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PubMed2006

Prognostic biomarkers in diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin's lymphoma. Although it represents a curable disease, less than half of the patients are cured with conventional chemotherapy. The highly variable outcome reflects a heterogeneous group of tumors, with different genetic abnormalities and response to therapy. The International Prognostic Index (IPI) is useful in predicting the outcome of DLBCL patients. However, patients with identical IPI still exhibit marked variability in survival, suggesting the presence of significant residual heterogeneity within each IPI category. The discovery of specific genetic alterations and the assessment of protein expression led to the identification of multiple novel single molecular markers capable of predicting the outcome of DLBCL patients independently of clinical variables. The recent application of DNA microarrays and tissue array technologies allowed a better understanding of the biology of lymphoma and the development of novel diagnostic tools capable of improving the current models for outcome prediction. However, much confusion exists in the literature regarding the importance of different prognostic biomarkers and their applicability in routine practice. This review summarizes the recent advances in our understanding of prognostic biomarkers in DLBCL and discusses whether this is the right time for biomarkers-guided risk-adjusted therapy.

Biomarkers, Tumor↗
PubMed2006

A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls.

BACKGROUND: Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. RESULTS: A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, and 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished from those of control groups. CONCLUSION: The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry experiments. It is expected that the higher resolution and mass accuracy of the FT-ICR mass spectrometry prevents the clustering of peaks of different peptides and allows the identification of differentially expressed proteins from the peptide profiles.

Algorithms↗
PubMed2000

Biomarkers of exposure to 1,3-butadiene as a basis for cancer risk assessment.

1,3-Butadiene (BD) is carcinogenic in mice and rats, with mice being considerably more sensitive than rats. Urine metabolites are 1, 2-dihydroxybutyl mercapturic acid (DHBMA) and a mixture of monohydroxy-3-butenyl mercapturic acids (MHBMA). The reactive metabolite 1,2-epoxy-3-butene forms 1- and 2-hydroxy-3-butenyl valine adducts in hemoglobin (MHBVal). The objectives of the study were (1) to compare the suitability of MHBMA, DHBMA, and MHBVal as biomarkers for low levels of exposure to BD, and (2) to explore relative pathways of metabolism of BD in humans for comparison with mice and rats, which is important in relation to cancer risk assessment in man. Analytical methods of measuring MHBMA, DHBMA, and MHBVal were modified and applied in 2 studies to workers engaged in the manufacture and use of BD. Airborne BD concentrations were assessed by personal air monitoring. MHBMA in urine was more sensitive for monitoring recent exposures to BD when compared to DHBMA and could measure 8-h time weighted average exposures as low as 0.13 ppm. Relatively high natural background levels in urine restricted the sensitivity of DHBMA. The origin of this background is currently unknown. The measurement of MHBVal adducts in hemoglobin was a sensitive method for monitoring cumulative exposures to BD at or above 0.35 ppm. Statistically significant relationships were found between urinary MHBMA and DHBMA concentrations, between either of these variables and 8-h airborne BD levels and between MHBVal adducts and average airborne BD levels over 60 days. The data on biomarkers demonstrated a much higher rate of hydrolytic metabolism of 1,2-epoxy-3-butene in humans compared to mice and rats, which was reflected in a much higher DHBMA/(DHBMA + MHBMA) ratio and in much lower levels of MHBVal in humans. Assuming a genotoxic mechanism, the data of this study, coupled with other published data on DNA and hemoglobin binding in mice and rats, suggest that the cancer risk for man from exposure to BD is expected to be less than for the rat and much less than for the mouse.

Acetylcysteine↗
PubMed2006

ZAP-70 by flow cytometry: a comparison of different antibodies, anticoagulants, and methods of analysis.

BACKGROUND: The clinical course of chronic lymphocytic leukaemia (CLL) is variable. ZAP-70 expression is believed to provide prognostic information. The flow cytometric detection of ZAP-70 is difficult because it is an intracellular antigen with weak expression in CLL. Consensus has not been reached as to the best method for measurement. METHODS: We analyzed 72 CLL patient samples for ZAP-70 expression and IgVH mutational status. Sensitivity and specificity of ZAP-70 expression against IgVH mutational status were assessed for two clones (2F3.2 and 1E7.2) and for four methods of analysis: percentage positivity (PP), comparing test to isotype control, ratio of geometric means of test and isotype control, and percentage and ratiometric methods comparing test and T/NK cell populations. The effects of anticoagulant, collection times, and time to analysis were also evaluated. RESULTS: Sensitivity and specificity were 85 and 88%, respectively, for Upstate PP; 70 and 88% for Caltag PP; 89 and 91% for Upstate ratio; 89 and 88% for Caltag ratio. Intraobserver variability was smaller when ZAP-70 expression was assessed using a ratiometric approach rather than the percentage method. By 48 h, we observed an average decrease of 13% in the Caltag ratio in the heparin preserved samples compared to an increase of 3% in those collected in EDTA. Within the first 24-h period, a greater percent variability was observed in those samples collected into EDTA compared with heparin. CONCLUSION: Our data support a rapid method for ZAP-70 measurement using commercially available fixation/permeabilization reagents, a conjugated antibody, and a ratiometric method of analysis that minimizes subjective interpretation of the results. This is a method of ZAP-70 assessment that could be included in a routine diagnostic CLL panel; however, the choice of anticoagulant and time of analysis after collection are critical factors in accurate assessment of ZAP-70 expression.

