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PubMed2006

Use of biomarkers to investigate toxicological effects of produced water treated with conventional and innovative methods.

The aim of this study was to develop and apply a multi-biomarker system to assess the toxicological effects of produced water (PW) from a Mediterranean off-shore oil platform. The selected bioindicator organism, mosquitofish (Gambusia affinis), was exposed in the laboratory to high concentrations of different PW: PW before treatment (BT), after conventional treatment (ACT) and after innovative treatment with zeolites in a prototype system (AIT). A set of biomarkers (benzo(alpha)pyrene monooxygenase, ethoxyresorufin-o-deethylase, vitellogenin, porphyrins, PAH bile metabolites, esterases, catalase, micronuclei) and PAH concentrations were measured in the experimental organism. The methodology proved to be appropriate and biomarker responses (CYP 1A1, PAH bile metabolites, micronuclei, esterases, porphyrins) affected by BT were less affected by ACT. PW treated with zeolites (AIT) had the lowest toxicological impact. The results obtained applying this multi-biomarker approach suggest that the system using zeolites is effective for treating produced water.

Acetylcholinesterase↗

PubMed2006

Sex steroids in the female zebrafish (Danio rerio). Effects of cyproterone acetate and leachate-contaminated sediment extract.

In Molnbyggen, a leachate-contaminated lake in Sweden, effects on the reproductive system of perch included a decreased frequency of sexually mature female perch, reduced gonadosomatic index and decreased plasma levels of androstenedione and testosterone, but the contaminants responsible for these effects have not yet been identified. A biomarker-directed fractionation approach could be used to narrow the search for the compound(s) responsible for the adverse effects in Molnbyggen female perch. Thus, it is important to develop and test a suitable biomarker, which can be used in this type of approach. We evaluated if decreased concentrations of sex steroids could work as an in vivo end-point in female zebrafish fed an organic extract of bottom sediments from Molnbyggen. The responsiveness of zebrafish to endocrine alteration was evaluated using a positive control substance, cyproterone acetate (CA), which is known to inhibit steroid biosynthesis. After the 21-day exposure period the concentrations of testosterone (T) and estradiol (E2) were successfully determined by HRGC/HRMS in whole-body homogenates of individual fish. Median T concentrations were 1.7pmol/g fish in controls and were decreased after exposure both to CA (0.55pmol/g fish) and Molnbyggen sediment extract (1.2-1.3pmol/g fish). Median E2 concentrations were 5.3pmol/g fish in controls and were decreased after CA exposure (2.3pmol/g fish) and after exposure to Molnbyggen sediment extract (4.0-4.5pmol/g fish). This suggests that sex steroid concentrations in zebrafish are responsive to endocrine alteration and indicates that compounds with endocrine altering potency are present in Molnbyggen sediments.

Androgen Antagonists↗

PubMed2006

Altered expression and localization of creatine kinase B, heterogeneous nuclear ribonucleoprotein F, and high mobility group box 1 protein in the nuclear matrix associated with colon cancer.

Identification of biomarkers could lead to the development of effective screening tests for colorectal cancer. A previous study from our laboratory showed specific alterations of nuclear structure in colon cancer. In an effort to characterize these biomarkers, protein spots were selected from separations made by two-dimensional gel electrophoresis, which were analyzed by mass spectrometry. The sequences obtained from the isolated spots revealed that they have close similarity to creatine kinase B (CKB) isoforms, heterogeneous nuclear ribonucleoprotein F (hnRNP F) and high mobility group box 1 protein (HMGB1) isoforms. To determine the expression of these proteins in colon cancer, expression was studied in 9 tumor and matched adjacent normal pairs, 5 donor colons, 16 polyps, 4 metastatic liver lesions and matched adjacent normal pairs, and 3 liver donors. CKB and hnRNP F were expressed in 78% and 89% of colon tumors, respectively. hnRNP F had a higher frequency of expression than CKB in premalignant polyps. With the establishment of differential expression of the proteins in colon cancer, their subcellular localization was analyzed. The subcellular fractions studied both showed high protein levels of hnRNP F in colon tumors compared with normal colon tissues. Surprisingly, subcellular levels of CKB were decreased in colon tumors, suggesting that the observed high CKB levels in nuclear matrix extracts are caused by the enhanced localization of CKB to the nuclear matrix during colon tumorigenesis. These results suggest an involvement of hnRNP F and CKB in colorectal cancer. Additionally, they suggest that hnRNP F is a potential marker for colorectal cancer progression.

