Microarray profiling of gene expression patterns in bladder tumor cells treated with genistein

Genistein: A promising phytoconstituent with reference to its bioactivities

Genistein, a potent phytoconstituent, has garnered significant attention for its diverse bioactivities, making it a subject of extensive research and exploration. This review delves into the multifaceted properties of genistein, encompassing its antioxidant and anticancer potential. Its ability to modulate various cellular pathways and interact with diverse molecular targets has positioned it as a promising candidate in the prevention and treatment of various diseases. This review provides a comprehensive examination of Genistein, covering its chemical properties, methods of isolation, synthesis, therapeutic attributes with regard to cancer management, and the proposed mechanisms of action as put forth by researchers.

Trends in urine biomarker discovery for urothelial bladder cancer: DNA, RNA, or protein?

Urothelial bladder cancer is a complex disease displaying a landscape of heterogenous molecular subtypes, mutation profiles and clinical presentations. Diagnosis and surveillance rely on flexible cystoscopy which has high accuracy, albeit accompanied by a high-cost burden for healthcare providers and discomfort for patients. Advances in "omic" technologies and computational biology have provided insights into the molecular pathogenesis of bladder cancer and provided powerful tools to identify markers for disease detection, risk stratification, and predicting responses to therapy. To date, numerous attempts have been made to discover and validate diagnostic biomarkers that could be deployed as an adjunct to the cystoscopic diagnosis and long-term surveillance of bladder cancer. We report a comprehensive literature analysis using PubMed to assess the changing trends in investigating DNA, RNA, or proteins as diagnostic urinary biomarkers over a period of 5 decades: 1970-2020. A gradual shift has been observed in research away from protein biomarkers to nucleic acids including different classes of RNA, and DNA methylation and mutation markers. Until 2000, publications involving protein biomarker discovery constituted 87% of the total number of research articles with DNA comprising 6% and RNA 7%. Since 2000 the proportion of protein biomarker articles has fallen to 40%, and DNA and RNA studies increased to 32% and 28%, respectively. Clearly research focus, perhaps driven by technological innovation, has shifted from proteins to nucleic acids. We optimistically hypothesise that, following thorough validation, a clinically useful detection test for bladder cancer based on a panel of DNA or RNA markers could become reality within 5-10 years.

Spectroscopic evaluation of the interaction between pesticides and chickpea cystatin: comparative binding and toxicity analyses

The binding study of pesticides with proteins is of great importance in ecotoxicology. In this study, a comparative interaction mechanism of phytocystatin with three pesticides has been presented, each from a different class-glyphosate herbicide (GPS), chlorpyrifos insecticide (CPF), and mancozeb fungicide (MCZ). The interaction of purified chickpea cystatin (CPC) has been characterized by fluorescence, UV, and circular dichroism (CD) spectroscopic methods. The study revealed association constants (Ka) of 52 M(-1), 1.145 × 10(3) M(-1), and 36.12 M(-1) for the interaction of CPF, MCZ, and GPS with CPC, respectively, signifying the high affinity interaction for MCZ. Structural changes (at tertiary and secondary levels) were confirmed by UV-visible, intrinsic fluorescence and CD spectroscopy. The results showed that the effect on the CPC structure was more pronounced in the case of MCZ, which was followed by CPF and then GPS. The functional analysis of the pesticide treated inhibitor showed a decline in antipapain activity which varied with the time and dose as well as the class of pesticide. MCZ was relatively much more toxic as compared to CPF and GPS. Reactive oxygen species responsible for inhibitor damage were also analyzed. The results obtained implicate that the exposure of plants to pesticides may lead to physicochemical changes in proteins such as phytocystatins leading to physiological damage to the plant system.

DNA microarray-based gene expression profiling of estrogenic chemicals

We summarize updated information about DNA microarray-based gene expression profiling by focusing on its application to estrogenic chemicals. First, estrogenic chemicals, including natural/industrial estrogens and phytoestrogens, and the methods for detection and evaluation of estrogenic chemicals were overviewed along with a comprehensive list of estrogenic chemicals of natural or industrial origin. Second, gene expression profiling of chemicals using a focused microarray containing estrogen-responsive genes is summarized. Third, silent estrogens, a new type of estrogenic chemicals characterized by their estrogenic gene expression profiles without growth stimulative or inhibitory effects, have been identified so far exclusively by DNA microarray assay. Lastly, the prospect of a microarray assay is discussed, including issues such as commercialization, future directions of applications and quality control methods.

