Matthew J. Baker

Using Fourier transform IR spectroscopy to analyze biological materials

IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.

5' splice site mutations in tau associated with the inherited dementia FTDP-17 affect a stem-loop structure that regulates alternative splicing of exon 10.

Missense and splice site mutations in the microtubule-associated protein tau gene were recently found associated with fronto-temporal dementia and parkinsonism linked to chromosome 17 (Poorkaj et al. (1998) Ann. Neurol. 43, 815–825; Hutton et al. (1998)Nature 393, 702–705; Spillantini et al. (1998)Proc. Natl. Acad. Sci. U. S. A. 95, 7737–7741). The mutations in the 5′ splice site of exon 10 were shown to increase the ratio of tau mRNAs containing exon 10 and thus the proportion of Tau protein isoforms with 4 microtubule binding repeat domains, although how this increase leads to neurodegeneration is presently unclear. The mechanism by which these mutations increasetau exon 10 splicing was not determined, although the mutations were predicted to disrupt a potential stem-loop structure that was likely involved in the regulation of exon 10 alternative splicing. Here we describe in vitro splicing assays and RNA structural analysis that demonstrate that the mutations do indeed act through disruption of the stem-loop structure and that the stability of this secondary structure feature at least partially determines the ratio of tau exon 10+/− transcripts. In addition, we provide evidence that the stability of the stem-loop structure underlies the alternative splicing of this exon in other species.

FTIR-based spectroscopic analysis in the identification of clinically aggressive prostate cancer

Fourier transform infrared (FTIR) spectroscopy is a vibrational spectroscopic technique that uses infrared radiation to vibrate molecular bonds within the sample that absorbs it. As different samples contain different molecular bonds or different configurations of molecular bonds, FTIR allows us to obtain chemical information on molecules within the sample. Fourier transform infrared microspectroscopy in conjunction with a principal component-discriminant function analysis (PC-DFA) algorithm was applied to the grading of prostate cancer (CaP) tissue specimens. The PC-DFA algorithm is used alongside the established diagnostic measures of Gleason grading and the tumour/node/metastasis system. Principal component-discriminant function analysis improved the sensitivity and specificity of a three-band Gleason score criterion diagnosis previously reported by attaining an overall sensitivity of 92.3% and specificity of 99.4%. For the first time, we present the use of a two-band criterion showing an association of FTIR-based spectral characteristics with clinically aggressive behaviour in CaP manifest as local and/or distal spread. This paper shows the potential for the use of spectroscopic analysis for the evaluation of the biopotential of CaP in an accurate and reproducible manner.

Investigating FTIR based histopathology for the diagnosis of prostate cancer.

Prostate cancer is the most common gender specific cancer. The current gold standard for diagnosis, histopathology, is subjective and limited by variation between different pathologists. The diagnostic problems associated with the correct grading and staging of prostate cancer (CaP) has led to an interest in the development of spectroscopic based diagnostic techniques. FTIR microspectroscopy used in combination with a Principal Component Discriminant Function Analysis (PC-DFA) was applied to investigate FTIR based histopathology for the diagnosis of CaP. In this paper we report the results of a large patient study in which FTIR has been proven to grade CaP tissue specimens to a high degree of sensitivity and specificity.

Improved Protocols for Vibrational Spectroscopic Analysis of Body Fluids

The applications of vibrational spectroscopy to the examination of human blood serum are explored. Although FTIR spectra can be recorded in aqueous solutions at (gelatin) concentrations as low as 100 mg/L, the high-wavenumber region remains obscured by water absorption. Using Raman spectroscopy, high quality spectra of gelatine solutions as low as 10 mg/L can be achieved, also covering the high-wavenumber regions. In human serum, spectral profiles are weak and partially obscured by water features. Dried deposits are shown to be physically and chemically inhomogeneous resulting in reduced measurement reproducibility. Concentration of the serum using commercially available centrifugal filter devices results in an improvement in the spectral intensity and quality. Additionally, in Raman spectroscopy, reduced background and significantly enhanced signal collection is achievable by measurement in an inverted geometry. The improved protocols for spectroscopic measurement of human serum are applicable to a range of bodily fluids and should accelerate potential clinical applications.

