Introduction
 In recent years, RNA interference (RNAi) has become an increasingly powerful research tool, and the introduction of small interfering (si)RNA screening libraries, targeted at the genomes of different species, has allowed real insight into previously unknown interactions.
The principal interests of the RNAi Screening Facility at the Beatson Institute are twofold. We aim to facilitate the translation of existing cancer research into cancer treatments, and to enhance the efficacy of existing cancer drugs, potentially through a combinatorial therapeutic approach.
Coupling screening of our human and mouse whole genome siRNA libraries with High Content Imaging, we aim to identify novel interactions, pathways and mechanisms in specific types of carcinoma. Our current portfolio includes a number of synthetic lethality approaches to targeting cancer.
The state-of-the-art laboratory is comprised of liquid handling robotics and readers and an Operetta High Content Imaging System (Perkin Elmer), to bring accuracy, precision and speed to the screening process.
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Lab Report
Key Publications
Shanks EJ, Ong HB, Robinson DA, Thompson S, Sienkiewicz N, Fairlamb AH, Frearson JA (2010). Development and validation of a cytochrome c-coupled assay for pteridine reductase 1 and dihydrofolate reductase. Analytical Biochemistry 396, 194–203.
Biography
Education and qualifications
2004: PhD, Molecular Biology, University of Dundee
2000: BSc (Hons), Neuroscience, University of Sussex
Appointments
2011-present: Head of Screening, Beatson Institute for Cancer Research
2005-2010: Postdoctoral Screening Scientist, DDU, University of Dundee
Recent Publications
Spinks D, Ong HB, Mpamhanga CP, Shanks EJ, Robinson DA, Collie IT, Read KD, Frearson JA, Wyatt PG, Brenk R, Fairlamb AH, Gilbert IH (2010). Design, Synthesis and Biological Evaluation of Novel Inhibitors of Trypanosoma brucei Pterine Reductase 1. ChemMedChem 6, 302-8.
Shanks EJ, Ong HB, Robinson DA, Thompson S, Sienkiewicz N, Fairlamb AH, Frearson JA (2010). Development and validation of a cytochrome c-coupled assay for pteridine reductase 1 and dihydrofolate reductase. Analytical Biochemistry 396, 194–203.
Spinks D, Shanks EJ, Cleghorn LAT, McElroy S, Jones D, James D, Fairlamb AH, Frearson JA, Wyatt PG, Gilbert IH (2009). Investigation of Trypanothione Reductase as a Drug Target in Trypanosoma brucei. ChemMedChem 4, 2060-9.
Patterson S, Jones DC, Shanks EJ, Frearson JA, Gilbert IH, Wyatt PG, Fairlamb AH (2009). Synthesis and Evaluation of 1-(1-(Benzo[b]thiophen-2-yl)cyclohexyl)piperidine (BTCP) Analogues as Inhibitors of Trypanothione Reductase. ChemMedChem 4, 1341-53.
Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E, Santoyo-Lopez J, Dunican DJ, Long A, Kelleher D, Smith Q, Beijersbergen RL, Ghazal P, Shamu CE (2009). Statistical methods for analysis of high-throughput RNA interference screens. Nature Methods 6, 569-75.
Mpamhanga CP, Spinks D, Tulloch LB, Shanks EJ, Robinson DA, Collie IT, Fairlamb AH, Wyatt PG, Frearson JA, Hunter WN, Gilbert IH, Brenk R (2009). One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening. J Med Chem. 52, 4454-65.
Lab Members
Senior Scientific Officer: Lynn McGarry
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Introduction
 During the development of cancer, cells frequently lose attributes of their tissue of origin and acquire some of the characteristics of stem cells, a process termed anaplasia. The aim of the research in our lab is to use stem cells to model the processes underlying cancer and to uncover the roles that novel stem cell and reprogramming factors play in the development of the disease. Using embryonic stem (ES) cells we are developing and improving models of human cancer. The targeted genetic modification of such cells allows us to study genes involved in cancer in fine detail so as to better understand their normal function and how these functions are compromised during the development of cancer.
Once modified ES cell lines are established, not only can gene function be analysed in the stem cells themselves but these cells can be differentiated into a wide variety of different cell types to allow the study of basic disease mechanisms in different tissues and potentially to establish screens for drug discovery.
