Download Genetics projects 2015

 Contents
Genetic Associations with Rheumatoid Arthritis in African Ancestry Individuals .................................... 3
HNF1A gene as a regulator of plasma protein glycosylation ...................................................................... 4
Tracing Tumour Lineage in Pre-invasive Breast Cancer ............................................................................ 5
Characterisation of how Sam68 regulates CD4 T cell gene expression in the presence and absence of HIV-1
infection ......................................................................................................................................................... 7
Genome wide promoter interactions in endocardial versus endothelial cell differentiation; implications for
heart development ......................................................................................................................................... 8
Mutations and mechanisms in cholestatic liver disease ............................................................................... 9
Genetic studies to understand the aetiology and pathogenesis of Poland Syndrome and improve treatment
..................................................................................................................................................................... 10
Functional Annotation of Susceptibility loci for SLE in Multiple Ancestries ........................................... 11
Targeting autophagy in the treatment of rare and severe forms of psoriasis ............................................. 12
Understanding the role of non-coding RNAs in the aetiology and pathogenesis of inflammatory bowel
disease .......................................................................................................................................................... 13
Transcriptional regulation of lung cancer metastasis ................................................................................. 14
External ear defects in mice and men ......................................................................................................... 15
Identification and validation of driver genes in oesophageal adenocarcinoma ......................................... 16
Discovery of Mutated Driver Pathways in Primary Cutaneous T-cell lymphoma ................................... 17
Genome-wide and epigenetic screen in drug metabolising (ADME) genes in twins ................................ 18
2
Genetic Associations with Rheumatoid Arthritis in African Ancestry Individuals
Theme: Genetics
Supervisor 1: Professor Cathryn Lewis
Research Division or CAG: Division of Medical and Molecular Genetics
E-mail: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/clewis/sgu/index.aspx
Supervisor 2 & Collaborating Clinician: Dr Ian Scott
Research Division or CAG: Division of Medical and Molecular Genetics
Email: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/clewis/sgu/index.aspx
Project description:
Scientific Basis - Rheumatoid arthritis (RA) arises when genetically predisposed individuals are exposed to
environmental risks. Most gene-environment studies in RA have focussed on European ancestry populations.
The causes of RA in African ancestry populations are uncertain.
We have established a study of African ancestry RA patients: the GENetics of Rheumatoid arthritis in African
ancestry individuals (GENRA) study. This comprises 220 and 1,000 African ancestry RA cases and controls,
respectively. This project will evaluate if European RA genetic risk factors are associated with RA in African
ancestry individuals. Dr Scott will supervise the clinical aspects of the study; Professor Lewis will supervise
statistical analysis and training.
Specific Objectives
1. Establish if European RA susceptibility variants increase the risk of RA in African populations
2. Establish if RA risk allele frequencies/effect sizes vary across populations
3. Evaluate if known European genetic interactions with smoking exist in African populations
4. Develop models that predict RA across populations
This project can be extended beyond this initial remit, to prognostic modelling and pharmacogenomics. We
have access to multiple RA genetic datasets, with longitudinal data on outcomes and treatment responses.
Skills Training - You will learn the following:
Managing “big data”: over 1,000 individuals and several hundred thousand genetic markers
Complex statistical analysis using multifunctional platforms such as “R” and “PLINK”
Analysing case-control data: a key genetic study design
An in-depth understanding of complex diseases through attending semester 1 lectures from the intercalated
BSc in Human Genetics, and the course 6BBYG306 “Complex Disease Genetics”.
Two representative publications:
1) Scott IC, Lewis CM et al. Do Genetic Susceptibility Variants Associate with Disease Severity in Early
Active Rheumatoid Arthritis? J Rheumatol 2015 [Epub ahead of print]
2) Scott IC, Lewis CM. Predicting the risk of rheumatoid arthritis and its age of onset through modelling
genetic risk variants with smoking. PLoS Genet. 2013; 9: e1003808
3
HNF1A gene as a regulator of plasma protein glycosylation
Theme: Genetics
Supervisor 1: Tim Spector
Research Division or CAG: Department of Twin Research and Genetic Epidemiology
E-mail: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/twin/about/people/spector.aspx
Supervisor 2: Frances Williams
Research Division or CAG: Department of Twin Research and Genetic Epidemiology
Email: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/twin/research/williams/index.aspx
Collaborating Statistician: Maxim Freydin
Research Division or CAG: Department of Twin Research and Genetic Epidemiology
Email: [email protected]
Summary of role: Co-supervision and help with the statistical analysis
Project description:
The project is aimed at identifying associations between glycan levels and polymorphisms if the HNF1A gene.
Glycosylation constitutes the most abundant and diverse form of post-translational modification of proteins.
Glycans can influence disease development such as congenital disorders of glycosylation, cancer, rheumatoid
arthritis and AIDS. Glycans are crucial for the immune system, development, and protein folding but currently
our understanding of glycosylation is very limited.
Some IgG N-glycans have been shown to influenced by genetic factors. A GWAS of the plasma
glycome identified HNF1A gene as a possible master regulator of plasma protein glycosylation [Lauc et al.,
2010]. Functional and pathogenetic relevance of the HNF1A gene as a regulator of glycosylation have been
assessed through the analysis of patients with different subtypes diabetes [Thanabalasingham et al., 2013].
Specific mutations in the HNF1A gene were associated both with variation of the DG9-glycan index and the
maturity onset diabetes of the young type (MODY), thus providing the links between genetic variation,
intermediate phenotype (glycans) and phenotype of interest (MODY). This study confirmed that the glycan
profile of plasma proteins is altered substantially in subjects with HNF1A mutations; however, it is not yet
known how widespread are mutations in HNF1A gene, which do not cause this rare form of diabetes mellitus,
but may have functional effect on glycome variation.
