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Background: One of the new roles for enzymes in personalized medicine builds on a rational approach to cancer biomarker discovery using enzyme-associated aberrant glycosylation. A hallmark of cancer, aberrant glycosylation is associated with differential expressions of enzymes such as glycosyltransferase and glycosidases. The aberrant expressions of the enzymes in turn cause cancer cells to produce glycoproteins with specific cancer-associated aberrations in glycan structures., Content: In this review we provide examples of cancer biomarker discovery using aberrant glycosylation in three areas. First, changes in glycosylation machinery such as glycosyltransferases/glycosidases could be used as cancer biomarkers. Second, most of the clinically useful cancer biomarkers are glycoproteins. Discovery of specific cancer-associated aberrations in glycan structures of these existing biomarkers could improve their cancer specificity, such as the discovery of AFP-L3, fucosylated glycoforms of AFP. Third, cancer-associated aberrations in glycan structures provide a compelling rationale for discovering new biomarkers using glycomic and glycoproteomic technologies., Summary: As a hallmark of cancer, aberrant glycosylation allows for the rational design of biomarker discovery efforts. But more important, we need to translate these biomarkers from discovery to clinical diagnostics using good strategies, such as the lessons learned from translating the biomarkers discovered using proteomic technologies to OVA 1, the first FDA-cleared In Vitro Diagnostic Multivariate Index Assay (IVDMIA). These lessons, providing important guidance in current efforts in biomarker discovery and translation, are applicable to the discovery of aberrant glycosylation associated with enzymes as cancer biomarkers as well.

Antibody-overlay lectin microarray (ALM) has been used for targeted glycan profiling to identify disease-related protein glycoforms. In this context, high sensitivity is desired because it allows for the identification of disease-related glycoforms that are often present at low concentrations. We describe a new tyramide signal amplification (TSA) for the antibody-overlay lectin microarray procedure for sensitive profiling of glycosylation patterns. We demonstrate that TSA increased the sensitivity of the microarray over 100 times for glycan profiling using the model protein prostate specific antigen (PSA). The glycan profile of PSA enriched from LNCAP cells, obtained at a subnanogram level with the aid of TSA, was consistent with the previous reports. We also established the glycan profile of prostate specific membrane antigen (PSMA) using the TSA and ALM. Thus, the TSA for antibody-overlay lectin microarray is a sensitive, rapid, comprehensive, and high-throughput method for targeted glycan profiling and can potentially be used for the identification of disease-related protein glycoforms.

Background: When creatinine concentrations determined by routine clinical assays are in question, reference methods can aid investigation. Currently available reference methods are significantly labor-intensive, which prevents implementation in a routine clinical laboratory., Methods: Creatinine D-3 internal standard was added to serum prior to chromatographic separation. A TurboFlow Cyclone MCX column was used for online solid phase extraction (SPE) to remove large biomolecules such as proteins, carbohydrates and phospholipids from the serum specimen. Creatinine and creatinine D-3 were then eluted onto a Hypercarb (porous graphitic carbon) column for separation. Analytes were detected using electrospray ionization tandem mass spectrometry and measured by monitoring parent ions of m/z 114 and 117, respectively., Results: Total precision at multiple levels was found to be less than 6% (1.0-7.5 mg/dl). Limit of detection (LOD) was 0.05 mg/dl and limit of quantitation (LOQ) was 0.20 mg/dl. Average recovery was 107.5% (0.37-5.95 mg/dl). Analysis of standard reference materials from The National Institute of Standards and Technology (NIST) confirmed accuracy of the method. No significant difference was found between the liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) method and the Roche Creatinine Plus enzymatic assay., Conclusion: The automated turbulent flow LC-IDMS method for quantitation of serum creatinine is accurate, robust, and easy to perform and may serve as a quick and inexpensive alternative to current creatinine reference methods., (2010 Elsevier B.V. All rights reserved.)