In addition, it is possible to reverse the differentiation process and reprogramme a variety of somatic cells to induced pluripotential stem (iPS) cells. This process is reminiscent of anaplasia, the loss of differentiation seen in cancer. Genes crucial for this type of reprogramming are often involved in cancer development.
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Lab Report
 Scientific Report 2010 Strathdee
Key Publications
Strathdee D, Whitelaw CB, Clark AJ (2008). Distal transgene insertion affects CpG island maintenance during differentiation. J Biol Chem. 283, 11509-15.
Strathdee D, Ibbotson H, Grant SG (2006). Expression of transgenes targeted to the Gt(ROSA)26Sor locus is orientation dependent. PLoS One 1, e4.
Brown K, Strathdee D, Bryson S, Lambie W, Balmain A (1998). The malignant capacity of skin tumours induced by expression of a mutant H-ras transgene depends on the cell type targeted. Curr Biol. 8, 516-24.
Biography
Education and qualifications
1995: PhD, University of Glasgow, Supervisor Allan Balmain
1989: BSc, Immunology (Honours), University of Glasgow
Appointments
2009-present: Head of Transgenic Technology, Beatson Institute for Cancer Research
2004-2009: Senior Research Associate, Wellcome Trust Sanger Institute
2000-2004: Postdoctoral Fellow, University of Edinburgh
1996-2000: Research Scientist, Roslin Institute
Recent Publications
Feyder M, Karlsson RM, Mathur P, Lyman M, Bock R, Momenan R, Munasinghe J, Scattoni ML, Ihne J, Camp M, et al. (2010). Association of mouse Dlg4 (PSD-95) gene deletion and human DLG4 gene variation with phenotypes relevant to autism spectrum disorders and Williams' syndrome. Am J Psychiatry 167, 1508-17.
Strathdee D, Whitelaw CB, Clark AJ (2008). Distal transgene insertion affects CpG island maintenance during differentiation. J Biol Chem. 283, 11509-15.
Strathdee D, Ibbotson H, Grant SG (2006). Expression of transgenes targeted to the Gt(ROSA)26Sor locus is orientation dependent. PLoS One 1, e4.
Komiyama NH, Watabe AM, Carlisle HJ, Porter K, Charlesworth P, Monti J, Strathdee DJ, O'Carroll CM, Martin SJ, Morris RG, et al. (2002). SynGAP regulates ERK/MAPK signaling, synaptic plasticity, and learning in the complex with postsynaptic density 95 and NMDA receptor. J Neurosci. 22, 9721-32.
Lab Members
Scientific Officers: Laurence Cadalbert, Farah Naz Ghaffar
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Introduction
 The Transgenic Models Lab develops and utilises sophisticated genetic models that recapitulate human cancer. Using models of intestinal cancer, pancreatic cancer, breast cancer and melanoma we can better understand how cancer cells behave and metastasise, and develop biologically relevant systems for testing novel therapeutic agents.
One of the genes our lab is particularly interested in is RUNX2, which belongs to the family of RUNX genes. These genes are essential regulators in mammalian development, most notably for bone and blood cell lineages. Like many genes important for normal development, the RUNX genes are linked to human cancer, but interestingly have been found to both promote and suppress tumour formation, a paradox we are exploring. Studies suggest that expression of RUNX2 correlates with metastatic breast and prostate cancer and we are investigating how this gene might confer these properties in cancer cells.
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Lab Report
Scientific Report 2010 Blyth
Key Publications
Kilbey A, Blyth K, Wotton S, Terry A, Jenkins A, Bell M, Hanlon L, Cameron ER, Neil JC (2007). Runx2 disruption promotes immortalization and confers resistance to oncogene-induced senescence in primary murine fibroblasts. Cancer Res. 67, 11263-71.
Blyth K, Vaillant F, Hanlon L, Mackay N, Bell M, Jenkins A, Neil JC, Cameron ER (2006). Runx2 and MYC collaborate in lymphoma development by suppressing apoptotic and growth arrest pathways in vivo. Cancer Res. 66, 2195-201.
Blyth K, Cameron ER, Neil JC (2005). The RUNX genes: gain or loss of function in cancer. Nat Rev Cancer 5, 376-87.
Vaillant F, Blyth K, Andrew L, Neil JC, Cameron ER (2002). Enforced expression of Runx2 perturbs T-cell development at a stage coincident with beta-selection. J Immunol. 169, 2866-74.
