Evaluation of cadmium-induced transcriptome alterations by three color cDNA labeling microarray analysis on a T-cell line

Modified Titanium Surfaces Alter Osteogenic Differentiation: A Comparative Microarray-Based Analysis of Human Mesenchymal Cell Response to Commercial Titanium Surfaces

The differential effects of dual-acid etched (Osseotite), hydroxyapatite coated (HA) and sand-blasted/acid-etched (SLA) titanium surfaces on human bone marrow-derived mesenchymal cells (hMSCs) were investigated. Proliferation was significantly promoted on the SLA surfaces. 16 genes were significantly upregulated when hMSCs were cultured on the Osseotite and the HA surfaces and 15 genes on the SLA surfaces. Upregulated genes control cell differentiation, signal transduction, cell cycle regulation, angiogenesis, cell adhesion, and extracellular matrix and bone formation.

Cadmium induces thymocyte apoptosis via caspase-dependent and caspase-independent pathways

Based on our recent findings that 25 µM cadmium triggers oxidative stress-mediated caspase-dependent apoptosis in murine thymocytes, this study is designed to explore whether Cd also induces caspase-independent apoptosis. We found that pretreatment with caspase inhibitors fails to prevent Cd-induced apoptosis completely, suggesting the possibility of an additional pathway. Western blot and flow cytometry techniques indicated marked expression of apoptosis-inducing factor and endonuclease G in nuclear fraction, signifying their translocation from mitochondria to nucleus. Intracellular Ca²⁺ and reactive oxygen species (ROS) levels significantly raised by Cd were restored by ruthenium red, which had no influence on mitochondrial membrane depolarization and caspase activity and apoptosis. Using cyclosporin A, ROS formation and mitochondrial membrane depolarization were completely abolished, whereas apoptosis was partly attenuated. These results clearly demonstrate more than one apoptotic pathway in thymocytes and support the role of mitochondrial permeability transition pore in the regulation of caspase-independent cell death triggered by Cd.

Searching for coexpressed genes in three-color cDNA microarray data using a probabilistic model-based Hough Transform

The effects of a drug on the genomic scale can be assessed in a three-color cDNA microarray with the three color intensities represented through the so-called hexaMplot. In our recent study, we have shown that the Hough Transform (HT) applied to the hexaMplot can be used to detect groups of coexpressed genes in the normal-disease-drug samples. However, the standard HT is not well suited for the purpose because 1) the assayed genes need first to be hard-partitioned into equally and differentially expressed genes, with HT ignoring possible information in the former group; 2) the hexaMplot coordinates are negatively correlated and there is no direct way of expressing this in the standard HT and 3) it is not clear how to quantify the association of coexpressed genes with the line along which they cluster. We address these deficiencies by formulating a dedicated probabilistic model-based HT. The approach is demonstrated by assessing effects of the drug Rg1 on homocysteine-treated human umbilical vein endothetial cells. Compared with our previous study, we robustly detect stronger natural groupings of coexpressed genes. Moreover, the gene groups show coherent biological functions with high significance, as detected by the Gene Ontology analysis.

Cadmium induces differentiation of RAW264.7 cells into osteoclasts in the presence of RANKL

The mechanism of cadmium effects on bone is not fully understood. In this study, we investigated the effects of cadmium on osteoclasts differentiation and the probable mechanism. RAW264.7 cells were exposed to cadmium (0-60 nmol/L) in the presence or absence of receptor-activated nuclear factor κ B ligand (RANKL) for 5 days. Then, the viability, tartrate-resistant acid phosphatase (TRAP) activity and the formation of TRAP positive multinucleated osteoclasts were observed. Receptor activator of nuclear factor κ B (RANK), tumor necrosis factor receptor associated factor 6 (TRAF6), c-src, c-fos, fos-related antigen 1 (Fra1) expression were determined by reverse transcription polymerase chain reaction. Cadmium increased TRAP activity (20-40%) and TRAP positive cell formation in the presence of RANKL, but had no obvious influence on them without RANKL. RANK, TRAF6, Fra1, c-src and c-fos (at 15-30 nmol/L) expression were enhanced (30-70%) by cadmium in the presence of RANKL, but cadmium had little influence on them in the absence of RANKL. This study demonstrated that cadmium could induce differentiation of osteoclasts precursor into osteoclasts in the presence of RANKL. Even though the changes of gene expression were small, RANKL/RANK and downstream genes may play an important role in cadmium effects on osteoclasts.

