Towards disease diagnosis through spectrochemical imaging of tissue architecture.

Lead Research Organisation: University of Manchester
Department Name: Chem Eng and Analytical Science


This proposal brings together a critical mass of scientists from the Universities of Cardiff, Lancaster, Liverpool and Manchester and clinicians from the Christie, Lancaster and Liverpool NHS Hospital Trusts with the complementary experience and expertise to advance the understanding, diagnosis and treatment of cervical, oesophageal and prostate cancers. Cervical and prostate cancer are very common and the incidence of oesophageal is rising rapidly. There are cytology, biopsy and endoscopy techniques for extracting tissue from individuals who are at risk of developing these diseases. However the analysis of tissue by the standard techniques is problematic and subjective. There is clearly a national and international need to develop more accurate diagnostics for these diseases and that is a primary aim of this proposal.
Experiments will be conducted on specimens from all three diseases using four different infrared based techniques which have complementary strengths and weaknesses: hyperspectral imaging, Raman spectroscopy, a new instrument to be developed by combining atomic force microscopy with infrared spectroscopy and a scanning near field microscope recently installed on the free electron laser on the ALICE accelerator at Daresbury. The latter instrument has recently been shown to have considerable potential for the study of oesophageal cancer yielding images which show the chemical composition with unprecedented spatial resolution (0.1 microns) while hyperspectral imaging and Raman spectroscopy have been shown by members of the team to provide high resolution spectra that provide insight into the nature of cervical and prostate cancers. The new instrument will be installed on the free electron laser at Daresbury and will yield images on the nanoscale. This combination of techniques will allow the team to probe the physical and chemical structure of these three cancers with unprecedented accuracy and this should reveal important information about their character and the chemical processes that underlie their malignant behavior. The results of the research will be of interest to the study of cancer generally particularly if it reveals feature common to all three cancers.
The infrared techniques have considerable medical potential and to differing extents are on the verge of finding practical applications. Newer terahertz techniques also have significant potential in this field and may be cheaper to implement. Unfortunately the development of cheap portable terahertz diagnositic instruments is being impeded by the weakness of existing sources of terahertz radiation. By exploiting the terahertz radiation from the ALICE accelerator, which is seven orders of magnitude more intense that conventional sources, the team will advance the design of two different terahertz instruments and assess their performance against the more developed infrared techniques in cancer diagnosis. However before any of these techniques can be used by medical professionals it is essential that their strengths and limitations of are fully understood. This is one of the objectives of the proposal and it will be realised by comparing the results of each technique in studies of specimens from the three cancers that are the primary focus of the research. This will be accompanied by developing data basis and algorithms for the automated analysis of spectral and imaging data thus removing subjectivity from the diagnostic procedure.
Finally the team will explore a new approach to monitoring the interactions between pathogens, pharmaceuticals and relevant cells or tissues at the cellular and subcellular level using the instruments deployed on the free electron laser at Daresbury together with Raman microscopy. If this is successful, it will be important in the longer term in developing new treatments for cancer and other diseases.
Description We have discovered that infrared spectroscopy can be used as an objective method to diagnose cancer in biopsy tissue samples. We have used a range of infrared sampling methodologies at various spatial resolutions and have seen that a basic cancer vs cancer classifier can be made at low resolution with a standard instrumentation. For more detailed analysis and sub-classification finer details are required.

As part of this project a new method of data analysis related to tissue has been developed
Exploitation Route We hope that infrared imaging will be commercialized so that it will be used routinely in the clinic.

In addition the university of Manchester has provided ~450K of funding for a high resolution optical photothermal IR microscope to continue with the high resolution tissue imaging work.