Epithelial membrane protein 2 is a prognostic indictor for patients with urothelial carcinoma of the upper urinary tract

Upper urinary tract urothelial carcinoma is a relatively uncommon disease and is diagnosed more frequently at advanced stages. The prognosis of these patients mainly has been related to tumor stage and grade. As a result, the definition of prognostic indicators enabling precise patient selection is mandatory for neoadjuvant or adjuvant therapies. The epithelial membrane protein (EMP2) was identified as one of the up-regulated genes by isoflavones. EMP2 overexpression suppressed foci formation, anchorage-independent growth in vitro, and tumorigenicity in severe combined immunodeficiency mice (all P < 0.05). In addition, a cross-talk between EMP2 and integrins αV and β3 was shown in the regulation of cell adhesion and migration. Higher EMP2 expression was associated with a better progression-free survival (P = 0.008) and cancer-related death (P < 0.001). EMP2 was identified as a tumor-suppressor gene in urinary tract urothelial carcinoma and may be an innovative co-targeting candidate for designing integrin-based cancer therapy.

Transcriptional activation of the Axl and PDGFR-α by c-Met through a ras- and Src-independent mechanism in human bladder cancer

BACKGROUND

A cross-talk between different receptor tyrosine kinases (RTKs) plays an important role in the pathogenesis of human cancers.

METHODS

Both NIH-Met5 and T24-Met3 cell lines harboring an inducible human c-Met gene were established. C-Met-related RTKs were screened by RTK microarray analysis. The cross-talk of RTKs was demonstrated by Western blotting and confirmed by small interfering RNA (siRNA) silencing, followed by elucidation of the underlying mechanism. The impact of this cross-talk on biological function was demonstrated by Trans-well migration assay. Finally, the potential clinical importance was examined in a cohort of 65 cases of locally advanced and metastatic bladder cancer patients.

RESULTS

A positive association of Axl or platelet-derived growth factor receptor-alpha (PDGFR-α) with c-Met expression was demonstrated at translational level, and confirmed by specific siRNA knock-down. The transactivation of c-Met on Axl or PDGFR-α in vitro was through a ras- and Src-independent activation of mitogen-activated protein kinase/extracellular signal-regulated kinase (MEK/ERK) pathway. In human bladder cancer, co-expression of these RTKs was associated with poor patient survival (p < 0.05), and overexpression of c-Met/Axl/PDGFR-α or c-Met alone showed the most significant correlation with poor survival (p < 0.01).

CONCLUSIONS

In addition to c-Met, the cross-talk with Axl and/or PDGFR-α also contributes to the progression of human bladder cancer. Evaluation of Axl and PDGFR-α expression status may identify a subset of c-Met-positive bladder cancer patients who may require co-targeting therapy.

Functional genomics of endothelial cells treated with anti-angiogenic or angiopreventive drugs

Angiogenesis is a highly regulated physiological process that has been studied in considerable detail given its importance in several chronic pathologies. Many endogenous factors and hormones intervene in the regulation of angiogensis and classical as well as targeted drugs have been developed for its control. Angiogenesis inhibition has come off the bench and entered into clinical application for cancer therapy, particularly for metastatic disease. While the clinical benefit is currently in terms of months, preclinical data suggest that novel drugs and drug combinations could lead to substantial improvement. The many targets of endogenous angiogenesis inhibitors reflect the complexity of the process; in contrast, current clinical therapies mainly target the vascular endothelial growth factor system. Cancer chemopreventive compounds can retard tumor insurgence and delay or prevent metastasis and many of these molecules hinder angiogenesis, a mechanism that we termed angioprevention. Angiopreventive drugs appear to prevalently act through the inhibition of the pro-inflammatory and anti-apoptotic player NFkappaB, thus contrasting inflammation dependent angiogenesis. Relatively little is known concerning the effects of these angiogenesis inhibitors on gene expression of endothelial cells, the main target of many of these molecules. Here we provide an exhaustive list of anti-angiogenic molecules, and summarize their effects, where known, on the transcriptome and functional genomics of endothelial cells. The regulation of specific genes can be crucial to preventive or therapeutic intervention. Further, novel targets might help to circumvent resistance to anti-angiogenic therapy. The studies we review are relevant not only to cancer but also to other chronic degenerative diseases involving endothelial cells, such as cardiovascular disorders, diabetes, rheumatoid arthritis and retinopaties, as well as vessel aging.

