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PubMed2005

Molecular target therapy for synovial sarcoma.

Although the specific chromosomal translocation and fusion gene SYT-SSX in synovial sarcoma (SS) has been identified, the molecular mechanism of its tumorigenesis is largely unknown. Recent gene-expression profiles of soft-tissue tumors using cDNA microarray demonstrated that SS has the distinct gene-expression pattern from other sarcomas and has a similar pattern to that of malignant peripheral nerve sheath tumors, indicating that the origin of SS is likely to be the neural crest cells. Through this analysis, several genes were found to be specifically upregulated in SS and considered to play an important role in the proliferation of SS cells. Among them, Frizzled homolog 10 was identified as a good candidate molecule for the development of novel therapies to treat SS patients.

Antineoplastic Agents↗
PubMed2004

Research issues and strategies for genomic and proteomic biomarker discovery and validation: a statistical perspective.

The development and validation of clinically useful biomarkers from high-dimensional genomic and proteomic information pose great research challenges. Present bottlenecks include: that few of the biomarkers showing promise in initial discovery were found to warrant subsequent validation; and biomarker validation is expensive and time consuming. Biomarker evaluation should proceed in an orderly fashion to enhance rigor and efficiency. A molecular profiling approach, although promising, has a high chance of yielding biased results and overfitted models. Specimens from cohorts or intervention trials are essential to eliminate biases. The high cost for biomarker validation motivates some novel study design features, including sequential filtering and DNA pooling. For data analysis, logistic regression (in particular, boosting logistic regression) has features of robustness against model misspecification, and has resistance to model overfitting. Model assessment and cross-validation are critical components of data analysis. Having an independent test set is a vital feature of study design.

Biomarkers, Tumor↗
PubMed2005

Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information.

MOTIVATION: It is important to predict the outcome of patients with diffuse large-B-cell lymphoma after chemotherapy, since the survival rate after treatment of this common lymphoma disease is <50%. Both clinically based outcome predictors and the gene expression-based molecular factors have been proposed independently in disease prognosis. However combining the high-dimensional genomic data and the clinically relevant information to predict disease outcome is challenging. RESULTS: We describe an integrated clinicogenomic modeling approach that combines gene expression profiles and the clinically based International Prognostic Index (IPI) for personalized prediction in disease outcome. Dimension reduction methods are proposed to produce linear combinations of gene expressions, while taking into account clinical IPI information. The extracted summary measures capture all the regression information of the censored survival phenotype given both genomic and clinical data, and are employed as covariates in the subsequent survival model formulation. A case study of diffuse large-B-cell lymphoma data, as well as Monte Carlo simulations, both demonstrate that the proposed integrative modeling improves the prediction accuracy, delivering predictions more accurate than those achieved by using either clinical data or molecular predictors alone.

Biomarkers, Tumor↗
PubMed2005

Immunoprofiles of 11 biomarkers using tissue microarrays identify prognostic subgroups in colorectal cancer.

BACKGROUND AND AIMS: Genomewide expression profiling has identified a number of genes expressed at higher levels in colorectal cancer (CRC) than in normal tissues. Our objectives in this study were: 1) to test whether genes were also distinct on the protein level; 2) to evaluate these biomarkers in a series of well-characterized CRCs; and 3) to apply hierarchical cluster analysis to the immunohistochemical data. METHODS: Tissue microarrays (TMAs) comprising 351 CRC specimens from 270 patients were constructed to evaluate the genes Adam10, Cyclin D1, Annexin II, NFKB, Casein kinase 2 beta (CK2B), YB-1, P32, Rad51, c-fos, IGFBP4, and Connexin26 (Cx26). In total, 3,797 samples were analyzed. RESULTS: Unsupervised hierarchical clustering discovered subgroups of CRC that differed by tumor stage and survival. Kaplan-Meier analysis showed that reduced Cx26 expression was significantly associated with shorter patient survival and higher tumor grade (G1/G2 vs G3, P = .02), and Adam10 expression with a higher tumor stage (pT1/2 vs pT3/4, P = .04). CONCLUSIONS: Our study highlights the potential of TMAs for a higher-dimensional analysis by evaluating serial sections of the same tissue core (three-dimensional TMA analysis). In addition, it endorses the use of immunohistochemistry supplemented by hierarchical clustering for the identification of tumor subgroups with diagnostic and prognostic signatures.