The project is devoted to the analysis of the sequence polymorphisms in HNF1A coding regions and the
analysis of functional significance of these variants on glycome composition. Positive findings would strongly
support for glycans as functional biomarkers of HNF1A activity. The project will be based on TwinsUK
dataset including exome sequences and glycan levels in approximately 4500 subjects. The project will include
the analysis of the exome of the twins to reveal single-nucleotide polymorphisms and other variations in the
HNF1A gene. The variants identified will be tested for their associations with glycan levels in twins. Further
exploration will be made of the region using expression data and epigenetic information, if indicated.
The project is for a person with strong interest in bioinformatics and statistical genetics.
Two representative publications:
1) Lauc G, Essafi A, Huffman JE et al. Genomics meets glycomics-the first GWAS study of human NGlycome identifies HNF1α as a master regulator of plasma protein fucosylation. PLoS Genet. 2010
Dec 23;6(12):e1001256. doi: 10.1371/journal.pgen.1001256
2) Thanabalasingham G, Huffman JE, Kattla JJ et al. Mutations in HNF1A result in marked alterations of
plasma glycan profile. Diabetes. 2013 Apr;62(4):1329-37. doi: 10.2337/db12-0880
4
Tracing Tumour Lineage in Pre-invasive Breast Cancer
Theme: Genetics
Supervisor 1: Elinor Sawyer
Research Division or CAG: Cancer
E-mail: [email protected]
Supervisor 2: Anita Grigoriadis
Research Division or CAG: Cancer
Email: [email protected]
Collaborating Clinician: Professor Sarah Pinder
Research Division or CAG: Cancer
Email: [email protected]
Project description:
The project will focus on understanding tumour progression in ductal and lobular breast cancer.
Invasive ductal cancer (no special type) (IDC) is the most common type of invasive breast cancer and in 60%
of cases is associated with ductal carcinoma in situ (DCIS), a form of non-invasive breast cancer. Similarly
invasive lobular cancer, which accounts for 10-15% of breast cancer, is often associated with lobular
carcinoma in situ (LCIS). Since the introduction of the breast screening programme there has been an increase
in the diagnosis of in situ disease and it is not clear which cases of in situ disease progress to invasive cancer.
The project will use genomics (SNP arrays, exome sequencing and RNA-seq) to look at copy number changes,
somatic mutations and gene expression in different stages of breast cancer (pre-invasive, invasive and
metastatic) in order to identify biomarkers of progression. Global analyses looking at mutation burden, genetic
diversity and clonal structure will also be studied in detail.
Skills training available:
Microdissection and DNA & RNA extraction from archival tumour samples;
Hybridization and analysis of SNP arrays;
Preparation of samples for next generation sequencing (NGS);
Bioinformatic analysis of data.
Objectives for each year:
Year 1: Analysis of SNP arrays and exome sequencing, optimization of exome sequencing in archival material
Year 2: Analysis of NGS and optimization of RNA-seq in archival material;
Year 3: Analysis of RNA-seq;
Year 4: Validation of potential biomarkers of progression in larger sample set.
Two representative publications:
1) Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous
Recombination Deficiency in Triple-Negative Breast Cancers. Watkins J, Weekes D, Shah V,
Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A,
Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis
A, Tutt AN. Cancer Discov. 2015;5:488-505
2) Genetic predisposition to in situ and invasive lobular carcinoma of the breast. Sawyer EJ, Roylance R,
Petridis C, Brook M, Nowinski S Papouli E, Fletcher O, Pinder S, Hanby A, Kohut K, Gorman P,
Caneppele M, Peto J, Dos Santos Silva I, Johnson N, Swann R, Dwek M, Perkins KA, Gillett C,
Houlston R, Ross G, De Ieso P, Southey MC, Hopper JL, Provenzano E, Apicella C, Wesseling J,
Cornelissen S, Keeman R, Fasching PA, Jud SM, Ekici AB, Beckmann MW, Kerin MJ, Marme F,
Schneeweiss A, Sohn C, Burwinkel B, Guénel P, Truong T, Laurent-Puig P, Kerbrat P, Bojesen SE,
5
Nordestgaard BG, Nielsen SF, Flyger H, Milne RL, Perez JI, Menéndez P, Benitez J, Brenner H,
Dieffenbach AK, Arndt V, Stegmaier C, Meindl A, Lichtner P, Schmutzler RK, Lochmann M,
Brauch H, Fischer HP, Ko YD; GENICA Network, Nevanlinna H, Muranen TA, Aittomäki K,
Blomqvist C, Bogdanova NV, Dörk T, Lindblom A, Margolin S, Mannermaa A, Kataja V, Kosma
VM, Hartikainen JM, Chenevix-Trench G, Investigators K, Lambrechts D, Weltens C, Van
Limbergen E, Hatse S, Chang-Claude J, Rudolph A, Seibold P, Flesch-Janys D, Radice P, Peterlongo
P, Bonanni B, Volorio S, Giles GG, Severi G, Baglietto L, McLean CA, Haiman CA, Henderson BE,
Schumacher F, Le Marchand L, Simard J, Goldberg MS, Labrèche F, Dumont M, Kristensen V,
Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Kauppila S, Andrulis IL, Knight JA, Glendon G, Mulligan
AM, Devillee P, Tollenaar RA, Seynaeve CM, Kriege M, Figueroa J, Chanock SJ, Sherman ME,
Hooning MJ, Hollestelle A, van den Ouweland AM, van Deurzen CH, Li J, Czene K, Humphreys K,
Cox A, Cross SS, Reed MW, Shah M, Jakubowska A, Lubinski J, Jaworska-Bieniek K, Durda K,
Swerdlow A, Ashworth A, Orr N, Schoemaker M, Couch FJ, Hallberg E, González-Neira A, Pita G,
Alonso MR, Tessier DC, Vincent D, Bacot F, Bolla MK, Wang Q, Dennis J, Michailidou K, Dunning
AM, Hall P, Easton D, Pharoah P, Schmidt MK, Tomlinson I, Garcia-Closas M. PLoS Genetics