Different mechanisms for phytoalexin induction by pathogen and wound signals in Medicago truncatula

Cell suspensions of the model legume Medicago truncatula accumulated the isoflavonoid phytoalexin medicarpin in response to yeast elicitor or methyl jasmonate (MJ), accompanied by decreased levels of isoflavone glycosides in MJ-treated cells. DNA microarray analysis revealed rapid, massive induction of early (iso)flavonoid pathway gene transcripts in response to yeast elicitor, but not MJ, and differential induction by the two elicitors of sets of genes encoding transcription factors, ABC transporters, and beta-glucosidases. In contrast, both elicitors induced genes encoding enzymes for conversion of the isoflavone formononetin to medicarpin. Four MJ-induced beta-glucosidases were expressed as recombinant enzymes in yeast, and three were active with isoflavone glucosides. The most highly induced beta-glucosidase was nuclear localized and preferred flavones to isoflavones. The results indicate that the genetic and biochemical mechanisms underlying accumulation of medicarpin differ depending on the nature of the stimulus and suggest a role for MJ as a signal for rapid hydrolysis of preformed, conjugated intermediates for antimicrobial biosynthesis during wound responses.

Molecular alterations associated with bladder cancer progression

Clinically, superficial tumors (stages Ta, Tis, and T1) account for 75% to 85% of bladder neoplasms, while the remaining 15% to 25% are invasive (T2, T3, T4) or metastatic lesions at the time of initial presentation. More than 70% of patients with superficial tumors will have one or more recurrences after initial treatment, and about one third of those patients will progress and eventually die of the disease. New methods are needed to identify and monitor patients presenting with "high-risk" superficial tumors likely to develop into invasive carcinoma. Once invasive into muscle, the natural history is quite variable but highly lethal. Despite aggressive surgical resection, radiotherapy, and/or chemotherapy, the overall cure rate remains in the range of 20% to 50%. New biological determinants are needed both for proper selection of therapy and monitoring. In this review, we describe and update molecular alterations reportedly associated with bladder tumorigenesis and cancer progression. We also review novel genes and "signaling networks" identified by the use of high-throughput technologies. The concept of alterations affecting "genetic pathways" is becoming more than just a molecular biology exercise. The challenge is to evaluate such targets for therapeutic development, as well as to translate progression and outcome biomarkers into improved clinical management. Integration of data generated from in-depth clinical evaluation, histologic tumor characteristics, and validated biomarkers could provide highly accurate, predictive tools for management of the bladder cancer patient.

hEGR1 is induced by EGF, inhibited by gefitinib in bladder cell lines and related to EGF receptor levels in bladder tumours

The effect of EGF and gefitinib on two EGFR-positive human bladder cancer cell lines has been investigated using array-based gene expression profiling. The most prominent transcript, increased up to 6.7-fold by EGF compared with controls in RT112 cells, was human early growth response protein 1 (hEGR1). This induction was prevented by gefitinib. The hEGR1 mRNA in EGF-treated samples was reduced in the presence of gefitinib, as was hEGR1 protein in cell lysates. In the RT4 cells, hEGR1 expression was halved in the presence of EGF and gefitinib in combination. In bladder tumour samples, there was a significant correlation between hEGR1 mRNA detected by RT-PCR and EGFR detected by ligand binding, (P=0.042). The induction by EGF of the hEGR1 gene, mRNA and protein in RT112 cells, and its inhibition by gefitinib, together with the detection of hEGR1 mRNA in bladder tumours, suggests that hEGR1 may be important in the EGFR growth-signalling pathway in bladder cancer and should be further investigated for its prognostic significance and as a potential therapeutic target.