Antibodies↗
PubMed1998

Use of DNA fingerprinting to detect genotoxic effects.

The effects of environmental pollutants on organisms may be monitored in a number of ways and at different levels. In the case of genotoxic chemicals, the effects on the DNA may be monitored using a number of biomarker assays capable of detecting phenotypic changes as a result of mutation, gross chromosomal abnormalities, unscheduled DNA synthesis, DNA adducts (e.g., by 32P postlabeling or by ELISA) and DNA strand breaks (e.g., by the alkaline unwinding assay or the comet assay); the sensitivity and specificity of these assays are variable. Recent developments in molecular biology such as DNA fingerprinting and gene amplification by the polymerase chain reaction (PCR) offer new possibilities for detecting DNA damage. In this laboratory, whether an alternative biomarker assay (using DNA fingerprinting by arbitrarily primed PCR) can reveal differences in the DNA fingerprints of individuals from control and polluted areas was investigated. The results indicate that DNA fingerprinting by arbitrarily primed PCR offers a useful alternative biomarker assay for detection of the genotoxic effects of environmental pollutants.

Animals↗
PubMed2004

B-cell chronic lymphocytic leukemia with aberrant CD8 expression: genetic and immunophenotypic analysis of prognostic factors.

B-cell chronic lymphocytic leukemia (B-CLL) is phenotypically characterized by cell surface co-expression of CD19, CD20, CD5, and CD23. However, the concomitant presence of other antigens distinctive of a particular leukocyte subset, e.g. T cells, is an unusual finding in B-CLL. In the present report, a case of B-CLL with aberrant expression of the T-cell-associated antigen CD8 is described. Flow cytometric analysis of the patient's cells demonstrated lack of CD38 expression, and cytogenetic analysis by FISH did not show any abnormalities of chromosomes 17p, 11q, and 12. Furthermore, the B-CLL cells expressed only low levels of the tyrosine kinase ZAP-70, which was in agreement with the mutated status of the immunoglobulin heavy-chain variable-region gene (IgVH). In summary, the determined profile of prognostic markers together with the highly stable and indolent disease in the described patient suggest a good prognosis of B-CLL with aberrant CD8 expression.

Aged↗
PubMed1999

Exposure estimates to disinfection by-products of chlorinated drinking water.

Exposure to disinfection by-products (DBPs) of drinking water is multiroute and occurs in households serviced by municipal water treatment facilities that disinfect the water as a necessary step to halt the spread of waterborne infectious diseases. Biomarkers of the two most abundant groups of DBPs of chlorination, exhaled breath levels of trihalomethanes (THMs) and urinary levels of two haloacetic acids, were compared to exposure estimates calculated from in-home tap water concentrations and responses to a questionnaire related to water usage. Background THM breath concentrations were uniformly low. Strong relationships were identified between the THM breath concentrations collected after a shower and both the THM water concentration and the THM exposure from a shower, after adjusting for the postshower delay time in collecting the breath sample. Urinary haloacetic acid excretion rates were not correlated to water concentrations. Urinary trichloroacetic acid excretion rates were correlated with ingestion exposure, and that correlation was stronger in a subset of individuals who consumed beverages primarily within their home where the concentration measurements were made. No correlation was observed between an average 48-hr exposure estimate and the urinary dichloroacetic acid excretion rate, presumably because of its short biological half-life. Valid biomarkers were identified for DBP exposures, but the time between the exposure and sample collection should be considered to account for different metabolic rates among the DBPs. Further, using water concentration as an exposure estimate can introduce misclassification of exposure for DBPs whose primary route is ingestion due to the great variability in the amount of water ingested across a population.

Adult↗
PubMed2003

Caffeine, an anthropogenic marker for wastewater comtamination of surface waters.

