UCL Institute for Women's Health (IfWH)

Cancer Proteomics Laboratory

Lead: Dr John Timms

Overview and Core Facilities

Our major research themes are the identification of cancer biomarkers and understanding the molecular basis of carcinogenesis through the application of quantitative proteomic technologies and other molecular biology techniques. This research is funded through the Eve Appeal Gynaecological Cancer Trust, CR UK, MRC and Pancreatic Cancer UK. Facilities include a biochemistry laboratory, dedicated clean rooms for high-sensitivity, low-contamination sample handling, fluorescence 2D difference gel electrophoresis (2D-DIGE) capability, liquid-handling robotics and liquid chromatography (LC) for protein and peptide separations. Mass spectrometry (MS) instrumentation for expression profiling, protein/peptide identification and characterisation includes a Thermo LTQ Orbitrap XL hybrid mass spectrometer with on-line Dionex3000 nano-LC system and Bruker Ultraflex MALDI-TOF/TOF instrument.

Our mission also is to establish a core resource in proteomics, to provide technical expertise and knowledge in proteomic applications and data interpretation, to promote interaction between clinical and basic scientists and to provide training for the next generation of proteomics research scientists. Above all, we wish to make a difference to healthcare by addressing important questions in disease through the application of proteomic methods.

Research Projects

Analysis of human serum proteomes for cancer biomarker discovery

Our work aims to establish the potential of the human serum proteome for screening and ealry diagnosis of cancer in large populations and uses samples collected as part of the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) and in other studies. By using samples that pre-date diagnosis, we hope to identify early detection markers in the absence of non-specific late stage changes. Biomarker discovery work uses multi-dimensional protein and peptide separations linked to tandem MS with isobaric mass tagging for quantification. By comparing profiles of serum from healthy volunteers, patients with benign and malignant cancer and samples that predate diagnosis, we hope to identify biomarkers for differential diagnosis and early detection of ovarian, breast, pancreaticobiliary and colorectal cancers and endometriosis. Promising markers are being further validated in independent sample sets using immune- and MS-based assays and multi-marker models developed for translation to the clinic.

ErbB2/HER2 signalling in breast cancer

Research is aimed at identifying targets of ErbB2 and the growth factors which activate the ErbB receptor family of tyrosine kinases. Parallel differential mRNA and protein expression analyses have been applied to compare gene and protein expression profiles in model breast cancer cell lines to understand how target genes are regulated by ErbB2 overexpression and specific ErbB receptor ligands. Targets of interest are being validated and functionally characterised using cell-based assays following siRNA-mediated knockdown. Further work, applying in-depth proteomic methods for improved detection and quantification of low-abundance proteins and their post-translational modifications is aimed at understanding ErbB signalling and regulated expression at the molecular level and relating this to cellular phenotype. Methods include SILAC and multi-dimensional phospho-peptide enrichment linked to tandem MS.

Ovarian cancer biology/carcinogenesis

This research is aimed at a better understanding of the molecular events required for ovarian cell carcinogenesis, tumour progression and chemoresistance, and to thereby identify potential diagnostic, prognostic and predictive biomarkers for ovarian cancer. Work involves the application of complementary proteomic technologies to profile novel cell models of early ovarian epithelial cell transformation, metastasis, tumour suppression and chemoresistance. Candidate genes of interest are further validated and functionally characterised using RNAi-mediated knockdown and assessment of phenotype using cell-based assays.