2014:10(4)
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6
Characterisation of how Sam68 regulates CD4 T cell gene expression in the presence and
absence of HIV-1 infection
Theme: Genetics
Supervisor 1: Reiner Schulz
Research Division or CAG: Genetics and Molecular Medicine
E-mail: [email protected]
Website: https://atlas.genetics.kcl.ac.uk/~rschulz/
Supervisor 2: Chad Swanson
Research Division or CAG: Division of Immunology, Infection and Inflammatory Disease
Email: [email protected]
Website:
http://www.kcl.ac.uk/medicine/research/divisions/diiid/departments/infectious/research/swanson/index.asp
x
Collaborating Clinician: Dr Julie Fox
Research Division or CAG: HIV Consultant, Guy’s and St Thomas’ NHS Foundation Trust; Division of
Immunology, Infection and Inflammatory Disease
Email: [email protected]
Website:
http://www.kcl.ac.uk/medicine/research/divisions/diiid/departments/infectious/research/juliefox.aspx
Summary of role: Identify opportunities for clinical translation of the changes in gene expression
Project description:
CD4 T cells orchestrate the immune response to pathogens, eliminate neoplastic growth and mediate immune
regulation. They are also the target for human immunodeficiency virus type 1 (HIV-1). Interestingly, HIV-1
infection reprograms a CD4 T cell by altering the expression and splicing of hundreds of cellular genes, though
the mechanisms by which it does so are unclear. This project will use CD4 T cells as a model system to
understand how changes in gene expression control cellular function.
Sam68 is a RNA binding protein that controls multiple steps of gene expression including transcription,
splicing and translation. It is phosphorylated upon CD4 T cell activation and, while a few of the genes that it
regulates are known, its genome wide targets have not been identified, which is essential to understand how it
regulates CD4 T cell function. Furthermore, Sam68 binds the HIV-1 Rev protein, regulates HIV-1 gene
expression, and is phosphorylated upon HIV-1 infection. However, it is not known how HIV-1 infection alters
Sam68-regulated cellular gene expression and therefore cellular function.
RNA-seq and ribosomal profiling have revolutionized our ability to analyse the abundance, identity and
translation of mRNAs. We are using these techniques to answer two questions:
1. How does Sam68 control transcription, splicing, and translation upon T cell activation?
2. How does HIV-1 infection alter CD4 T cell gene expression and are Sam68-regulated genes affected?
This project will involve both experimental and bioinformatic analyses with the appropriate division between
these activities determined by the student’s interests.
Two representative publications:
1) Goujon C, Moncorgé O, Bauby H, Doyle T, Ward CC, Schaller T, Hué S, Barclay WS, Schulz R and
Malim MH. Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection. Nature.
2013. 502:559-62
2) Swanson, C.M., Sherer, N.M., Malim, M.H. SRp40 and SRp55 promote the translation of unspliced
human immunodeficiency virus type 1 RNA. J Virol. 2010. 84:6748-59
7
Genome wide promoter interactions in endocardial versus endothelial cell differentiation;
implications for heart development
Theme: Genetics
Supervisor 1: Rebecca Oakey
Research Division or CAG: Genetics & Molecular Medicine
E-mail: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/OakeyLab/index.aspx
Supervisor 2: Ajay Shah
Research Division or CAG: Head of Cardiovascular Division
Email: [email protected]
Collaborating Bioinformatician: Reiner Schulz
Research Division or CAG: Genetics & Molecular Medicine
Email: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/OakeyLab/index.aspx
Summary of role: Dr Schulz will provide bioinformatics t raining for the PhD student
Project description:
Epigenetic mechanisms of gene regulation include DNA methylation and histone modifications. The
endocardium, composed of endothelial cells lining the heart, is one of the earliest cardiac populations and is
essential for cardiac development. Understanding the processes that direct endocardial differentiation is
essential for understanding the aetiology of congenital heart disease. We have compared the transcriptome (by
RNA-seq) and the methylome (by BS-seq) of endocardial versus endothelial cells to identify DNA
methylation differences that have been correlated with transcriptional profiles. This project proposal hinges on
the idea that genome organisation influences transcriptional regulation by facilitating interactions between
promoters and distal regulatory elements such as enhancers. Accordingly we will use capture Hi-C (CHi-C) to
assay genome-wide promoter interactions at unprecedented resolution. We will generate CHi-C interaction
libraries for next generation sequencing from our in vitro cultured endocardial and endothelial cells, with
computational and bioinformatics analyses, to integrate findings with our existing genome-wide epigenomic
and transcription datasets. These analyses will offer crucial novel insight into the genes and factors that direct
the cell fate decisions between endocardial and endothelial cells. The delineation of the events that steer
differentiation will provide an understanding of the mechanisms at work in normal heart development and
identify key regulatory factors that when perturbed, result in congenital heart disease. This information will be
used to develop efforts towards therapeutic pluripotent cell-based regenerative strategies.
