FTIR, Raman and SIMS Imaging for Lipidomic Analysis of Cellular Systems
Deadline 17 November 2017
The role of lipid metabolism in a number of cellular processes including (i) stem cell differentiation, (ii) drugcell interactions and (iii) epithelial/adipocyte cell interactions, is generally poorly understood. For example it has been recently shown that PC3 cells when co-cultured with adipocyte cells, sequestrate omega-6 lipids and their metabolites which subsequently stimulate cell migration and whilst promoting proliferation . Similarly lipids have been shown to play a key role in the differentiation of stem-cells, and recent investigations using FTIR have shown that lipid signatures may indicate early signs of differentiation . These fundamental cell processes, mediated by lipids, are currently a major focus of research.
We propose to use Fourier Transform Infrared (FTIR) hyperspectral imaging, high resolution Raman imaging and time of flight-secondary ion mass spectrometry (ToF-SIMS) alongside established co-culture protocols to examine the role of lipids and their metabolites in cells. FTIR imaging of cells has become possible through the recent development of scatter correction algorithms . In addition, the evolution of new high magnification optics coupled with an array detector means that for the first time infrared hyperspectral images with similar pixel resolution similar to that of Raman and ToF-SIMS can be obtained. This means that full multimodal chemical image characterisation can be achieved. The new state of the art Raman system was funded through the BBSRC and has a spatial resolution that spans that of the FTIR and SIMS. The ToF-SIMS instrument developed in Manchester also has unique capabilities in the UK [4,5]. This multimodal imaging approach will facilitate unique lipidomic studies of cellular systems.
This project is to be funded under the BBSRC Doctoral Training Programme. If you are interested in this project, please make direct contact with the Principal Supervisor to arrange to discuss the project further as soon as possible. You MUST also submit an online application form – full details on how to apply can be found on the BBSRC DTP website https://www.bmh.manchester.ac.uk/study/research/bbsrc-dtp/
Applications are invited from UK/EU nationals only. Applicants must have obtained, or be about to obtain, at least an upper second class honours degree (or equivalent) in a relevant subject.
- M. Brown, C. Hart, E. Gazi, P. Gardner, N. Lockyer, N. Clarke,
The influence of the omega 6 PUFA arachidonic acid and bone marrow adipocytes on the metastatic spread of prostate cancer,
British Journal of Cancer, 102 (2010) 403–413
- G. Clemens, K. R. Flower, A. P. Henderson, A. Whiting, S. A. Przyborski, M. Jimenez-Hernandez, F. Ball, P. Bassan, G. Cinque, P. Gardner.
Application of Infrared Microspectroscopy to Monitor the Differentiation of Human Pluripotent Stem Cells in Response to Retinoic Acid and Synthetic Retinoid Analogues.
Molecular BioSystems, 2013, 9 (4), 677 – 692
- P. Bassan, A. Sachdeva, A. Kohler, C. Hughes, A. Henderson, J. Boyle, J. H. Shanks, M. Brown, N. W. Clarke P.Gardner,
FTIR Microscopy of biological cells and tissue: data analysis using resonant Mie scattering (RMieS) EMSC algorithm,
Analyst 137, (2012) 1370-1377
- S. Rabbani, J. S. Fletcher, N. P. Lockyer, J. C. Vickerman,
Exploring subcellular imaging on the buncher-ToF J105 3D chemical imager,
Surface and Interface Analysis 43 (2011) 380-384
- John S. Fletcher, Nicholas P. Lockyer, John C. Vickerman,
Developments in molecular SIMS depth profiling and 3D imaging of biological systems using polyatomic primary ions,
Mass Spectrometry Reviews 30(1) (2011) 142-174
Probing the secondary effects of Tp53 and BRCA gene mutations upon cellular physiology using advanced analytical techniques.
Prof R Edmondson, Prof P Gardner, Dr N Lockyer, Dr J Denbigh
Deadline: 17 November 2017
Cancer is a disease of DNA in which genomic events allow the cell to develop the autonomy, increased proliferation and other fundamental hallmarks of the disease. This process is often initiated by mutation of one or two key driver genes. Understanding the effects of these driver mutations is crucial in order to not only improve our understanding of the disease process but also to develop new screening and detection methods for cancer. In this exciting PhD the student will develop a novel cell model using primary human tissue to replicate the earliest phases in the development of high grade serous cancer, the commonest and most deadly pelvic cancer. The model will be created using fallopian tube epithelial cells which will be cultured ex vivo. Tp53 and BRCA1 genes will then be silenced using Crispr technology.