Cadmium induces transcription independently of intracellular calcium mobilization

BACKGROUND

Exposure to cadmium is associated with human pathologies and altered gene expression. The molecular mechanisms by which cadmium affects transcription remain unclear. It has been proposed that cadmium activates transcription by altering intracellular calcium concentration ([Ca(2+)](i)) and disrupting calcium-mediated intracellular signaling processes. This hypothesis is based on several studies that may be technically problematic; including the use of BAPTA chelators, BAPTA-based fluorescent sensors, and cytotoxic concentrations of metal.

METHODOLOGY/PRINCIPAL FINDING

In the present report, the effects of cadmium on [Ca(2+)](i) under non-cytotoxic and cytotoxic conditions was monitored using the protein-based calcium sensor yellow cameleon (YC3.60), which was stably expressed in HEK293 cells. In HEK293 constitutively expressing YC3.60, this calcium sensor was found to be insensitive to cadmium. Exposing HEK293::YC3.60 cells to non-cytotoxic cadmium concentrations was sufficient to induce transcription of cadmium-responsive genes but did not affect [Ca(2+)](i) mobilization or increase steady-state mRNA levels of calcium-responsive genes. In contrast, exposure to cytotoxic concentrations of cadmium significantly reduced intracellular calcium stores and altered calcium-responsive gene expression.

CONCLUSIONS/SIGNIFICANCE

These data indicate that at low levels, cadmium induces transcription independently of intracellular calcium mobilization. The results also support a model whereby cytotoxic levels of cadmium activate calcium-responsive transcription as a general response to metal-induced intracellular damage and not via a specific mechanism. Thus, the modulation of intracellular calcium may not be a primary mechanism by which cadmium regulates transcription.

Analysis of osteoblastic gene expression in the early human mesenchymal cell response to a chemically modified implant surface: an in vitro study

OBJECTIVES

The effect of a chemical modification of the SLA surface (SLActive surface) on human bone marrow-derived mesenchymal cells (hMSCs) on; (1) adhesion, (2) proliferation and (3) early transcriptional control of osteogenic differentiation was investigated. We are based on the hypothesis that expression patterns of genes responsible for osteogenesis might be dependent on the characteristics of the implant surface.

MATERIAL AND METHODS

hMSCs were allowed to grow on smooth (SMO-control), SLA and SLActive implant surfaces (chemically modified). Cell attachment and proliferation were assessed at 3 and 24 h using a MTT dye reduction assay. At 24 h of culture, DNA microarray analysis examined alterations in early gene expression using a human osteogenesis gene array, including 109 cDNAs in quadruplicates of major regulatory genes for osteogenesis.

RESULTS

Initial attachment and proliferation were found to be significantly reduced. Nineteen genes were significantly upregulated when hMSCs were cultured on the SLA surfaces and 27 genes were significantly upregulated when hMSCs were cultured on the SLActive surfaces. Upregulated genes control cell differentiation, signal transduction, cell cycle regulation, angiogenesis, cell adhesion and extracellular matrix and bone formation.

DISCUSSION

Chemical modification decreases further cell attachment and proliferation and upregulates early osteoblastic differentiation genes. Hence, a microenvironment is created around chemically modified implants that may enhance osseointegration.

Cadmium-induced alterations of gene expression in human cells

We have reported the changes in gene expression in human HeLa cells exposed to a low concentration (5μM) of Cd. In the present study, cells exposed to a higher concentration of Cd were analyzed using a DNA microarray with 9182 human cDNA probes, in an attempt to obtain a comprehensive view on the biological effects of Cd. After a 6h exposure to 50μM Cd, 48 genes were up-regulated 2.5-fold or greater and 14 genes were down-regulated to 40% or less. Marked up-regulation of genes coding for metallothioneins, anti-oxidant proteins, and heat shock proteins was observed. Cd appeared to repress cell proliferation by modulating genes involved in multiple pathways. Cd also affected a number of genes related to apoptosis. Interestingly, it appeared that a series of genes were regulated to accelerate the intrinsic pathway of apoptosis, while others were directed to suppress the extrinsic pathway. Of these, rapid and transient induction of the TR3 gene was noted as a possible key process in Cd-induced apoptosis. Effects on several genes that may reflect mechanistic backgrounds of Cd toxicity were also observed. The present study disclosed a complex pleiotypic response of human cells to Cd, which was composed of a variety of changes in gene expression directed to defense, growth arrest, recovery from damage, apoptosis and so on.

Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity

BACKGROUND

Exposure to cadmium is associated with a variety of human diseases. At low concentrations, cadmium activates the transcription of stress-responsive genes, which can prevent or repair the adverse effects caused by this metal.

RESULTS

Using Caenorhabditis elegans, 290 genes were identified that are differentially expressed (>1.5-fold) following a 4 or 24 hour exposure to cadmium. Several of these genes are known to be involved in metal detoxification, including mtl-1, mtl-2, cdr-1 and ttm-1, confirming the efficacy of the study. The majority, however, were not previously associated with metal-responsiveness and are novel. Gene Ontology analysis mapped these genes to cellular/ion trafficking, metabolic enzymes and proteolysis categories. RNA interference-mediated inhibition of 50 cadmium-responsive genes resulted in an increased sensitivity to cadmium toxicity, demonstrating that these genes are involved in the resistance to cadmium toxicity. Several functional protein interacting networks were identified by interactome analysis. Within one network, the signaling protein KEL-8 was identified. Kel-8 protects C. elegans from cadmium toxicity in a mek-1 (MAPKK)-dependent manner.

CONCLUSION

Because many C. elegans genes and signal transduction pathways are evolutionarily conserved, these results may contribute to the understanding of the functional roles of various genes in cadmium toxicity in higher organisms.

HoughFeature, a novel method for assessing drug effects in three-color cDNA microarray experiments

BACKGROUND

Three-color microarray experiments can be performed to assess drug effects on the genomic scale. The methodology may be useful in shortening the cycle, reducing the cost, and improving the efficiency in drug discovery and development compared with the commonly used dual-color technology. A visualization tool, the hexaMplot, is able to show the interrelations of gene expressions in normal-disease-drug samples in three-color microarray data. However, it is not enough to assess the complicated drug therapeutic effects based on the plot alone. It is important to explore more effective tools so that a deeper insight into gene expression patterns can be gained with three-color microarrays.

RESULTS

Based on the celebrated Hough transform, a novel algorithm, HoughFeature, is proposed to extract line features in the hexaMplot corresponding to different drug effects. Drug therapy results can then be divided into a number of levels in relation to different groups of genes. We apply the framework to experimental microarray data to assess the complex effects of Rg1 (an extract of Chinese medicine) on Hcy-related HUVECs in details. Differentially expressed genes are classified into 15 functional groups corresponding to different levels of drug effects.

CONCLUSION

Our study shows that the HoughFeature algorithm can reveal natural cluster patterns in gene expression data of normal-disease-drug samples. It provides both qualitative and quantitative information about up- or down-regulated genes. The methodology can be employed to predict disease susceptibility in gene therapy and assess drug effects on the disease based on three-color microarray data.

Toxicogenomics in the assessment of immunotoxicity

Microarray analysis is used for simultaneous measurement of expression of thousands of genes in a given sample and as such extends and deepens our understanding of biological processes. Application of the technique in toxicology is referred to as toxicogenomics. The examples of assessment of immunotoxicity by gene expression profiling presented and discussed here, show that microarray analysis is able to detect known and novel effects of a wide range of immunomodulating agents. Besides the elucidation of mechanisms of action, toxicogenomics is also applied to predict consequences of exposing biological systems to toxic agents. Successful attempts to classify compounds using signature gene expression profiles have been reported. These did, however, not specifically focus on immunotoxicity. Databases containing expression profiles can facilitate the applications of toxicogenomics. Platforms and methodologies for gene expression profiling may vary, however, hampering data compiling across different laboratories. Therefore, attention is paid to standardization of the generation, reporting, and management of microarray data. Obtained gene expression profiles should be anchored to pathological and functional endpoints for correct interpretation of results. These issues are also important when using toxicogenomics in risk assessment. The application of toxicogenomics in evaluation of immunotoxicity is thus not yet without challenges. It already contributes to the understanding of immunotoxic processes and the development of in vitro screening assays, though, and is therefore expected to be of value for mechanistic insight into immunotoxicity and hazard identification of existing and novel compounds.

Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity

BACKGROUND

Exposure to cadmium is associated with a variety of human diseases. At low concentrations, cadmium activates the transcription of stress-responsive genes, which can prevent or repair the adverse effects caused by this metal.