Regulation of HOXA10 expression by phytoestrogens

HOXA10 is necessary for normal development of the Müllerian duct, and continued adult expression in the uterus is necessary for female fertility. HOXA10 expression is altered by diethylstilbestrol, leading to uterine anomalies. Other endocrine disruptors may potentially lead to reproductive anomalies or dysfunction by altering HOXA10 expression. Here we investigated the effect of isoflavones on HOXA10 expression after in utero or adult exposure in the mouse. Genistein, but not diadzein, regulated HOXA10 mRNA and protein expression in the adult mouse uterus. In contrast, in utero genistein or diadzein exposure had no lasting effect on HOXA10 expression in the exposed offspring. Reporter gene expression driven by the HOXA10 estrogen response element was increased in a dose-responsive manner by genistein, but not daidzein. Neither estrogen receptor-alpha nor estrogen receptor-beta binding to the HOXA10 estrogen response element was affected by genistein or daidzein. In utero exposure to isoflavones is unlikely to result in HOXA10-mediated developmental anomalies. Adult genistein exposure alters uterine HOXA10 expression, a potential mechanism by which this agent affects fertility.

Dietary isoflavones differentially induce gene expression changes in lymphocytes from postmenopausal women who form equol as compared with those who do not

Human and animal studies suggest that dietary soy isoflavones reduce cancer risk, ameliorate postmenopausal syndrome and decrease bone resorption in postmenopausal women. The capacity to form the metabolite equol from daidzein is suggested as an important modulator of response to isoflavones; this capacity depends on gut colonization with appropriate bacteria. We administered a dietary supplement containing high-dose purified soy isoflavones (genistein, 558 mg/day; daidzein, 296 mg/day; and glycitein, 44 mg/day) to 30 postmenopausal women for 84 days and collected peripheral lymphocytes at timed intervals. Using microarray analysis, we determined whether changes in gene expression associated with this treatment support existing hypotheses as to isoflavones' mechanisms of action. Expression of a large number of genes was altered by isoflavone treatment, including induction of genes associated with cyclic adenosine 3',5'-monophosphate (cAMP) signaling and cell differentiation and decreased expression of genes associated with cyclin-dependent kinase activity and cell division. We report that isoflavone treatment in subjects who have the capacity to produce equol differentially affects gene expression as compared with nonproducers, supporting the plausibility of the importance of equol production. In general, isoflavones had a stronger effect on some putative estrogen-responsive genes in equol producers than in nonproducers. Our study suggests that, in humans, isoflavone changes are related to increased cell differentiation, increased cAMP signaling and G-protein-coupled protein metabolism and increased steroid hormone receptor activity and have some estrogen agonist effects; equol-production status is likely to be an important modulator of responses to isoflavones.

Antiviral effect of Phyllanthus nanus ethanolic extract against hepatitis B virus (HBV) by expression microarray analysis

Ethanolic extract of Phyllanthus nanus (P. nanus) treatment exhibited potent antiviral activity against Hepatitis B virus (HBV). The effects of these extracts on HBV in the HBV genome integrated cell lines--Alexander cells and HepG2 2.2.15 cells were examined. Experimental results showed that the ethanolic extract of P. nanus produced suppressive effect on HBsAg secretion and HBsAg mRNA expression. The extract also inhibited HBV replication as measured by HBV DNA level in vitro. In addition, using a duck HBV (DHBV) primary culture model, the P. nanus ethanolic extract suppressed viral replication of DHBV in DHBV infected primary duck hepatocytes. The gene expression pattern in Alexander cells that had been treated with the ethanolic extract of P. nanus was also revealed by microarray techniques. The microarray results indicated that there was up-regulation of expression of several genes, including annexin A7 (Axn7). The subcellular localization of Axn7 and anti-HBV effect of Axn7 over-expression in Alexander cells were also investigated. Results showed that expression of Axn7-GFP fusion protein are localized around the secretory vesicles and could cause a decrease in HBsAg secretion in Alexander cells. Axn7 protein might play an important role in the medicinal effect of the active principle(s) of P. nanus.

Detection of Epstein–Barr virus infection and gene expression in human tumors by microarray analysis

Epstein-Barr virus (EBV) genome-chips are employed to determine the EBV infection rate and to reveal the gene expression patterns of EBV in tumor biopsies. These chips are produced with 71 consecutive PCR-amplified EBV DNA fragments of 1-3 kbp covering the entire EBV genome. The specificity of the EBV-chips is determined by hybridizing the DNA on the chips with biotin-labeled cDNA probes reverse transcribed from the mRNA of P3HR1 cells, which were B-cell infected latently by EBV. Hybridization results revealed only the expression of EBNA1, EBNA2, EBER1 and EBER2 in these cells. On the other hand, EBV lytic genes are expressed after the cells are treated with 12-O-tetradecanoylphorbol-13-acetate and sodium butyrate to induce the EBV lytic cycle. Fourty-four tumor biopsies from different organs are assayed with these chips, which showed many defined and interesting EBV gene expression patterns. This study demonstrates that the EBV-chip is useful for screening infection with EBV in tumors, which may lead to insights into tumorigenesis associated with this virus.