BACKGROUND: Plasma tumor biomarkers are widely used clinically for monitoring response to therapy and detecting cancer recurrence. However, only a limited number of them have been effectively used for the early detection of cancer. OBJECTIVE: To review plasma tumor markers used clinically for the early detection of cancer and to provide expert opinion about future directions. METHODS: Literature review, as well as our expert opinion, of plasma tumor markers that have been widely accepted for the early detection of cancer. RESULTS: In the United States, only prostate specific antigen (PSA), cancer antigen 125 (CA125), and alpha-fetoprotein (AFP) have been clinically used for the early detection of prostate, ovarian, and liver cancers, respectively. Both analytical and clinical issues related to the use of these three markers were discussed. CONCLUSION: Few plasma tumor markers have been used effectively for the early detection of cancer, mainly due to their limited sensitivity and/or specificity. Multiple approaches have been developed to improve the clinical performance of tumor markers for the early detection of cancer. Metrological traceability and antibody specificity are important issues to ensure comparability of immunoassays for the measurement of plasma tumor markers.

Formalin-fixed, paraffin-embedded (FFPE) tissues have been used to discover disease-associated protein changes using mass spectrometry. Protein post-translational modifications such as glycosylation are known to associate with disease development. In this study, we investigated whether FFPE tissues preserve such modifications and therefore can be used as specimen of choice to identify the disease-associated modifications. We isolated the glycopeptides from the tryptic digest of frozen and FFPE lung tissues using solid-phase extraction of glycopeptides and analyzed them using mass spectrometry. The glycopeptides identified from FFPE lung tissue were compared to the ones from frozen lung tissue regarding their relative abundance, unique glycosylation sites, and subcellular locations. The results from our study confirmed that glycosylation in FFPE tissues are preserved and FFPE tissues can be used for discovery of new disease associated changes in protein modifications. Furthermore, we demonstrated the feasibility of applying the strategy of glycopeptide isolation from tryptic peptides of FFPE tissue to other tissues such as liver and heart.

Currently, serum prostate-specific antigen (PSA) is used for the early detection of prostate cancer despite its low specificity in the range of 4-10 ng/mL. Because aberrant glycosylation is a fundamental characteristic of tumor genesis, the objective of this study was to investigate whether changes in PSA glycosylation may be used to improve the cancer specificity of PSA. We developed five lectin immunosorbant assays to analyze the glycosylation patterns of PSA in serum. Each assay sandwiches serum PSA between a PSA monoclonal antibody and a biotinylated lectin and then tags the biotin complex using a streptavidin SULFO TAG for electrochemiluminescence detection. Low limits of detection (0.04-1.35 ng/mL), good reproducibility (%CVs < 10%), and direct analysis of PSA glycosylation in sera suggest these assays may have a potential role in improving PSA's cancer specificity. Clinical performance was evaluated in 52 human subjects (26 cancer and 26 noncancer). ROC analysis showed that the total SNA assay (AUC = 0.71) appeared to perform better than percent free PSA (AUC = 0.54) in its diagnostic gray zone between 10 and 20% in a subset of 21 subjects. A separate study of 16 additional subjects showed similar findings.

Carbonylation is a highly prevalent protein modification in skeletal muscle mitochondria, possibly contributing to its functional decline with age. Using quantitative proteomics, we identified mitochondrial proteins susceptible to carbonylation in a muscle type (slow- vs fast-twitch)-dependent and age-dependent manner from Fischer 344 rat skeletal muscle. Fast-twitch muscle contained twice as many carbonylated mitochondrial proteins than did slow-twitch muscle, with 22 proteins showing significant changes in carbonylation state with age, the majority of these increasing in their amount of carbonylation. Ingenuity pathway analysis revealed that these proteins belong to functional classes and pathways known to be impaired in muscle aging, including cellular function and maintenance, fatty acid metabolism, and citrate cycle. Although our studies do not conclusively link protein carbonylation to these functional changes in aging muscle, they provide a unique catalogue of promising protein targets deserving further investigation because of their potential role in aging muscle decline.

