Online coupling of capillary electrophoresis with mass spectrometry for the identification of biomarkers for clinical diagnosis

Proteomic screening of complex biologic samples is of increasing importance in clinical research and diagnosis. In the postgenomic area it is evident that changes of the composition of body fluids, as well as post-translational modifications of proteins and peptides, provide more information than genetic typing. The study of these changes allows the state of health or disease of particular organs, and consequently, the whole organism, to be described. This review describes the application of capillary electrophoresis coupled online to an electrospray ionization time-of-flight mass spectrometer to the analysis of body fluids obtained from patients for the identification of biomarkers for diagnostic purposes.     

Quantitative analysis of DNA methylation after whole bisulfitome amplification of a minute amount of DNA from body fluids

Cell-free circulating DNA isolated from the plasma of individuals with cancer has been shown to harbor cancer-associated changes in DNA methylation, and thus it represents an attractive target for biomarker discovery. However, the reliable detection of DNA methylation changes in body fluids has proven to be technically challenging. Here we describe a novel combination of methods that allows quantitative and sensitive detection of DNA methylation in minute amounts of DNA present in body fluids (quantitative Methylation Analysis of Minute DNA amounts after whole Bisulfitome Amplification, qMAMBA). This method involves genome-wide amplification of bisulphite-modified DNA template followed by quantitative methylation detection using pyrosequencing and allows analysis of multiple genes from a small amount of starting DNA. To validate our method we used qMAMBA assays for four genes and LINE1 repetitive sequences combined with plasma DNA samples as a model system. qMAMBA offered high efficacy in the analysis of methylation levels and patterns in plasma samples with extremely small amounts of DNA and low concentrations of methylated alleles. Therefore, qMAMBA will facilitate methylation studies aiming to discover epigenetic biomarkers, and should prove particularly valuable in profiling a large sample series of body fluids from molecular epidemiology studies as well as in tracking disease in early diagnostics.     

Quantitation of desmosine and isodesmosine in urine, plasma, and sputum by LC-MS/MS as biomarkers for elastin degradation

The aim of this study is to develop a standardized LC-MS/MS method for accurate measurement of desmosine (DES) and isodesmosine (IDS) in all body fluids as biomarkers for in vivo degradation of matrix tissue elastin in man and animals. A reproducible three-step analytical procedure: (1) sample hydrolysis in 6N HCl, (2) SPE by a CF1 cartridge with addition of acetylated pyridinoline as internal standard (IS), and (3) LC/MSMS analysis by SRM monitoring of transition ions; DES or IDS (m/z 526-481+397) and IS (m/z 471-128) was developed. The method achieves accurate measurements of DES/IDS in accessible body fluids (i.e. urine, plasma, and sputum). LOQ of DES/IDS in body fluids is 0.1 ng/ml. The % recoveries and reproducibility from urine, plasma, and sputum samples are above 99 ± 8% (n = 3), 94 ± 9% (n = 3) and 87 ± 11% (n = 3), with imprecision 8%, 9% and 10%, respectively. The proposed method was applied to measure DES/IDS in body fluids of patients with chronic obstructive pulmonary disease (COPD) and healthy controls. Total DES/IDS in sputum and plasma is increased over normal controls along with the free DES/IDS in urine in patients. DES/IDS can be used to study the course of COPD and the response to therapy. This practical and reliable LC-MS/MS method is proposed as a standardized method to measure DES and IDS in body fluids. This method can have wide application for investigating diseases which involve elastic tissue degradation.     

Peroxidase-labeled antibody staining for carcinoembryonic antigen of cytologic specimens for light and electron microscopy

Immunohistochemical staining methods suitable for light and electron microscopic examination of cytologic specimens are described. Application of the methods clearly demonstrated the localization of carcinoembryonic antigen (CEA) in adenocarcinoma cells in body fluids. The use of a peroxidase-labeled antibody method permits rapid penetration of the cells by the antibody, which is not achieved by the peroxidase-antiperoxidase or avidin-biotin-peroxidase-complex staining methods. Since mesothelial and inflammatory cells are negative for CEA, the staining of body fluids for CEA is expected to be an extremely useful tool for the differential diagnosis of adenocarcinoma.     

