Mater. 14, 532 (2015)
41.1 Regulation of gene expression in fat tissue and its contributions
to Type 2 Diabetes and Obesity
Co-Supervisor 1A: Dr Kerrin Small
School/Division or CAG: School of Life Course Sciences
E-mail: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/twin/research/small/index.aspx Co-Supervisor 1B: Dr Alan Hodgkinson
School/Division or CAG: School of Basic & Biomedical Sciences
Email: https://www.hodgkinsonlab.org/
Website: https://www.hodgkinsonlab.org/ Project description
Type 2 Diabetes and obesity-related traits are global epidemics. In the UK alone, ~4 million people are living with diabetes and 10% of the NHS budget is spent on diabetes. Understanding the molecular mechanisms underlying genetic risk of diabetes will help direct novel treatments and prevention. We have previously shown that gene expression in adipose (fat) tissue mediates a subset of Type 2 Diabetes associated GWAS loci, including a master trans-regulator at the KLF14 locus which regulates 400 genes. This project will seek to identify novel regulatory variants that influence gene expression and use them to 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-centre 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. One representative publication from each co-supervisor:
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.
42.1 Lineage reprogramming of hepatocytes into pancreatic beta-
cells
Co-Supervisor 1A: Dr Francesca M. Spagnoli
School/Division or CAG: School of Basic and Medical Biosciences
E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/stemcells/index.aspx Co-Supervisor 1B: Professor Benedikt Berninger School/Division or CAG: Psychology & Neuroscience Email: [email protected] Website: https://www.kcl.ac.uk/ioppn/depts/devneuro/index.aspx Project description
The discovery of cellular reprogramming towards pluripotency and across lineages has revolutionized
our thinking about cell plasticity and cell fate control. Lineage reprogrammed cells are now an
indispensable and versatile platform for both basic developmental studies and regenerative medicine.
The aim of this PhD project is to establish a reprogramming approach to convert hepatocytes into
functional pancreatic beta-cells. This knowledge will be valuable for developing cell-replacement
therapies to treat diabetes.
My laboratory previously established a strategy to reprogram liver cells into pancreatic progenitors
based on a single transcriptional regulator (Cerda-Esteban et al. 2017). This represents a powerful
platform for dissecting mechanistic aspects of lineage reprogramming and provides a starting point
for production of differentiated pancreatic beta-cells.
The candidate will investigate the reprogramming competence of hepatocytes and how the tissue
microenvironment can influence this conversion, with the final goal to improve the efficiency and
functional properties of reprogrammed pancreatic beta-cells for therapeutic purposes.
During the rotation project, the student will learn lineage reprogramming approaches and generation
of iPSC-derived hepatocytes.
Years 1/2: Genetic lineage tracing will be used to in vivo target and isolate different types of
hepatocytes from the mouse liver (e.g. peri-portal or centrolobular hepatocytes); the different
hepatocyte populations will be reprogrammed using our established strategy and efficiency of
reprogramming and differentiation properties will be measured.
Year 2/3: Next, the candidate will study reprogramming competence in human using liver organoids
generated from iPSCs, which provide a new experimental platform to reproduce distinct liver tissue
microenvironments. CRISPR/CAS9 genome-editing technologies will be used to introduce fluorescent
reporters and monitor cell fate changes.
Final year: Molecular and functional properties of the reprogrammed cells, obtained from different
liver populations, will be benchmarked against endogenous beta-cells.
The PhD student will acquire cutting-edge techniques in Reprogramming, iPSCs culturing, confocal microscopy, transcriptome analyses, Crispr/Cas9 established in both labs.
One representative publication from each co-supervisor:
Cerdá-Esteban N, Naumann N, Ruzzittu, S, Cozzitorto, C., Pongrac IM, Hommel A, Mah N, Andrade-
Navarro MA, Bonifacio E, Spagnoli FM. Step-wise reprogramming of liver to pancreas progenitor
state by a single transcriptional regulator. Nature Communications. 2017 8:14127
doi:10.1038/ncomms14127.