The student will learn about, molecular biology, next generations sequencing (RO), bioinformatic analysis
(RS), heart development and cell differentiation and congenital cardiac malformations (AS).
Two representative publications:
1) CHiC technique: Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L,
Wingett SW, Andrews S, Grey W, Ewels PA, Herman B, Happe S, Higgs A, LeProust E, Follows
GA, Fraser P, Luscombe NM, Osborne CS. Mapping long-range promoter contacts in human cells
with high-resolution capture Hi-C. Nat Genet. 2015 Jun;47(6):598-606. doi: 10.1038/ng.3286. Epub
2015 May 4. PMID: 25938943
2) Genomics and bioinformatics: Prickett, A.R., 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 Res 2013. 23(10):1624-1635. PMID: 23804403
8
Mutations and mechanisms in cholestatic liver disease
Theme: Genetics
Supervisor 1: Richard Thompson (Clinical Scientist)
Research Division or CAG: Division of Transplantation Immunology and Mucosal Biology
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/richard.j.thompson.html
Supervisor 2: Emer Fitzpatrick (Clinical Scientist)
Research Division or CAG: Division of Transplantation Immunology and Mucosal Biology
Email: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/emer.fitzpatrick.html
Project description:
The project will combine the identification of new disease genes, and the in vitro investigation of the
consequences of mutations in those genes.
We have identified several new causes of liver disease, and have others to find. This component of the work
will involve the identification of suitable patients and samples, and the analysis of whole exome and whole
genome data. Over 500 patients with cholestatic liver disease are available for testing. The feature common to
all is failure of normal bile formation. This work will lead to the identification of new disease genes. Equally
important is the understanding of the mechanisms by which mutations lead to disease. Previously the
investigation of mutations has been through mRNA analysis, Western Blotting, immunohistochemistry and in
vitro expression. Currently in vitro models are being used, including gene knockdown in human hepatocytes
and cell lines. This is being expanded to include the study of hepatocyte-like cells derived from induced
pluripotent cells generated from patients.
During the 12 week attachment the student will analyse whole exome data for new disease causing mutations
and work with a post-doctoral scientist in the study of cells for in vitro studies. They will learn the principles of
next generation sequence analysis, cell culture and the examination of protein distribution in normal and
abnormal cells.
The project will be far reaching. Dr Thompson will bring the genetic expertise, Dr Fitzpatrick that of work
with human hepatocytes. Other work will require assistance from established collaborators within KCL,
London, USA and Canada.
Two representative publications:
1) Missense mutations and single nucleotide polymorphisms in ABCB11 impair BSEP processing and
function or disrupt pre-mRNA splicing. JA Byrne, SS Strautnieks, G Ihrke, F Pagani, AS Knisely, KJ
Linton, G Mieli-Vergani, RJ Thompson. Hepatology 49, 553-567 (2009)
2) Mutations in TJP2 cause progressive cholestatic liver disease. Melissa Sambrotta, Sandra Strautnieks,
Efterpi Papouli, Peter Rushton, Barnaby E. Clark, David A. Parry, Clare V. Logan, Lucy J. Newbury,
Binita M. Kamath, Simon Ling, Tassos Grammatikopoulos, Bart E. Wagner, John C. Magee, Ronald J.
Sokol, Giorgina Mieli-Vergani, University of Washington Center for Mendelian Genomics, Joshua D.
Smith, Colin A. Johnson, Patricia McClean, Michael A. Simpson, A.S. Knisely, Laura N. Bull,
Richard J. Thompson. Nature Genetics 46, 326-328 (2014)
9
Genetic studies to understand the aetiology and pathogenesis of Poland Syndrome and
improve treatment
Theme: Genetics
Supervisor 1: Malcolm Logan
Research Division or CAG: Randall
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/malcolm.logan.html
Supervisor 2 & Collaborating Clinician: Muriel Holder-Espinasse
Research Division or CAG: Clinical Genetics, Guy’s Hospital
Email: [email protected]
Website: http://www.guysandstthomas.nhs.uk/our-services/genetics/overview.aspx
Project description:
Poland syndrome (PS) was first diagnosed and named by clinicians working at Guy's Hospital. The syndrome
presents as unilateral underdevelopment/absence of the pectoralis major muscle with variable degree of
ipsilateral hand anomalies. PS is usually sporadic, but familial cases have been reported with an apparent
autosomal dominant mode of inheritance. PS has been proposed to have a vascular origin, resulting from a
disruption in the blood supply from the subclavian artery, but no detailed studies have been undertaken to
support this conclusion and the aetiology remains unknown. In addition, long-term outcomes have not been
described and treatments are limited.
Work in animal models (chick and mouse) (Supervisor 1) has demonstrated an embryological and genetic link
between forelimb appendicular structures and thoracic elements such as pectoral muscles that provide clues to
the origins of the defects found in PS.
The project aims to explain the aetiology of PS, better define the features of PS and reveal the embryological
mechanisms disrupted in PS toward improving diagnosis and treatment of PS patients.
The work will be designed as follows:
Year 1 and 2: Begin chelating PS patient data and establishing common/diagnostic features. Initiate work
using chick and mouse models to study the events of embryogenesis/genetic mechanisms that have been
disrupted.
Year 3 and 4: Building a patient database and analyse results in combination with initial experimental work.
The project will benefit from external collaborations with clinicians specialising in treating limb abnormalities
at GOSH/RFH who will provide clinical/radiological data and patient samples.
