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At least 343 records · Page 19Linked to original sources
PubMed2003

The development of CpG island methylation biomarkers using restriction landmark genomic scanning.

CpG island hypermethylation is a common occurrence in cancer. Because this is a stable molecular alteration of the DNA, which can be detected easily from very small amounts, DNA methylation is an attractive candidate to use as a molecular biomarker. Recent studies have used DNA methylation of genes known to be targets of genetic disruption in cancer as biomarkers for early detection of cancer, classification of malignancies, response to drug treatment, and as markers predictive of outcome. Since many of the currently used targets of methylation are methylated at rather low frequencies in various cancer types even though the gene may be frequently disrupted by other mechanisms, it would be useful to develop additional markers that are methylated at high frequency in the cancer being studied. Restriction landmark genomic scanning has been used for the identification of frequent targets of methylation in multiple malignancies. These markers, which can be either cancer type-specific or nonspecific, may prove to be effective biomarkers for diagnostic or prognostic purposes, or for midpoint analysis of intervention strategies.

Biomarkers↗
PubMed2006

Vitellogenin 1 mRNA as an early molecular biomarker for endocrine disruption in developing zebrafish (Danio rerio).

Contemporary ecotoxicology is faced with the challenge of mechanistic understanding, a prerequisite for advanced risk assessment where acute toxicity is not the main issue. To achieve this, bioassay systems that are fast and biologically integrating and that detect a multitude of effects on a molecular level are needed. We present here the concept of such a novel test system that is built on the Danio rerio teratogenicity (DarT) assay but is extended in time and is based on testing molecular effects in the subacute toxicity range, named MolDarT. As proof of principle, we show the use of measuring vitellogenin 1 gene (vtg1) mRNA levels as a molecular marker for estrogenicity in developing zebrafish, a first module of MolDarT. Fertilized zebrafish eggs were exposed to 100, 1,000, and 2,000 ng/L (6.75 nM) 17 alpha-ethinylestradiol (EE2), and total RNA was isolated every 24 h up to 120 h postfertilization (hpf). Abundance of vtg1 mRNA was detected using reverse transcription real-time polymerase chain reaction and normalized to beta-actin mRNA abundance. Between 48 and 120 hpf, beta-actin mRNA levels were constant, making this gene a suitable reference gene for normalization. A significant up-regulation of vtg1 expression was detected at 48 hpf for 1,000 and 2,000 ng/L EE2. At 72, 96, and 120 hpf, vtg1 was significantly induced for all EE2 concentrations. Expression of vtg1 was also measured in unexposed developing zebrafish. At 24 hpf and at all later time points, zebrafish embryos contained vtg1 transcripts. These findings show that vtg1 is regularly expressed in developing zebrafish and that it is inducible by EE2. We propose the use of vtg1 as molecular target for estrogenicity in the MolDarT.

Actins↗
PubMed2004

Genomic and proteomic profiling for biomarkers and signature profiles of toxicity.

Toxicity profiling measures and compares all gene expression changes among biological samples after toxicant exposure. Toxicity profiling with DNA microarrays to measure all mRNA transcripts (transcriptomics), or by global separation and identification of proteins (proteomics), has led to the discovery of better descriptors of toxicity, toxicant classification and exposure monitoring than current indicators. A shared goal in transcript and proteomic profiling is the development of biomarkers and signatures of chemical toxicity. In this review, biomarkers and signature profiles are described for specific chemical toxicants that affect target organs such as liver, kidney, neural tissues, gastrointestinal tract and skeletal muscle, for specific disease models such as cancer and inflammation, and for unique chemical-protein adducts underlying cell injury. The recent introduction of toxicogenomics databases support researchers in sharing, analyzing, visualizing and mining expression data, assist the integration of transcriptomics, proteomics and toxicology datasets, and eventually will permit in silico biomarker and signature pattern discovery.

Animals↗
PubMed2002

Saliva and inhibition of HIV-1 infection: molecular mechanisms.