Adenocarcinoma↗

PubMed2006

Biomarker discovery from body fluids using mass spectrometry.

Systems analysis of body fluids by mass spectrometry (MS) is an upcoming field of biomarker research. This approach is extremely attractive because it does not require biomarker candidates and the sample preparation is simple. However, during the development of the technique strong critical comments were made on the poor reproducibility, the special characteristics of blood as a source of peptides and on the frequent non-adequate statistical analysis of the data. Here we discuss the efforts made in the last few years to develop suitable protocols, which could lead to biomarker discovery from body fluids by mass spectrometry. Our review focuses on the systems analysis of non-digested blood serum or plasma samples by MALDI-TOF and SELDI-TOF.

Animals↗

PubMed2005

Risk factors associated with beta-amyloid(1-42) immunotherapy in preimmunization gene expression patterns of blood cells.

BACKGROUND: A phase 2a, double-blind, placebo-controlled, multicenter study was conducted to evaluate safety, tolerability, and pilot efficacy of immunization with beta-amyloid((1-42)) in patients with Alzheimer disease. Six immunizations were planned but were halted when meningoencephalitis was recognized as an adverse event in 6% of immunized patients. OBJECTIVE: To identify biomarkers associated with both the risk of meningoencephalitis and antibody responsiveness. PARTICIPANTS: One hundred fifty-three patients with mild to moderate Alzheimer disease.Main Outcome Measure Association between response to immunization and preimmunization expression levels of 8239 messenger RNA transcripts expressed in peripheral blood mononuclear cells that had been collected at the screening visit. RESULTS: Expression patterns of genes related to apoptosis and proinflammatory pathways (tumor necrosis factor pathway in particular) were identified as biomarkers of risk for the development of meningoencephalitis. Expression patterns of genes related to protein synthesis, protein trafficking, DNA recombination, DNA repair, and cell cycle were strongly associated with IgG response to immunization. CONCLUSIONS: Candidate biomarkers associated with risk of immunotherapy-related meningoencephalitis were detected in blood collected prior to treatment. In addition, a different set of biomarkers were identified that were associated with the desired outcome of IgG response.

Alzheimer Disease↗

PubMed1998

Biomarkers in toxicology.

The use of biomarkers in toxicology is becoming increasingly important. This article briefly reviews some of the aspects in an attempt to give an overall view of the field. Some of the new developments, particularly in relation to biomarkers of exposure and response, are mentioned. Specific DNA and protein adducts can now be used as biomarkers of the effective exposure so incorporating variations in environmental levels and individual disposition. Analysis of urinary metabolite profiles by NMR can highlight novel markers and allow recognition of patterns of metabolite changes as biomarkers of a toxic response. Novel urinary markers for liver and testicular dysfunction are discussed. Finally, the acetylator phenotype as a biomarker of susceptibility is described.

Animals↗

PubMed2004

Clinical proteomics and biomarker discovery.

Early detection of disease generally provides much-improved outcomes by a definitive medical procedure or through lifestyle modification along with specific medical management strategies. For serum biomarkers, which are central to the diagnosis of many diseases, to become truly useful sentinels of pathogenesis, their sensitivity and specificity in both early detection and recurrence monitoring must be improved. Currently, the detection and monitoring of disease markers is based on solitary proteins, and this approach is not always reliable. New classes of biomarkers derived from mass spectroscopy analysis of the low molecular weight proteome have shown improved abilities in the early detection of disease and hence in patient risk stratification and outcome. The development of a modular platform technology with sufficient flexibility and design abstractions allowing for concurrent experimentation, test, and refinement will help speed the progress of mass spectroscopy-derived proteomic pattern-based diagnostics from the scientific laboratory to the medical clinic. For acceptance by scientists, physicians, and regulatory personnel, new bioinformatic tools are essential system components for data management, analysis, and intuitive display of these new and complex data. Clinically engineered mass spectroscopy systems are essential for the further development and validation of multiplexed biomarkers that have shown tremendous promise for the early detection of disease.

Biomarkers↗

PubMed2005

Quantification of trimethylsilyl derivatives of amino acid disease biomarkers in neonatal blood samples by gas chromatography-mass spectrometry.