Blyth K, Terry A, Mackay N, Vaillant F, Bell M, Cameron ER, Neil JC, Stewart M (2001). Runx2: a novel oncogenic effector revealed by in vivo complementation and retroviral tagging. Oncogene 20, 295-302.
Stewart M, Terry A, Hu M, O’Hara M, Blyth K, Baxter E, Cameron E, Onions DE, Neil JC (1997). Proviral insertions induce the expression of bone-specific isoforms of PEBP2alphaA (CBFA1): evidence for a new myc collaborating oncogene. Proc Natl Acad Sci USA 94, 8646-51.
Biography
Education and qualifications
1997: PhD, University of Glasgow, Supervisors Ewan Cameron & Moyra Campbell
1991: BSc, Biochemistry (Honours), University of Glasgow
Appointments
2009-present: Head of Transgenic Models, Beatson Institute for Cancer Research
2009-present: Honorary Senior Lecturer, University of Glasgow
1997-2008: Postdoctoral Fellow, Molecular Oncology Lab, University of Glasgow
1991-1996: Research Assistant, University of Glasgow
Recent Publications
Blyth K, Vaillant F, Jenkins A, McDonald L, Pringle MA, Huser C, Stein T, Neil J, Cameron ER (2010). Runx2 in normal tissues and cancer cells: A developing story. Blood Cells Mol Dis. 45, 117-23.
Woodcock SA, Rushton HJ, Castaneda-Saucedo E, Myant K, White GR, Blyth K, Sansom OJ, Malliri A (2010). Tiam1-Rac signalling counteracts Eg5 during bipolar spindle assembly to facilitate chromosome congression. Curr Biol. 20, 669-75.
Blyth K, Slater N, Hanlon L, Bell M, Mackay N, Stewart M, Neil JC, Cameron ER (2009). Runx1 promotes B-cell survival and lymphoma development. Blood Cells Mol Dis. 43, 12-9.
Scobie L, Hector RD, Grant L, Bell M, Nielsen AA, Meikle S, Philbey A, Thrasher AJ, Cameron ER, Blyth K, Neil JC (2009). A novel model of SCID-X1 reconstitution reveals predisposition to retrovirus-induced lymphoma but no evidence of gammaC gene oncogenicity. Mol Ther. 17, 1031-8.
Kilbey A, Blyth K, Wotton S, Terry A, Jenkins A, Bell M, Hanlon L, Cameron ER, Neil JC (2007). Runx2 disruption promotes immortalization and confers resistance to oncogene-induced senescence in primary murine fibroblasts. Cancer Res. 67, 11263-71.
Stewart M, Mackay N, Hanlon L, Blyth K, Scobie L, Cameron E, Neil JC (2007). Insertional mutagenesis reveals progression genes and checkpoints in MYC/Runx2 lymphomas. Cancer Res. 67, 5126-33.
Blyth K, Vaillant F, Hanlon L, Mackay N, Bell M, Jenkins A, Neil JC, Cameron ER (2006). Runx2 and MYC collaborate in lymphoma development by suppressing apoptotic and growth arrest pathways in vivo. Cancer Res. 66, 2195-201.
Thrasher AJ, Gaspar HB, Baum C, Modlich U, Schambach A, Candotti F, Otsu M, Sorrentino B, Scobie L, Cameron E, Blyth K, Neil J, Abina SH, Cavazzana-Calco M, Fischer A (2006). Gene Therapy: X-SCID transgene leukaemogenicity. Nature 443, E5-6.
Blyth K, Cameron ER, Neil JC (2005). The RUNX genes: gain or loss of function in cancer. Nat Rev Cancer 5, 376-87.
Lab Members
Post-doc: Laura McDonald
Scientific Officers: Dimitris Athineos, Susan Mason
PhD Student: Nicola Ferrari
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Introduction
 The study of changes in the cellular protein content is called proteomics. In diseases such as cancer, diabetes or cardiovascular disease, the expression of proteins or their post-translational modification (PTM) can lead to changes in the activity of proteins and enzymes. These activity changes can be markers of a particular disease and quantifying them by proteomic technologies is a major challenge. In my group, we are particularly interested in changes in PTMs such as phosphorylation. Protein phosphorylation is regulated in human cells by some five hundred protein kinases (enzymes that add phosphate to serine, threonine or tyrosine residues) and over one hundred protein phosphatases (enzymes that remove phosphate from serine, threonine or tyrosine residues). This PTM is highly dynamic and to quantify the changes at individual phosphorylation sites we use quantitative proteomics methods using high mass accuracy mass spectrometers.