Karow, M., Camp, J. G., Falk, S., Gerber, T., Pataskar, . A., Gac-Santel, M., Kageyama, J., Brazovskaja, . A., Garding, A., Fan, W., Riedemann, T., Casamassa, A., Smiyakin, A., Schichor, C., Götz, M., Tiwari, V. K., Treutlein, B., Berninger, B. Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. Nature Neuroscience. 2018 21:932-940.
43.1 Dissecting the role and regulation of contact inhibition of
locomotion in cancer Co-Supervisor 1A: Dr Brian Stramer
School/Division or CAG: School of Basic and Medical Sciences
E-mail: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/motility/stramer/index.aspx Co-Supervisor 1B: Dr Claudia Linker
School/Division or CAG: School of Basic and Medical Sciences
Email: [email protected]
Website: https://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/motility/linker/index.aspx Project description
Many cell types will repel each other through a process of contact inhibition of locomotion (CIL) and
an alteration in CIL dynamics has been hypothesized to be involved in a number of pathologies, such
as cancer. This project will examine the CIL properties of a number of cancer cell types with the
goal of understanding whether a loss of this repulsive mechanism is involved in the metastatic
cascade. Preliminary evidence in the laboratory has revealed that different cancer cells have unique
CIL dynamics in response to normal epithelial cells. Uniquely, melanoma cells appear to have a
complete loss of CIL, which leads to their invasion of the surrounding epithelial monolayer. The aim
of this work is to understand the mechanisms behind the control of these distinct CIL behaviors with
the hope of preventing the initial outgrowth of the cancer.
Yearly Objectives-
Year 1: screen through a panel of cancer cell types that have a range of metastatic capabilities to
examine whether CIL behaviors (or a loss of CIL) is correlated with their invasiveness.
Year 2: Characterize the ability of the various cell types, such as human melanoma cells, to invade
epithelial cells using a combination of 2D and 3D model systems.
Year 3-4: Examine the mechanisms behind this cellular invasion and the reasons for the altered CIL
behaviour.
Skillset: The student will gain exposure to cell culture, molecular biology, and timelapse microscopy.
One representative publication from each co-supervisor:
Stramer B, and Mayor R. (2016) Mechanisms and in vivo functions of contact inhibition of
locomotion. Nat. Rev. Mol. Cell Biol. 18:43-55.
Richardson J, Gauert A, Briones L, Fanlo L, Alhashem Z, Assar R, Marti E, Kabla A, Hartel S, Linker S.
(2016) Leader cells define directionality of trunk, but not cranial, neural crest cell migration. Cell Rep.
15:2076
44.1 Gene editing approaches for treating sickle cell disease
Co-Supervisor 1A:Professor John Strouboulis PhD
School/Division or CAG: School of Cancer and Pharmaceutical Sciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/john.strouboulis.html
Co-Supervisor 1B: Professor David Rees MD
School/Division or CAG: School of Cancer and Pharmaceutical Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/david.rees.html
Project description
Sickle cell disease (SCD) is a severe inherited disease, affecting more than 300 000 new-born babies
per year. More than 80% of SCD patients die in childhood in African countries, where SCD is most
common. Sickle haemoglobin (HbS) polymerises when deoxygenated and damages red cells which
become rigid and dehydrated. Treatment options remain very limited, however the emergence of
CRISPR/Cas9 gene editing techniques offers exciting opportunities. The aim of this project is to use
CRISPR/Cas9 to edit specific genes in primary erythroid cultures established from patients with
different types of SCD, to study their effects on red cell pathophysiology and to assess their potential
as therapeutic targets. SCD cell lines will be fully characterised in terms of haemoglobin expression,
cation transport, red cell membrane properties, transcriptome and proteome. Specific genes will be
targeted by gene editing, to investigate their role in SCD pathophysiology and to assess their
potential as novel therapeutic candidates in halting/reversing SCD. Targets will include genes
involved in haemoglobin expression and switching, red cell cation transport and membrane
structure.