A novel analytical procedure was developed for the rapid determination of disease biomarkers of maple syrup urine disease (MSUD), L-valine, L-leucine, L-isoleucine, and L-phenylalanine in dried blood spots. Amino acids extracted from neonatal dried blood spots were rapidly derivatized with bis-(trimethylsilyl)trifluoroacetamide (BSTFA) and then analyzed by gas chromatography-mass spectrometry (GC-MS). Derivatization conditions and the method validation were studied: optimal derivatization conditions were acetonitrile as reaction solvent, a temperature of 100 degrees C, and a reaction time of 30 min. The proposed method provided a detection limit lower than 2.0 microM, recovery between 92% and 106%, and relative standard deviation less than 8.0%. The method was further tested in screening for neonatal MSUD by determination of L-valine, L-leucine, L-isoleucine, and L-phenylalanine in blood samples. The experimental results show that GC-MS following BSTFA derivatization is a rapid, simple, and sensitive method for the determination of amino acid disease biomarkers in blood samples, and is a potential tool for fast screening of MSUD.

Amino Acids↗

PubMed2006

Development of a mass spectrometry method for the determination of a melanoma biomarker, 5-S-cysteinyldopa, in human plasma using solid phase extraction for sample clean-up.

5-S-cysteinyldopa is a well-known pigment intermediate and analysis of its plasma concentration is interesting for the early diagnosis, as well as for evaluation of treatment and follow-up of malignant melanoma. A determination method of 5-SCD in human plasma was developed using solid phase extraction (SPE) on disposable cartridges and liquid chromatography electrospray mass spectrometry (LC-ESI-MS-MS). Compound's sensitivity to light and oxidation requires the addition of anti-oxidative agents (AO), to work in acidic media at 4 degrees C and to avoid light exposure of samples since blood collection. Different solid phases involving covalent binding to phenylboronic groups or dual retention mechanisms were evaluated and extraction cartridges containing both hydrophobic and strong cation exchange functionalities were finally selected. The LC separation of 5-SCD from endogenous catecholamines was achieved by gradient elution on a C18 stationary phase. 5-SCD was detected by multiple reaction monitoring (MRM) performed on ES(+) generated ions. Finally, the method was prevalidated in the lower ng/ml range. Good results with respect to accuracy, trueness and precision were obtained.

Biomarkers, Tumor↗

PubMed2006

The role of mass spectrometry in biomarker discovery and measurement.

Recent advances in the biological and analytical sciences have led to unprecedented interest in the discovery and quantitation of endogenous molecules that serve as indicators of drug safety, mechanism of action, efficacy, and disease state progression. By allowing for improved decision-making, these indicators, referred to as biomarkers, can dramatically improve the efficiency of drug discovery and development. Mass spectrometry has been a key part of biomarker discovery and evaluation owing to several important attributes, which include sensitive and selective detection, multi-analyte analysis, and the ability to provide structural information. Because of these capabilities, mass spectrometry has been widely deployed in search for new markers both through the analysis of large molecules (proteomics) and small molecules (metabonomics). In addition, mass spectrometry is increasingly being used to support quantitative measurement to assist in the evaluation and validation of biomarker leads. In this review, the dual role of mass spectrometry for biomarker discovery and measurement is explored for both large and small molecules by examining the key technologies and methods used along the continuum from drug discovery through clinical development.

Amino Acid Sequence↗

PubMed2007

One-pot solid-phase glycoblotting and probing by transoximization for high-throughput glycomics and glycoproteomics.