If protein expression or protein PTMs are modulated this can lead to changes in enzyme activity. This in turn can lead to changes in metabolites in the cell, such as those involved in glycolysis, gluconogenesis or lipolysis. Quantitative mass spectrometry can again be used to measure these changes and this technique is called metabonomics. We are in the process of setting up mass spectrometry systems to analyse the metabolites from cancer biopsies as well as mouse models of cancer. With these techniques in place we should be able to gain an insight into the metabolic changes in cancer cells compared to healthy cells and then monitor the impact of anti-cancer drugs on the metabolome of cancer cells.
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Lab Report
Scientific Report 2010 Morrice
Key Publications
Yan L, Mieulet V, Burgess D, Findlay GM, Sully K, Procter J, Goris J,
Janssens V, Morrice NA, Lamb RF (2010). PP2A T61 epsilon is an
inhibitor of MAP4K3 in nutrient signaling to mTOR. Mol Cell 37, 633-42.
von Kriegsheim A, Baiocchi D, Birtwistle M, Sumpton D, Bienvenut W,
Morrice N, Yamada K, Lamond A, Kalna G, Orton R, Gilbert D, Kolch W
(2009). Cell fate decisions are specified by the dynamic ERK
interactome. Nat Cell Biol. 11, 1458-64.
Dubois F, Vandermoere F, Gernez A, Murphy J, Toth R, Chen S, Geraghty
KM, Morrice NA, MacKintosh C (2009). Differential 14-3-3 affinity
capture reveals new downstream targets of phosphatidylinositol 3-kinase
signalling. Mol Cell Proteomics 8, 2487-99.
Trinkle-Mulcahy L, Boulon S, Lam YW, Urcia R, Boisvert FM, Vandermoere
F, Morrice NA, Swift S, Rothbauer U, Leonhardt H, Lamond A (2008).
Identifying specific protein interaction partners using quantitative
mass spectrometry and bead proteomes.
J Cell Biol. 183, 223-39.
Elderkin S, Maertens GN, Endoh M, Mallery DL, Morrice N, Koseki H,
Peters G, Brockdorff N, Hiom K (2007). A phosphorylated form of Mel-18
targets the Ring1B histone H2A ubiquitin ligase to chromatin. Mol Cell
28, 107-20.
Williamson BL, Marchese J, Morrice N (2006). Automated Identification and Quantification of Protein Phosphorylation Sites by LC/MS on a Hybrid Triple Quadrupole Linear Ion Trap Mass Spectrometer. Mol Cell Proteomics 5, 337-46.
Biography
Education and qualifications
1987: PhD, University of London, Supervisor Alastair Aitken
1983: MSc in Analytical Chemistry, University of Bristol
1982: BSc, Chemistry (Second Class Honours), University of Bristol
Appointments
2010-present: Head of Proteomics, Beatson Institute for Cancer Research
2002-2010: Group Leader and Head of Proteomics, MRCPPU, University of Dundee
1994-2002: Senior Support Scientist, MRCPPU, University of Dundee
1987-1994: Postdoctoral Research Assistant, La Trobe University and Melbourne University, Australia
Recent Publications
Yan L, Mieulet V, Burgess D, Findlay GM, Sully K, Procter J, Goris J, Janssens V, Morrice NA, Lamb RF (2010). PP2A T61 epsilon is an inhibitor of MAP4K3 in nutrient signaling to mTOR. Mol Cell 37, 633-42.
Blomster HA, Imanishi SY, Siimes J, Kastu J, Morrice NA, Eriksson JE, Sistonen L (2010). In vivo identification of sumoylation sites by a signature tag and cysteine-targeted affinity purification. J Biol Chem. 285, 19324-9.
Nichols RJ, Dzamko N, Morrice NA, Campbell DG, Deak M, Ordureau A, Macartney T, Tong Y, Shen J, Prescott AR, Alessi DR (2010). 14-3-3 binding to LRRK2 is disrupted by multiple Parkinson's disease-associated mutations and regulates cytoplasmic localization. Biochem J. 430, 393-404.
Martin DM, Nett IR, Vandermoere F, Barber JD, Morrice NA, Ferguson MA (2010). Prophossi: automating expert validation of phosphopeptide-spectrum matches from tandem mass spectrometry. Bioinformatics 26, 2153-9.