The following skills will be learnt: immortalisation of primary erythroid cell lines, gene editing, red
cell physiology, transcriptomic (RNAseq) and proteomic (mass spectrometry) analysis, clinical
aspects of SCD.
Objectives
Year 1: basic laboratory techniques, establishing erythroid cell lines from 3 – 5 patients using
lentivirally transduced Tet-inducible HPV16-E6/E7 cell immortalisation system.
Year 2: Characterisation of primary erythroid cell lines, choosing genetic targets and gene editing.
Year 3: Characterisation of edited cell lines, publication, thesis.
One representative publication from each co-supervisor:
Papageorgiou D.N., Karkoulia E., Amaral-Psarris A., Burda P., Kolodziej K., Demmers J., Bungert J., Stopka T., Strouboulis J. Distinct and overlapping DNMT1 interactions with multiple transcription factors in erythroid cells: evidence for co-repressor functions. Biochim Biophys Acta, 2016, 1859(12):1515-1526.
Tewari S, Renney G, Brewin J, Gardner K, Kirkham F, Inusa B, Barrett JE, Menzel S, Thein SL, Ward M,
Rees DC. Proteomic analysis of plasma from children with sickle cell anemia and silent cerebral
infarction. Haematologica. 2018;103(7):1136-1142.
45.1 Inhibition of human immunodeficiency virus (HIV) replication by
CpG dinucleotides, the cellular antiviral protein ZAP and its cofactors
Co-Supervisor 1A: Dr Chad Swanson
School/Division or CAG: School of Immunology & Microbial Sciences
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/swanson/inde
x.aspx
Co-Supervisor 1B: Dr John Cason
School/Division or CAG: School of Immunology & Microbial Sciences
Email: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/diiid/departments/infectious/research/cason/index.a
spx
Project description
ZAP is a cellular protein that inhibits the replication of diverse viruses including Ebola virus, hepatitis
B virus and Japanese encephalitis virus. It has recently been shown to bind to viral RNA containing
CpG dinucleotides. The frequency of CpG dinucleotides is supressed in HIV, potentially to avoid being
targeted by ZAP, and increasing the CpG abundance in HIV inhibits viral replication. Introduction of
CpG dinucleotides into viral genomes using synthetic biology techniques may be a new way to
develop live attenuated virus vaccines, but a full understanding of how ZAP and CpG dinucleotides
inhibit viral replication is necessary to develop this approach. Furthermore, ZAP interacts with
several other cellular proteins but it is unclear how these regulate ZAP antiviral activity.
In this PhD project, the student will characterise how CpG dinucleotides, ZAP and its interacting
proteins inhibit HIV replication. Specific experiments will address three major questions:
1) How does the HIV sequence influence how ZAP and its cofactors bind the viral RNA?
2) What are the mechanisms by which ZAP and its cofactors inhibit viral gene expression?
3) How do the abundance and location of CpGs in the HIV genome modulate disease progression
using archived samples from the Infectious Diseases BioBank from patients with extremes of clinical
progression?
Overall, this project will analyse how ZAP interacts with CpG dinucleotides and other cellular
proteins to inhibit HIV replication. This will further our understanding of how HIV evades the innate
immune response and promote the development of new vaccines.
One representative publication from each co-supervisor:
Antzin-Anduetza I, Mahiet C, Granger LA, Odendall C, Swanson CM. (2017) Increasing the CpG
dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication. Retrovirology. 14:49.
Sobolev O, Binda E, O'Farrell S, Lorenc A, Pradines J, Huang Y, Duffner J, Schulz R, Cason J, Zambon
M, Malim MH, Peakman M, Cope A, Capila I, Kaundinya GV, Hayday AC. Adjuvanted influenza-H1N1
vaccination reveals lymphoid signatures of age-dependent early responses and of clinical adverse
events. Nat Immunol. 2016 Feb;17(2):204-13.