Relevant Publications

1. Nagano K, Akpan A, Warnasuriya G, Yang A, Stein R, Zvelebil M, Corless S, Totty N, Cramer R, Burlingame A, Waterfield M, Timms JF and Naaby-Hansen S. Functional proteomic analysis of long-term growth factor stimulation and receptor tyrosine kinase co-activation in Swiss 3T3 fibroblasts Mol Cell Proteomics 2012, published on line 06 Sept
2. Devetyarov D, Nouretdinov I, Burford B, Camuzeaux S, Gentry-Maharaj A, Tiss A, Smith C, Luo Z, Chervonenkis A, Hallett R, Vovk V, Waterfield M, Cramer R, Timms JF, Sinclair J, Menon U, Jacobs I and Gammerman A. Conformal predictors in early diagnostics of ovarian and breast cancers. Progress in Artificial Intelligence 2012, published on line 08 July
3. Chou H-C, Lu Y-C, Cheng C-S, Chen Y-W, Lyu P-C, Lin C-W, Timms JF and Chan H-L. Proteomic and redox-proteomic analysis of berberine-induced cytotoxicity in breast cancer cells. Journal of Proteomics 2012 75(11): 3158-3176
4. Dumartin L, Whiteman HJ, Weeks ME, Hariharan D, Dmitrovic B, Brentnall T, Bronner MP, Feakins RM, Timms JF, Brennan C, Lemoine NR and Crnogorac-Jurcevic T. AGR2 is a novel surface antigen that promotes the dissemination of pancreatic cancer cells through regulation of cathepsins B and D. Cancer Research 2011 71(22): 7091-7102
5. Timms JF, Menon U, Devetyarov D, Tiss A, Camuzeaux S, McCurrie K, Nouretdinov I, Burford B, Smith C, Gentry-Maharaj A, Hallett R, Ford J, Luo Z, Vovk V, Gammerman A, Cramer R and Jacobs I. Early detection of ovarian cancer in pre-diagnosis samples using CA125 and MALDI-MS peaks. Cancer Genomics and Proteomics 2011 8(6): 289-305
6. Sandanayake NS, Sinclair J, Andreola F, Chapman MH, Xue A, Webster GJ, Clarkson A, Gill A, Norton I, Smith RC, Timms JF and Pereira SP. A combination of serum leucine-rich alpha-2-glycoprotein 1, CA19-9 and interleukin-6 differentiate biliary tract cancer from benign biliary strictures. British J. Cancer 2011 105: 1370-1378
7. Worthington J, Cutillas PR and Timms JF. IMAC/TiO2 enrich for peptide modifications other than phosphorylation: Implications for chromatographic choice and database searching in phosphoproteomics. Proteomics 2011 11: 1-5
8. Fry SA, Afrough B, Lomax-Browne HJ, Timms JF, Velentzis LS and Leathem AJC. Lectin microarray profiling of metastatic breast cancer glycans. Glycobiology 2011 21(8):1060-1070
9. Sinclair J and Timms JF. Quantitative profiling of serum samples using TMT protein labelling, fractionation and LC-MS/MS. Methods 2011 54(4): 361-369
10. Díez-Dacal B, Gayarre J, Gharbi S, Timms JF, Coderch C, Gago F and Pérez-Sala D. Identification of aldo-keto reductase AKR1B10 as a selective target for modification and inhibition by PGA1. Implications for antitumoral activity. Cancer Research 2011 71(12): 4161-4171
11. Sinclair J, Metodieva G, Dafou D, Gayther S and Timms JF. Profiling signatures of ovarian cancer tumour suppression using 2D-DIGE and 2D-LC-MS/MS with tandem mass tagging. Journal of Proteomics 2011 74(4): 451-465
12. Tiss A*, Timms JF*, Smith C, Devetyarov D, Gentry-Maharaj A, Camuzeaux S, Burford B, Nouretdinov I, Ford J, Luo Z, Jacobs I, Menon U, Gammerman A and Cramer R. Highly accurate detection of ovarian cancer using CA125 but limited improvement with serum MALDI-TOF MS profiling. Int J Gynecological Cancer 2010 20(9): 1518-1524
13. Worthington J*, Bertani M*, Chan H-L, Gerrits B and Timms JF. Transcriptional profiling of ErbB signalling in mammary luminal epithelial cells – interplay of ErbB and IGF1 signalling through IGFBP3 regulation. BMC Cancer 2010 10: 490
14. Tiss A, Smith C, Menon U, Jacobs I, Timms JF and Cramer R. A well-characterised peak identification list of MALDI MS profile peaks for human blood serum. Proteomics 2010 10(18): 3388-3392