Biomarkers, Tumor↗
PubMed2004

Two-dimensional electrophoretic protein profile analysis following exposure of human uroepithelial cells to occupational bladder carcinogens.

Protein biomarkers to occupational carcinogens were investigated using a transformable human uroepithelial cell system, SV-HUC.PC. SV-HUC.PC was treated with N-hydroxy-4,4'-methylene bis (2-chloroaniline) (N-OH-MOCA) or N-hydroxy-4 aminobiphenyl (N-OH-ABP). Two-dimensional gel electrophoresis of cell lysates compared protein changes across treatments. Increasing N-OH-MOCA resulted in a dose-related increase in protein spots altered. Comparing cell profiles treated with either carcinogen revealed alterations in the expression of nine proteins, identified using the TagIdent database. These demonstrated isoelectric point shift (1) or quantity change (8). Our investigation may be useful in identifying biomarkers of effects of exposure to bladder carcinogens.

Biomarkers↗
PubMed2005

Identification of novel biomarker candidates by differential peptidomics analysis of cerebrospinal fluid in Alzheimer's disease.

The objective of this work was the application of peptidomics technologies for the detection and identification of reliable and robust biomarkers for Alzheimer's disease (AD) contributing to facilitate and further improve the diagnosis of AD. Using a new method for the comprehensive and comparative profiling of peptides, the differential peptide display (DPD), 312 cerebrospinal fluid (CSF) samples from AD patients, cognitively unimpaired subjects and from patients suffering from other primary dementia disorders were analysed as four independent analytical sets. By combination with a cross validation procedure, candidates were selected from a total of more than 6,000 different peptide signals based on their discriminating power. Twelve candidates were identified using mass-spectrometric techniques as fragments of the possibly neuroprotective neuroendocrine protein VGF and another one as the complement factor C3 descendent C3f. The combination of peptide profiling and cross validation resulted in the detection of novel potential biomarkers with remarkable robustness and a close relation to AD pathophysiology.

Algorithms↗
PubMed2003

A combined comparative genomic hybridization and expression microarray analysis of gastric cancer reveals novel molecular subtypes.

Comparative genomic hybridization (CGH), microsatellite instability (MSI) assays, and expression microarrays were used to molecularly subclassify a common set of gastric tumor samples. We identified a number of novel genomic aberrations associated with gastric cancer and discovered that gastric tumors could be grouped by their expression profiles into three broad classes: "tumorigenic," "reactive," and "gastric-like." Patients with gastric-like tumors exhibited a significantly better overall survival than patients belonging to the other two classes (P < 0.05). A novel supervised learning methodology for multiclass prediction was used to identify optimal predictor gene sets that accurately predicted the class of an unknown tumor sample. These predictor sets may prove useful in the development of new diagnostic applications for gastric cancer staging and prognostication.

Adenocarcinoma↗
PubMed2004

Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling.

Trends in increased tuberculosis infection and a fatality rate of approximately 23% have necessitated the search for alternative biomarkers using newly developed postgenomic approaches. Here we provide a systematic analysis of Mycobacterium tuberculosis (Mtb) by directly profiling its gene products. This analysis combines high-throughput proteomics and computational approaches to elucidate the globally expressed complements of the three subcellular compartments (the cell wall, membrane, and cytosol) of Mtb. We report the identifications of 1044 proteins and their corresponding localizations in these compartments. Genome-based computational and metabolic pathways analyses were performed and integrated with proteomics data to reconstruct response networks. From the reconstructed response networks for fatty acid degradation and lipid biosynthesis pathways in Mtb, we identified proteins whose involvements in these pathways were not previously suspected. Furthermore, the subcellular localizations of these expressed proteins provide interesting insights into the compartmentalization of these pathways, which appear to traverse from cell wall to cytoplasm. Results of this large-scale subcellular proteome profile of Mtb have confirmed and validated the computational network hypothesis that functionally related proteins work together in larger organizational structures.