The development of rapid and efficient methods for high-throughput protein glycomics is of growing importance because the glycoform-focused reverse proteomics/genomics strategy will greatly contribute to the discovery of novel biomarkers closely related to cellular development, differentiation, growth, and aging as well as a variety of diseases such as cancers and viral infection. Recently, we communicated that rapid and efficient purification of carbohydrates can be achieved by employing sugar-specific chemical ligation with aminooxy-functionalized polymers, which we termed "glycoblotting" (see S.-I. Nishimura et al., Angew. Chem. 2005, 117, 93-98; Angew. Chem. Int. Ed. 2005, 44, 91-96). The chemoselective blotting of oligosaccharides present in crude biological materials onto synthetic polymers relies on the unique oxime-bond formation between aminooxy group displayed on the supporting materials and aldehyde/ketone group at the reducing terminal of all oligosaccharides, thus enabling highly selective and rapid oligosaccharide purification. Aiming to improve the detection sensitivity of the released oligosaccharides, we introduce here a novel strategy for one-pot solid-phase glycoblotting and probing by transoximization. We found that oligosaccharides captured by the polymer supports via the oxime bond can be released in the presence of excess O-substituted aminooxy derivatives in a weakly acidic condition. The released oligosaccharides could be recovered as newly formed oxime derivatives of the O-substituted aminooxy compound added, thus demonstrating the simultaneous releasing and probing. In addition, we synthesized a novel aminooxy-functionalized monomer, N-[2-[2-(2-tert-butoxycarbonylaminooxyacetylamino-ethoxy)ethoxy]ethyl]-2-methacrylamide, which allows for the large-scale preparation of a versatile polymer characterized by its high stability, high blotting capacity, and easy use. The one-pot protocol allowed to profile 23 kinds of N-glycan chains of human serum glycoproteins. This concept was further applied for the glycopeptides analysis in a crude mixture followed by galactose oxidase treatment to generate free aldehyde group at the non-reducing terminal of oligosaccharide moiety of glycopeptides. Our technique may be implemented in existing biochemistry and molecular diagnostics laboratories because enriched oligosaccharides and glycopeptides by solid-phase transoximization with high-sensitive labeling reagents are widely applicable in a variety of common analytical methods using two-dimensional HPLC, LC/MS, and capillary electrophoresis as well as modern mass spectrometry.

Acrylamides↗

PubMed2006

Surrogate outcomes in neurology, psychiatry, and psychopharmacology.

A surrogate outcome can be defined as an outcome that can be observed sooner, at lower cost, or less invasively than the true outcome, and that enables valid inferences about the effect of intervention on the true outcome. There is increasing interest in the use of surrogate outcomes of treatment efficacy measurement in investigational drug trials. However, the significance of surrogate markers of treatment outcome in neurology and psychiatry has not yet been sufficiently demonstrated. Few such markers have been adequately "validated, " that is, shown to predict the effect of the treatment on the clinical outcome of interest. In this article, evidence that would support the validation of such markers is discussed. Biomarkers used during early clinical development programs of new psychotropic compounds are considered in the contexts of Parkinson's disease, affective disorder, and schizophrenia. The particular case of neuroprotective trials is exemplified by Parkinson's disease, where a biomarker substituting for a clinical measure of progression could be considered as a surrogate treatment outcome.

Animals↗

PubMed2003

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

BACKGROUND: As a biomarker of cellular activities, the transcriptome of a specific tissue or cell type during development and disease is of great biomedical interest. We have generated and analyzed 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries: embryonic day 15.5 (M15E) eye, postnatal day 2 (M2PN) eye and adult retina (MRA). RESULTS: Annotation of 8,633 non-mitochondrial and non-ribosomal high-quality ESTs revealed that 57% of the sequences represent known genes and 43% are unknown or novel ESTs, with M15E having the highest percentage of novel ESTs. Of these, 2,361 ESTs correspond to 747 unique genes and the remaining 6,272 are represented only once. Phototransduction genes are preferentially identified in MRA, whereas transcripts for cell structure and regulatory proteins are highly expressed in the developing eye. Map locations of human orthologs of known genes uncovered a high density of ocular genes on chromosome 17, and identified 277 genes in the critical regions of 37 retinal disease loci. In silico expression profiling identified 210 genes and/or ESTs over-expressed in the eye; of these, more than 26 are known to have vital retinal function. Comparisons between libraries provided a list of temporally regulated genes and/or ESTs. A few of these were validated by qRT-PCR analysis. CONCLUSIONS: Our studies present a large number of potentially interesting genes for biological investigation, and the annotated EST set provides a useful resource for microarray and functional genomic studies.

Aging↗

PubMed2006

Ecotoxicity testing of chemicals with particular reference to pesticides.