The suitability of caffeine as a chemical marker for surface water pollution by domestic wastewaters was assessed in this study. Caffeine concentrations in influents and effluents of Swiss wastewater treatment plants (WWTPs, 7-73 and 0.03-9.5 microg/L, respectively) indicated an efficient elimination of 81-99.9%. Corresponding loads in untreated wastewater showed small variations when normalized forthe population discharging to the WWTPs (15.8 +/- 3.8 mg person(-1) d(-1)), reflecting a rather constant consumption. WWTP effluent loads were considerably lower (0.06 +/- 0.03 mg person(-1) d(-1)), apart from installations with low sludge age (< or = 5 d, loads up to 4.4 mg person(-1) d(-1)). Despite the efficient removal in most WWTPs, caffeine was ubiquitously found in Swiss lakes and rivers (6-250 ng/ L), except for remote mountain lakes (<2 ng/L; analytical procedure for wastewater and natural waters: SPE, GC-MS-SIM or GC-MS-MS-MRM, internal standard 13C3-labeled caffeine). Caffeine concentrations in lakes correlated with the anthropogenic burden by domestic wastewaters, demonstrating the suitability of caffeine as a marker. A mass balance for Greifensee revealed that approximately 1-4% of the wastewaters had been discharged without treatment, presumably on rainy days when the capacity of WWTPs had been exceeded. For Zürichsee, it could be shown that the monthly inputs of caffeine correlated with precipitation data. The depth- and seasonal-dependent concentrations in this lake were adequately rationalized by a numerical model considering flushing, biodegradation, and indirect photodegradation via HO. radicals as elimination processes and caffeine inputs as fitting variables.

Biomarkers↗
PubMedDate not supplied

[Use of regression analysis in the study of the association between different mercury exposure routes and some functional variables].

AIMS: The "Mercury Multicentric Project" data-set was analysed with the aim to identify a group of biological variables associated with different types of Hg exposure (occupational exposure, fish dietary intake, exposure due to amalgam restorations). The distribution of socio-demographic, biological and surrogate outcome variables was rather different among the collaborating Units. METHODS: Mixed linear models (MLM) were used to overcome the problems related to the heterogeneity of variances among Units. MLM are a generalization of the standard linear models, the generalization being that the data are permitted to exhibit correlation and non constant variability. MLM therefore provide with the flexibility of modelling not only the means of the dependent variable, but also their variances and co-variances as well. This allows to represent the total variability of the dependent variable as a sum of two components: the first attributable to the Units and the other one to the random error. RESULTS AND CONCLUSIONS: A set of biological variables significantly associated with at least one of the Hg exposure variables or with the HgU/creatinine ratio (as surrogate variable for Hg exposure) was identified by means of MLM. This set includes beta 2-MG, sIL8, CD4+, sPRL, FT dominant, BAMT, and some variables related to neurological behaviour. An extension of this analysis will be performed with a structural equations approach in order to study the dose-response relationships among the various variables according to a hierarchical path defined on biological basis. One of the possible simplified general models including all the selected variables is described.

Adult↗
PubMed1992

Prospective screening in multiple endocrine neoplasia type 1.

To assess the age of clinically detectable onset of multiple endocrine neoplasia type 1 (MEN 1), 88 members of four families were invited to participate in a ten-year biochemical screening program. Evidence for clinically detectable MEN 1 was found in adolescence. Pancreatic endocrine dysfunction constituted the presenting lesion in a majority of these individuals. The age at diagnosis of pancreatic endocrine tumors averaged 25 years and was lowered by almost two decades by prospective investigation. Furthermore, the penetrance of the pancreatic endocrine and parathyroid lesions equaled the penetrance found in autopsy studies. The use of a standardized meal stimulation test with the measurement of serum pancreatic polypeptide (PP) and gastrin responses resulted in diagnostic sensitivities of 75% and 100%, respectively. In addition to basal serum PP and insulin values, the proinsulin level was predictive for early pancreatic involvement in MEN 1. Serum gastrin was another useful tumor marker but only in the patients with pancreatic tumors diagnosed outside the prospective investigation. Two of the four MEN 1 kindreds selected for the screening investigation displayed homogeneity within families with respect to the profile of peptide excess and malignant potential of the pancreatic endocrine lesion, while the remaining kindreds demonstrated variable MEN 1 traits.

Adolescent↗
PubMed2004

Emerging biomarker technologies.

New technology offers great potential for advances in cancer biomarker research. Here, we describe a number of new technologies and discuss their potential for use in molecular cancer epidemiology. The successful sequencing of the human genome has revealed several new insights, including the fact that the human genome consists of only 40,000 genes and is highly variable, with approximately 60,000 functional polymorphisms. High-throughput genomic technologies continue to facilitate the identification and analysis of mutations and polymorphisms in key genes and expand the spectrum of available genomic biomarkers. The next major challenge is the identification of novel proteins and understanding the structure, function and interaction of proteins and other molecules--information that cannot be obtained from genomics alone. Emerging technologies including arrays, proteomics and nanotechnology provide new platforms for high-throughput, highly sensitive, functional assays. These technologies will complement existing and emerging genomic technologies and result in the identification of new biomarkers of cancer risk. They will, however, require extensive validation in epidemiological studies.