Oral fluids are rarely a vehicle for HIV-1 infection in vivo, unlike other mucosal secretions. This unique property raises questions regarding (1) the molecular mechanisms responsible for the lack of salivary transmission, (2) the extent to which oral immunological responses mirror responses at other mucosal sites, (3) the use of promising salivary markers of HIV-1 disease progression, (4) the relationship between oral and blood viral loads, (5) cofactors that influence oro-genital transmission, and (6) the feasibility of oral-based antibody testing for HIV-1 diagnosis in the home. This paper discusses these questions and provides background summaries, findings from new studies, consensus opinions, practical relevance to developing countries, and suggestions for future research agenda on each of the key topics.

Antibodies, Viral↗
PubMed2001

Standardization, analytical validation, and quality control of intermediate endpoint biomarkers.

Standardized processes should be used in the identification and development of intermediate endpoint biomarkers (IEB) for the prediction of patient-specific disease outcomes. Using our own experiences, we outline some of our standardized processes. Using computer-assisted image analysis, we developed a new biomarker of genetic instability, termed quantitative nuclear grade (QNG). The QNG biomarker is derived using nuclear images analyzed from the tumor areas of Feulgen-stained 5-microm biopsy or radical prostatectomy tissue sections. From the variances of 41 to 60 different nuclear size, shape, and chromatin organization features, a QNG solution is computed using either logistic regression or artificial neural networks. QNG can then be used as an input for models that solve for a patient-specific probability to accurately predict disease outcomes. Preoperatively, QNG predicted both the pathologic stage and progression of prostate cancer using biopsies (P <0.0001). Postoperatively, QNG proved extremely valuable in the prediction of biochemical progression using radical prostatectomy specimens with more than 10 years of follow-up (P <0.0001). We also demonstrate the identification of novel, differentially expressed, prostate cancer genes using RNA fingerprinting methods and the clinical utility of testing for these genes in both blood and tissue samples. Also illustrated is the improvement of serum biomarker performance by combining molecular forms of PSA with new biomarkers. In conclusion, the development of new IEBs requires planning based upon an understanding of the molecular pathogenesis of disease. IEB selection and clinical evaluation should employ standardized methods of testing and validation, followed by publication. QNG is 1 example of a new, highly predictive, IEB for prostate cancer that has been developed using these processes.

Analysis of Variance↗
PubMed1993

Stress protein synthesis induced by cadmium-cysteine in rat kidney.

Biomarkers are important tools which enable toxicologists to reliably predict and detect exposures to xenobiotics and resultant cell injury, ultimately improving risk assessments. Since the de novo synthesis of stress proteins can be detected early after exposure to some agents, analysis of toxicant-induced changes in gene expression, i.e. alterations in patterns of protein synthesis, may be useful to develop as biomarkers of exposure and toxicity. We are utilizing various xenobiotics as tools to study stress protein synthesis in target organs in order to evaluate the target tissue-specificity of this response. Previous data from this laboratory have demonstrated that induction of stress proteins in rat liver, but not kidney, after acute exposure to CdCl2 precedes hepatoxicity. Since kidney is a target tissue after chronic Cd exposure, it was of interest to examine stress protein synthesis in this tissue. However, dose-limiting hepatotoxicity precluded this evaluation. Cd complexed with molecules such as cysteine (cys) or metallothionein has been used in acute dosing regimens as a tool in order to study the nephrotoxicity of Cd. Therefore, this study was undertaken in order to evaluate Cd-induced stress protein synthesis in an important tissue known to be injured after chronic exposure, i.e. kidney. Specific objectives included comparing stress protein synthesis in rat kidney and liver after acute exposure to Cd-cys and CdCl2, determining the Cd threshold concentration for renal stress protein synthesis and assessing the relationship between stress protein synthesis and nephropathy. Male rats were exposed to equivalent doses of Cd as CdCl2 or Cd-cysteine (molar ratio Cd:cys = 1:15). Kidney Cd concentrations increased 5-fold after i.v. injection of Cd-cys compared to CdCl2, mimicking Cd distribution following chronic exposure. After exposure to Cd, tissue slices were incubated with 35S-methionine. Slices were subsequently homogenized and centrifuged, and the 16,000 g supernatants were subjected to SDS-polyacrylamide gel electrophoresis. Proteins which had incorporated 35S-methionine were detected by autoradiography. De novo synthesis of 70, 90 and 110 kDa proteins was enhanced in liver, but not in kidney, 4 h after injection of 2 mg Cd/kg as CdCl2. In contrast, dose-related increases in synthesis of these proteins were observed in kidney 4 h after injection of 1 and 2mg Cd/kg as Cd-cys, but not at lower dosages. In addition, synthesis of a 68 kDa kidney protein was inhibited at 2 mg Cd/kg as Cd-cys. The threshold for Cd-induced stress protein synthesis was shown to be between 4 and 8 micrograms Cd/g tissue.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2006

Validation of pharmacogenomic biomarker classifiers for treatment selection.