Respiring mitochondria produce superoxide and release it into both sides of the mitochondrial inner membrane: the mitochondrial matrix and the extramitochondrial space. These two pools of superoxide are expected to have very distinctive effects on cellular function. Currently, separate measurements are required to measure superoxide in both pools, which complicates the comparison of superoxide's effects and roles in physiology and pathology. In this study, we describe a highly sensitive strategy to monitor simultaneously these two pools of superoxide in respiring isolated rat skeletal muscle mitochondria using hydroethidine. The oxidation of hydroethidine by superoxide forms the membrane-impermeable 2-hydroxyethidium in these two superoxide pools that can be separated by differential centrifugation. Two technical limitations in using 2-hydroxyethidium as a superoxide reporter are (i) the uncontrolled fluorescence enhancement due to intercalation of 2-hydroxyethidium with variable amounts of mitochondrial DNA and (ii) the spectral interference of ethidium fluorescence. These complications were eliminated by digestion of mitochondrial DNA with DNase and by separation of ethidium and 2-hydroxyethidium using cationic micellar electrokinetic capillary chromatography with laser-induced fluorescence, respectively. Using this method, which has subattomole limits of detection, we compared the levels of 2-hydroxyethidium in normally respiring and antimycin A-treated mitochondria and demonstrated that the strategy can be extended to observe how menadione induces superoxide generation in mitochondria.

We describe a strategy for the identification of carbonylated proteins from complex protein mixtures that combines biotin hydrazide labeling of protein carbonyl groups, avidin affinity chromatography, multiplexed iTRAQ reagent stable isotope labeling, and analysis using pulsed Q dissociation (PQD) operation on an LTQ linear ion trap mass spectrometer. This strategy provided the ability to distinguish biotin hydrazide labeled, avidin purified, carbonylated proteins from non-carbonylated background proteins with affinity for the avidin column, derived from a control sample. Applying this strategy to the identification of crudely enriched rat skeletal muscle mitochondrial protein isolates, we generated a catalogue of over 200 carbonylated proteins by virtue of their quantitative enrichment compared to the control sample. The catalogue contains many mitochondrial localized proteins shown to be susceptible to carbonyl modification for the first time, including numerous transmembrane proteins involved in oxidative phosphorylation. Other oxidative modifications (e.g. nitrosylation, hydroxylation) were also identified on many of the carbonylated proteins, providing further evidence of the susceptibility of these proteins to oxidative damage. The results also demonstrate the utility of PQD operation on the LTQ instrument for quantitative analysis of iTRAQ reagent-labeled peptide mixtures, as well as the quantitative reproducibility of the avidin-affinity enrichment method.

Reactive oxygen species (ROS) that are produced by mitochondria are released toward the mitochondrial matrix or the intermembrane space. Each ROS pool is likely involved in different cellular mechanisms and damage. Unfortunately, it is difficult to distinguish the provenance and effects of ROS. Here we introduce a method to semiquantitate the steady-state levels of superoxide produced in the matrix of mitochondria. Superoxide produced during cellular respiration is capable of oxidizing hydroethidine, a probe that is membrane permeant. The poor membrane permeability of the hydroethidine oxidation products causes accumulation of these fluorescent products within the mitochondria. After isolation of mitochondria, a method based on the capillary electrophoretic separation of individual organelles and their detection by laser-induced fluorescence detection is used to determine their fluorescent contents. Use of this method for the analysis of organelle fractions obtained from cells treated with antimycin A or rotenone confirms that the detected fluorescence is associated with superoxide produced by mitochondria. Furthermore, using this method the superoxide levels in the mitochondrial matrix of a cytoplasmic hybrid (cybrid) cell line (DeltaH2-1) and one of its parent cell lines (143B) were compared.