Detection of preclinical scrapie from serum by infrared spectroscopy and chemometrics

Developing and understanding biofluid vibrational spectroscopy: a critical review

Biofluid vibrational spectroscopy, a promising tool for rapid disease diagnosis.

Application of mid-infrared (MIR) microscopy imaging for discrimination between follicular hyperplasia and follicular lymphoma in transgenic mice

Mid-infrared (MIR) microscopy imaging is a vibrational spectroscopic technique that uses infrared radiation to image molecules of interest in thin tissue sections. A major advantage of this technology is the acquisition of local molecular expression profiles, while maintaining the topographic integrity of the tissue. Therefore, this technology has become an essential tool for the detection and characterization of the molecular components of many biological processes. Using this method, it is possible to investigate the spatial distribution of proteins and small molecules within biological systems by in situ analysis. In this study, we have evaluated the potential of mid-infrared microscopy imaging to study biochemical changes which distinguish between reactive lymphadenopathy and cancer in genetically modified mice with different phenotypes. We were able to demonstrate that MIR microscopy imaging and multivariate image analyses of different mouse genotypes correlated well with the morphological tissue features derived from HE staining. Using principal component analyses, we were also able to distinguish spectral clusters from different phenotype samples, particularly from reactive lymphadenopathy (follicular hyperplasia) and cancer (follicular lymphoma).

Measuring similarity and improving stability in biomarker identification methods applied to Fourier-transform infrared (FTIR) spectroscopy

FTIR spectroscopy is a powerful diagnostic tool that can also derive biochemical signatures of a wide range of cellular materials, such as cytology, histology, live cells, and biofluids. However, while classification is a well-established subject, biomarker identification lacks standards and validation of its methods. Validation of biomarker identification methods is difficult because, unlike classification, there is usually no reference biomarker against which to test the biomarkers extracted by a method. In this paper, we propose a framework to assess and improve the stability of biomarkers derived by a method, and to compare biomarkers derived by different method set-ups and between different methods by means of a proposed "biomarkers similarity index".

ATR-FTIR spectroscopy reveals genomic loci regulating the tissue response in high fat diet fed BXD recombinant inbred mouse strains

Background

Obesity-associated organ-specific pathological states can be ensued from the dysregulation of the functions of the adipose tissues, liver and muscle. However, the influence of genetic differences underlying gross-compositional differences in these tissues is largely unknown. In the present study, the analytical method of ATR-FTIR spectroscopy has been combined with a genetic approach to identify genetic differences responsible for phenotypic alterations in adipose, liver and muscle tissues.

Results

Mice from 29 BXD recombinant inbred mouse strains were put on high fat diet and gross-compositional changes in adipose, liver and muscle tissues were measured by ATR-FTIR spectroscopy. The analysis of genotype-phenotype correlations revealed significant quantitative trait loci (QTL) on chromosome 12 for the content of fat and collagen, collagen integrity, and the lipid to protein ratio in adipose tissue and on chromosome 17 for lipid to protein ratio in liver. Using gene expression and sequence information, we suggest Rsad2 (viperin) and Colec11 (collectin-11) on chromosome 12 as potential quantitative trait candidate genes. Rsad2 may act as a modulator of lipid droplet contents and lipid biosynthesis; Colec11 might play a role in apoptopic cell clearance and maintenance of adipose tissue. An increased level of Rsad2 transcripts in adipose tissue of DBA/2J compared to C57BL/6J mice suggests a cis-acting genetic variant leading to differential gene activation.

Conclusion

The results demonstrate that the analytical method of ATR-FTIR spectroscopy effectively contributed to decompose the macromolecular composition of tissues that accumulate fat and to link this information with genetic determinants. The candidate genes in the QTL regions may contribute to obesity-related diseases in humans, in particular if the results can be verified in a bigger BXD cohort.

FTIR spectroscopic imaging of protein aggregation in living cells

Protein misfolding and aggregation are the hallmark of a number of diseases including Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and the prion diseases. In all cases, a naturally-occurring protein misfolds and forms aggregates that are thought to disrupt cell function through a wide range of mechanisms that are yet to be fully unraveled. Fourier transform infrared (FTIR) spectroscopy is a technique that is sensitive to the secondary structure of proteins and has been widely used to investigate the process of misfolding and aggregate formation. This review focuses on how FTIR spectroscopy and spectroscopic microscopy are being used to evaluate the structural changes in disease-related proteins both in vitro and directly within cells and tissues. Finally, ongoing technological advances will be presented that are enabling time-resolved FTIR imaging of protein aggregation directly within living cells, which can provide insight into the structural intermediates, time scale, and mechanisms of cell toxicity associated with aggregate formation. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.