Sectors Healthcare

Description It is part due to this work that we have set up the international society for clinical spectroscopy
Sector Healthcare
Impact Types Societal

Title Quantum Cascade Laser Spectral Histopathology: Breast Cancer Diagnostics Using High Throughput Chemical Imaging 
Description Fourier transform infrared (FT-IR) microscopy, coupled with machine learning approaches, has been demonstrated to be a powerful technique for identifying abnormalities in human tissue.  The ability to objectively identify the prediseased state, and diagnose cancer with high levels of accuracy, has the potential to revolutionise current histopathological practice.  Despite recent technological advances in FT-IR microscopy, sample throughput and speed of acquisition are key barriers to clinical translation. Wide-field quantum cascade laser (QCL) infrared imaging systems with large focal plane array detectors utilising discrete frequency imaging, have demonstrated that large tissue microarrays (TMA) can be imaged in a matter of minutes.  However this ground breaking technology is still in its infancy and its applicability for routine disease diagnosis is, as yet, unproven. In light of this we report on a large study utilising a breast cancer TMA comprised of 207 different patients.  We show that by using QCL imaging with continuous spectra acquired between 912 and 1800 cm -1, we can accurately differentiate between 4 different histological classes.  We demonstrate that we can discriminate between malignant and non-malignant stroma spectra with high sensitivity (93.56%) and specificity (85.64%) for an independent test set.   Finally, we classify each core in the TMA and achieve high diagnostic accuracy on a patient basis with 100% sensitivity and 86.67% specificity.  The absence of false negatives reported here opens up the possibility of utilising high throughput chemical imaging for cancer screening, thereby reducing pathologist workload and improving patient care. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Description Agilent 
Organisation Agilent Technologies
Country United States 
Sector Private 
PI Contribution We have been working with Agilent on a number of projects to speed up data collection. We have provided know-how in data analysis
Collaborator Contribution Agilent have provided many hours of consultation regarding the software.
Impact This paper was ca direct result of our EPSRC Impact Acceleration award. P. Bassan, A. Sachdeva, J. H. Shanks, M. D. Brown, N. W. Clarke, P. Gardner, Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging, Proc. SPIE 9041, Medical Imaging 2014: Digital Pathology, 90410D We have also presented at numerous conferences and workshops. High-throughput assessment of biopsy tissue using infrared spectroscopic chemical imaging, Agilent FTIR imaging workshop, Montreal, Canada, 26 June 2016 Rapid assessment of breast and prostate biopsy tissue using infrared spectroscopic chemical imaging. Agilent FTIR imaging workshop, Krakow, Poland 17th August 2014 The use of infrared imaging in urological pathology. Agilent International Imaging Workshop 2012, 11th November, Chiang Mai, Thailand
Start Year 2010
Description Noel Clarke 
Organisation The Christie NHS Foundation Trust
Country United Kingdom 
Sector Public 
PI Contribution We have had a number of joint projects and joint studentship over the last 18 years. We have provided access to state of the art infrared imaging systems.
Collaborator Contribution Noel's group have provided access to tissue samples, and numerous consultations regarding our work. We have regular project meeting at the Christie.