Microarray analyses in bladder cancer cells: Inhibition of hTERT expression down-regulates EGFR

The human telomerase reverse transcriptase (hTERT) contributes to the immortal phenotype of the majority of cancers. Targeting hTERT by transfection with antisense oligonucleotides (AS-ODNs) induced immediate growth inhibition in human bladder cancer (BCa) cells. The molecular basis of the antiproliferative capacity of hTERT AS-ODNs was investigated by oligonucleotide microarray analyses and was compared to effects caused by siRNA-mediated knock-down of hTERT in EJ28 BCa cells. Two different AS-ODNs -- both down-regulated the expression of hTERT -- changed the expression of different genes mainly involved in stress response (including EGR1, ATF3 and GDF15), but without an association to telomerase function. This indicates that the immediate growth inhibition was caused, at least in part, by off-target effects. In comparison to that the blockade of the expression of hTERT using 2 different siRNAs was accompanied by the down-regulation of the oncogenes FOS-like antigen 1 (FOSL1) and epidermal growth factor receptor (EGFR), known to be overexpressed in BCa. We show here for the first time that repression of the hTERT transcript number decreased the expression of EGFR both at the mRNA and protein levels, suggesting a potential new function of hTERT in the regulation of EGFR-stimulated proliferation. Furthermore, the suppression of hTERT by siRNAs caused an enhancement of the antiproliferative capacity of the chemotherapeutics mitomycin C and cisplatin. The results presented herein may support the hypothesis that hTERT promotes the growth of tumor cells by mechanisms independent from telomere lengthening. The detailed clarification of these processes will shed light on the question, whether telomerase inhibitors might constitute suitable anticancer tools.

Hepatitis B virus pre-S2 mutant upregulates cyclin A expression and induces nodular proliferation of hepatocytes

Naturally occurring mutants with a deletion in the pre-S2 region of the large surface protein (Delta S2-LHBs) are prevalent in serum and livers of patients with chronic hepatitis B virus (HBV) infection associated with cirrhosis. The Delta S2-LHBs protein is retained in the endoplasmic reticulum (ER) and may induce ER stress. One interesting observation is the consistently clustered distribution of hepatocytes expressing Delta S2-LHBs. In this study, complementary DNA microarray analysis identified cyclin A and several groups of genes as being significantly upregulated by Delta S2-LHBs in the HuH-7 cell line. This observation was confirmed in liver tissues. The induction of cyclin A expression may occur via the specific transactivator function of Delta S2-LHBs independent of ER stress. In the presence of Delta S2-LHBs, hepatocytes sustained cyclin A expression and cell cycle progression under ER stress and displayed increased BrdU incorporation with multinuclear formation. Furthermore, Delta S2-LHBs could enhance anchorage-independent cell growth in a nontransformed human hepatocyte line and induced nodular proliferation of hepatocytes in transgenic mice. In conclusion, these in vitro and in vivo data support a role for Delta S2-LHBs in the hepatocyte hyperplasia and a likely role in the process of HBV-related tumorigenesis.

Microfabricated systems for nucleic acid analysis

High throughput and automation of nucleic acid analysis are required in order to exploit the information that has been accumulated from the Human Genome Project. Microfabricated analytical systems enable parallel sample processing, reduced analysis-times, low consumption of sample and reagents, portability, integration of various analytical procedures and automation. This review article discusses miniaturized analytical systems for nucleic acid amplification, separation by capillary electrophoresis, sequencing and hybridization. Microarrays are also covered as a new analytical tool for global analysis of gene expression. Thus. instead of studying the expression of a single gene or a few genes at a time we can now obtain the expression profiles of thousands of genes in a single experiment.

