PhD studentship – FTIR, Raman and SIMS Imaging for Lipidomic Analysis

FTIR, Raman and SIMS Imaging for Lipidomic Analysis of Cellular Systems

Prof P Gardner, Dr N Lockyer, Dr J Denbigh

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 [1]. 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 [2]. 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 [3]. 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.

Funding Notes

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.

FindAPhD

https://www.findaphd.com/search/ProjectDetails.aspx?PJID=89950&LID=1040

References

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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

PhD studentship – Secondary effects of gene mutations

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.

Links

https://www.research.manchester.ac.uk/portal/en/researchers/richard-edmondson
http://www.manchester.ac.uk/research/peter.gardner/
http://www.sarc.manchester.ac.uk/index.php/group-members/nick-lockyer/
http://www.chemistry.manchester.ac.uk/people/staff/profile/?ea=nick.lockyer
http://www.salford.ac.uk/environment-life-sciences/els-academics/joanna-denbigh

Funding Notes

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/

FindAPhD

https://www.findaphd.com/search/ProjectDetails.aspx?PJID=89927&LID=1020

References

  1. 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.
  2. 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
  3. McCormick, A., Edmondson RJ et al.,
    Ovarian Cancers Harbour Defects in Non-Homologous End Joining Resulting in Resistance to Rucaparib.
    Clin Cancer Res, 2016
  4. 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
  5. M. Pilling and P. Gardner,
    Fundamental developments in infrared spectroscopic imaging for biomedical applications.
    Chemical Society Reviews, 2016, 45, 1935 – 1957

CLIRCON17

 

 

The CLIRCON17 Conference will be held in Manchester, UK, 2–5 April 2017. It is hosted by the Clinical Infrared and Raman Spectroscopy (CLIRSPEC) Network and the Analytical and Biomedical Spectroscopy groups at the University of Manchester, UK.

The conference is for researchers and industrialists in the multidisciplinary area of clinical infrared and Raman spectroscopy. For more information, please visit:
https://clirspec.org/uk-network/clircon17/

Review Paper – Single cell analysis using Fourier transform infrared microspectroscopy

James Doherty, Gianfelice Cinque & Peter Gardner
Applied Spectroscopy Reviews(Oct 2016)
Abstract
Fourier transform infrared spectroscopy (FTIR) is a well-established, non-destructive method of obtaining chemical information from biological samples such as tissues and cells. This review focuses specifically on the development of infrared spectroscopic microanalysis at the single cell level. Technological developments, including that of the infrared microscope, synchrotron radiation (SR)-FTIR, and focal plane array (FPA) detectors, and their impact on the field are discussed along with the various data processing procedures that are currently used to extract meaningful information. There is then an emphasis on live cell IR imaging, including developments in water correction and microfluidic device design. The review concludes with look to future directions, highlighting the potential impact of quantum cascade lasers.

Welcome!

We are delighted to welcome our new PhD students:

Thomas Gladwell, Jiayi ‘Jennie’ Tang, Nga-Tsing ‘Kayto’ Tang and Widad Al Rawahi!

Paper – The Dynamic Nature of Hypertrophic and Fibrotic Remodeling of the Fish Ventricle

The Dynamic Nature of Hypertrophic and Fibrotic Remodeling of the Fish Ventricle

A. N. Keen, A. J. Fenna,  J. C. McConnell,  M. J. Sherratt, P. Gardner, H. A. Shiels
Front Physiol. 2016 Jan 21;6:427
DOI: 10.3389/fphys.2015.00427

Abstract

Chronic pressure or volume overload can cause the vertebrate heart to remodel. The hearts of fish remodel in response to seasonal temperature change. Here we focus on the passive properties of the fish heart. Building upon our previous work on thermal-remodeling of the rainbow trout ventricle, we hypothesized that chronic cooling would initiate fibrotic cardiac remodeling, with increased myocardial stiffness, similar to that seen with pathological hypertrophy in mammals. We hypothesized that, in contrast to pathological hypertrophy in mammals, the remodeling response in fish would be plastic and the opposite response would occur following chronic warming. Continue reading

Review Paper – Fundamental Developments in IR Spectroscopic Imaging for Biomedical Applications

Fundamental developments in infrared spectroscopic imaging for biomedical applications
Michael Pilling and Peter Gardner
Chem. Soc. Rev., 2016,45, 1935-1957
DOI: 10.1039/C5CS00846H

Abstract

Infrared chemical imaging is a rapidly emerging field with new advances in instrumentation, data acquisition and data analysis. These developments have had significant impact in biomedical applications and numerous studies have now shown that this technology offers great promise for the improved diagnosis of the diseased state. Relying on purely biochemical signatures rather than contrast from exogenous dyes and stains, infrared chemical imaging has the potential to revolutionise histopathology for improved disease diagnosis. In this review we discuss the recent advances in infrared spectroscopic imaging specifically related to spectral histopathology (SHP) and consider the current state of the field. Finally we consider the practical application of SHP for disease diagnosis and consider potential barriers to clinical translation highlighting current directions and the future outlook.

Graphical abstract: Fundamental developments in infrared spectroscopic imaging for biomedical applications

Paper – Chemotherapeutic Response in Human Breast Cancer Cells

Chemotherapeutic response to cisplatin-like drugs in human breast cancer cells probed by vibrational microspectroscopy

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. Marques
Faraday Discuss., 2016,187, 273-298

DOI: 10.1039/C5FD00148J

FD187_Frontispiece_PUBLICITY
Abstract
Studies of drug–cell interactions in cancer model systems are essential in the preclinical stage of rational drug design, which relies on a thorough understanding of the mechanisms underlying cytotoxic activity and biological effects, at a molecular level. This study aimed at applying complementary vibrational spectroscopy methods to evaluate the cellular impact of two Pt(II) and Pd(II) dinuclear chelates with spermine (Pt2Spm and Pd2Spm), using cisplatin (cis-Pt(NH3)2Cl2) as a reference compound. Their effects on cellular metabolism were monitored in a human triple-negative metastatic breast cancer cell line (MDA-MB-231) by Raman and synchrotron-radiation infrared microspectroscopies, for different drug concentrations (2–8 μM) at 48 h exposure. Continue reading

Paper – High-Throughput QCL Spectral Histopathology

High-throughput quantum cascade laser (QCL) spectral histopathology: a practical approach towards clinical translation

M. J. Pilling, A. Henderson, B. Bird,  M. D. Brown, N. W. Clarke and P. Gardner
Faraday Discuss., 2016,187, 135-154

DOI: 10.1039/C5FD00176E

FD187_Frontispiece_PUBLICITY

Abstract
Infrared microscopy has become one of the key techniques in the biomedical research field for interrogating tissue. In partnership with multivariate analysis and machine learning techniques, it has become widely accepted as a method that can distinguish between normal and cancerous tissue with both high sensitivity and high specificity. While spectral histopathology (SHP) is highly promising for improved clinical diagnosis, several practical barriers currently exist, which need to be addressed before successful implementation in the clinic. Sample throughput and speed of acquisition are key barriers and have been driven by the high volume of samples awaiting histopathological examination.