Physicians need improved tools for selecting treatments for individual patients. Many syndromes traditionally viewed as individual diseases are heterogeneous in molecular pathogenesis and treatment responsiveness. This results in treatment of many patients with ineffective drugs and leads to the conduct of large clinical trials to identify small average treatment benefits for heterogeneous groups of patients. New genomic and proteomic technologies provide powerful tools for the selection of patients likely to benefit from a therapeutic without unacceptable adverse events. In spite of the large literature on developing predictive biomarkers and on statistical methodology for analysis of high dimensional data, there is considerable uncertainty about the validation of biomarker based diagnostic classifiers for treatment selection. In this paper we attempt to clarify these issues and to provide guidance on the design of clinical trials for evaluating the clinical utility and robustness of pharmacogenomic classifiers.

Biomarkers↗
PubMed2002

Small- and large-scale biosimulation applied to drug discovery and development.

Biosimulation uses mathematics to quantitatively represent the dynamics of biological systems and thereby analyze and predict system behavior. Biosimulations can be classified into two general categories: small-scale models designed to address a specific problem, and large-scale models of detailed regulatory mechanisms used to address a broad scope of questions. Both classes of biosimulations have been applied to problems important for drug discovery and development. Small-scale biosimulations have been particularly useful for interpreting clinical data and developing novel biomarkers. Large-scale biosimulations typically integrate a wide variety of data and can provide insights into how complex biological systems are regulated in both health and disease. Because large-scale biosimulations represent detailed regulatory mechanisms and their interactions, they can predict the overall clinical effect of modulating individual pathways or targets. In this mini-review, we describe several examples of how small- and large-scale biosimulations have been applied to problems important for drug development in diabetes, HIV, heart disease and asthma.

Animals↗
PubMedDate not supplied

Flow cytometry in the preclinical development of biopharmaceuticals.

Novel biomarkers are often required in the preclinical development of biopharmaceuticals in order to characterize pharmacologic and toxicologic effects and to establish pharmacodynamic and pharmacokinetic relationships. Flow cytometry is uniquely suited for measurement of these biomarkers. Large numbers of single cells in a heterogeneous population can be rapidly identified and characterized with high accuracy and reproducibility. Cells are not damaged by the detection system and can be subsequently sorted for further morphologic or functional analysis. The availability of clinical instruments and a wide range of fluorescent probes have made this technology applicable for use in toxicologic clinical pathology. Flow cytometry has played an integral role in the development of a monoclonal antibody to human CD4 (keliximab, IDEC-CE9.1, SB 210396). Lymphocyte subset analysis and assays for expression, coating, and modulation of human CD4 were used for sequential assessment of the pharmacologic activity of keliximab in transgenic mice expressing human CD4.

Animals↗
PubMed2006

4-nitroquinoline-1-oxide induced experimental oral carcinogenesis.

Human oral cancer is the sixth largest group of malignancies worldwide and single largest group of malignancies in the Indian subcontinent. Seventy percent of premalignant cancers appear from premalignant lesions. Only 8-10% of these lesions finally turn into malignancy. The appearance of these premalignant lesions is one distinct feature of human oral cancer. At present there is dearth of biomarkers to identify which of these lesions will turn into malignancy. Regional lymph node metastasis and locoregional recurrence are the major factors responsible for the limited survival of patients with oral cancer. Paucity of early diagnostic and prognostic markers is one of the contributory factors for higher mortality rates. Cancer is a multistep process and because of constrain in availability of human tissues from multiple stages of oral carcinogenesis including normal tissues, animal models are being widely used, aiming for the development of diagnostic and prognostic markers. A number of chemical carcinogens like coal tar, 20 methyl cholanthrene (20MC), 9,10-dimethyl-1,2-benzanthracene (DMBA) and 4-nitroquinoline-1-oxide (4NQO) have been used in experimental oral carcinogenesis. However, 4NQO is the preferred carcinogen apart from DMBA in the development of experimental oral carcinogenesis. 4NQO is a water soluble carcinogen, which induces tumors predominantly in the oral cavity. It produces all the stages of oral carcinogenesis and several lines of evidences suggest that similar histological as well as molecular changes are observed in the human system. In the present review an attempt has been made to collate the information available on mechanisms of action of 4NQO, studies carried out for the development of biomarkers and chemopreventives agents using 4NQO animal models.