46.1 Predictive Immune Atlas of Cancer Resistance to Radiotherapy
Co-Supervisor 1A: Prof Mahvash Tavassoli
School/Division or CAG: Dental Institute
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/mahvash.tavassoli.html
Co-Supervisor 1B: Dr. Shahram Kordasti
School/Division or CAG: School of Cancer and Pharmaceutical Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/shahram.kordasti.html
Collaborating Clinician: Dr Teresa Guerrero, Consultant Clinical Oncologist
School/Division or CAG: School of Cancer Studies
Email: [email protected] Website: https://www.guysandstthomas.nhs.uk/our-services/consultant-profiles/cancer/clinical-
oncology/teresa-guerrerourbano.aspx
Summary of role: Patient selection, follow up and outcome analysis, regular discussion and meetings
with the student on clinical translational aspects of the project.
Project description
Radiation therapy is the pillar of standard therapy for many types of solid cancers however, resistance to the ionizing radiation is a current problem in the treatment and clinical management of various cancers. The biological and molecular mechanisms responsible for resistance of the tumours to radiotherapy remain unknown. Recently the immune system in tumour microenvironment has been found to influence patient response to RT and disease outcome. Further investigation is necessary to take advantage of these mechanisms in order to develop more tailored therapeutic strategies.
The primary objective of this study is to perform deep phenotyping of immune cells in HNC tumour microenvironment to identify an immune signature to predict RT response
Flowcytometry (conventional and mass cytometry, CyTOF), following tumour biopsy dissociation (using BD Tumour Dissociation Reagent), will be used as the primary methods to identify specific immune signatures for the prediction of disease progression and RT response. Unbiased data analysis will be performed by the supervisor’s already established pipeline to identify immunophenotypic heterogeneity within tumour microenvironment. This pipeline includes dimension reduction by T-distributed Stochastic Neighbour Embedding (t-SNE) followed by a clustering algorithm (ie. SPADE or FlowSOM) based on t-SNE scores. In house developed pipeline (CytoClustR) will then be used to further characterise the identified cell clusters and compare the frequency and expression intensities among samples. This pipeline can be used for both multidimensional conventional cytometry (ie BD Symphony) as well as mass cytometry (CyTOF). This strategy will help to predict patients response to RT and RT plus other treatments such as immune checkpoint blockers, development of tailored treatment plans, and assessment of adverse effects of such therapy.
This interdisciplinary project will provide in-depth training in cancer biology/ immunology, and in
a range of cellular, molecular, imaging, biochemical and bioinformatics methods.
One representative publication from each co-supervisor:
Association between hypoxic volume and underlying hypoxia-induced gene expression in oropharyngeal squamous cell carcinoma. Suh YE, Lawler K, Henley-Smith R, Pike L, Leek R, Barrington S, Odell EW, Ng T, Pezzella F, Guerrero-Urbano T and Tavassoli M. Br J Cancer. 2017 Apr 11;116(8):1057-1064. doi: 10.1038/bjc.2017.66. Epub 2017 Mar 21. Deep phenotyping of Tregs identifies an immune signature for idiopathic aplastic anemia and predicts response to treatment. Kordasti S, Costantini B, Seidl T, Perez Abellan P, Martinez Llordella M, McLornan D, Diggins KE, Kulasekararaj A, Benfatto C, Feng X, Smith A, Mian SA, Melchiotti R, de Rinaldis E, Ellis R, Petrov N, Povoleri GA, Chung SS, Thomas NS, Farzaneh F, Irish JM, Heck S, Young NS, Marsh JC and Mufti GJ. Blood. 2016 Sep 1;128(9):1193-205. doi: 10.1182/blood-2016-03-703702. Epub 2016 Jun 8.
