Differential gene expression of livers from ApoE deficient mice

Genomic Expression for Rat Model of Damp Obstruction in Chinese Medicine: Application of Microarray Technology

Damp obstruction refers to the stagnation of vital energy (qi) caused by dampness resulting in dysfunction of body and limbs movement, as well as impairment of spleen and stomach digestive function. Damp obstruction is the dampness-induced imbalance of five elements; thus it serves as an ideal model for genomic study using cDNA microarray. We have performed microarray analyses to major organs of damp-obstructed rats. Cluster analysis for the expression profiles of major organs indicated that spleen, stomach, and kidney respond to dampness differently from heart, liver, lung, and brain. Gene expression profile specific to each element or group of elements was also identified. Our results are consistent with the philosophy of Chinese medicine that the five elements, metal (lung), wood (liver), water (kidney), fire (heart), and earth (spleen and stomach) coordinate by subjugation or restriction to maintain a healthy, physiological state. This is the first time that a powerful genomic tool was applied to probe the ancient theory of Chinese medicine.

Modulation of miRNA expression by dietary polyphenols in apoE deficient mice: a new mechanism of the action of polyphenols

BACKGROUND

Polyphenols are the most abundant antioxidants in the human diet and are widespread constituents of fruits and beverages, such as tea, coffee or wine. Epidemiological, clinical and animal studies support a role of polyphenols in the prevention of various diseases, such as cardiovascular diseases, cancers or neurodegenerative diseases. Recent findings suggest that polyphenols could interact with cellular signaling cascades regulating the activity of transcription factors and consequently affecting the expression of genes. However, the impact of polyphenol on the expression of microRNA, small non-coding RNAs, has not yet been studied. The aim of this study was to investigate the impact of dietary supplementation with polyphenols at nutritional doses on miRNA expression in the livers of apolipoprotein E-deficient mice (apoE⁻/⁻) jointly with mRNA expression profiling.

METHODOLOGY/PRINCIPAL FINDINGS

Using microarrays, we measured the global miRNA expression in the livers of wild-type (C57B6/J) mice or apoE⁻/⁻ mice fed diets supplemented with one of nine different polyphenols or a control diet. This analysis revealed that knock-out of the apoE gene induced significant modulation in the expression of miRNA. Moreover, changes in miRNA expression were observed after polyphenol supplementation, and five miRNAs (mmu-miR-291b-5p, mmu-miR-296-5p, mmu-miR-30c-1*, mmu-miR-467b* and mmu-miR-374*) were identified as being commonly modulated by these polyphenols. We also observed that these polyphenols counteracted the modulation of miRNA expression induced by apoE mutation. Pathway analyses on these five miRNA-target genes revealed common pathways, some of which were also identified from a pathway analysis on mRNA profiles.

CONCLUSION

This in vivo study demonstrated for the first time that polyphenols at nutritional doses modulate the expression of miRNA in the liver. Even if structurally different, all polyphenols induced a similar miRNA expression profile. Common pathways were identified from both miRNA-target and mRNA analysis, revealing cellular functions that could be regulated by polyphenols at both the miRNA and mRNA level.

Dietary deficiency increases presenilin expression, gamma-secretase activity, and Abeta levels: potentiation by ApoE genotype and alleviation by S-adenosyl methionine

Apolipoprotein E4 (ApoE4) is a risk factor for Alzheimer's disease (AD). Whether this risk arises from a deficient function of E4 or the lack of protection provided by E2 or E3 is unclear. Previous studies demonstrate that deprivation of folate and vitamin E, coupled with dietary iron as a pro-oxidant, for 1 month displayed increased presenilin 1 (PS-1) expression, gamma-secretase, and Abeta generation in mice lacking ApoE (ApoE-/- mice). While ApoE-/- mice are a model for ApoE deficiency, they may not reflect the entire range of consequences of E4 expression. We therefore compared herein the impact of the above deficient diet on mice expressing human E2, E3, or E4. As folate deficiency is accompanied by a decrease in the major methyl donor, S-adenosyl methionine (SAM), additional mice received the deficient diet plus SAM. E2 was more protective than murine ApoE or E3 and E4. Surprisingly, PS-1 and gamma-secretase were over-expressed in E3 to the same extent as in E4 even under a complete diet, and were not alleviated by SAM supplementation. Abeta increased only in E4 mice maintained under the complete diet, and was alleviated by SAM supplementation. These findings suggest dietary compromise can potentiate latent risk factors for AD.

The genetics of cerebrovascular atherosclerosis

Ischemic stroke attributable to atherosclerosis remains a major public health problem. Genetic factors are increasingly recognized as influencing risk for atherosclerosis directly and indirectly. Genetic makeup may influence the development of major vascular risk factors or alter susceptibility of the cerebral vasculature to these risk factors. More recently, newly identified risk factors for atherosclerosis, such as plasma homocysteine and infection, have also been reported to be influenced by important genetic determinants. This article reviews the current nature on genetics of cerebral and precerebral atherosclerosis and seeks to identify areas of promise for future clinical application.