Automation↗
PubMed2006

Effect of multiple oral doses of androgenic anabolic steroids on endurance performance and serum indices of physical stress in healthy male subjects.

Anabolic androgenic steroids (AAS) are doping agents that are mostly used for improvement of strength and muscle hypertrophy. In some sports, athletes reported that the intake of AAS is associated with a better recovery, a higher training load capacity and therefore an increase in physical and mental performances. The purpose of this study was to evaluate, the effect of multiple doses of AAS on different physiological parameters that could indirectly relate the physical state of athletes during a hard endurance training program. In a double blind settings, three groups (n = 9, 8 and 8) were orally administered placebo, testosterone undecanoate or 19-norandrostenedione, 12 times during 1 month. Serum biomarkers (creatine kinase, ASAT and urea), serum hormone profiles (testosterone, cortisol and LH) and urinary catecholamines (noradrenalin, adrenalin and dopamine) were evaluated during the treatment. Running performance was assessed before and after the intervention phase by means of a standardized treadmill test. None of the measured biochemical variables showed significant impact of AAS on physical stress level. Data from exercise testing on submaximal and maximal level did not reveal any performance differences between the three groups or their response to the treatment. In the present study, no effect of multiple oral doses of AAS on endurance performance or bioserum recovery markers was found.

Adult↗
PubMed2005

Molecular prognostic factors in diffuse large B-cell lymphoma.

The treatment of patients with diffuse large B-cell lymphoma (DLBCL) has been guided traditionally by clinical parameters such as the Ann Arbor Staging Classification for Hodgkin's disease. Although the International Prognostic Index (IPI) represents the most widely accepted prognostic model, there is still a marked variability in outcome within identical IPI subgroups, reflecting the heterogeneity of this malignancy. Use of DNA microarray, real-time reverse transcription polymerase chain reaction, and tissue array immunohistochemistry methodologies makes the development of new classifications possible based on molecular profiling. The molecular classification of DLBCL may lead to the grouping of specific disease entities sharing similar biologic features, clinical behavior, and outcome. Once tested and validated, this new generation of prognostic models should become an integral part of the daily practice, providing valuable additional information to the currently existing clinically based predictive models. To accomplish these goals and to be in a position in which existing or new prognostic models can be easily tested and validated, there is a strong need to collect frozen and paraffin-embedded material that can be used for RNA extraction and construction of tissue arrays, respectively. Such materials should be gathered as an integral part of any planned study.

Biomarkers, Tumor↗
PubMed2004

How are biomarkers related to physical and mental well-being?

We investigate how biological markers of individual responses to stressful experiences are associated with profiles of physical and mental functioning in a national sample of middle-aged and elderly Taiwanese. Data come from a population-based sample of middle-aged and elderly Taiwanese in 2000. The data combine rich biological measures with self-reported information on physical and mental health. Grade of membership methods are used to summarize functional status, and multinomial logit models provide information on the association between biological measures and function. The analysis identifies significant associations between biomarkers of stressful experience and profiles of physical and mental functioning. The estimates reveal the potential importance for health of both low and high values of biological parameters. The findings point to directions for future research regarding development of aggregate measures of cumulative dysregulation across multiple physiological systems.

Aged↗
PubMed2004

Stratification of acute myeloid leukemia based on gene expression profiles.

Acute myeloid leukemia (AML) is characterized by clonal growth of immature leukemic blasts and develops either de novo or secondarily to anticancer treatment or to other hematologic disorders. Given that the current classification of AML, which is based on blast karyotype and morphology, is not sufficiently robust to predict the prognosis of each affected individual, new stratification schemes that are of better prognostic value are needed. Global profiling of gene expression in AML blasts has the potential both to identify a small number of genes whose expression is associated with clinical outcome and to provide insight into the molecular pathogenesis of this condition. Emerging genomics tools, especially DNA microarray analysis, have been applied in attempts to isolate new molecular markers for the differential diagnosis of AML and to identify genes that contribute to leukemogenesis. Progress in bioinformatics has also yielded means with which to classify patients according to clinical parameters such as long-term prognosis. The application of such analysis to large sets of gene expression data has begun to provide the basis for a new AML classification that is more powerful with regard to prediction of prognosis.