RESULTS

Using Caenorhabditis elegans, 290 genes were identified that are differentially expressed (>1.5-fold) following a 4 or 24 hour exposure to cadmium. Several of these genes are known to be involved in metal detoxification, including mtl-1, mtl-2, cdr-1 and ttm-1, confirming the efficacy of the study. The majority, however, were not previously associated with metal-responsiveness and are novel. Gene Ontology analysis mapped these genes to cellular/ion trafficking, metabolic enzymes and proteolysis categories. RNA interference-mediated inhibition of 50 cadmium-responsive genes resulted in an increased sensitivity to cadmium toxicity, demonstrating that these genes are involved in the resistance to cadmium toxicity. Several functional protein interacting networks were identified by interactome analysis. Within one network, the signaling protein KEL-8 was identified. Kel-8 protects C. elegans from cadmium toxicity in a mek-1 (MAPKK)-dependent manner.

CONCLUSION

Because many C. elegans genes and signal transduction pathways are evolutionarily conserved, these results may contribute to the understanding of the functional roles of various genes in cadmium toxicity in higher organisms.

Sub-chronic administration of diphenyl diselenide potentiates cadmium-induced testicular damage in mice

Sub-chronic cadmium (Cd) exposure causes testicular damage in mice. The mode of action may involve oxidative stress and especially lipid peroxidation. The present study has monitored the pathogenesis of testicular damage during sub-chronic Cd exposure and has evaluated the potential protective effect of antioxidant therapy with diphenyl diselenide (PhSe)(2). Male mice were dosed with 2.5 mg/kg CdCl(2) (2.5 mg/kg) with or without (PhSe)(2) (5 micromol/kg) at 30 min post-exposure using a model of five weekly subcutaneous injections. Histological evaluation of the testis was performed across a 4 week test period. Animals exposed to CdCl(2) and CdCl(2) plus (PhSe)(2) displayed a reduction in body weight gain and testicular weight. Progressive damage and histolopathological changes in the testis were not remedied with, but rather were potentiated by, (PhSe)(2) therapy. We conclude that (PhSe)(2) enhances testicular injury in an animal model for sub-chronic Cd exposure mice.

Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues

MicroRNAs (miRNAs) are a non-coding family of genes involved in post-transcriptional gene regulation. These transcripts are associated with cell proliferation, cell differentiation, cell death and carcinogenesis. We analysed the miRNA expression profiles in 25 pairs of hepatocellular carcinoma (HCC) and adjacent non-tumorous tissue (NT) and nine additional chronic hepatitis (CH) specimens using a human miRNA microarray. Targets and references samples were co-hybridized to a microarray containing whole human mature and precursor miRNA sequences. Whereas three miRNAs exhibited higher expression in the HCC samples than that in the NT samples, five miRNAs demonstrated lower expression in the HCC samples than in the NT samples (P<0.0001). Classification of samples as HCC or NT by using support vector machine algorithms based on these data provided an overall prediction accuracy of 97.8% (45/46). In addition, the expression levels of four miRNAs were inversely correlated with the degree of HCC differentiation (P<0.01). A comparison of CH and liver cirrhosis samples revealed significantly different pattern of miRNA expression (P<0.01). There were no differences, however, between hepatitis B-positive and hepatitis C-positive samples. This information may help clarify the molecular mechanisms involved in the progression of liver disease, potentially serving as a diagnostic tool of HCC.

MARS: microarray analysis, retrieval, and storage system

Background

Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells.

Results

MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents.

Conclusion

We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at .

Transcriptome profiling reveals similarities and differences in plant responses to cadmium and lead

We analyzed the influence of salts of two heavy metals--lead and cadmium (Pb2+ and Cd2+) on plants, including plant and root size, plant genome stability as well as global genome expression. Measurement of the metal uptake showed that there was a significantly higher incorporation of Cd than of Pb, 0.6 and 0.15 uM per gram of dry weight, respectively. The analysis of the root length and plant size showed a dose dependent decrease in plants exposed to cadmium. In contrast there was little difference in the size of plants exposed to lead, although there was nearly four-fold increase of the root length. Analysis of the genome stability revealed that cadmium led to a dose dependent increase of homologous recombination whereas lead had no effect. Analysis of the global genome expression of plants chronically exposed to 50 uM of Cd and Pb revealed 65 and 338 up- and down-regulated genes by Cd and 19 and 76 by Pb, respectively. Interestingly, half of the genes that changed their expression in Pb-treated plants also changed their expression in Cd-treated ones. The greater number of genes regulated by Cd reflects generally higher genome instability of plants as well as higher uptake as compared to Pb.