15. Chan H-L, Chou H-C, Durán MaC, Gruenewald J, Waterfield MD, Ridley A and Timms JF. Major role of EGFR and Src kinases in promoting oxidative stress-dependent loss of adhesion and apoptosis. J Biol Chem. 2010 285(7): 4307-4318
16. Timms JF, Cramer R, Camuzeaux S, Tiss A, Smith C, Burford B, Nouretdinov I, Devetyarov D, Gentry-Maharaj A, Ford J, Luo Z, Gammerman A, Menon U and Jacobs I. Peptides generated ex vivo from serum proteins by tumour-specific exopeptidases are not useful biomarkers in ovarian cancer. Clinical Chem. 2010 56(2): 262-271
17. Gammerman A, Vovk V, Burford B, Nouretdinov I, Luo Z, Chervonenkis A, Waterfield M, Cramer R, Tempst P, Villanueva J, Kabir M, Camuzeaux S, Timms J, Menon U and Jacobs I. Serum proteomic abnormality predating screen detection of ovarian cancer. The Computer Journal 2009 52: 326-333
18. Grun B, Benjamin E, Sinclair J, Timms JF, Jacobs IJ, Gayther SA and Dafou D. Three dimensional in vitro cell biology models of ovarian and endometrial cancer. Cell Proliferation 2009 42 (2): 219-228
19. Timms JF and Cramer R. Difference gel electrophoresis. Proteomics 2008 8: 4886–4897
20. Durán MaC, Vega F, Moreno-Bueno G, Artiga MaJ, Sanchez L, Palacios J, Ridley A and Timms JF. Characterisation of tumoral markers correlated with ErbB2 (HER2/Neu) overexpression and metastasis in breast cancer. Proteomics: Clinical Applications 2008 2(9): 1313-1326
21. Weeks ME, Hariharan D, Petronijevic L, Radon TP, Whiteman HJ, Kocher H, Timms JF, Lemoine NR and Crnogorac-Jurcevic T. Analysis of the urine proteome in patients with pancreatic ductal adenocarcinoma. Proteomics: Clinical Applications. 2008. 2(7-8): 1047–1057
22. Tiss A, Smith C, Camuzeaux S, Kabir M, Gayther S, Menon U, Waterfield M, Timms JF, Jacobs I and Cramer R. Serum peptide profiling using MALDI mass spectrometry: Avoiding the pitfalls of coated magnetic beads using well-established Ziptip technology. Proteomics 2007. 7: 77-89
23. Jovceva E, Larsen MR, Waterfield MD, Baum B and Timms JF. Dynamic cofilin phosphorylation in the control of lamellipodial actin homeostasis. Journal of Cell Science 2007 120(11): 1888-1897
24. Gharbi SI, Zvelebil MJ, Shuttleworth SJ, Hancox T, Saghir N, Timms JF and Waterfield MD. Exploring the specificity of the PI3K family inhibitor LY294002. Biochemical Journal 2007. 404(1): 15-21
25. Timms JF, Arslan-Low E, Gentry-Maharaj A, Luo Z, T’Jampens D, Podust VN, Ford J, Fung ET, Gammerman A, Jacobs IJ and Menon U. Pre-analytic influence of sample handling on SELDI-TOF serum protein profiles. Clinical Chem 2007 53: 645-656
26. Whiteman HJ, Weeks ME, Dowen SE, Barr, S, Timms JF, Lemoine NR and Crnogorac-Jurcevic T. The role of S100P in the invasion of pancreatic cancer cells is mediated through cytoskeletal changes and regulation of cathepsin D. Cancer Research 2007 67: 8633-8642
27. Chan H-L, Gharbi S, Gaffney PR, Cramer R, Waterfield MD and Timms JF. Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis. Proteomics 2005 5(11): 2908-2926
28. White SL, Gharbi S, Bertani MF, Chan H-L, Waterfield MD and Timms JF. Cellular responses to ErbB-2 overexpression in human mammary luminal epithelial cells: comparison of mRNA and protein expression. Br J Cancer 2004 90(1): 173-81
29. Timms JF, White SL, O’Hare MJ and Waterfield MD. Effects of ErbB-2 overexpression on mitogenic signalling and cell cycle progression in human breast luminal epithelial cells. Oncogene 2002 21: 6573-6586
30. Gharbi S, Gaffney P, Yang A, Zvelebil MJ, Cramer R, Waterfield MD and Timms JF. Evaluation of 2D-differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol Cell Proteomics 2002 1(2): 91-98