Biomarkers, Tumor↗
PubMed2006

Dose-response relationships in gene expression profiles in rainbow trout, Oncorhyncus mykiss, exposed to ethynylestradiol.

Determining how gene expression profiles change with toxicant dose will improve the utility of arrays in identifying biomarkers and modes of toxic action. Isogenic rainbow trout, Oncorhyncus mykiss,were exposed to 10, 50 or 100 ng/L ethynylestradiol (a xeno-estrogen) for 7 days. Following exposure hepatic RNA was extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNAs. Transcript expression in treated vs control fish was analyzed via Genespring (Silicon Genetics) to identify genes with altered expression, as well as to determine gene clustering patterns that can be used as "expression signatures". Array results were confirmed via qRT PCR. Our analysis indicates that gene expression profiles varied somewhat with dose. Established biomarkers of exposure to estrogenic chemicals, such as vitellogenin, vitelline envelope proteins, and the estrogen receptor alpha, were induced at every dose. Other genes were dose specific, suggesting that different doses induce distinct physiological responses. These findings demonstrate that cDNA microarrays could be used to identify both toxicant class and relative dose.

Animals↗
PubMed2003

Hepsin and maspin are inversely expressed in laser capture microdissectioned prostate cancer.

PURPOSE: Recent studies have shown that hepsin, a serine protease, is over expressed in prostate cancers, implicating hepsin activity in tumor invasion. Using microarray technology we have previously identified 22 genes that were up-regulated in high grade prostate cancers compared with benign prostatic hyperplasia. Of them hepsin was the most differentially over expressed. In the current report we compare hepsin to maspin (BD Transduction Laboratories, San Diego, California), a serine protease inhibitor (serpin), to measure the balance between levels of serine proteases and serpins, which are considered to be a critical determinant of net proteolytic activity. MATERIALS AND METHODS: We combined the technique of laser capture microdissection with gene expression monitoring by micro-array analysis to investigate the gene expression profiles of prostate cells of different histological types. We also studied maspin immunohistochemically. RESULTS: We observed that hepsin as well as 7 of 22 previously reported up-regulated genes demonstrated a pattern of increasing expression with increasing malignant phenotype. In contrast, the expression of maspin (a serpin) decreased with increasing malignancy of prostate cancers. Using immunohistochemistry we observed that maspin protein is expressed strongly in benign prostatic tissues and slightly in grade 3 prostate cancers, and is absent in grade 4/5 cancers. CONCLUSIONS: We conclude that the increased ratio of hepsin-to-maspin may have an important role in prostate cancer progression and invasion.

Biomarkers, Tumor↗
PubMed2005

Comparison of genome profiles for identification of distinct subgroups of diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) comprises molecularly distinct subgroups such as activated B-cell-like (ABC) and germinal center B-cell-like (GCB) DLBCLs. We previously reported that CD5(+) and CD5(-)CD10(+) DLBCL constitute clinically relevant subgroups. To determine whether these 2 subgroups are related to ABC and GCB DLBCLs, we analyzed the genomic imbalance of 99 cases (36 CD5(+), 19 CD5(-)CD10(+), and 44 CD5(-)CD10(-)) using array-based comparative genomic hybridization (CGH). Forty-six of these cases (22 CD5(+), 7 CD5(-)CD10(+), and 17 CD5(-)CD10(-)) were subsequently subjected to gene-expression profiling, resulting in their division into 28 ABC (19 CD5(+) and 9 CD5(-)CD10(-)) and 18 GCB (3 CD5(+), 7 CD5(-)CD10(+), and 8 CD5(-)CD10(-)) types. A comparison of genome profiles of distinct subgroups of DLBCL demonstrated that (1) ABC DLBCL is characterized by gain of 3q, 18q, and 19q and loss of 6q and 9p21, and GCB DLBCL is characterized by gain of 1q, 2p, 7q, and 12q; (2) the genomic imbalances characteristic of the CD5(+) and CD5(-)CD10(+) groups were similar to those of the ABC and GCB types, respectively. These findings suggest that CD5(+) and CD5(-)CD10(+) subgroups are included, respectively, in the ABC and GCB types. Finally, when searching for genomic imbalances that affect patients' prognosis, we found that 9p21 loss (p16(INK4a) locus) marks the most aggressive type of DLBCL.