Impact This has been a very successful collaboration resulting in 34 peer reviewed publications and numerous presentations at international conferences. Publications 1. M. J Pilling, A. Henderson, J. H. Shanks, M. D. Brown, N. W. Clarke and P. Gardner, Infrared Spectral Histopathology Using Haematoxylin and Eosin (H&E) Stained Glass Slides: A major step forward towards clinical translation. Analyst on line 2. M. Jimenez-Hernandez, M. D. Brown , C. Hughes, N. W. Clarke, P. Gardner, Characterising cytotoxic agent action as a function of the cell cycle using Fourier Transform Infrared Mircospectroscopy, Analyst, 2015, 140, 4453 - 4464 3. C. Hughes, A. Henderson, M. Kansiz, K. M. Dorling, M. Jimenez-Hernandez, M. D. Brown, N. W. Clarkeb, and P. Gardner, Enhanced FTIR benchtop imaging of single biological cells, Analyst, 2015, 140, 2080 - 2085. DOI: 10.1039/C4AN02053G 4. P. Bassan, A. Sachdeva, J. H. Shanks, M. D. Brown, N. W. Clarke, P. Gardner, Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging, Proc. SPIE 9041, Medical Imaging 2014: Digital Pathology, 90410D 5. C. Hughes, M. Brown, G. Clemens, A. Henderson, G. Monjardez, N.W. Clarke, P. Gardner, Assessing the challenges of Fourier transform infrared spectroscopic analysis of blood serum, J Biophotonics 2014 7(3-4) 180-188 6. C. Hughes, L. Gaunt, M. Brown, N.W. Clarke, P. Gardner, Assessment of Paraffin Removal from prostate FFPE Sections using transmission mode FTIR-FPA Imaging, Analytical Methods. 2014, 6 (4), 1028 - 1035 7. P. Bassan, A. Sachdeva, J. Shanks, Mick D. Brown, N.W. Clarke, P.Gardner, Whole organ cross-section chemical imaging using label-free mega-mosaic FTIR microscopy, Analyst 2013, 138(23), 7066-7069 8. M. Jimenez-Hernandez, C. Hughes, P. Bassan, F. Ball, M.D. Brown, N.W Clarke, P. Gardner. Exploring the spectroscopic differences of Caki-2 cells progressing through the cell cycle while proliferating in-vitro. Analyst 2013, 138(14), 3957-3966 9. C. Hughes, M. Brown, J. H Shanks J. Iqbal-Wahid, A. Eustac, H. Denley, P. J Hoskin, C. West, N. W Clarke, P. Gardner, FTIR microspectroscopy of diverse sub-variants of carcinoma of the urinary bladder: a pilot study. J Biophotonics, 6(1) (2013) 73-87 10. C. Hughes , M. D. Brown , F. Ball , G. Monjardez, P. Dumas, N. W. Clarke, K. R. Flower and P Gardner, Highlighting a Need to Distinguish Cell Cycle Signatures from Cellular Responses to Chemotherapeutics in SR-FTIR Spectroscopy, Analyst 137 (24),(2012), 5736 - 5742 11. C. Hughes , M. D. Brown , P. Dumas, N. W. Clarke, K. R. Flower and P Gardner, Tracking Cellular Responses to Chemotherapeutics in Renal Cell Carcinoma using Synchrotron and Benchtop FTIR Spectroscopy, Analyst, 137 (20), (2012), 4720 - 4726 12. 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 13. C. Hughes, M. Liew, M. D. Brown, A. Sachdeva, P. Bassan, P. Dumas, C.Hart, N. W. Clarke, P.Gardner, SR-FTIR Spectroscopy of Renal Epithelial Carcinoma Cells Displaying Stem Cell Characteristics, Analyst, 135, (2010) 3133-3141 14. P. Bassan, A. Kohler, H. Martens, J. Lee, E. Jackson, N. Lockyer, P. Dumas, M. Brown, N. Clarke, P. Gardner RMieS-EMSC correction for infrared spectra of biological cells: Extension using full Mie theory and GPU computing, J. Biophotonics, 3 (2010) 609-620 15. M.J. Baker, C. Clarke, D. Démoulin, J. Nicholson, F. Lyng, H.J. Byrne, C.A. Hart, M.D. Brown, N.W. Clarke, P. Gardner, An Investigation of the RWPE Prostate Derived Family of Cell Lines Using FTIR Spectroscopy, Analyst, 135, (2010) 887- 894 16. P. Bassan, A. Kohler, H. Martens, J. Lee, H. J. Byrne, P. Dumas, E. Gazi, M. Brown, N. Clarke, P. Gardner, Resonant Mie Scattering (RMieS) Correction of Infrared Spectra from Highly Scattering Biological Samples, Analyst, 135 (2010) 268-277 (Front Cover) 17. 