Simultaneous extraction and rapid visualization of peptidomic and lipidomic body fluids fingerprints using mesoporous aluminosilicate and MALDI‐TOF MS

Herein we report the use of mesoporous aluminosilicate (MPAS) for the simultaneous extraction of peptides and lipids from complex body fluids such as human plasma and synovial fluid. We show that MPAS particles, given their mesostructural features with nanometric pore size and high surface area, are an efficient device for simultaneous extraction of peptidome and lipidome from as little as a few microliters of body fluids. The peptides and the lipids, selected and enriched by MPAS particles and rapidly visualized by MALDI‐TOF MS, could form part of a diagnostic profile of the “peptidome” and the “lipidome” of healthy versus diseased subjects in comparative studies. The ability of this approach to rapidly reveal the overall pattern of changes in both lipidome and peptidome signatures of complex biofluids could be of valuable interest for handling large numbers of samples required in ‐omics studies for the purpose of finding novel biomarkers.     

Methylation Markers for the Identification of Body Fluids and Tissues from Forensic Trace Evidence

The identification of body fluids is an essential tool for clarifying the course of events at a criminal site. The analytical problem is the fact that the biological material has been very often exposed to detrimental exogenous influences. Thereby, the molecular substrates used for the identification of the traces may become degraded. So far, most protocols utilize cell specific proteins or RNAs. Instead of measuring these more sensitive compounds this paper describes the application of the differential DNA-methylation. As a result of two genome wide screenings with the Illumina HumanMethylation BeadChips 27 and 450k we identified 150 candidate loci revealing differential methylation with regard to the body fluids venous blood, menstrual blood, vaginal fluid, saliva and sperm. Among them we selected 9 loci as the most promising markers. For the final determination of the methylation degree we applied the SNuPE-method. Because the degree of methylation might be modified by various endogenous and exogenous factors, we tested each marker with approximately 100 samples of each target fluid in a validation study. The stability of the detection procedure is proved in various simulated forensic surroundings according to standardized conditions. We studied the potential influence of 12 relatively common tumors on the methylation of the 9 markers. For this purpose the target fluids of 34 patients have been analysed. Only the cervix carcinoma might have an remarkable effect because impairing the signal of both vaginal markers. Using the Illumina MiSeq device we tested the potential influence of cis acting sequence variants on the methylation degree of the 9 markers in the specific body fluid DNA of 50 individuals. For 4 marker loci we observed such an influence either by sole SNPs or haplotypes. The identification of each target fluid is possible in arbitrary mixtures with the remaining four body fluids. The sensitivity of the individual body fluid tests is in the same range as for the forensic STR-analysis. It is the first forensic body fluid protocol which considers the exogenic and endogenic parameters potentially interfering with the true results.     

Circulating RNAs as predictive markers for the progression of type 2 diabetes

Type 2 Diabetes Mellitus (T2DM) is the most prevalent form of diabetes in the USA, thus, the identification of biomarkers that could be used to predict the progression from prediabetes to T2DM would be greatly beneficial. Recently, circulating RNA including microRNAs (miRNAs) present in various body fluids have emerged as potential biomarkers for various health conditions, including T2DM. Whereas studies that examine the changes of miRNA spectra between healthy controls and T2DM individuals have been reported, the goal of this study is to conduct a baseline comparison of prediabetic individuals who either progress to T2DM, or remain prediabetic. Using an advanced small RNA sequencing library construction method that improves the detection of miRNA species, we identified 57 miRNAs that showed significant concentration differences between progressors (progress from prediabetes to T2DM) and non‐progressors. Among them, 26 have been previously reported to be associated with T2DM in either body fluids or tissue samples. Some of the miRNAs identified were also affected by obesity. Furthermore, we identified miRNA panels that are able to discriminate progressors from non‐progressors. These results suggest that upon further validation these miRNAs may be useful to predict the risk of conversion to T2DM from prediabetes.     