Adult↗
PubMed2006

[DNA-chips in the diagnosis of hematological malignancies].

In hematological malignancies, gene expression profiling using DNA-microarrays led to the discovery of novel lymphoma and leukemia subgroups. The heterogeneous entity of diffuse large B-cell lymphoma could be subdivided into the germinal center B-cell-like and the activated B-cell-like subtype which differ in pathogenesis and clinical behavior. In leukemia, existing entities defined by morphological, cytogenetic, molecular and immunophenotypic criteria were confirmed on the global gene expression level; in addition, new important molecular subgroups could be identified. In retrospective clinical lymphoma and leukemia studies, robust gene expression signatures were discovered that predict the clinical course at the time of diagnosis. Given the huge potential of the DNA-microarray technology, application in the routine diagnostic setting appears possible.

Biomarkers, Tumor↗
PubMed2005

ProteinChip technology reveals distinctive protein expression profiles in the urine of bladder cancer patients.

OBJECTIVE: Since accurate biomarkers for the early diagnosis or individual prognosis of the bladder carcinoma are still not available, we used the ProteinChip technology, to search for discriminating protein expressions associated with this cancer and its subtypes. METHODS: A training set consisting of 30 archival urine samples from bladder carcinoma patients and 30 urinary samples from healthy volunteers, was analyzed via ProteinChip technology and computer based data mining. Mass clusters of differentially expressed proteins were verified by a second set (test set) comprising 21 bladder carcinoma urine samples and 21 non-tumor urinary samples. Expression differences between carcinoma subtype sample groups of the initial training set were assessed by a trend test. RESULTS: Bladder carcinoma was segregated from control with a sensitivity and specificity of 80% and 90 to 97% in the trainings set, as well as 52 to 57% and 57 to 62% in the test set, respectively. Segregation of pooled tumor stages pT2-pT3 from stages pT1 and pTa was possible at the 53.3 kDa cluster of the CM10-chip array data derived rule base. CONCLUSION: ProteinChip technology together with adapted computer based data mining tools are useful for the rapid establishment of potential protein biomarkers.

Biomarkers, Tumor↗
PubMed2006

Daily immunoactive and bioactive human chorionic gonadotropin profiles in periimplantation urine samples.

A need exists for broadly applicable biomarkers of pregnancy outcome in population-based studies that assess environmental hazards to human reproduction. Previous studies have demonstrated that during the periimplantation period, measures of the circulating levels of immunoreactive hCG (IhCG) are not predictive of pregnancy outcome, whereas measurements of the circulating levels of bioactive hCG (BhCG) provide information relating to pregnancy outcome and might provide the basis for an early biomarker of pregnancy outcome. However, for this biomarker to have broad application in population-based studies, it must be adapted to urinary hCG metabolites. The principle objective of the present study was to characterize the periimplantation excretion patterns of urinary hCG metabolites of pregnancies that resulted in live birth (LB), early pregnancy loss (EPL), and recognized clinical abortion (CAB) with an immunoenzymometric assay specific to intact hCG and an LH/chorionic gonadotropin cellular bioassay as the basis for a preliminary comparison between successful (LB) and failing (EPL and CAB) outcome groups. Automated immunoassays for FSH and hCG were used to define each conceptive cycle's implantation window. The timing of first hCG detection was significantly later for the EPL group. Pregnancies that resulted in LB had consistently rising average daily IhCG and BhCG levels, with no significant differences when average daily IhCG and BhCG measurements were compared (Student t-test, P>0.05), whereas pregnancies that resulted in CAB and EFL had lower average daily IhCG and BhCG levels that increased inconsistently. These findings demonstrate that critical information related to pregnancy outcome may be present when multiple urinary hCG isoforms are measured. Further data suggest that the rate of change for the ratio of daily BhCG over IhCG levels might be useful as the basis of a broadly applicable early biomarker for pregnancy outcome.

Abortion, Spontaneous↗