Ecotoxicity tests are performed on vertebrates and invertebrates for the environmental risk assessment of pesticides and other chemicals and for a variety of ecotoxicological studies in the laboratory and in the field. Existing practices and strategies in ecotoxicity testing are reviewed, including an account of current requirements of the European Commission for the testing of pesticides and the recent REACH (Registration, Evaluation, Authorisation and Restrictions of Chemicals) proposals for industrial chemicals. Criticisms of existing practices have been made on both scientific and ethical grounds, and these are considered before dealing with the question of possible alternative methods and strategies both for environmental risk assessment and for ecotoxicological studies more generally. New approaches from an ecological point of view are compared with recent developments in laboratory-based methods such as toxicity tests, biomarker assays and bioassays. With regard to the development of new strategies for risk assessment, it is suggested that full consideration should be given to the findings of earlier long-term studies of pollution, which identified mechanisms of action by which environmental chemicals can cause natural populations to decline. Neurotoxicity and endocrine disruption are two cases in point, and biomarker assays for them could have an important role in testing new chemicals suspected of having these properties. In a concluding discussion, possible ways of improving testing protocols are discussed, having regard for current issues in the field of environmental risk assessment as exemplified by the debate over the REACH proposals. The importance of flexibility and the roles of ecologists and ecotoxicologists are stressed in the context of environmental risk assessment.

Animals↗

PubMed1997

Molecular epidemiology: carcinogen-DNA adducts and genetic susceptibility.

Molecular epidemiological studies assess individual chemical exposures and genetic susceptibility in order to identify cancer risk. Such studies incorporate the development, application, and validation of biomarkers of cancer risk in order to enhance cancer risk assessments, focus cancer prevention strategies, and elucidate mechanisms of carcinogenesis. Current studies of molecular epidemiology are based upon an understanding of the complex, multistage process of carcinogenesis and interindividual variations in response to carcinogenic exposures. Quantitative methods to measure human exposures to carcinogens continue to improve and have been successfully applied to a number of epidemiological studies. Genetic predispositions to cancer, both inherited and acquired, have been and continue to be identified. The combined approach of associating genetic polymorphisms with carcinogen-DNA adduct measurements, in order to assess cancer risk, is showing considerable promise. It is hoped that, in the future, molecular epidemiologists will be able to develop a risk profile for an individual that includes assessment of multiple biomarkers. The field has the near-term potential to have a significant impact on regulatory quantitative risk assessments, which may aid in the determination of allowable exposures. Molecular epidemiological data may also aid in the identification of individuals who will most benefit by cancer prevention strategies.

Biomarkers, Tumor↗

PubMedDate not supplied

Use of response biomarkers in milk for assessing exposure to environmental contaminants: the case for dioxin-like compounds.

Screening for environmental contaminants in milk is generally conducted by chemical analysis, yet such an approach may be time-consuming and expensive, and is not indicative of the physiological consequences of such exposure. The focus of this review is to summarize those constituents of milk that may be altered by maternal exposure to one of the most biologically active environmental pollutants, 2,3,7,8-tetrachlorodibenzo-p-dioxin, and to develop the case for their use as biomarkers of response. Several chemical and/or cellular components of milk are potentially useful as biomarkers, and may be developed as convenient, biologically relevant indicators of maternal exposure to dioxin-like compounds.

Biomarkers↗

PubMedDate not supplied

Intermediate biomarkers in the colorectal tumor progression.

Intermediate biomarkers are biological alterations in tissue which signal a stage of carcinogenesis between initiation and the development of a malignant tumor. Proliferation biomarkers are those that most satisfy the requisites for premorphological intermediate markers in the colorectal tumor progression. Cell proliferation changes in histologically normal intestinal mucosa are early events directly and closely associated with the morphogenesis of colorectal neoplasia. The transition from the morphological stage and the latter's further progression can be reliably monitored through the use of differentiation and genomic markers. In particular the incidence and the degree of DNA aneuploidy are indicators of the risk of malignant transformation in colorectal adenomas. New "regression-related" biomarkers should be investigated for the planning of measures designed to bring about the regression of premalignant lesions.

Biomarkers, Tumor↗

PubMed1997

The use of biological markers as predictive early-outcome measures in epidemiological research.

One of the possible uses of biomarkers in epidemiological research is as early-outcome measures to predict the occurrence of clinical disease and to elucidate the biological mechanism of pathogenesis. This use is conceptually less straightforward than the well established use of biomarkers to improve or extend exposure assessment or to study interindividual variations in disease susceptibility. In principle, this form of use could accelerate or otherwise facilitate etiological research. However, in practice, the recent review literature suggests that this mode of biomarker use, especially in cancer epidemiology, is the least clear-cut and the least well developed. The recurrent problem is identifying biomarkers that: (1) are on the causal pathway, (2) have a high probability of progression to clinical disease, and (3) account for all or most of the cases of the specified clinical outcome. Such biomarkers would be most useful if they conferred a long lead-time relative to clinical disease occurrence.

Biomarkers, Tumor↗