4-Nitroquinoline-1-oxide↗
PubMedDate not supplied

Pro-inflammatory alterations and status of blood plasma iron in a model of blast-induced lung trauma.

Impact of blast shock waves (SW) with the body wall produces blast lung injuries characterized by bilateral traumatic hemorrhages. Such injuries often have no external signs, are difficult to diagnose, and therefore, are frequently underestimated. Predictive assessment of acute respiratory distress syndrome outcome in SW-related accidents should be based on experimental data from appropriate animal models. Blood plasma transferrin is a major carrier of blood iron essential for proliferative "emergency" response of hematopoietic and immune systems as well as injured tissue in major trauma. Iron-transferrin complexes (Fe3+ TRF) can be quantitatively analyzed in blood and tissue samples with low-temperature EPR techniques. We hypothesized that use of EPR techniques in combination with assays for pro-inflammatory cytokines and granulocytes in the peripheral blood and BAL would reveal a pattern of systemic sequestration of (Fe3+)TRF that could be useful for development of biomarkers of the systemic inflammatory response to lung injury. With this goal we (i) analyzed time-dependent dynamics of (Fe3+)TRF in the peripheral blood of rats after impacts of SW generated in a laboratory shock-tube and (ii) assayed the fluctuation of granulocyte (PMN) counts and expression of CD11b adhesion molecules on the surface of PMNs during the first 24 h after SW induced injury. Sham-treated animals were used as control. Exposure to SW led to a significant decrease in the amount of blood (Fe3+)TRF that correlated with the extent of lung injury and developed gradually during the first 24 h. Thus, sequestration of (Fe3+)TRF occurred as early as 3 h post-exposure. At that time, the steady state concentration of (Fe3+)TRF in blood samples decreased from 19.7+/-0.6 microM in controls to 7.5+/-1.3 microM in exposed animals. The levels of (Fe3+)TRF remained decreased throughout the entire study period. PMN counts increased 5-fold and 3.5-fold over controls respectively, at 3 and 6 h postexposure. These effects were accompanied by an increase in expression of CD11b on the surface membrane of PMNs. Extensive release of cytokines IL-1, IL-6, MCP-1, and MIP-2 was observed in BAL fluid and blood plasma during 24 h postexposure. We conclude that EPR monitoring of blood (Fe3+)TRF can be a useful approach for assessment of systemic pro-inflammatory alterations due to SW-induced lung injury.

Air Pressure↗
PubMed2001

Enamel lead biomarker for prenatal exposure assessment.

The development of the enamel biomarker for heavy metal exposure assessment is designed to improve studies of dose-effect relationships to embryonic anomalies, particularly neurotoxic dysfunction. This report documents initial demonstrations of ambient lead (Pb) relative to calcium (Ca) in histological cross sections of deciduous tooth enamel of three human subjects, by use of ion mass spectrometry. The goal of this research was to measure Pb and Ca in tooth enamel for use as a temporal biomarker in assessing prenatal and postnatal exposure. This involves measurement of these heavy metals in enamel at high spatial resolution along histological transects following the temporal pattern of enamel growth. The technique may be applied when completely developed to cross-sectional and longitudinal research.

Biomarkers↗
PubMed1998

Biomarker strategies to evaluate the environmental effects of chemicals.