Two representative publications:
1) Hasson, P., Delaurier, A., Bennet, M., Grigorieva, E., Naiche, L.A., Papaioannou, V.E., Mohun T.J.
and Logan, M.P. 2010. Tbx4 and Tbx5 acting in connective tissue are required for limb muscle and
tendon patterning. Developmental Cell 18, 148-156
2) Petit F, Escande F, Jourdain A, Porchet N, Amiel J, Doray B, Delrue M, Flori E, Kim C, Marlin S,
Robertson S, Manouvrier-Hanu S, Holder-Espinasse M. 2013. Nager syndrome: confirmation of
SF3B4 haploinsufficiency as the major cause. Clinic Genet, Epub ahead of print
10
Functional Annotation of Susceptibility loci for SLE in Multiple Ancestries
Theme: Genetics
Supervisor 1: Deborah Cunninghame Graham
Research Division or CAG: Genetics and Molecular Medicine & Immunology, Infection & Inflammatory
Disease
E-mail: [email protected]
Website: http://www.kcl.ac.uk/medicine/research/divisions/gmm/sections/clusters/cdc/vyse/dcgraham.aspx
Supervisor 2: David Morris
Research Division or CAG: Genetics and Molecular Medicine
Email: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/gmm/archive/clusters/cdc/vyse/dmorris.aspx
Collaborating Clinician: Timothy Vyse
Research Division or CAG: Research Division or CAG: Genetics and Molecular Medicine & Immunology,
Infection & Inflammatory Disease
Email: [email protected]
Website: http://www.kcl.ac.uk/medicine/research/divisions/gmm/sections/clusters/cdc/vyse/index.aspx
Project description:
The complex autoimmune disease Systemic Lupus Erythematosus (SLE) has both genetic and environmental
risk factors. Following a meta-analysis of our group’s large genome-wide association study, with two previous
smaller studies, we now have 75 risk loci for lupus in Europeans. We also have access to a large trans-ancestral
ImmunoChip study, split between Europeans, African-Americans (AA) and Hispanic-Americans (HA) and
additional GWAS studies in cohorts of AA and HA samples. The genetic risk-factors for SLE contribute to
diverse molecular pathways in a range of immune cell-types. The aim is to annotate these risk-factors using
bioinformatics tools and then verify the findings for selected loci through laboratory investigation using
immune cells from lupus patients.
In the short rotation/first year, the student will identify the LD regions surrounding each associated variant in
the European GWAS/ImmunoChip datasets. S/he will prioritise these regions based on tissue-specificity, class
of risk variant and expression data, using the major bioinformatics databases, including the Roadmap and
ENCODE resources as well as expression datasets within the laboratory.
In the second year, the student will undertake a meta-analysis of the ImmunoChip/GWAS studies with the
AA and HA ancestries to narrow the association signals shared with European samples and to define ancestryspecific signals. The student will undertake a trans-ancestral targeted sequencing project of the novel loci s/he
identifies.
In the third year the student will select 1-2 loci with cell-type specific expression to identify disease specific
functional differences between purified immune cell-types in lupus cases and controls, using gene expression
analyses and/or Chromatin Immunoprecipitation.
Two representative publications:
1) Aberrant gene regulation in innate and adaptive immunity implicated by genetics in SLE pathogenesis.
Bentham J, Morris, DL, Cunninghame Graham DS, Pinder CL, Tombleson P, Behrens TW, Gaffney
PM, Martín J, Fairfax B, Knight J, Syvänen A-C, Rönnblom, L, Graham RR, Wither JE, Rioux JD,
Alarcón-Riquelme MA, Vyse, TJ (under review, Nature Genetics)
2) Integrative analysis of 111 reference human epigenomes (2015). Roadmap Epigenomics Consortium,
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z,
Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom
RS, Eaton ML, Wu Y-C, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa, C et al. Nature 518,
317–330
11
Targeting autophagy in the treatment of rare and severe forms of psoriasis
Theme: Genetics
Supervisor 1: Francesca Capon
Research Division or CAG: Division of Genetics and Molecular Medicine
E-mail: [email protected]
Website: http://tinyurl.com/CaponLab
Supervisor 2 & Collaborating Clinician: Jonathan Barker
Research Division or CAG: Division of Genetics and Molecular Medicine
Email: [email protected]
Website:
www.kcl.ac.uk/lsm/research/divisions/gmm/departments/dermatology/Research/stru/about/people/barkerjonathan.aspx
Project description:
Pustular psoriasis (PP) is a rare, but potentially life-threatening form of psoriasis that is characterised by
repeated eruptions of painful skin pustules. PP is notoriously difficult to treat, underscoring the need to
elucidate disease processes and identify novel therapeutic targets.
We have recently demonstrated that pustular psoriasis is associated with mutations of the AP1S3 gene. We
have also shown that AP1S3 deficiency disrupts autophagy, a process that has a well-documented antiinflammatory function. The aim of the rotation project is to build on these interesting results to further
investigate the pathogenic consequences of impaired autophagy. This will be achieved by measuring the
induction of key cytokines in AP1S3 knockout cell lines (previously generated by the group) exposed to a
range of inflammatory stimuli. Thus, the student will be trained in cell culture, RNA isolation, cDNA synthesis
and real-time PCR. They will also be taught how to analyse and interpret their data.
In subsequent years, the study will aim to:
Identify further autophagy-related disease genes, through the whole-exome sequencing of carefully selected
patient subsets (Year 1)
Investigate the impact of PP mutations in-vitro, through the characterization of knock-out or knock-in cell
lines, generated by CRISPR-Cas9 genome editing (Year 2)
Determine whether the effect of PP mutations can be reversed ex-vivo, by treating patient keratinocytes with
pharmacological modulators of autophagy (Year 3)
These experiments are expected to elucidate the role of impaired autophagy in the pathogenesis of PP, paving
the way for the development of novel targeted therapeutics.