47.1 Understanding and enhancing repair of the ear
Co-Supervisor 1A: Professor Abigail Tucker
School/Division or CAG: Dental Institute
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/dentistry/research/divisions/craniofac/researchgroups/tuckerlab/tuckerlab.a
spx
Co-Supervisor 1B: Mr Dan Jiang PhD FRCSI(Otol) FRCS(ORL-HNS)
School/Division or CAG: Otolaryngology, Head & Neck Surgery, Guys and St Thomas’s Hospital Honorary Prof: Dental Institute Email: [email protected]
Website: http://www.guysandstthomas.nhs.uk/our-services/consultant-profiles/audiology/dan-
jiang.aspx
Project description
In between the external and middle ear sits the ear-drum, a thin transparent membrane that
converts sound waves into vibrations. This membrane is very susceptible to damage caused by ear
infections, pressure changes or head trauma. Most holes in the membrane heal rapidly without any
intervention. Some holes, however, do not heal leading to ear pain, ringing in the ears (tinnitus), ear
infections, and hearing loss. These chronic perforations may be due to the size or position of the
initial damage, or the presence of infectious agents. Such chronic perforations have to be corrected
using surgery with tissue from elsewhere in the body grafted into the ear to bridge the gap.
Aim: To analyse the effect of pharmacological inhibitors on stem/progenitor cell populations within
the ear-drum and to their subsequent effect on healing.
Year 1: Document natural repair of ear-drums in murine explant culture, and map the role of stem
cells.
Year 2: Investigate the ability of pharmacological inhibitors to enhance repair of perforations in
explant culture.
Year 3: Move to in vivo model to repair holes using topical application of successful reagents to
mouse ears.
The project takes a novel approach (explant culture of the ear-drum) to allow visualization of the ear
as it heals and aims to create new and innovative therapies to prevent chronic perforations.
Skills training: The student will be trained in molecular biology techniques, stem cell biology, and
immersed in clinically relevant problems. Critical thinking, presentation and writing skills will be
taught.
One representative publication from each co-supervisor:
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.
48.1 Uncovering the properties of human Liver Stem Progenitor Cells
(hLSPC) and surrounding microenvironment during development,
homeostasis and disease.
Co-Supervisor 1A: Dr Alessandra Vigilante
School/Division or CAG: School of Basic & Medical Biosciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/alessandra.vigilante.html
Co-Supervisor 1B: Dr Tamir Rashid
School/Division or CAG: School of Basic & Medical Biosciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/tamir.rashid.html
Project description
The existence of a specialised cell type in the liver capable of replenishing dead or damaged tissue is
an exciting paradigm for researchers. Knowing the properties of this ‘stem/progenitor cell’ and the
microenvironment holding it in place is essential to our ambitions for using pluripotent stem cell
derived hepatocytes in cell therapy. We previously performed single cell RNA-seq on human fetal liver
and normal adult liver and we identified a putative stem / progenitor cell (hLSPC) suggesting the
existence of a sub-population of stem cells within normal human adult liver (Segal et al., BiorXiv 2018).
The main goal of this project is to demonstrate that as yet unidentified cell types (niche) make
essential contributions defining the cellular microenvironment surrounding LSPCs and change during
development, homeostasis and disease, inducing hLSPCs to proliferate, differentiate or remain
quiescent
We will isolate, sequence and profile parenchymal progenitors, stromal & immune cells in human fetal
liver and in diseases where progenitor cells expand (chronic liver disease with ductular reaction and
de-differentiated cancer). The student will use the following techniques: (i) single cell RNA -seq (ii)
multi-probe RNA scope of tissue microarray samples and (ii) 3D computational reconstruction. To
show that the niche exerts different biomechanical forces on LSPCs during development, homeostasis
and disease we will also generate mechanical forces AFM data to measure stiffness in the micro-
environment surrounding progenitors.
The student will perform bioinformatics analyses for the analysis of the raw data and for the
integration of the obtained datasets. In particular, we will implement a bioinformatics pipeline able
to integrate gene expression and cell biology datasets obtained (Vigilante et al, BiorXiv 2018) and we
will apply a multidimensional correlation strategy together with linear and nonlinear principal
component analysis of the parameters describing the phenotype of the cells (i.e. adhesion, stiffness,
friction, dissipation, …). With this approach we will decompose different aspects of the niche during
development, homeostasis and disease and correlate these features with the correspondent
patterns of differential gene expression. This will finally allow us to identify molecules secreted from
niche cells in conditions where LSPCs proliferate in cases like aggressive tumors and severe liver
injury.