Expression profiling of the estrogen responsive genes in response to phytoestrogens using a customized DNA microarray

Here, we examined phytoestrogens, isoflavones (genistein, daidzein, glycitein, biochanin A and ipriflavone), flavones (chrysin, luteolin and apigenin), flavonols (kaempferol and quercetin), and a coumestan, a flavanone and a chalcone (coumestrol, naringenin and phloretin, respectively) by means of a DNA microarray assay. A total of 172 estrogen responsive genes were monitored with a customized DNA microarray and their expression profiles for the above phytoestrogens were compared with that for 17beta-estradiol (E2) using correlation coefficients, or R values, after a correlation analysis by linear regression. While R values indicate the similarity of the response by the genes, we also examined the genes by cluster analysis and by their specificity to phytoestrogens (specific to genistein, daidzein or glycitein) or gene functions. Several genes were selected from p53-related genes (CDKN1A, TP53I11 and CDC14), Akt2-related genes (PRKCD, BRCA1, TRIB3 and APPL), mitogen-activated protein kinase-related genes (RSK and SH3BP5), Ras superfamily genes (RAP1GA1, RHOC and ARHGDIA) and AP-1 family and related genes (RIP140, FOS, ATF3, JUN and FRA2). We further examined the extracts from two local crops of soy beans (Kuro-daizu or Mochi-daizu) by comparing the gene expression profiles with those of E2 or phytoestrogens as a first step in utilizing the expression profiles for various applications.

H-Ras oncogene counteracts the growth-inhibitory effect of genistein in T24 bladder carcinoma cells

Among eight human bladder cancer cell lines we examined, only T24 cells were resistant to the growth inhibition effect of genistein, an isoflavone and potent anticancer drug. Since the T24 cell line was the only cell line known to overexpress oncogenic H-Ras(val 12), we investigated the role of H-Ras(val 12) in mediating drug resistance. Herein, we demonstrate that the phenotype of T24 cells could be dramatically reversed and became relatively susceptible to growth inhibition by genistein if the synthesis of H-Ras(val 12) or its downstream effector c-Fos had been suppressed. The inhibition of Ras-mediated signalling with protein kinase inhibitors, such as PD58059 and U0126 which inhibited MEK and ERK, in T24 cells also rendered the identical phenotypic reversion. However, this reversion was not observed when an inhibitor was used to suppress the protein phosphorylation function of PI3 K or PKC. These results suggest that the signal mediated by H-Ras(val 12) is predominantly responsible for the resistance of the cells to the anticancer drug genistein.

Recent advances in bladder cancer diagnostics

Transitional cell carcinoma of the bladder is a significant cause of morbidity and mortality worldwide. The diagnosis of bladder cancer is based on the information provided by cystoscopy, the gold standard, in combination with urinary cytology findings. Many tumor markers have been evaluated for detecting and monitoring of the disease in serum, bladder washes, and urinary specimens. However, none of these biomarkers reported to date has shown sufficient sensitivity and specificity for the detection of the whole spectrum of bladder cancer diseases in routine clinical practice. The advent of high-throughput microarrays is accelerating the identification process of the molecular events characteristic of bladder tumors' phenotype and subsequent clinical behavior. The information provided by these analyses is resulting not only in the identification of novel therapeutic targets for bladder cancer, but also in the development of diagnostic tools. This review summarizes the reports utilizing high-throughput microarrays in bladder cancer and the implications of these analyses in the diagnosis and clinical management of patients with bladder cancer.

Identifying Superficial, Muscle-Invasive, and Metastasizing Transitional Cell Carcinoma of the Bladder

PURPOSE

Expression profiling by DNA microarray technology permits the identification of genes underlying clinical heterogeneity of bladder cancer and which might contribute to disease progression, thereby improving assessment of treatment and prediction of patient outcome.

EXPERIMENTAL DESIGN

Invasive (20) and superficial (22) human bladder tumors from 34 patients with known outcome regarding disease recurrence and progression were analyzed by filter-based cDNA arrays (Atlas Human Cancer 1.2; BD Biosciences Clontech) containing 1185 genes. For 9 genes, array data were confirmed using real-time reverse transcription-PCR. Additionally, Atlas array data were validated using Affymetrix GeneChip oligonucleotide arrays with 22,283 human gene fragments and expressed sequence tags sequences in a subset of three superficial and six invasive bladder tumors.