Two representative publications:
1) Hussain S, Berki DM, Choon SE, Burden AD, Allen MH, Arostegui JI, Chaves A, Duckworth M,
Irvine AD, Mockenhaupt M, Navarini AA, Seyger MMB, Soler-Palacin P, Prins C, Valeyrie-Allanore
L, Vicente MA, Trembath RC, Smith CH, Barker JN, Capon F. IL36RN mutations define a severe
auto-inflammatory phenotype of generalized pustular psoriasis. J Allergy Clin Immunol 2015
135:1067-1070
2) Setta-Kaffetzi N, Simpson MA, Navarini AA, Patel VP, Lu HC, Allen MH, Duckworth M,Bachelez
H, Burden AD, Choon SE, Griifths CEM, Kirby B, Kolios A, Seyger MMB, Prins C, Smahi A,
Trembath RC, Fraternali F, Smith CH, Barker JN, Capon F. AP1S3 mutations are associated with
pustular psoriasis and impaired Toll-like receptor 3 trafficking. Am J Hum Genet, 2014 94:790-7
12
Understanding the role of non-coding RNAs in the aetiology and pathogenesis of
inflammatory bowel disease
Theme: Genetics
Supervisor 1: Dr Natalie Prescott
Research Division or CAG: Genetics and Molecular Medicine
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/natalie.prescott.html
Supervisor 2: Professor Christopher Mathew
Research Division or CAG: Genetics and Molecular Medicine
Email: [email protected]
Website:
http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/MathewLab/index.as
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Collaborating Clinician: Dr Nicholas Powell
Research Division or CAG: Liver, Renal, Urology, Transplant, Gastro/Gastro Intestinal Surgery Clinical
Academic Group
Email: [email protected]
Summary of role: Provide access to patients for sample procurement, interpret clinical phenotype data, advise
on immunological aspects of IBD and deliver training in immunological assays.
Project description:
Crohn’s disease and ulcerative colitis are two forms of inflammatory bowel disease (IBD) in which both genes
and environment contribute to development of symptoms. Many common DNA sequence variants have been
shown to increase risk for IBD but only a very small proportion lie within protein coding genes. We expect the
remaining variants are most-likely to influence regulation of gene expression directly or via epigenetic
mechanisms such as non-coding regulatory RNAs. MicroRNAs are small non-coding RNAs which act as posttranscriptional regulators of gene expression and a number of examples of these have now been implicated in
key mechanisms involved in the pathogenesis of IBD.
We will use next generation sequencing (NGS) to profile cell-type specific miRNAs using total RNA isolated
from separated immune cells from blood and intestinal biopsy samples collected from our extensive cohort of
IBD patients and controls. We will look for tissue specific differential expression of miRNAs between
individuals with different risk genotypes at key IBD-associated loci. We will validate key miRNAs using
qPCR and follow up with cell-based techniques on immune-cell subsets.
We will provide training in laboratory-based genetic and genomic techniques, including; NGS, and gene
expression analysis, bioinformatics, separation and characterization of cells from patient samples and functional
immunological assays.
Year 1 and 2 will involve generation and analysis of small RNA sequencing data. In year 2 will involve
validation and replication of key findings and in year 3 functional immunoassays will be completed and models
developed to link aberrant miRNA expression to pathogenesis.
Two representative publications:
1) Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, et al, Host-microbe interactions have
shaped the genetic architecture of inflammatory bowel disease (2012) Nature 491: 119-24
2) MicroRNAs: new players in IBD (2014) Gut 64:504-51
13
Transcriptional regulation of lung cancer metastasis
Theme: Genetics
Supervisor 1: Fiona Wardle
Research Division or CAG: Randall Division of Cell & Molecular Biophysics
E-mail: [email protected]
Website: http://www.kcl.ac.uk/biohealth/research/divisions/randall/sections/signalling/wardle/index.aspx
Supervisor 2 & Collaborating Clinician: George Santis
Research Division or CAG: Asthma, Allergy and Lung Biology
Email: [email protected]
Website: http://www.kcl.ac.uk/medicine/research/divisions/aalb/about/people/profiles/santisg.aspx
Project description:
Lung cancer is the second most common cancer in the UK, with over 40,000 people being diagnosed each
year. Although, if diagnosed and treated at early stages before the cancer becomes metastatic, 5 year survival
rates can be up to 80%, if diagnosed at stage 4 (metastatic) 5 year survival rates are less than 10%.
T/Brachyury plays a central role in regulating the normal migration of cells during early vertebrate
embryogenesis, and interestingly Brachyury has recently been implicated in metastasis of several cancers,
including non small cell lung cancer [e.g. 1]. This project aims to test the hypothesis that Brachyury regulates
cell migration genes in lung cancer and aims to identify these target genes in order to discover new therapeutic
targets. This will be achieved through analysis of gene expression by RNA-seq in lung cancer lines knocked
down for Brachyury combined with chromatin immunoprecipitation (ChIP) for Brachyury [e.g. 2] to identify
potential downstream targets. Targets will then be analysed in primary lung cancer samples and the regulation
and activity of targets determined through promoter analysis and knockdown or overexpression in cell lines.