Bioimpedance analysis of fluids and body composition under the conditions of short-term space flight or hypokinesia

Hydration status of humans was assessed by means of bioimpedancemetry on board the space station or under the conditions of antiorthostatic hypokinesia (AOSH). Water compartments of the body were decreased in a cosmonaut at the seventh day of a ten-day-long flight to the same degree as in a group of six testers by the seventh day of AOSH (?8°): the amount of total body fluids and intracellular and extracellular volumes were decreased by 5.6–6.5% as compared to the baseline level. The changes in body composition of a cosmonaut during flight were similar to the changes observed in testers during AOSH: lean body weight, which was determined by bioimpedancemetry, was insignificantly decreased, whereas the adipose component of body weight was, on the contrary, increased. It was concluded that the hydration level of the human body was decreased and the amount of body fat was increased during a short-term space flight. It was also shown that the hydration status and composition of the human body were changed in a similar way under the conditions of both AOSH and space flight, which indicates that this ground-based model is adequate for simulation of hydration changes caused by microgravity.     

Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry

A main objective of proteomics research is to systematically identify and quantify proteins in a given proteome (cells, subcellular fractions, protein complexes, tissues or body fluids). Protein labeling with isotope-coded affinity tags (ICAT) followed by tandem mass spectrometry allows sequence identification and accurate quantification of proteins in complex mixtures, and has been applied to the analysis of global protein expression changes, protein changes in subcellular fractions, components of protein complexes, protein secretion and body fluids. This protocol describes protein-sample labeling with ICAT reagents, chromatographic fractionation of the ICAT-labeled tryptic peptides, and protein identification and quantification using tandem mass spectrometry. The method is suitable for both large-scale analysis of complex samples including whole proteomes and small-scale analysis of subproteomes, and allows quantitative analysis of proteins, including those that are difficult to analyze by gel-based proteomics technology.     

Amino acid composition of the lymph and blood in allergic transformations of the body

The time-course of changes in the content of free amino acids and total protein in lymph of the thoracic duct and peripheral blood was studied in dogs during sensitization and anaphylactic shock (AS). Allergic rearrangement of the body during AS was accompanied by considerable disorders in redistribution of free amino acids in body fluids (blood, interstitial fluid and lymph). It is assumed that changes in the quantitative ratios occurring between individual amino acids during metabolic processes under sensitization are likely to cause protein biosynthesis disorders in the body experiencing allergic rearrangement.     

Urinary Biomarkers of Brain Diseases

Biomarkers are the measurable changes associated with a physiological or pathophysiological process. Unlike blood, urine is not subject to homeostatic mechanisms. Therefore, greater fluctuations could occur in urine than in blood, better reflecting the changes in human body. The roadmap of urine biomarker era was proposed. Although urine analysis has been attempted for clinical diagnosis, and urine has been monitored during the progression of many diseases, particularly urinary system diseases, whether urine can reflect brain disease status remains uncertain. As some biomarkers of brain diseases can be detected in the body fluids such as cerebrospinal fluid and blood,there is a possibility that urine also contain biomarkers of brain diseases. This review summarizes the clues of brain diseases reflected in the urine proteome and metabolome.     

Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer

DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.     

Evidence for Two Extremes of Ciliary Motor Response in a Single Swimming Microorganism

Because arrays of motile cilia drive fluids for a range of processes, the versatile mechano-chemical mechanism coordinating them has been under scrutiny. The protist Paramecium presents opportunities to compare how groups of cilia perform two distinct functions, swimming propulsion and nutrient uptake. We present how the body cilia responsible for propulsion and the oral-groove cilia responsible for nutrient uptake respond to changes in their mechanical environment accomplished by varying the fluid viscosity over a factor of 7. Analysis with a phenomenological model of trajectories of swimmers made neutrally buoyant with magnetic forces combined with high-speed imaging of ciliary beating reveal that the body cilia exert a nearly constant propulsive force primarily by reducing their beat frequency as viscosity increases. By contrast, the oral-groove cilia beat at a nearly constant frequency. The existence of two extremes of motor response in a unicellular organism prompts unique investigations of factors controlling ciliary beating.     