One representative publication from each co-supervisor:
Identifying extrinsic versus intrinsic drivers of variation in cell behaviour in human iPS cell lines from
healthy donors. Alessandra Vigilante, Anna Laddach, Nathalie Moens, Ruta Meleckyte, Andreas Leha,
Arsham Ghahramani, Oliver J. Culley, Annie Kathuria, Chloe Hurling, Alice Vickers, Mukul Tewary,
Peter Zandstra, HipSci Consortium, Richard Durbin, Franca Fraternali, Oliver Stegle, Ewan Birney,
Nicholas M Luscombe, Davide Danovi, Fiona M Watt. BiorXiv 2018, doi:
https://doi.org/10.1101/285627
Single-cell analysis identifies EpCAM+/CDH6+/TROP-2- cells as human liver progenitors.
Joe M Segal, Daniel J Wesche, Maria Paola Serra, Bénédicte Oulés, Deniz Kent, Soon Seng Ng, Gozde
Kar, Guy Emerton, Samuel Blackford, Spyros Darmanis, Rosa Miquel, Tu Vinh, Ryo Yamamoto,
Andrew Bonham, Alessandra Vigilante, Sarah Teichmann, Stephen R Quake, Hiromitsu Nakauchi, S
Tamir Rashid. BiorXiv 2018, doi: https://doi.org/10.1101/294272
49.1 Transcriptional regulation of cardiac progenitor cell fate
Co-Supervisor 1A: Dr Fiona Wardle
School/Division or CAG: School of Basic and Medical Biosciences
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/signalling/wardle/index.as
px
Co-Supervisor 1B: Dr Elisabeth Ehler
School/Division or CAG: School of Basic and Medical Biosciences
Email: [email protected]
Website:
https://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/signalling/ehler/index.aspx
Project description
Mesp1 is central to cardiac lineage formation. It is transiently expressed in cardiac progenitor cells
during gastrulation, and overexpression of Mesp1 in mouse embryonic stem cells causes
differentiation to cardiovascular cell types.
However, we know very little about the factors and pathways that ensure the correct spatial and temporal expression of Mesp1. To elucidate the regulation of human MESP1, which will lead to a better knowledge of the conditions for cardiac cell formation in regenerative medicine, this project aims to identify and characterise MESP1 regulatory elements in cardiac differentiation. Year 1: Identify regulatory regions for MESP1. Genomic regions interacting with the MESP1
promoter in differentiating human induced pluripotent stem cells (hiPSCs) will be identified using 4C-
seq. In parallel, published genomics datasets, such as ChIP-seq and ATAC-seq, will be used to identify
putative MESP1 regulatory elements, which will help confirm 4C-seq interactions and identify
potential transcription factor binding.
Year 2: Test sufficiency of regulatory elements. Reporter assays in differentiating hiPSCs will be used to identify which elements are active (enhancers). Those found to be active in cells will be tested in transgenic reporter mice and zebrafish for the spatial and temporal pattern they drive.
Year 3+: Test necessity of regulatory elements. Using genome editing techniques (CRISPR) the effect
of ablating regulatory elements on MESP1 expression and hiPSC differentiation will be tested. To test
the role in MESP1 regulation of transcription factors bound to each element knockdown
experiments will be performed.
One representative publication from each co-supervisor:
FW: Nelson A. C., Cutty S.J., Gasiunas S.N., Deplae I., Stemple D.L., Wardle F.C. (2017). In vivo
regulation of the zebrafish endoderm progenitor niche by T-box transcription factors. Cell Reports,
19:2782-95.
EE: Lange, S, Gehmlich, K, Lun, AS, Blondelle, J, Hooper, C, Dalton, ND, Alvarez, EA, Zhang, X, Bang,
M-L, Abassi, YA, dos Remedios, CG, Peterson, KL, Chen, J, Ehler E (2016). MLP and CARP are linked to
chronic PKCalpha signalling in dilated cardiomyopathy. Nat. Commun., 7:12120.