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 18. P. Bassan, H. J. Byrne, J. Lee, F. Bonnier, C. Clarke, P. Dumas, E. Gazi, M. D. Brown, N. W. Clarke, P. Gardner., Reflection contributions to dispersion artefact in FTIR spectra of cellular samples, Analyst, 134, (2009), 1171-1175 19. T. J. Harvey, E. Gazi, A. Henderson, R. D Snook, N. W. Clarke, M. Brown, P Gardner. Factors Influencing the Discrimination and Classification of Prostate Cancer Cells Lines by FTIR Microspectroscopy, Analyst 134, (2009) 1083-1091 20. M.J. Baker, E.Gazi, M.D. Brown, J.H. Shanks, N.W. Clarke, P. Gardner, Investigating FTIR Based Histopathology for the Diagnosis of Prostate Cancer, J. Biophotonics, 2 (2009) 104-113 21. T J Harvey, C Hughes, A D Ward, E Correia Faria, A Henderson, N W Clarke, M D Brown, R D Snook P. Gardner, Classification of Fixed Urological Cells using Raman Tweezers, J. Biophotonics, 2 (2009) 47-69 22. E. Gazi, T.J. Harvey, M.D.Brown, N.W. Clarke, N.P. Lockyer, P. Gardner, A FTIR Microspectroscopic Study of the Uptake and Metabolism of Isotopically Labelled Fatty Acids by Metastatic Prostate Cancer, Vibrational Spectroscopy, 50 (2009) 99-105 23. T. J. Harvey, E Correia Faria, E Gazi, A D Ward, N W Clarke, M D Brown, R.D. Snook, P Gardner, The Spectral Discrimination of Live Prostate and Bladder Cancer Cell Lines Using Raman Optical Tweezers, Journal of Biomedical Optics, 13 (2008) 064004 24. 76. M.J. Baker, E.Gazi, M.D. Brown, J.H. Shanks, P. Gardner, N.W. Clarke, FTIR Based Spectroscopic Analysis in the Identification of Clinically Aggressive Prostate Cancer, British Journal of Cancer, 99 (2008) 1859-1866 25. 74. E. Gazi, P. Gardner, N.P Lockyer, C.A Hart, N.W. Clarke, M.D Brown, Probing Lipid Translocation Between Adipocytes and Prostate Cancer Cells with Imaging FTIR Microspectroscopy, J. Lipid Research 48 (2007) 1846 26. 73. J. Lee, E Gazi, J Dwyer, M. D. Brown, N. W. Clarke, P. Gardner, Optical artefacts in transflection mode FTIR microspectroscopic images of single cells on a biological support: the effect of back-scattering into collection optics. Analyst 132 (2007) 750-755 27. T. J. Harvey, A. Henderson, E. Gazi, N. W. Clarke, M. Brown, E Correia Faria, R. D. Snook P. Gardner, Discrimination of prostate cancer cells by reflection mode FTIR photo-acoustic spectroscopy, Analyst 132 (2007) 292-295 28. E. Gazi, J. Dwyer, N.P Lockyer, P. Gardner, J.H Shanks, Jo-An Roulson, C.A Hart, N.W Clarke, M.D Brown, Biomolecular Profiling of Metastatic Prostate Cancer Cells in Bone Marrow Tissue Using FTIR Microspectroscopy: A Pilot Study, Analytical and Bioanalytical Chemistry, 387 (2007) 1621-1631. 29. E. Gazi, M. Baker, J. Dwyer, N. P. Lockyer, P. Gardner, J.H. Shanks, R. S. Reeve, C. Hart, N.W. Clarke M. Brown, A Correlation of FTIR Spectra Derived from Prostate Cancer Tissue with Gleason Grade, and Tumour Stage, 30. E. Gazi, J. Dwyer, N. P. Lockyer. J. Miyan, P. Gardner, C.A Hart, M.D Brown, N.W. Clarke, A Study of Cytokinetic and Motile Prostate Cancer Cells Using Synchrotron Based FTIR - Microspectroscopic Imaging, Vibrational Spectroscopy 38 (2005) 193 - 201 31. E. Gazi, J. Dwyer, J. Miyan, P. Gardner, C. Hart, M. Brown, N.W. Clarke, Fixation Protocols for Sub-cellular Imaging by Synchrotron Based FTIR Microspectroscopy, Biopolymers 77 (2005) 18-30 32. E. Gazi, N. P. Lockyer, J. C. Vickerman, P. Gardner, J. Dwyer, C. A. Hart, M. B. Brown, N. W. Clarke J. Miyan, Imaging ToF-SIMS and synchrotron based FTIR-microspectroscopic studies of prostate cancer cell lines, Applied Surface Science 231 - 232 (2004) 452 - 456 33. E. Gazi, J. Dwyer, N. Lockyer, P. Gardner, J.C. Vickerman, J. Miyan, C. Hart, M. Brown and N. Clarke, Application of FTIR Microspectroscopy and ToF-SIMS Imaging in the Study of Prostate Cancer, Faraday Discussions 126 (2004) 41 - 59 34. E. Gazi, J. Dwyer, P. Gardner, A. Ghanbari-Siakhali, A. P. Wade. J. Myan. N.P.Lockyer, J. C. Vickerman, N. W. Clarke, J. H. Shanks, C. Hart, M.Brown, Applications of Fourier Transform Infrared Microspectroscopy in Studies of Benign Prostate & Prostate Cancer. A pilot Study, J. Pathology 201 (2003) 99-108