Evidence for Two Extremes of Ciliary Motor Response in a Single Swimming Microorganism

Because arrays of motile cilia drive fluids for a range of processes, the versatile mechano-chemical mechanism coordinating them has been under scrutiny. The protist Paramecium presents opportunities to compare how groups of cilia perform two distinct functions, swimming propulsion and nutrient uptake. We present how the body cilia responsible for propulsion and the oral-groove cilia responsible for nutrient uptake respond to changes in their mechanical environment accomplished by varying the fluid viscosity over a factor of 7. Analysis with a phenomenological model of trajectories of swimmers made neutrally buoyant with magnetic forces combined with high-speed imaging of ciliary beating reveal that the body cilia exert a nearly constant propulsive force primarily by reducing their beat frequency as viscosity increases. By contrast, the oral-groove cilia beat at a nearly constant frequency. The existence of two extremes of motor response in a unicellular organism prompts unique investigations of factors controlling ciliary beating.     

Diagnostic accuracy of the immunocytochemical study of body fluids

The diagnostic accuracy of the immunocytochemical characterization of body fluids was evaluated in 100 specimens (35 pleural, 40 peritoneal, 7 pericardial and 18 cerebrospinal [CSF] fluids) in comparison with routine morphologic examination. The immunochemical markers used for all specimens were common-leukocyte antigen, epithelial membrane antigen, epithelial keratin and desmin. Additional immunocytochemical studies for neurofilaments, glial fibrillary acidic protein, vimentin and melanoma-associated antigen were performed on the CSF specimens. The study confirmed the accuracy of the immunocytochemical characterization of cells in body fluids using a panel of immunocytochemical stains. These methods are recommended as an adjunct to improve the accuracy of the cytologic diagnosis of body fluids, especially in cases with diagnostically difficult morphologic features.     

Simplified equations for the distribution of chloride in body water

According to the theory of Boyle and Conway, chloride leaves the extracellular fluid to enter cells, particularly muscle, when the plasma potassium concentrationK rises. Simplified equations are presented to describe in terms ofK the distribution of chloride expected when the quantity of the saltKp in the body fluids changes in health and disease.     

The Hemolymph Proteome of Fed and Starved Drosophila Larvae

The co-operation of specialized organ systems in complex multicellular organisms depends on effective chemical communication. Thus, body fluids (like blood, lymph or intraspinal fluid) contain myriads of signaling mediators apart from metabolites. Moreover, these fluids are also of crucial importance for immune and wound responses. Compositional analyses of human body fluids are therefore of paramount diagnostic importance. Further improving their comprehensiveness should increase our understanding of inter-organ communication. In arthropods, which have trachea for gas exchange and an open circulatory system, the single dominating interstitial fluid is the hemolymph. Accordingly, a detailed analysis of hemolymph composition should provide an especially comprehensive picture of chemical communication and defense in animals. Therefore we used an extensive protein fractionation workflow in combination with a discovery-driven proteomic approach to map out the detectable protein composition of hemolymph isolated from Drosophila larvae. Combined mass spectrometric analysis revealed more than 700 proteins extending far beyond the previously known Drosophila hemolymph proteome. Moreover, by comparing hemolymph isolated from either fed or starved larvae, we provide initial provisional insights concerning compositional changes in response to nutritional state. Storage proteins in particular were observed to be strongly reduced by starvation. Our hemolymph proteome catalog provides a rich basis for data mining, as exemplified by our identification of potential novel cytokines, as well as for future quantitative analyses by targeted proteomics.     