Attenuated total reflection fourier transform infrared (ATR-FTIR) spectral discrimination of brain tumour severity from serum samples

Gliomas are the most frequent primary brain tumours in adults with over 9,000 people diagnosed each year in the UK. A rapid, reagent-free and cost-effective diagnostic regime using serum spectroscopy would allow for rapid diagnostic results and for swift treatment planning and monitoring within the clinical environment. We report the use of ATR-FTIR spectral data combined with a RBF-SVM for the diagnosis of gliomas (high-grade and low-grade) from non-cancer with sensitivities and specificities on average of 93.75 and 96.53% respectively. The proposed diagnostic regime has the ability to reduce mortality and morbidity rates.

An investigation of the RWPE prostate derived family of cell lines using FTIR spectroscopy.

Interest in developing robust, quicker and easier diagnostic tests for cancer has lead to an increased use of Fourier transform infrared (FTIR) spectroscopy to meet that need. In this study we present the use of different experimental modes of infrared spectroscopy to investigate the RWPE human prostate epithelial cell line family which are derived from the same source but differ in their mode of transformation and their mode of invasive phenotype. Importantly, analysis of the infrared spectra obtained using different experimental modes of infrared spectroscopy produces similar results. The RWPE family of cell lines can be separated into groups based upon the method of cell transformation rather than the resulting invasiveness/aggressiveness of the cell line. The study also demonstrates the possibility of using a genetic algorithm as a possible standardised pre-processing step and raises the important question of the usefulness of cell lines to create a biochemical model of prostate cancer progression.

Mass spectral imaging of glycophospholipids, cholesterol, and glycophorin A in model cell membranes

Time of flight secondary ion mass spectrometry (ToF-SIMS) and the Langmuir-Blodgett (LB) technique have been used to create and analyze reproducible membrane mimics of the inner and outer leaflets of a cellular membrane to investigate lipid-protein and lipid-lipid interactions. Films composed of phospholipids, cholesterol and an integral membrane protein were utilized. The results show the outer membrane leaflet mimic (DPPC/cholesterol/glycophorin A LB film) consisting of a single homogeneous phase whereas the inner membrane leaflet mimic (DPPE/cholesterol/glycophorin A LB film) displays heterogeneity in the form of two separate phases. A DPPE/cholesterol phase and a glycophorin A phase. This points to differences in membrane domain formation based upon the different chemical composition of the leaflets of a cell membrane. The reliability of the measurements was enhanced by establishing the influence of the matrix effect upon the measurement and by utlilizing PCA to enhance the contrast of the images.

Rapid FTIR chemical imaging: highlighting FPA detectors

Fourier transform infrared (FTIR) spectroscopy is an established analytical technique that measures molecular bond vibrations via infrared absorption. The technique traditionally obtains single spectra from a sample, averaging the absorption information over a pre-determined aperture size. However, this averaging of information can be detrimental to pure biochemical analysis. The coupling of focal plane array (FPA) detectors to conventional FTIR systems and recent technical advances in FPA technology have allowed the concurrent rapid collection of thousands of infrared spectra over large areas of a sample, which has been particularly useful in tissue analysis. This novel technique presents a strong case for its use as a potential tool to aid in the clinic for disease diagnosis and assessment.

Highlighting attenuated total reflection Fourier transform infrared spectroscopy for rapid serum analysis

Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy is an excellent vibrational spectroscopic technique for the analysis of serum due to its rapidity and ease of translation into the clinical environment. FTIR is an analytical technique that produces spectra summarising infrared absorption peaks over a limited wavelength range that can be explained by molecular vibrations within a sample that has been exposed to a source of infrared radiation. FTIR spectroscopy combined with appropriate data handling frameworks over the years has proved a useful tool in biomedical research, particularly in the identification and diagnosis of cancer and other diseases, through the discovery of diagnostic biomarkers from the complexity of the biological background [1]. Current methods for cancer diagnosis look at several criteria, with the gold standard for cancer detection being histopathology. Histopathology is a subjective method for cancer diagnosis which is invasive, time consuming, and requires experienced interpretation. Here, we focus on the findings and the potential of serum analysis for cancer diagnosis using a specific method of FTIR spectroscopy called ATR-FTIR, offering point-of-care testing with minimal interpretation.