Cerebrospinal fluid biomarkers in human prion diseases

Cerebrospinal fluid (CSF) is the main component of the brain extracellular space and participates in the exchange of many biochemical products in the CNS. Consequently, CSF contains a dynamic and complex mixture of proteins that reflect the physiological or pathological state of the CNS. Changes in the CSF proteome have been described in various neurodegenerative disorders. These alterations are also thought to reflect pathological changes in the brain, and thus understanding them will contribute to a better awareness of the pathophysiology that underlies these disorders. Proteomics offers a new methodology for the analysis of pathological changes and mechanisms occurring in neurodegenerative processes and provides the possibility of novel biomarker discovery in order to supplement faster, earlier and more precise diagnosis. In general, the following criteria have to be applied in order to qualify a protein or a gene as a potential biomarker: the selected parameters have to be sensitive (able to detect the abnormalities at early stage of disease), specific (to allow differential diagnosis), reproducible with a high positive predictive value, and should allow for disease monitoring as well as a potential therapeutic response. In Creutzfeldt–Jakob disease, two major approaches have been followed that aim to detect the pathological form of the prion protein (PrPSc) in various peripheral tissues, while other approaches look for surrogate parameters that are a consequence of the neurodegenerative process. While the amount of abnormal disease-related PrPSc in CSF and blood in human transmissible spongiform encephalopathies appears to be extremely low, the development of a PrPSc-based biomarker was hampered by technical problems and detection limits. However, a variety of other proteins have been investigated in the CSF, and recently a variety of potential biomarkers have been reported that contribute to clinical diagnosis. Already established markers are 14-3-3, β-amyloid, tau-protein and phosphorylated isoforms, S100b, as well as neuron-specific enolase. Since some of these markers display certain limitations, the search continues. This review summarizes current knowledge of biomarker development in prion diseases and discusses perspectives for new approaches.

Toward point-of-care diagnostic metabolic fingerprinting: quantification of plasma creatinine by infrared spectroscopy of microfluidic-preprocessed samples

Infrared (IR) spectroscopy has previously been established as a means to accurately quantify several serum and urine metabolites, based upon spectroscopy of dry films. The same technique has also provided the basis to develop certain diagnostic tests, developed in the 'metabolomics' spirit. Here, we report on the further development of an integrated microfluidic-IR technology and technique, customized with the aim of dramatically extending the capabilities of IR spectroscopy in both analytical and diagnostic (metabolomic) applications. By exploiting the laminar fluid diffusion interface (LFDI), serum specimens are processed to yield product streams that are better suited for metabolic fingerprinting; metabolites are captured within the aqueous product stream, while proteins (which otherwise dominate the spectra of films dried from serum) are present in much reduced concentration. Spectroscopy of films dried from the aqueous stream then provides enhanced diagnostic and analytical sensitivity. The manuscript introduces an LFDI card design that is customized for integration with IR spectroscopy, and details the development of a quantitative assay for serum creatinine--based upon LFDI-processed serum samples--that is substantially more accurate (standard error of calibration, SEC = 43 micromol/L) than the corresponding assay based upon unprocessed serum specimens (SEC = 138 micromol/L). Preliminary results of diffusion modeling are reported, and the prospects for further optimization of the technique, guided by accurate modeling, are discussed.

Disease recognition by infrared and Raman spectroscopy

Infrared (IR) and Raman spectroscopy are emerging biophotonic tools to recognize various diseases. The current review gives an overview of the experimental techniques, data-classification algorithms and applications to assess soft tissues, hard tissues and body fluids. The methodology section presents the principles to combine vibrational spectroscopy with microscopy, lateral information and fiber-optic probes. A crucial step is the classification of spectral data by a variety of algorithms. We discuss unsupervised algorithms such as cluster analysis or principal component analysis and supervised algorithms such as linear discriminant analysis, soft independent modeling of class analogies, artificial neural networks support vector machines, Bayesian classification, partial least-squares regression and ensemble methods. The selected topics include tumors of epithelial tissue, brain tumors, prion diseases, bone diseases, atherosclerosis, kidney stones and gallstones, skin tumors, diabetes and osteoarthritis.