Biomarkers↗
PubMed1998

A strategy for identifying biomarkers of aging: further evaluation of hematology and blood chemistry data from a calorie restriction study in rhesus monkeys.

We examined a dataset derived from a battery of hematology and blood chemistry tests to identify candidate biomarkers of aging in a sample of 33 male rhesus monkeys (Macaca mulatta) ranging in age from 4-27 years. About half this sample comprised an experimental group subjected to 30% calorie restriction for six to seven years compared to the control group fed the same nutritionally fortified diet to approximate ad lib levels. Variables that met the following criteria were selected: (1) longitudinal change within the cohorts of control monkeys; (2) cross-sectional correlation with age across the adult lifespan in the control group; (3) stability of individual differences within all groups; and (4) no obvious redundancy with other selected variables. Five variables emerged from this step-wise selection, including the percentage lymphocytes, and serum levels of alkaline phosphatase, albumin, creatinine, and calcium. These variables were then submitted to a principal component analysis, which yielded a single component accounting for about 58% of the total variance. Based on this marked degree of covariance, these candidate biomarkers of aging could be combined into a biological age score (BAS) for the control and experimental groups. When chronological age was regressed onto BAS, the slopes of the control and experimental groups could be compared. Although a trend toward a slower aging rate in calorie-restricted monkeys was apparent, this analysis did not detect a statistically significant difference in the rate of aging between these groups estimated by this index. Despite this result, a logical strategy was confirmed for expanding the search for candidate biomarkers of aging to apply to this and to other studies assessing interventions that purport to affect the rate of aging in long-lived species.

Aging↗
PubMed2002

Effect of sorbic acid administration on urinary trans,trans-muconic acid excretion in rats exposed to low levels of benzene.

Trans,trans-muconic acid (t,t-MA) is a biomarker of benzene exposure reflecting metabolic activation to trans,trans-muconaldehyde. t,t-MA background urinary levels are highly variable, thus limiting its use to exposure monitoring of levels over 1 ppm of benzene. Actually, sorbic acid (SA) is known to influence background excretion of t,t-MA in man, but only a few examples suggest that SA ingestion can enhance t,t-MA levels occurring together with benzene exposure. In this study, the effect of SA was investigated in benzene-exposed male Sprague-Dawley rats exposed to 1 ppm benzene for 6 h. Exposed animals had a 24-h urinary t,t-MA excretion higher than that observed in non-exposed animals (87+/-13 microg/kg vs 19+/-3 microg/kg body weight). The oral dose of 8 mg/kg body weight SA had no effect on urinary t,t-MA both in control and in benzene-exposed rats. Increases of t,t-MA levels in urine occurred at SA doses of 50-200 mg/kg body weight, and co-exposure to benzene and SA (50 and 100 mg/kg body weight) produced additive enhancement of t,t-MA excretion. These data demonstrate the dose-response relationship between SA administration and t,t-MA excretion. Our study showed that SA ingestion at doses equal to or greater than 50 mg/kg body weight significantly affects the t,t-MA urinary levels in rats exposed to 1 ppm of benzene for 6 h. These data support the conclusion that in man t,t-MA is not suitable for biomonitoring of low levels of benzene exposure.

Animals↗
PubMedDate not supplied

Exhaled biomarkers in COPD: their potential role in diagnosis, treatment and prognosis.

Several diagnostic tools have been developed for diagnosing, monitoring and evaluating Chronic Obstructive Pulmonary Disease (COPD). There is an increasing interest in the use of non or less invasive biological markers (biomarkers) which reflect the character and intensity of the pathological processes in the lungs of COPD patients. The main goal of this review was to discuss the origin and current role of exhaled biomarkers in the diagnosis, evaluation of treatment and prognosis of COPD. Data of cross-sectional, cohort and intervention studies on exhaled biomarkers were studied. These studies were identified by a Medline search on papers in the English language published from 1990 to November 2001. The following markers were discussed: exhaled nitric oxide (NO), exhaled carbon monoxide (CO), exhaled alkanes, exhaled hydrogen peroxide (H2O2), exhaled isoprostanes, exhaled NO metabolites and exhaled thiobarbituric acid-reactive substances (TBARs). Data on these markers were summarized. The origin of each marker, the technique of analysis, the values in healthy controls and COPD patients, the effect of treatment and the correlation with other parameters were presented. Most studies, however, were cross-sectional studies with small populations. It was also difficult to compare studies because of differences in technique and study population. This review shows that exhaled biomarkers need to be studied further before using them in clinical practice. There is a need for standardization of the measurements, for comparison of COPD patients with healthy persons matched for age and smoking-status, for data on reproducibility and variability of all markers, for correlation of exhaled markers with other parameters and for intervention studies.

Biomarkers↗