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Synthesis of 2'-deoxy-2'-[18F]fluoro-5-bromo-1-beta-D-arabinofuranosyluracil ([18F]-FBAU) and 2'-deoxy-2'-[18F]fluoro-5-chloro-1-beta-D-arabinofuranosyl-uracil ([18F]-FCAU), and their biological evaluation as markers for gene expression.

[(18)F]-FBAU and [(18)F]-FCAU have been synthesized and evaluated in vivo as markers for HSV1-tk gene expression. At 2 hours, uptake of [(18)F]-FBAU and [(18)F]-FCAU in HSV1-tk-positive tumors was 7.9-fold and 6.0-fold higher than the control tumors, respectively. Micro-PET images also showed very high uptake in HSV-tk tumors. Compared to [(14)C]-FMAU, total uptake of [(18)F]-FBAU and [(18)F]-FCAU was similar in tk-positive cells, but the uptake ratio (tk+/wild) was higher. [(18)F]-FBAU and [(18)F]-FCAU appear to be potential PET imaging agents for gene expression.

Animals↗

Molecular biomarkers for the study of childhood leukemia.

Various specific chromosome rearrangements, including t(8;21), t(15;17), and inv(16), are found in acute myeloid leukemia (AML) and in childhood acute lymphocytic leukemia (ALL), t(12;21) and t(1;19) are common. We sequenced the translocation breakpoints of 56 patients with childhood ALL or AML harboring t(12;21), t(8;21), t(15;17), inv(16), and t(1;19), and demonstrated, with the notable exception of t(1;19), that these rearrangements are commonly detected in the neonatal blood spots (Guthrie cards) of the cases. These findings show that most childhood leukemias begin before birth and that maternal and perinatal exposures such as chemical and infectious agents are likely to be critical. Indeed, we have reported that exposure to indoor pesticides during pregnancy and the first year of life raises leukemia risk, but that later exposures do not. We have also examined aberrant gene methylation in different cytogenetic subgroups and have found striking differences between them, suggesting that epigenetic events are also important in the development of some forms of childhood leukemia. Further, at least two studies now show that the inactivating NAD(P)H:quinone acceptor oxidoreductase (NQO1) C609T polymorphism is positively associated with leukemias arising in the first 1-2 years of life and polymorphisms in the 5,10-methylenetetrahydrofolate reductase (MTHFR) gene have been associated with adult and childhood ALL. Thus, low folate intake and compounds that are detoxified by NQO1 may be important in elevating leukemia risk in children. Finally, we are exploring the use of proteomics to subclassify leukemia, because cytogenetic analysis is costly and time-consuming. Several proteins have been identified that may serve as useful biomarkers for rapidly identifying different forms of childhood leukemia.

Biomarkers↗

An overview of the kallikrein gene families in humans and other species: emerging candidate tumour markers.

Kallikreins are serine proteases with diverse physiologic functions. They are represented by multigene families in many animal species, especially in rat and mouse. Recently, the human kallikrein gene family has been fully characterized and includes 15 members, tandemly localized on chromosome 19q13.4. A new definition has now been proposed for kallikreins, which is not based on function but, rather, on close proximity and structural similarities. In this review, we summarize available information about kallikreins in many animal species with special emphasis on human kallikreins. We discuss the common structural features of kallikreins at the DNA, mRNA and protein levels and overview their evolutionary history. Kallikreins are expressed in a wide range of tissues including the salivary gland, endocrine or endocrine-related tissues such as testis, prostate, breast and endometrium and in the central nervous system. Most, if not all, genes are under steroid hormone regulation. Accumulating evidence indicates that kallikreins are involved in many pathologic conditions. Of special interest is the potential role of kallikreins in the central nervous system. In addition, many kallikreins seem to be candidate tumor markers for many malignancies, especially those of endocrine-related organs.

Animals↗

Sequence databases and microarrays as tools for identifying prostate cancer biomarkers.

Identification, acquisition, and assessment of molecular markers that could be adopted as surrogate endpoints for evaluating a response to prostate cancer intervention strategies is highly desirable. Recent advances in the fields of genomics and biotechnology have dramatically increased the quantity and accessibility of molecular information that is relevant to the study of prostate carcinogenesis. One major advance involves the construction of comprehensive databases that archive gene sequences and gene expression data. This information is in a format suitable for virtual queries designed to distinguish the molecular differences between normal and cancer cells. A second major advance uses robotic tools to construct microarrays comprising thousands of distinct genes expressed in prostate tissues. Such arrays offer a powerful approach for monitoring the expression of thousands of genes simultaneously and provide access for techniques designed to assess patterns or "fingerprints" of gene expression that may ultimately be used as signatures of response to therapeutic intervention.

Base Sequence↗

Exploring the quantitative relationship between the level of MDR1 transcript, protein and function using digoxin as a marker of MDR1-dependent drug efflux activity.