Figure depicting ChIP experimental and analysis pipeline. Two representative publications:
1) Fernando, R.I., et al., 2010. The T-box transcription factor Brachyury promotes epithelialmesenchymal transition in human tumor cells. J Clin Invest, 120: 533-44
2) Nelson, A.C., et al. 2012. A gene regulatory network directed by T, brachyury gives insight into the
pathogenesis of chordoma. J Pathol, 228, 274-85
14
External ear defects in mice and men
Theme: Genetics
Supervisor 1: Dr Abigail Tucker
Research Division or CAG: Dentistry and Oral Science
E-mail: [email protected]
Website: http://rg.kcl.ac.uk/staffprofiles/staffprofile.php?pid=370
Supervisor 2 & Collaborating Clinician: Mr Dan Jiang PhD FRCSI(Otol) FRCS(ORL-HNS)
Research Division or CAG: Otolaryngology, Guys and St Thomas’s Hospital
Email: [email protected], [email protected]
Website: http://www.guysandstthomas.nhs.uk/our-services/consultant-profiles/audiology/dan-jiang.aspx
Project description:
Defects in the external ear can affect the ear canal, or the auricle, or both. The ear canal can be missing
(atresia) or narrow (stenosis). In cases of atresia (1 in 10,000-15,000 births) canal reconstruction is sometimes
attempted (atresiaplasty), or the external ear is bypassed by a bone-anchored hearing aid (BAHA). We are
interested in how the ear canal forms during normal development and what goes wrong in cases of atresia. We
aim to study the development of the external ear taking advantage of mouse mutants with external ear defects.
In addition we aim to study external ear defects in patients from the Ear Clinic at St Thomas’ Hospital. The
project is a collaboration between an expert in ear development and conductive hearing loss in mice (Dr
Tucker) and a clinical expert specialising in ear surgery (Prof Jiang).
Aim 1: To investigate the normal process of ear canal and pinna formation during mouse embryonic
development.
Aim 2: To understand the mechanisms behind ear defects using mouse models of human syndromes associated
with external ear defects. These will include 22q11.2 deletion syndrome (Tbx1 mice), Branchio-oto-renal
syndrome (Eya1 mice), LADD syndrome (Fgf10 mice).
Aim 3: To analyse CT scans from patients with external ear defects to correlate the findings from the mouse in
humans.
Skills training: The student will be trained in a range of molecular biology techniques and anatomy, while
having access to clinical data. In addition critical thinking, presentation and writing skills will be taught.
Two representative publications:
1) Thompson, H. Tucker, A.S. (2013). Dual origin of the epithelium of the middle ear. Science 339,
1453-1456
2) 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
15
Identification and validation of driver genes in oesophageal adenocarcinoma
Theme: Genetics
Supervisor 1: Dr Francesca Ciccarelli (Reader in Cancer Genomics, basic scientist)
Research Division or CAG: Cancer Studies
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/francesca.ciccarelli.html
Supervisor 2 & Collaborating Clinician: Professor Jesper Lagergren (academic consultant surgeon)
Research Division or CAG: Cancer Studies
Email: [email protected]
Website: www.kcl.ac.uk/lsm/research/divisions/cancer/research/sections/gastro/index.aspx
Project description:
Oesophageal adenocarcinoma (OAC) is characterised by poor prognosis and rapidly increasing incidence, with
the highest incidence globally in the UK. This project aims to analyse whole genome sequence (WGS) data of
several hundred OACs to predict mutated genes that drive or co-drive cancer development. Predicted drivers
will be experimentally validated using a combination of cell-based and tissue-based assays.
WGS data derive from OCCAMS, a network of 20 clinical UK centres recruiting OAC patients for tissue and
data collection with the aim to identify clinical, demographic and molecular factors affecting disease
progression. St Thomas’ Hospital is a key centre in OCCAMS under the supervision of Prof. Lagergren. This
provides unique opportunities to test predicted driver genes on OAC samples where they are found altered. It
also allows relating genomics findings with clinical factors.
In year one, the student will primarily learn computational biology techniques, mainly for analysis of next
generation sequencing data (alignment, quality control, variant calling and annotation).
In year two, the student will apply the computational approach developed in Ciccarelli’s group
(D’antonio&Ciccarelli Genome Biol 2013) to predict sample-specific cancer drivers in OAC.
In year three, the student will validate predicted drivers by perturbing the genes and measuring the effect of
this perturbation on cell growth. Gene perturbation will be performed through gene editing, RNA interference
and gene overexpression, depending on whether the gene is predicted to have oncogenic or tumour suppressor
activity. The student will also verify abnormal staining and overexpression of the mutated proteins in cancer
tissue blocks.
Two representative publications:
1) D’antonio M, Ciccarelli FD Integrated analysis of recurrent properties of cancer genes to identify novel
drivers 2013, Genome Biology 14:R52 (Highly accessed)
2) Lagergren J, Lagergren P Recent developments in esophageal adenocarcinoma. CA Cancer J Clin.