Some aspects of the mechanism of thermal acclimation in the earthworm Lampito mauritii

Summary Inorganic ions (Ca, Mg, Na, K, Cl, SO₄) and free amino acids of the body fluids of the normal, cold and warm acclimated worms (laboratory as well as seasonal populations) are estimated. Calcium increased and chloride and sodium decreased on both cold and warm acclimation in relation to normal. But magnesium and sulphate and free amino acids increased on warm acclimation whereas potassium increased and magnesium decreased on cold acclimation. Changes in different ions in the same direction are observed in the seasonal populations. Attention is drawn to the adaptive significance of these changes in the different ions during thermal acclimation.Changes in the glycogen, RNA, protein and non-protein nitrogen, and water content in the tissues of normal and acclimated worms are studied. Glycogen increased on warm and cold acclimation, whereas RNA content, protein nitrogen and dry weight of the cold worms increased over normal. No change is observed in non-protein nitrogen on thermal acclimation. The role of these substances and the significance of the changes observed, in the operation of homeostatic mechanism compensating to temperature changes in the metabolic rate of the worms, are also discussed.Changes in the pattern of neurosecretory activity are followed with thermal acclimation and it is shown that the activity of the neurosecretory cells increased on cold and warm acclimation, but the positions of these cells, which are active, are different from normal worms in warm acclimated worms.Studies on the effect of the body fluids of acclimated worms on the tissues of normal and acclimated worms showed that the body fluids of cold acclimated worms increased the respiration of the tissues of normal and warm acclimated worms and vice-versa.     

Is mitochondrial DNA content a potential biomarker of mitochondrial dysfunction?

Mitochondrial dysfunction is central to numerous diseases of oxidative stress. Changes in mitochondrial DNA (MtDNA) content, often measured as mitochondrial genome to nuclear genome ratio (Mt/N) using real time quantitative PCR, have been reported in a broad range of human diseases, such as diabetes and its complications, obesity, cancer, HIV complications, and ageing. We propose the hypothesis that MtDNA content in body fluids and tissues could be a biomarker of mitochondrial dysfunction and review the evidence supporting this theory. Increased reactive oxygen species resulting from an external trigger such as hyperglycaemia or increased fat in conditions of oxidative stress could lead to enhanced mitochondrial biogenesis, and increased Mt/N. Altered MtDNA levels may contribute to enhanced oxidative stress and inflammation and could play a pathogenic role in mitochondrial dysfunction and disease. Changes in Mt/N are detectable in circulating cells such as peripheral blood mononuclear cells and these could be used as surrogate to predict global changes in tissues and organs. We review a large number of studies reporting changes in MtDNA levels in body fluids such as circulating blood cells, cell free serum, saliva, sperm, and cerebrospinal fluid as well as in tumour and normal tissue samples. However, the data are often conflicting as the current methodology used to measure Mt/N can give false results because of one or more of the following reasons (1) use of mitochondrial primers which co-amplify nuclear pseudogenes (2) use of nuclear genes which are variable and/or duplicated in numerous locations (3) a dilution bias caused by the differing genome sizes of the mitochondrial and nuclear genome and (4) template preparation protocols which affect the yields of nuclear and mitochondrial genomes. Development of robust and reproducible methodology is needed to test the hypothesis that MtDNA content in body fluids is biomarker of mitochondrial dysfunction.     

Influence of uterine secretions on the chromatin of ram spermatozoa at different stages of maturation: Cytophotometric study of Feulgen-DNA after in vitro incubation

Ram spermatozoa taken from the epididymal head, body, or tail or from the ejaculate were examined by microspectrometry after incubation in vitro with ewe uterine fluids at 37°C for 20 hours. Compared with incubation in Ringer's solution, uterine fluid incubation resulted in a decrease in nuclear Feulgen-DNA content. This decrease was greater for more immature spermatozoa (29.0 and 47.3% for spermatozoa from head and body, respectively) than for more mature spermatozoa (17.7 and 4.0% for spermatozoa from the tail and the ejaculate, respectively). In parallel with this decrease, there was a condensation of the chromatin which resulted in a decreased nuclear surface area, especially in spermatozoa taken from the epididymal body. Therefore, it would appear that, during epididymal maturation, changes in the ability of spermatozoa to maintain embryonic development as the spermatozoa mature are due to changes in chromatin structure.