Suppression of cadmium-induced JNK/p38 activation and HSP70 family gene expression by LL-Z1640-2 in NIH3T3 cells

When NIH3T3 cells were exposed to CdCl(2), the three major mitogen-activated protein kinases (MAPKs), extracellular signal-regulated protein kinase (ERK), c-Jun NH(2)-terminal kinase (JNK), and p38, were phosphorylated in a time (1-9 h)- and dose (1-20 microM)-dependent manner. Treatment with a macrocyclic nonaketide compound, LL-Z1640-2 (10-100 ng/ml), suppressed the phosphorylation of MAPKs without affecting the total protein level in cells exposed to 10 microM CdCl(2) for 6 h. CdCl(2)-induced phosphorylation of c-Jun on Ser63 and that on Ser73, and resultant accumulation of total c-Jun protein were also suppressed by LL-Z1640-2 treatment. The in vitro kinase assays also showed significant inhibitory effects of LL-Z1640-2 (at 10 or 25 ng/ml) on JNK and p38 but less markedly. In contrast to JNK and p38, ERK activity was inhibited moderately only at 50 or 100 ng/ml LL-Z1640-2. On the other hand, other JNK inhibitors, SP600125 and L-JNKI1, failed to suppress CdCl(2)-induced activation of the JNK pathway. Among the mouse stress response genes upregulated in response to CdCl(2) exposure, the expressions of hsp68 (encoding for heat shock 70 kDa protein 1; Hsp70-1) and grp78 (encoding for 78 kDa glucose-regulated protein; Grp78) genes were suppressed by treatment with 25 ng/ml LL-Z1640-2. Thus, LL-Z1640-2 could suppress CdCl(2)-induced activation of JNK/p38 pathways and expression of HSP70 family genes in NIH3T3 cells. LL-Z1640-2 seems to be useful to analyze functions of toxic metal-induced JNK/p38 activation.

DNA Microarray Analysis of Altered Gene Expression in Cadmium‐exposed Human Cells

Cadmium (Cd) is a heavy metal known to be toxic and carcinogenic, but its mechanism of action remains to be elucidated. Development of the DNA microarray technology has recently made the comprehensive analysis of gene expression possible, and it could be a powerful tool also in toxicological studies. With microarray slides containing 7,000-9,000 genes, we have been studying the gene expression profiles of a human cell line exposed to Cd. By exposure to a non-lethal concentration of Cd, 46 upregulated and 10 downregulated genes whose expression levels changed twofold or greater were observed. The expression of genes related to cellular protection and damage control mechanisms such as those encoding metallothioneins, anti-oxidant proteins and heat shock proteins was simultaneously induced. In addition, altered expression of many genes involved in signaling, metabolism and so on was newly observed. As a whole, a number of genes appear to be coordinately regulated toward survival from Cd toxicity. When cells were exposed to a higher concentration of Cd, more remarkable effects were observed both in the number of affected genes and in the extent of altered expression. These findings will contribute to the understanding of the complicated biological effects of Cd.

Identification of genes that are induced after cadmium exposure by suppression subtractive hybridization

The heavy metal cadmium is a xenobiotic toxicant of environmental and occupational concern and it has been classified as a human carcinogen. Inhalation of cadmium has been implicated in the development of emphysema and pulmonary fibrosis, but, the detailed mechanism by which cadmium induces adverse biological effects is not yet known. Therefore, we undertook the investigation of genes that are induced after cadmium exposure to illustrate the mechanism of cadmium toxicity. For this purpose, we employed the polymerase chain reaction (PCR)-based suppression subtractive hybridization (SSH) technique. We identified 29 different cadmium-inducible genes in human peripheral blood mononuclear cells (PBMCs), such as macrophage migration inhibitory factor (MIF), lysophosphatidic acid acyltransferase-alpha, enolase-1alpha, VEGF, Bax, and neuron-derived orphan receptor-1 (Nor-1), which are known to be associated with inflammation, cell survival, and apoptosis. Induction of these genes by cadmium treatment was further confirmed by semi-quantitative reverse-transcription PCR. Further, we found that these genes were also induced after cadmium exposure in normal human lung fibroblast cell line, WI-38, suggesting potential use of this induction profile to monitor cadmium toxicity in the lung.