People

Dr John F. Timms (Group Leader). John is a Lecturer at the UCL EGA Institute for Women’s Health (IfWH) and Head of the Cancer Proteomics Group. He obtained his PhD in biochemistry from the University of Oxford. In 1995 he joined the laboratory of Prof Benjamin Neel at Harvard Medical School as a Leukemia Society of America Junior Research Fellow studying the role of tyrosine phosphatases in cellular signalling. He returned to the UK in 1999 as a Postdoctoral Research Fellow in the laboratory of Prof Mike Waterfield at the Ludwig Institute for Cancer Research (LICR), UCL Branch, working on ErbB receptor signalling in cancer and the development and application of proteomic technologies. In 2002, he was appointed Assistant Member of the Institute and Leader of the Cancer Proteomics Group and held a joint appointment as Lecturer in the UCL Dept of Biochemistry and Molecular Biology. In 2006 he moved to the EGA Institute for Women’s Health. His group's research activities are focused on elucidating the molecular mechanisms of cell signalling in cancer cells and the discovery of cancer biomarkers using proteomics-based methods and other molecular biology techniques.

Dr Jenny Worthington (Research Associate). Jenny graduated from the University of Newcastle with a BSc. Hons in Human Genetics in 2006 and then undertook a Masters in Medical Research in 2007, with a project investigating IGF1 signalling in gastric cancer. She joined the Cancer Proteomics Group as a PhD student in October 2007 working on a project entitled ‘Characterisation of ErbB2-dependant breast cancer markers’. She is currently a Research Associate in the group using proteomic technologies for the discovery and validation of biomarkers for the early detection of ovarian cancer.

Dr Darragh O’Brien (Postdoctoral Research Associate). Darragh obtained his BSc. Hons in Biochemistry from the Conway Institute of Biomolecular and Biomedical Research, University College Dublin in 2004. He then worked as a research technician at Proteome Sciences Plc., using mass spectrometry for biomarker discovery and assay development. He then undertook a PhD in 2007 at the Institute of Psychiatry, King’s College London, where he developed and implemented TMT-SRM assays for the validation of candidate biomarkers of Alzheimer’s disease. He joined the Cancer Proteomics Group in 2011 and works on the discovery and validation of biomarkers for the early detection and differential diagnosis of pancreatic cancer.

Mr Darren Thomas (PhD Student). Darren joined the Cancer Proteomics Group as an MRC Industrial Case PhD Student in October 2012 after completing a BSc Hons in Biomedical Science at Nottingham Trent University. He spent a year as a student intern at the Institute of Food Safety, Wageningen University, Netherlands, where he developed a rapid multiplex immunoassay for the determination of mycotoxins in foodstuffs with confirmation by LC-QqQ/MS analysis. His PhD project involves the identification of risk factors and biomarkers for colorectal cancer.

Ms Stella Irungu (PhD Student). Stella completed a BSc in Biomedical Technology at the University of Nairobi, Kenya in 2007 and then an MSc in Biomedical Sciences, specialising in Medical Microbiology, at Middlesex University in 2009. Her research project was on the correlation between Human Papilloma Virus infection and endometriosis/adenomyosis. Before joining the Cancer Proteomics Group in October 2012 as a Commonwealth Scholar, she worked on a food safety project at the Centre for Microbiology Research of the Kenya Medical Research Institute, and has undertaken several industrial placements. Her PhD project is aimed at the identification of non-invasive diagnostic biomarkers of endometriosis.