Metabolic profiling of serum using Ultra Performance Liquid Chromatography and the LTQ-Orbitrap mass spectrometry system

Advances in analytical instrumentation can provide significant advantages to the volume and quality of biological knowledge acquired in metabolomic investigations. The interfacing of sub-2 microm liquid chromatography (UPLC ACQUITY) and LTQ-Orbitrap mass spectrometry systems provides many theoretical advantages. The applicability of the interfaced systems was investigated using a simple 11-component metabolite mix and a complex mammalian biofluid, serum. Metabolites were detected in the metabolite mix with signals that were linear with their concentration over 2.5-3.5 orders of magnitude, with correlation coefficients greater than 0.993 and limits of detection less than 1 micromol L(-1). Reproducibility of retention time (RSD<3%) and chromatographic peak area (RSD<15%) and a high mass accuracy (<2 ppm) were observed for 14 QC serum samples interdispersed with other serum samples, analysed over a period of 40 h. The evaluation of a single deconvolution software package (XCMS) was performed and showed that two parameters (snthresh and bw) provided significant changes to the number of peaks detected and the peak area reproducibility for the dataset used. The data were used to indicate possible biomarkers of pre-eclampsia and showed both the instruments and XCMS to be applicable to the reproducible and valid detection of disease biomarkers present in serum.

Progress and limits of TSE diagnostic tools

Following the two "mad cow" crises of 1996 and 2000, there was an urgent need for rapid and sensitive diagnostic methods to identify animals infected with the bovine spongiform encephalopathy (BSE) agent. This stimulated research in the field of prion diagnosis and led to the establishment of numerous so-called "rapid tests" which have been in use in Europe since 2001 for monitoring at-risk populations (rendering plants) and animals slaughtered for human consumption (slaughterhouse). These rapid tests have played a critical role in the management of the mad cow crisis by allowing the removal of prion infected carcasses from the human food chain, and by allowing a precise epidemiological monitoring of the BSE epizootic. They are all based on the detection of the abnormal form of the prion protein (PrP(Sc) or PrP(res)) in brain tissues and consequently are only suitable for post-mortem diagnosis. Since it is now very clear that variant Creutzfeldt-Jakob disease (vCJD) can be transmitted by blood transfusion, the development of a blood test for the diagnosis of vCJD is a top priority. Although significant progress has been made in this direction, including the development of the protein misfolding cyclic amplification (PMCA) technology, at the time this paper was written, this objective had not yet been achieved. This is the most important challenge for the years to come in this field of prion research.

Analytical applications of Fourier transform-infrared (FT-IR) spectroscopy in microbiology and prion research

A genuine biophysical method, Fourier transform-infrared (FT-IR) spectroscopy has become a versatile research tool in biochemistry and biomedicine. Topical applications in microbiology and prion research are impressive illustrations of the vigorous evolution of the technique. FT-IR spectroscopy has established itself as a powerful method for the rapid differentiation and identification of microorganisms, thereby contributing to both clinical medicine and the prevention of bioterrorism. It has also led to considerable progress in various other fields of basic research, not least in prion sciences. In this field, FT-IR spectroscopy has been increasingly applied as a tool for elucidating structural features of the pathological prion protein, and also to study the molecular changes induced by prions in neuronal tissue and blood. This article sets out to give a review of current examples of the analytical potential of FT-IR spectroscopy in microbiology and prion research.

Application of Atomic Dielectric Resonance Spectroscopy for the screening of blood samples from patients with clinical variant and sporadic CJD

BACKGROUND

Sub-clinical variant Creutzfeldt-Jakob disease (vCJD) infection and reports of vCJD transmission through blood transfusion emphasise the need for blood screening assays to ensure the safety of blood and transplanted tissues. Most assays aim to detect abnormal prion protein (PrPSc), although achieving required sensitivity is a challenge.

METHODS

We have used innovative Atomic Dielectric Resonance Spectroscopy (ADRS), which determines dielectric properties of materials which are established by reflectivity and penetration of radio/micro waves, to analyse blood samples from patients and controls to identify characteristic ADR signatures unique to blood from vCJD and to sCJD patients. Initial sets of blood samples from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors) were screened as training samples to determine group-specific ADR characteristics, and provided a basis for classification of blinded sets of samples.

RESULTS

Blood sample groups from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors) screened by ADRS were classified with 100% specificity and sensitivity, discriminating these by a co-variance expert analysis system.

CONCLUSION

ADRS appears capable of recognising and discriminating serum samples from vCJD, sCJD, non-CJD neurological diseases, and normal healthy adults, and might be developed to provide a system for primary screening or confirmatory assay complementary to other screening systems.