RESULTS

A two-way clustering algorithm using different subsets of gene expression data, including a subset of 41 genes validated by the oligonucleotide array (Affymetrix), classified tumor samples according to clinical outcome as superficial, invasive, or metastasizing. Furthermore, (a) a clonal origin of superficial tumors, (b) highly similar gene expression patterns in different areas of invasive tumors, and (c) an invasive-like pattern was observed in bladder mucosas derived from patients with locally advanced disease. Several gene clusters that characterized invasive or superficial tumors were identified. In superficial bladder tumors, increased mRNA levels of genes encoding transcription factors, molecules involved in protein synthesis and metabolism, and some proteins involved into cell cycle progression and differentiation were observed, whereas transcripts for immune, extracellular matrix, adhesion, peritumoral stroma and muscle tissue components, proliferation, and cell cycle controllers were up-regulated in invasive tumors.

CONCLUSIONS

Gene expression profiling of human bladder cancers provides insight into the biology of bladder cancer progression and identifies patients with distinct clinical phenotypes.

Applications of array technology: identification of molecular targets in bladder cancer

High-throughput microarrays are being used in expression profiling analyses with the objectives of gene and pathway discovery, functional characterization of genes, and tumor subclassification. This review summarizes bladder cancer studies dealing with both in vitro models and clinical specimens, using distinct microarray platforms for target discovery.

A design and statistical perspective on microarray gene expression studies in nutrition: the need for playful creativity and scientific hard-mindedness

OBJECTIVES

Our purpose is to highlight some of the past and potential future uses of microarray in nutrition research, while also commenting on some aspects of the design conduct and analysis of microarray data that will leave to improved data quality.

METHODS

In this review article we outline some of the aspects of microarray experimentation that must be considered before and during these experiments. These topics include: identification of the experiment's objective (hypothesis), the experimental design, sample size, statistical analysis, data verification, data handling, and experimental interpretation.

RESULTS

In order to illustrate the principles we outline in this article we use the methods to layout the design of a microarray experiment to study one aspect of the observation that a diet high in soy is associated with lower rates of breast cancer.

CONCLUSIONS

Microarrays are a very powerful tool for studying virtually every nutrition-related disease and trait and can provide valuable insights that are not obtainable with other techniques. However, unless nutrition researchers conduct their studies with scientific hard-mindedness, the studies will be of lower power at least if not completely misleading.

Differential UVC-induced gadd45 gene expression in xeroderma pigmentosum cells

Xeroderma pigmentosum C (XPC) is a DNA repair factor essential for global genome repair (GGR) in nucleotide excision repair (NER). In the present study we screened for factors regulated by XPC after DNA damage. Ultraviolet C (UVC) irradiation-induced stress response factors were analyzed by a cDNA microarray chip system in HeLa and XP4PA-SV xpc mutant cell lines. The principal component analysis (PCA) method was employed to identify groups of genes with similar expression patterns over time after UVC irradiation. The growth arrest and DNA damage-inducible gene gadd45, as well as a small group of other genes, was found to exhibit an inducible expression pattern after 30min of incubation in xpc mutants but not in HeLa cells. Subsequent studies showed that gadd45 gene expression post-UVC irradiation was also present in the GGR mutant cells xpa and xpd, but not in TCR mutant csb cells. This evidence indicates that gadd45 plays a regulatory role in GGR of NER.

Comparative study of enterovirus 71 infection of human cell lines

The cell tropism of enterovirus 71 (Enteroviridae) in neuronal, glial and laryngeal cells. The 4643 strain, an enterovirus 71 isolate from a patient in Taiwan, was used to infect three human cell lines representing neuronal cells (SK-N-SH, neuroblastoma), glial cells (U373MG, glioblastoma), and laryngeal cells (HEp-2, larynx epidermoid carcinoma). Immunofluorescent staining and transmission electron microscopy (TEM) were used to detect mature enterovirus 71 4643 virions in these cell lines. The three cell lines were also compared for presence of virus-mediated cytopathic effect (CPE), synthesis of infected cell-specific proteins, viral (-) RNA, and virus replication rate. Virus particles were detected by TEM, and viral replication increased over time, indicating the existence and release of mature viruses from all three infected cell lines. The most severe CPE and the highest viral replication rate were observed in the SK-N-SH cells. Further screening of the infected cell lines by microarray analysis revealed that the neuron growth factor receptor (NGFR) gene was uniquely upregulated in infected SK-N-SH cells, implying that the receptor encoded by this gene may be involved in cell tropism. The data show that neurons are vulnerable to enterovirus 71 4643 infection and are consistent with the clinical observation that enterovirus 71 4643 targets mainly neuronal cells but is also found in many organs in conjunction with an inflammatory reaction.