A limited number of gene expression studies have investigated the quantitative relationships between the amount of transcript, level of protein or activity/function, with disparate conclusions regarding these relationships. Collectively these studies indicate that the relevance of quantitative transcript analysis as a predictor of phenotype has to be evaluated on a gene-by-gene or even a case-by-case basis. The purpose of this study was to define a suitable marker for MDR1-dependent drug efflux, and to quantitatively investigate the relationships between the amount of transcript, protein and drug efflux in the frequently used Caco-2 cell model. The substrate specificity of digoxin, a commonly used marker for MDR1, was investigated using transgenic MDCK II or LLC-PK1 cell lines expressing the efflux proteins MDR1, BCRP and MRP2, since these proteins are localised to the apical part of the enterocyte plasma membrane and exhibit comparatively high transcript levels in the human small intestine. Relationships between levels of transcript, protein and function were investigated quantitatively using real-time RT-PCR, ECL western blot analysis and basolateral-to-apical and apical-to-basolateral efflux ratios. Our results indicate that digoxin is a specific marker for MDR1-dependent drug efflux in the Caco-2 cell drug absorption model and that MDR1 transcript abundance is at least as valid as MDR1 protein abundance as a predictor of MDR1 efflux activity.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

Cardiovascular genomics.

The ongoing explosion of genomic information is revolutionizing cardiovascular science. More complete genomic maps allow easier identification of genes that cause monogenic inherited diseases. In addition, analyses of variations in gene expression in cardiovascular diseases are revealing new potential candidate genes as well as novel biomarkers for many common, multifactorial diseases. While experiments are revealing new pathophysiologic pathways, these genomic studies are also generating enormous amounts of data. Even as we learn how to sift through mountains of genomic information, new technologies in proteomics are rapidly advancing and promise to provide additional critical tools for diagnosis and for identifying new therapies.

Biomarkers↗

Angiogenic wisdom.

Explore the source record for details and available documents.

Biomarkers, Tumor↗

Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression.

The prognostication of head and neck squamous cell carcinoma (HNSCC) is largely based upon the tumor size and location and the presence of lymph node metastases. Here we show that gene expression patterns from 60 HNSCC samples assayed on cDNA microarrays allowed categorization of these tumors into four distinct subtypes. These subtypes showed statistically significant differences in recurrence-free survival and included a subtype with a possible EGFR-pathway signature, a mesenchymal-enriched subtype, a normal epithelium-like subtype, and a subtype with high levels of antioxidant enzymes. Supervised analyses to predict lymph node metastasis status were approximately 80% accurate when tumor subsite and pathological node status were considered simultaneously. This work represents an important step toward the identification of clinically significant biomarkers for HNSCC.

Adult↗

Genetics of malignant pleural mesothelioma: molecular markers and biologic targets.

MPM is a poorly understood lethal malignancy. Although the pathobiology of MPM is not completely elucidated, new genomic technology is likely to help shed light on the mechanisms of carcinogenesis through genome-wide screening of tumor-specific gene expression. Related efforts to identify the molecular markers of mesothelioma are pursued with the aim of refining current diagnostic capabilities, predicting prognosis, and designing appropriate trimodality programs. These new genomic tools also will assist efforts to tailor current adjuvant and neoadjuvant therapies, optimizing their effect and furthering research that may lead to new therapeutic options.

Apoptosis↗

Novel gene expression domains reveal early patterning of the Xenopus endoderm.

The endoderm gives rise the respiratory and digestive tract epithelia as well as associated organs such as the liver, lungs and pancreas. Investigations examining the molecular basis of embryonic endodermal patterning and organogenesis have been hampered by the lack of regionally expressed molecular markers in the early endoderm. By differentially screening an arrayed cDNA library, combined with an in situ hybridization screen we identified 13 new genes regionally expressed in the early tailbud endoderm of the Xenopus embryo. The putative proteins encoded by these cDNAs include a cell surface transporter, secreted proteins, a protease, a protease inhibitor, an RNA-binding protein, a phosphatase inhibitor and several enzymes. We find that the expression of these genes falls into one of three re-occurring domains in the tailbud embryo; (1). a ventral midgut, (2). posterior to the midgut and (3). in the dorsal endoderm beneath the notochord. Several of these genes are also regionally expressed at gastrula and neurula stages and appear to mark territories that were previously only predicted by the endoderm fate map. This indicates that there is significant positional identity in the early endoderm long before stages 28-32 when regional specification of the endoderm is thought to occur. These new genes provide valuable tools for studying endodermal patterning and organogenesis in Xenopus.

Animals↗

A yeast DNA microarray for the evaluation of toxicity in environmental water containing burned ash.

Numerous studies on the hazard assessment and epidemiological health responses to burned ash have been reported. However, there is little information on the potential toxicity of unknown chemical complexes in burned ash. For an overall evaluation of the multiple toxicities of burned ash, a DNA microarray was used in this study, as a new attempt to assess these toxicities. Using the global gene expression on yeast DNA chip to reflect the changes in mRNA levels, our study discovered a lot of evidences for the action of cell homeostasis and stress response etc., against the toxic effects on yeast cells. On the genes of 5,117 open reading frames (ORFs), as valid spots in a microarray, 997 were up-regulated, 1,259 were down-regulated and 2,861 remained unchanged. A detailed analysis of the microarray revealed the genes that were dynamically correlated to the function of the subcellular localization, energy/metabolism, various stress responses/cell homeostasis and detoxification. Significantly, the toxicities, caused by reactive oxygen species (ROS), metals and the other xenobiotics, were indicated in burned ash. Also, the possibility of mutagenicity of the burned ash was suggested on the basis of the DNA repair related genes.