Environmental risk assessment of chemicals depends on the production of toxicity data for surrogate species of mammals, birds, and fish and on making comparisons between these and estimated or predicted environmental concentrations of the chemicals. This paper gives an overview of biomarker assays and strategies that might be used as alternatives, that is, to replace, reduce, or refine currently used ecotoxicity tests that cause suffering to vertebrates. In the present context a biomarker is a biologic response to an environmental chemical at the individual level or below which demonstrates a departure from normal status. Of immediate interest and relevance are nondestructive assays that provide a measure of toxic effect in vertebrate species and that can be used in both laboratory and parallel field studies. A major shortcoming of this approach is that such assays are currently only available for a limited number of chemicals, primarily when the mode of action is known. Nondestructive assays can be performed on blood, skin, excreta, and eggs of birds, fish, reptiles, and amphibians. An interesting recent development is the use of vertebrate cell cultures, including transgenic cell lines that have been developed specifically for toxicity testing. The ultimate concern in ecotoxicology is the effects of chemicals at the level of populations and above. Current risk assessment practices do not address this problem. The development of biomarker strategies could be part of a movement toward more ecologic end points in the safety evaluation of chemicals, which would effect a reduction in animal tests that cause suffering.

Animal Testing Alternatives↗
PubMed1987

Reproductive immunology: biomarkers of compromised pregnancies.

The objective of this paper is to consider several categories of biomarkers of human pregnancy. The design of the report is to discuss useful and promising markers and techniques. Research gaps, needs, and priorities are also defined. Useful markers are mixed lymphocyte culture reactions, measures of lymphocytotoxic antibodies, histocompatibility (HLA) typing, and immunohematological evaluations. Promising markers are measures of major basic protein and early pregnancy factor, as well as determinations of trophoblast-lymphocyte cross-reactive (TLX) antigens. Promising techniques are fluorescence-activated cell-sorter analysis of maternal blood for fetal and extraembryonic tissues and immunotherapy with TLX and other antigens to prevent spontaneous abortion. It is concluded that immunology has much to offer the development of biomarkers of human pregnancy.

Antibodies↗
PubMed2006

Prolonged dormancy of human liposarcoma is associated with impaired tumor angiogenesis.

The disease state of cancer appears late in tumor development. Before being diagnosed, a tumor can remain for prolonged periods of time in a dormant state. Dormant human cancer is commonly defined as a microscopic tumor that does not expand in size and remains asymptomatic. Dormant tumors represent an early stage in tumor development and may therefore be a potential target for nontoxic, antiangiogenic therapy that could prevent tumor recurrence. Here, we characterize an experimental model that recapitulates the clinical dormancy of human tumors in mice. We demonstrate that these microscopic dormant cancers switch to the angiogenic phenotype at a predictable time. We further show that while angiogenic liposarcomas expand rapidly after inoculation of tumor cells in mice, nonangiogenic dormant liposarcomas remain microscopic up to one-third of the normal severe combined immune deficiency (SCID) mouse life span, although they contain proliferating tumor cells. Nonangiogenic dormant tumors follow a similar growth pattern in subcutaneous (s.c.) and orthotopic environments. Throughout the dormancy period, development of intratumoral vessels is impaired. In nonangogenic dormant tumors, small clusters of endothelial cells without lumens are observed early after tumor cell inoculation, but the nonangiogenic tumor cannot sustain these vessels, and they disappear within weeks. There is a concomitant decrease in microvessel density, and the nonangiogenic dormant tumor remains harmless to the host. In contrast, microvessel density in tumors increases rapidly after the angiogenic switch and correlates with rapid expansion of tumor mass. Both tumor types cultured in vitro contain fully transformed cells, but only cells from the nonangiogenic human liposarcoma secrete relatively high levels of the angiogenesis inhibitors thrombospondin-1 and TIMP-1. This model suggests that as improved blood or urine molecular biomarkers are developed, the microscopic, nonangiogenic, dormant phase of human cancer may be vulnerable to antiangiogenic therapy years before symptoms, or before anatomical location of a tumor can be detected, by conventional methods.

Animals↗
PubMed2003

Haem peroxidase activity in Daphnia magna: a biomarker for sub-lethal toxicity assessments of kerosene-contaminated groundwater.