The student will then apply novel bioanalytical tools to these models to probe the effects of each of the mutations, alone and in combination. Specifically the student will use a combination of mass spectrometry and vibrational spectroscopy approaches that are being pioneered in Manchester for biomolecular characterization. Signatures generated using these techniques will then be validated using RNAseq.
Taken together these studies represent a novel approach and make use of an existing collaboration to integrate advanced cell culture modelling with a unique analytical strategy. Results from these studies will provide important insights into the effect of these driver mutations upon cellular physiology which will pave the way for development of novel screening and detection methodologies.
The student will develop a wide range of transferable lab and analytical skills to enhance their career development.
This project is to be funded under the BBSRC Doctoral Training Programme. If you are interested in this project, please make direct contact with the Principal Supervisor to arrange to discuss the project further as soon as possible. You MUST also submit an online application form – full details on how to apply can be found on the BBSRC DTP website: http://www.manchester.ac.uk/bbsrcdtpstudentships
Applications are invited from UK/EU nationals only. Applicants must have obtained, or be about to obtain, at least an upper second class honours degree (or equivalent) in a relevant subject. https://www.bmh.manchester.ac.uk/study/research/bbsrc-dtp/apply/
- Bowtell, D.D., Edmondson RJ et al.,
Rethinking ovarian cancer II: reducing mortality from high-grade serous ovarian cancer.
Nat Rev Cancer, 2015. 15(11): p. 668-79.
- Denbigh, J. L., Perez-Guaita, D., Vernooij, R., Tobin, M., Bambery, K., Xu, Y., Southam, A., Khanim, F., Drayson, M., Lockyer, N., Goodacre, R., and Wood, B.
Probing the action of a novel anti-leukaemic drug therapy at the single cell level using modern vibrational spectroscopy techniques,
Scientific Reports, 2017. 7(1): 2649
- McCormick, A., Edmondson RJ et al.,
Ovarian Cancers Harbour Defects in Non-Homologous End Joining Resulting in Resistance to Rucaparib.
Clin Cancer Res, 2016
- A. L. M. Batista de Carvalho, M. Pilling, P. Gardner, J. Doherty, G. Cinque, K. Wehbe, C. Kelley, L. A. E. Batista de Carvalho and M. P. M. Marquesa,
Chemotherapeutic Response to Cisplatin-like Drugs in Human Breast Cancer Cells Probed by Vibrational Microspectroscopy.
Faraday Discussion, 2016, 187, 273-298
- M. Pilling and P. Gardner,
Fundamental developments in infrared spectroscopic imaging for biomedical applications.
Chemical Society Reviews, 2016, 45, 1935 – 1957
Analyst 140 (2015) 2080-2085
Large scale infrared imaging of tissue micro arrays (TMAs) using a tunable Quantum Cascade Laser (QCL) based microscope
Chemical imaging in the field of vibrational spectroscopy is developing into a promising tool to complement digital histopathology. Applications include screening of biopsy tissue via automated recognition of tissue/cell type and disease state based on the chemical information from the spectrum. For integration into clinical practice, data acquisition needs to be speeded up to implement a rack based system where specimens are rapidly imaged to compete with current visible scanners where 100’s of slides can be scanned overnight. Continue reading
Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging
Paul Bassan, Ashwin Sachdeva, Jonathan H. Shanks, Mick D. Brown, Noel W. Clarke and Peter Gardner
Proc. SPIE 9041, Medical Imaging 2014: Digital Pathology, 90410D 9041 (2014)
Fourier transform infrared (FT-IR) chemical imaging has been demonstrated as a promising technique to complement histopathological assessment of biomedical tissue samples. Current histopathology practice involves preparing thin tissue sections and staining them using hematoxylin and eosin (H&E) after which a histopathologist manually assess the tissue architecture under a visible microscope. Studies have shown that there is disagreement between operators viewing the same tissue suggesting that a complementary technique for verification could improve the robustness of the evaluation, and improve patient care. Continue reading
Assessing the challenges of Fourier transform infrared spectroscopic analysis of blood serum
Caryn Hughes, Michael Brown, Graeme Clemens, Alex Henderson, Geraldine Monjardez, Noel W. Clarke and Peter Gardner
Journal of Biophotonics (2014) [OPEN ACCESS]
There are many approaches to measuring the infrared spectrum of a blood serum sample. Naturally, each approach will have both advantages and disadvantages. We report on the progress of the application of infrared spectroscopy in the field of blood serum analysis towards clinical application, with a focus on prostate cancer. In order to perform a high-powered study with clinical relevance, choosing the most suitable approach must undergo careful consideration. We review the possibilities of using different sample preparation methods and speculate upon the potential pitfalls of both transmission and attenuated total reflectance (ATR) techniques.