Biomarkers↗

Common markers of proliferation.

When normal tissue and tumour samples are compared by microarray analysis, the biggest differences most often occur in the expression levels of genes that control cell proliferation. However, this difference is detected whenever mRNA samples that are taken from two cell populations with different proliferation rates are compared. Although the exact genes that comprise this 'proliferation signature' often differ, they are almost always genes that are involved in the fundamental process of cell proliferation. Can the proliferation signature be used to improve our understanding of the cell cycle and cancer pathogenesis, as well as being used as a biomarker for cancer diagnosis and prognosis?

Biomarkers, Tumor↗

Metallothionein - overexpression as a highly significant prognostic factor in melanoma: a prospective study on 1270 patients.

Metallothioneins (MT) are ubiquitous, intracellular small proteins with high affinity for heavy metal ions. In the last decades, it was shown that MT overexpression in a variety of cancers is associated with resistance to anticancer drugs and is combined with a poor prognosis. In this prospective study, we examined the role of MT overexpression in melanoma patients as a prognostic factor for progression and survival. Between 1993 and 2004, 3386 patients with primary cutaneous melanoma were investigated by using a monoclonal antibody against MT on routinely fixed, paraffin-embedded tissues. In all, 1270 patients could be followed up for further statistical analysis (Fisher's exact test, Mantel-Haenszel chi2 test, Kaplan-Meier curves). The MT data of disease-free interval and overall survival were compared univariately and multivariately in Cox regression analysis. Immunohistochemical overexpression of MT in tumour cells of patients with primary melanoma (310 of 1270; 24.4%) was associated with a higher risk for progression (117 of 167; 70.1%) and reduced survival (80 of 110; 72.7%) of the disease (P<0.0001). Similarly, Kaplan-Meier curves gave highly significant disadvantages for the MT-positive group. Univariate analysis (relative risk 7.4; 95% confidence interval (CI) 5.2-10.2; P<0.0001 for progression; relative risk 7.1; 95% CI 4.7-10.9; P<0.0001 for survival), as well as multivariate analysis with other prognostic markers resulted in MT overexpression as a highly significant and independent factor for prognosis in primary melanoma.

Adolescent↗

Pregnane X receptor prevents hepatorenal toxicity from cholesterol metabolites.

Efficient detoxification and clearance of cholesterol metabolites such as oxysterols, bile alcohols, and bile acids are critical for survival because they can promote liver and cardiovascular disease. We report here that loss of the nuclear xenobiotic receptor PXR (pregnane X receptor), a regulator of enterohepatic drug metabolism and clearance, results in an unexpected acute lethality associated with signs of severe hepatorenal failure when mice are fed with a diet that elicits accumulation of cholesterol and its metabolites. Induction of a distinct drug clearance program by a high-affinity ligand for the related nuclear receptor, the constitutive androstane receptor, does not overcome the lethality, indicating the unique requirement of PXR for detoxification. We propose that the PXR signaling pathway protects the body from toxic dietary cholesterol metabolites, and, by extension, PXR ligands may ameliorate human diseases such as cholestatic liver diseases and the associating acute renal failure.

Animals↗

Comparison of dietary intakes of micro- and macronutrients in rural, suburban and urban populations in Costa Rica.

OBJECTIVE: To compare, along with behavioural habits, the potential atherogenicity of diets in rural and urban areas in Costa Rica. DESIGN: Subjects were randomly selected from the general population in Costa Rica. A validated food-frequency questionnaire that inquired about dietary intake in the previous year was administered once to each subject. Each subject provided plasma and an adipose tissue biopsy, which were used as biomarkers for carotenoid, tocopherol and/or fatty acid intakes. Each subject also answered another questionnaire on personal profile and household characteristics. SETTING: A dietitian visited all subjects and conducted the interviews at their homes. SUBJECTS: Adult male and female free-living rural, suburban and urban Costa Ricans without a history of physical or mental disability. RESULTS: Subjects in rural areas were significantly (P < 0.05) more active physically, earned less income and had a higher intake of dietary fibre than urban dwellers. Urban residents reported a significantly (P < 0.05) higher consumption of total fat, specifically unsaturated fat mostly from soyabean oil, and had higher plasma and adipose tissue tocopherol and lycopene concentrations. Interestingly, no differences in body mass index were observed. CONCLUSIONS: These data show differences in cardiovascular disease (CVD) risk factors of rural and urban populations in Costa Rica. In rural areas, low socio-economic status and low intake of unsaturated fatty acids appear to be the prevalent CVD risk factors, while in urban areas they were low physical activity, high trans-fatty acids in the diet and adipose tissue, and low dietary fibre intake.

Cardiovascular Diseases↗