Pozo-Guisado E, Campbell DG, Deak M, Alvarez-Barrientos A, Morrice NA, Alvarez IS, Alessi DR, Martín-Romero FJ (2010). Phosphorylation of STIM1 at ERK1/2 target sites modulates store-operated calcium entry. J Cell Sci. 123, 3084-93.
Peirce MJ, Brook M, Morrice N, Snelgrove R, Begum S, Lanfrancotti A, Notley C, Hussell T, Cope AP, Wait R (2010). Themis2/ICB1 is a signaling scaffold that selectively regulates macrophage Toll-like receptor signaling and cytokine production. PLoS One 5, e11465.
Dunne A, Carpenter S, Brikos C, Gray P, Strelow A, Wesche H, Morrice N, O'Neill LA (2010). IRAK1 and IRAK4 promote phosphorylation, ubiquitination, and degradation of MyD88 adaptor-like (Mal). J Biol Chem. 285, 18276-82.
Lewis AE, Sommer L, Arntzen MO, Strahm Y, Morrice NA, Divecha N, D'Santos CS (2010). Identification of nuclear phosphatidylinositol 4,5-bisphosphate-interacting proteins by neomycin extraction. Mol Cell Proteomics, in press.
Lab Members
Scientific Officers: Sergio Lilla, David Sumpton
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At the Beatson Institute, we are fortunate in being supported not only
by outstanding core services but also in having access to the advanced
technologies required for cutting edge science.
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 The Beatson Advanced Imaging Resource provides a full range of support from basic imaging to the development of advanced applications. We specialise in live cell imaging and mouse in vivo imaging, using a variety of techniques including photo-activation and photo-bleaching, FLIM and FRET.
Access
- Priority given to Beatson users, followed by University of Glasgow
- Outside access primarily on a collaborative basis
Expertise
- Live cell imaging, including time and frequency domain FLIM, TIRF, photo-activation, photo-bleaching and photo-conversion
- Mouse in vivo imaging, including collagen SHG and use of photo-activation and photo-bleaching, FLIM and FRET
Confocal MicroscopyOlympus FV1000 (x2)
Nikon A1R
Leica TCS SP2
Zeiss LSM 710 |
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Live CellCustom TIRF
Olympus / Volocity deconvolution system
Micro-injection
Medium Throughput Long Term Time Lapse (x4)
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FLIMLaVision Bio-Tec TRIM scope
Lambert Instruments custom Spinning Disk
Lambert Instruments custom TIRF
Leica TCS SP2 with Becker & Hickle TCSPC 730 |
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OtherOlympus OV100
Leica AF6000 micro-dissection
FacsAria
Upright stands for histology and immunofluorescence (x4)
Off-line image analysis (x8)
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The last few years have seen a huge rise in the range of fields that require computational analysis or bioinformatics. In order to to properly manage and process large datasets, the Institute is currently building a team of four or five informaticists with complementary skills that will be overseen by an informatics committee.
The focus of skills for each of these individuals will be:
- Microarrays and relatives such as high throughput screening;
- Mass spectrometry – including installation and maintenance of user tools, and automated data extraction and data mining;
- Computational modelling; and
- Image analysis of microscope and screening data.
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 The Proteomics and Mass Spectrometry service has a new laboratory on level 2 housing three new LC-MS systems (LTQ orbitrap velos and Exactive) for proteomic and metabolomic analyses. In March 2011, we took delivery of the first 5600 tripleTOF mass spectrometer installed in a UK research laboratory and this system will provide a state-of-the-art platform for quantitative proteomics (SILAC, iTRAQ, label-free) and metabolomics.
The facility’s activities also include the training of users in
bi-dimensional gel separation of proteins using the Ettan IPGphor and
DALT systems from GE Healthcare as well as DiGE™ quantitation
techniques. Visualisation of fluorescence is performed using the
TYPHOON fluorescent imager. Image treatment to quantify differential
protein expression is done using DeCyder™ software.
Data processing after acquisition on the mass spectrometer requires
extensive computer-based treatment. A dedicated informatician manages
the on-site Mascot server, and implements and develops new user
analysis tools. We also maintain our interaction with the Swiss-Prot
group in Geneva, which allows us to annotate and update protein
sequence information in the UniProt-KB/Swiss-Prot database.
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