A novel biomarker was developed in Daphnia magna to detect organic pollution in groundwater. The haem peroxidase assay, which is an indirect means of measuring oxidase activity, was particularly sensitive to kerosene contamination. Exposure to sub-lethal concentrations of kerosene-contaminated groundwater resulted in a haem peroxidase activity increase by dose with a two-fold activity peak at 25%. Reproduction in D. magna remained unimpaired when exposed to concentrations below 25% for 21 days, and a decline in fecundity was only observed at concentrations above the peak in enzyme activity. The measurement of haem peroxidase activity in D. magna detected sublethal effects of kerosene in just 24 h, whilst offering information on the health status of the organisms. The biomarker may be useful in determining concentrations above which detrimental effects would occur from long-term exposure for fuel hydrocarbons. Moreover, this novel assay detects exposure to chemicals in samples that would normally be classified as non-toxic by acute toxicity tests.

Animals↗
PubMed2003

Analytical and clinical evaluation of a new urinary tumor marker: bladder tumor fibronectin in diagnosis and follow-up of bladder cancer.

Bladder cancer is the fourth most common malignant neoplasm in men and the tenth most common in women. Cystoscopy presents the gold standard for detection and monitoring of bladder cancer. However, it is an invasive and expensive procedure. Therefore, development of biomarkers for the purposes of screening, diagnosis and prediction of the prognosis in bladder cancer is required. Bladder tumor fibronectin is one of the new urinary tumor markers. The aim of this study is to evaluate the diagnostic performance of urinary bladder tumor fibronectin in detecting and monitoring bladder cancer. A total of 75 patients with the diagnosis of bladder cancer, 20 patients with the diagnosis of benign prostatic hyperplasia, 7 patients with the diagnosis of prostate cancer between the years 1996-2000, and 28 age-matched healthy individuals, were enrolled in the study. The patients were diagnosed by cystoscopy, with histopathological evaluation of the tumor, as having superficial or invasive bladder cancer. Patients were followed-up clinically with data pertinent to disease recurrence and progression. Bladder tumor fibronectin (BTF; ng/ml) was determined by solid phase, two-site chemiluminescent immunometric commercial diagnostic assay developed for the Immulite automated immunoassay system (Diagnostic Products Corporation, Los Angeles, CA, USA). All measured values were normalized by urinary creatinine, and the obtained data were evaluated by receiver-operating characteristics (ROC) curve analysis. Optimal cut-off was established at 43.4 ng/mg. This cut-off rendered overall sensitivities of 72% and specificity of 82.1%. The analytical evaluation of the BTF test displayed promising results in terms of a non-invasive in vitro test in the diagnosis of bladder cancer. Although it was not satisfactory in prediction of recurrence or progression of the disease, it correlated well with the stage, one of the most reliable prognostic factors. In conclusion, the urinary bladder tumor fibronectin test warrants further clinical evaluation.

Biomarkers, Tumor↗
PubMed2006

Anti-glycan antibodies as biomarkers for diagnosis and prognosis.

Glycans (sugars or carbohydrates) are predominant surface components of cells such as erythrocytes, immune cells and microorganisms. As such, they give rise to high levels of anti-glycan antibodies of all classes. Antibodies to certain defined mono, di and oligosaccharides that are common in bacterial, fungal and parasite cells exist in human sera and can be profiled using glycan arrays. The use of glycan arrays for systematic screening of blood samples from multiple sclerosis (MS) and Crohn's disease (CD) patients in versus to blood samples from control groups, have lead to the discovery of a few anti glycan antibodies biomarkers enabling diagnosis and prognosis in MS and CD patients. Anti-Glc(alpha1,4)Glc(alpha) IgM antibodies were found to be specific for MS patients, enabling differentiation between MS patients and patients with other neurological diseases, with 54% sensitivity and 85% specificity. Anti-Glc(alpha1,4)Glc(alpha) IgM were found to be predictive for the conversion of patients in first acute neurological event to clinically defined MS. Anti-laminaribioside (ALCA), anti-mannobioside (AMCA) and anti-chitobioside (ACCA) antibodies were found to be specific for CD. The combined use of these antibodies enables improved diagnosis of CD versus ulcerative colitis and other gastrointestinal diseases, as well as stratification of CD patients with a more complicated disease and high risk for surgery. Anti-glycan antibodies profiling (AGAP) is a new and promising approach for development of biomarkers for diagnosis and prognosis.

Antibodies↗