51.1 Identification of novel immunomodulatory target checkpoints
for Prostate Cancer therapeutics
Co-Supervisor 1A: Dr Christine Galustian
School/Division or CAG: School of Immunology & Microbial Sciences
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/christine.galustian.html
Co-Supervisor 1B: Dr Susan John
School/Division or CAG: School of Immunology & Microbial Sciences
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/susan.john.html
Collaborating Clinician: Professor Prokar Dasgupta
Research School/Division or CAG: Immunology and Microbial Sciences/MRC Centre for
transplantation
Email: [email protected]
Website: http://www.prokar.co.uk/
Project Description
Prostate cancer is the most common cancer among men. Immunotherapies such as Provenge™ have
improved end-stage prostate cancer survival1. However, although immune-cells such as CD8 T-cells
can infiltrate the prostate, this microenvironment renders these cells suppressive2. The cause of this
immunosuppression is not clear, although many immune-checkpoint proteins have been recently
discovered3.
The project aims to use a novel syngeneic human prostate tumour/immune-cell model to identify
immunomodulatory molecules in the cancerous prostate. Using syngeneic PBMCs and cells from
patient tumours (of varying stagings), mechanisms of immune-tolerance and molecules
differentiating indolent/aggressive disease can be determined. Moreover, potent
immunotherapeutic agents modifiable to localise to cell-membranes can be assessed using this
model (see below). The supervisors provide training in Immunology and Molecular Biology
(Genomics/Proteomics), Protein Chemistry, and Clinical Cancer diagnostics.
Objectives/methodologies:
Years 1-2: Studying immune-effector function of cells from patients with different stagings: This
will involve training including flow-cytometry, ELISA, and isolation/culture of primary-tumour cells.
Years 2-3: Immunome profiling from patient effector/tumour cells to determine markers of
disease progression. Training will be provided in technologies such as genomic/proteomic
microarrays. Antibodies will be raised/obtained to selected inhibitory markers.
Years 3-4: Assessing novel immunotherapeutic agents in the above model. We have developed a
cytotopic-tailing technology to localise therapeutic proteins/peptides to tissues/organs to reduce
systemic-toxicity and increase agent avidity4. Training will be provided in protein chemistry to
prepare agents modified with cytotopic “tails” (e.g antibodies from years 2-3) and will assay efficacy
of these agents on immune-cell function using assays described in year 1.
References for project
1. Dawson N. Immunotherapeutic approaches in prostate cancer: PROVENGE. Clin Adv Hematol
Oncol 2010;8:419-421.
2. Shafer-Weaver KA, Anderson MJ, Stagliano K, Malyguine A, Greenberg NM, Hurwitz AA. Cutting
Edge: Tumor-Specific CD8+ T Cells Infiltrating Prostatic Tumors Are Induced to Become Suppressor
Cells. The Journal of Immunology 2009;183:4848-4852.
3. Galustian C, Vyakarnam A, Elhage O, Hickman O, Dasgupta P, Smith RA. Immunotherapy of
prostate cancer: identification of new treatments and targets for therapy, and role of WAP domain-
containing proteins. Biochem Soc Trans 2011;39:1433-1436.
4. Smith GP, Smith RAG. Membrane-targeted complement inhibitors. Molecular Immunology
2001;38:249-255.
One representative publication from each co-supervisor:
Galustian C, Vyakarnam A, Elhage O, Hickman O, Dasgupta P, Smith RA. Immunotherapy of prostate
cancer: identification of new treatments and targets for therapy, and role of WAP domain-containing
proteins. Biochem Soc Trans 2011;39:1433-1436.
Afzali B, Mitchell PJ, Edozie FC et al. and John S* Lombardi G*. CD161 expression characterizes a sub-
population of human regulatory T cells that produces IL-17 in a STAT3 dependent manner. (2013) EJI,
32:2043.