2013;63(4):232-48. (Journal Impact Factor 162.5)
16
Discovery of Mutated Driver Pathways in Primary Cutaneous T-cell lymphoma
Theme: Genetics
Supervisor 1: Dr Tracey Mitchell
Research Division or CAG: Genetics and Molecular Medicine
E-mail: [email protected]
Website:
https://www.kcl.ac.uk/medicine/research/divisions/gmm/departments/dermatology/Groups/WhittakerLab/
index.aspx
Supervisor 2 & Collaborating Clinician: Professor Sean Whittaker
Research Division or CAG: Genetics and Molecular Medicine/GRIDA
Email: [email protected]
Website:
https://www.kcl.ac.uk/medicine/research/divisions/gmm/departments/dermatology/Groups/WhittakerLab/
index.aspx
Project description:
All cancers are characterised by the presence of somatic mutations in their genomes. Mutations that confer a
clonal selective advantage on cancer cells and are causally implicated in oncogenesis are known as ‘driver’
mutations. The focus of our research and clinical units is primary cutaneous T-Cell lymphoma (CTCL), a
heterogeneous malignancy of mature memory type, skin homing T-cells. The primary goal of our laboratory is
to identify the driver gene mutations and pathways involved in the initiation and progression of CTCL. To
achieve this we have used next generation sequencing to sequence whole exomes of CTCL cells, which has
identified a panel of genes carrying novel mutations involved in key process in oncogenesis including: T-cell
signalling; cell survival; regulation of cell death and DNA damage repair pathways. Consistent with studies of
other cancers, our data shows that each individual tumour harbours several driver gene mutations. For the
rotation project we will select a group of candidate genes based on their function and start to identify what
pathways, mutations in these genes affect. The work will utilise our large tissue bank of primary tumour cells
and use fundamental techniques in molecular genetics including PCR, cell culture and gene silencing. The
project will form the basis of a thesis to identify how driver gene mutations affect common pathways and to
look at how affected pathways co-occur and cooperate in the pathogenesis of CTCL (years 1/2). In year 3,
specific pathways will be screened against small molecule libraries to identify potential therapeutic targets.
Two representative publications:
1) Jones CL, Ferreira S, McKenzie RC, Tosi I, Caesar JA, Bagot M, Whittaker SJ, Mitchell TJ.
Regulation of T-Plastin Expression by Promoter Hypomethylation in Primary Cutaneous T-Cell
Lymphoma. J Invest Dermatol. 2012 Aug;132(8):2042-9
2) Agar NS, Wedgeworth E, Crichton S, Mitchell TJ, Cox M, Ferreira S, Robson A,Calonje E, Stefanato
CM, Wain EM, Wilkins B, Fields PA, Dean A, Webb K,Scarisbrick J, Morris S, Whittaker SJ.
Survival outcomes and prognostic factors in mycosis fungoides/Sézary syndrome: validation of the
revised International Society for Cutaneous Lymphomas/European Organisation for Research and
Treatment of Cancer staging proposal. J Clin Oncol. 2010 Nov 1;28(31):4730-9
17
Genome-wide and epigenetic screen in drug metabolising (ADME) genes in twins
Theme: Genetics
Supervisor 1 & Collaborating Clinician: Dr. Mariam Molokhia
Research Division or CAG: HSCR/Medicine CAG
E-mail: [email protected]
Website: https://kclpure.kcl.ac.uk/portal/mariam.molokhia.html
Supervisor 2: Dr. Jordana Bell
Research Division or CAG: GMM
Email: [email protected]
Website: http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/twin/research/bell/index.aspx
Project description:
Scientific basis: This proposal will examine a genome-wide screen of relevant gene expression and DNA
methylation quantitative trait loci (eQTL and meQTL) across multiple tissues in drug metabolising ADME
(absorption, distribution, metabolism, and excretion) genes in the TwinsUK cohort. We will use genetic
analysis to detect relationships between genetic polymorphisms, epigenetic and gene expression, adjusting for
confounders, focusing on enrichment of signals at ADME genes. Heritability of metabolic signatures,
associated with genetic variation in ADME will also be explored. TwinsUK is the biggest UK adult twin
registry (12,000) to study genetic and environmental aetiology of age related complex traits, drug metabolism
and diseases.
Skills training
1. Translational pharmacogenetics
Study design overview: Translational pharmacogenetics; large datasets; data resources & methods for handling
bias and confounding - including analytical models; GWAS; eQTL; meQTL; meta-analysis; evidence
synthesis.
2. Use and application of epigenetics
How epigenetic change (heritable changes in gene expression) can affect phenotype via DNA methylation,
histone modification and micro regulation (miRNA) processes. Explore role of factors such as age, environment
and disease on epigenetic and gene expression profiles at ADME genes CYP3A4/CYP1A2/CYP1B1/MDR.
Objectives
Yr 1: Explore GWAS for eQTL and meQTL in major drug metabolising (ADME) genes focusing on targeted
analyses of specific genes, e.g. genes affecting drug metabolism through renal and hepatic pathways.
Yr 2: Determine heritability and genetic basis (mQTLs) of metabolomics profiles in ADME genes.
Yr 3: Examine links across genetic, epigenetic, expression, and metabolomic signatures at identified ADME
QTLs across multiple layers of omic data.
Two representative publications:
1) Epigenetics of discordant monozygotic twins: implications for disease. Castillo-Fernandez, J.
E., Spector, T. D. & Bell, J. T. 31 Jul 2014 In : Genome medicine. 6, 7, 60
2) Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs
Thomas J. Urban, Yufeng Shen, Andrew Stolz, Naga Chalasan, Robert J. Fontana, James Rochon,
Dongliang Ge, Kevin V. Shianna, Ann K. Daly, M. Isabel Lucena, Matthew R. Nelson, Mariam
Molokhia, Guruprasad P. Aithal, Aris Floratos, Itsik Pe’er, Jose Serrano, Herbert Bonkovsky, Timothy
J. Davern, William M. Lee, Victor J. Navarro, Jayant A. Talwalkar, David B. Goldstein, Paul B.
Watkins , on behalf of the Drug Induced Liver Injury Network, EUDRAGENE and the International
Serious Adverse Events Consortium. Pharmacogenet Genomics. 2012 Nov;22(11):784-95. doi:
10.1097/FPC.0b013e3283589a76
18