Inhibition of Epstein-Barr virus lytic cycle by (-)-epigallocatechin gallate

(-)-Epigallocatechin gallate (EGCG), abundant in green tea, is a potent anti-microbial and anti-tumor compound. This investigation used immunoblot, flow cytometry, microarray, and indirect immunofluorescence analyses to show that at concentrations exceeding 50 microM, EGCG inhibits the expression of Epstein-Barr virus (EBV) lytic proteins, including Rta, Zta, and EA-D, but does not affect the expression of EBNA-1. Moreover, DNA microarray and transient transfection analyses demonstrated that EGCG blocks EBV lytic cycle by inhibiting the transcription of immediate-early genes, thus inhibiting the initiation of EBV lytic cascade.

Use of high-throughput DNA microarrays to identify biomarkers for bladder cancer

BACKGROUND

Numerous markers have been described to correlate to some extent with tumor stage and prognosis of patients with bladder cancer. The power of many of these biomarkers in detecting superficial disease or predicting the clinical outcome of individual tumors is limited, and alternative markers are still in demand. High-throughput microarrays represent novel means for cancer research and tumor marker discovery.

APPROACH

The aim of this report was to discuss the application of DNA technologies to provide novel biomarkers for bladder cancer.

CONTENT

Specific bladder tumor subtypes have distinct gene expression profiles. The use of high-throughput DNA microarrays allows identification of the most prevalent and relevant alterations within bladder tumors. Clusters of differentially expressed genes will become biomarkers to discriminate subgroups of patients with different histopathology or clinical outcome. Additionally, the identified individual molecular targets might be further validated and developed into novel serum or urinary biomarkers for the diagnosis and/or as prognostic factors to be applied in clinical practice. The diagnosis and prognosis of bladder cancer would be enhanced by the use of such markers, and the marker itself may constitute a therapeutic target when studied in appropriate patients and control groups.

SUMMARY

Expression profiling with high-throughput DNA microarrays has the potential of providing critical clues for the management of bladder cancer patients. As the quality, standardization, and ease of use of the technology increase and the costs decrease, DNA microarrays will move from being a technology restricted to research to clinical laboratories in the near future.

Nutrigenomics: exploiting systems biology in the nutrition and health arena

Nutritional sciences are discovering the application of the so-called "omics" sciences. Propelled by the recent unravelling of the human genome and the coinciding technological developments, genotyping, transcriptomics, proteomics and metabolomics are now available to nutritional research. In the future we are likely to see new screening tools for the selection of bioactive nutrients, new biomarkers for the in vivo efficacy of nutrients, and better insight into the influence of genetic polymorphisms on nutrient metabolism. However, are these promises just based on biotechnological hype or is a real fundamental change in human nutritional sciences at hand?

Two UVC-induced stress response pathways in HeLa cells identified by cDNA microarray

Environmental toxins induce multiple effects in vivo, involving various molecular pathways. The ultraviolet C (UVC, 254 nm) component of sunlight can cause strong cytotoxic and genotoxic effects. In this study, UVC-induced stress response factors were analyzed by cDNA microarray, using the Millennium(R) Nylon membrane chip system. HeLa cells were irradiated with 30 Joule/m(2)/sec UVC, incubated for 30 or 60 minutes and then subjected to the analysis. Multiple chips were used for each experimental condition so that the data could be analyzed statistically. Principal component analysis (PCA) was used to identify groups of genes whose expression changed in a similar manner with time post-UVC irradiation. Three major factors were identified, depending on the directionality of expression changes in each gene. The factor loadings in all three identified gene groups were high, indicating that genes within each group were highly correlated. Two factors exhibited significantly changed expression patterns after 30 minutes of incubation but in the opposite direction. This indicates that the "immediate early" UVC-induced stress response was elicited by two major pathways. Interestingly, expression of the genomic damage-inducible GADD genes, as well as p53, was initially decreased, unlike the "immediate early" genes Fos/Jun and Egr-1, which were strongly increased after 30 minutes of incubation. The results indicate that PCA used in the analysis of pre-hypothesized, functionally related genes can identify the potential subpathways in a group. This method provides a novel approach for identifying functionally-related genes in microarray studies.