Application of DNA array technology to mammalian embryos

Early embryogenesis depends on a tightly choreographed succession of gene expression patterns which define normal development. Fertilization and the first zygotic cleavage involve major changes to paternal and maternal chromatin and translation of maternal RNAs which have been sequestered in the oocyte during oogenesis. At a critical species-specific point known as the major onset of embryonic expression, there is a dramatic increase in expression from the new diploid genome. The advent of array technology has, for the first time, made possible to determine the transcriptional profile of all approximately 20,000 mammalian genes during embryogenesis, although the small amount of mRNA in a single embryo necessitates either pooling large numbers of embryos or a global amplification procedure to give sufficient labeled RNA for analysis. Following array hybridization, various bioinformatic tools must be employed to determine the expression level for each gene, often based on multiple oligonucleotide probes and complex background estimation protocols. The grouped analysis of clusters of genes which represent specific biological pathways provides the key to understanding embryonic development, embryonic stem cell proliferation and the reprogramming of gene expression after somatic cloning. Arrays are being developed to address specific biological questions related to embryonic development including DNA methylation and microRNA expression. Array technology in its various facets is an important diagnostic tool for the early detection of developmental aberrations; for improving the safety of assisted reproduction technologies for man; and for improving the efficiency of producing cloned and/or transgenic farm animals. This review discusses current approaches and limitations of DNA microarray technology with emphasis on bovine embryos.

Folate deprivation increases presenilin expression, gamma-secretase activity, and Abeta levels in murine brain: potentiation by ApoE deficiency and alleviation by dietary S-adenosyl methionine

Folate deficiency has been associated with age-related neurodegeneration. One direct consequence of folate deficiency is a decline in the major methyl donor, S-adenosyl methionine (SAM). We demonstrate herein that dietary deficiency in folate and vitamin E, coupled pro-oxidant stress induced by dietary iron, increased presenilin-1 expression, gamma-secretase activity, and Abeta levels in normal adult mice. These increases were potentiated by apolipoprotein E deficiency as shown by treatment of transgenic mice homozygously lacking murine apolipoprotein E. Dietary supplementation with SAM in the absence of folate attenuated or alleviated these deleterious consequences. These findings link nutritional and genetic risk factors for age-related neurodegeneration and underscore that dietary supplementation with SAM may be useful to augment therapeutic approaches.

Cross-species microarray hybridizations: a developing tool for studying species diversity

The use of cross-species hybridization (CSH) to DNA microarrays, in which the target RNA and microarray probe are from different species, has increased in the past few years. CSH is used in comparative, evolutionary and ecological studies of closely related species, and for gene-expression profiling of many species that lack a representative microarray platform. However, unlike species-specific hybridization, CSH is still considered a non-standard use of microarrays. Here, we present the recent developments in the field of CSH for cDNA and oligomer microarray platforms. We discuss issues that influence the quality of CSH results, including platform choice, experiment design and data analysis, and suggest strategies that can lead to improvement of CSH studies to investigate species diversity.

Senescence-associated genes induced during compatible viral interactions with grapevine and Arabidopsis

The senescence process is the last stage in leaf development and is characterized by dramatic changes in cellular metabolism and the degeneration of cellular structures. Several reports of senescence-associated genes (SAGs) have appeared, and an overlap in some of the genes induced during senescence and pathogen infections has been observed. For example, the enhanced expression of SAGs in response to diseases caused by fungi, bacteria, and viruses that trigger the hypersensitive response (HR) or during infections induced by virulent fungi and bacteria that elicit necrotic symptoms has been observed. The present work broadens the search for SAGs induced during compatible viral interactions with both the model plant Arabidopsis thaliana and a commercially important grapevine cultivar. The transcript profiles of Arabidopsis ecotype Uk-4 infected with tobacco mosaic virus strain Cg (TMV-Cg) and Vitis vinifera cv. Carménère infected with grapevine leafroll-associated virus strain 3 (GLRaV-3) were analysed using microarray slides of the reference species Arabidopsis. A large number of SAGs exhibited altered expression during these two compatible interactions. Among the SAGs were genes that encode proteins such as proteases, lipases, proteins involved in the mobilization of nutrients and minerals, transporters, transcription factors, proteins related to translation and antioxidant enzymes, among others. Thus, part of the plant's response to virus infection appears to be the activation of the senescence programme. Finally, it was demonstrated that several virus-induced genes are also expressed at elevated levels during natural senescence in healthy plants.

Multisite promiscuity in the processing of endogenous substrates by human carboxylesterase 1

Human carboxylesterase 1 (hCE1) is a drug and endobiotic-processing serine hydrolase that exhibits relatively broad substrate specificity. It has been implicated in a variety of endogenous cholesterol metabolism pathways including the following apparently disparate reactions: cholesterol ester hydrolysis (CEH), fatty acyl Coenzyme A hydrolysis (FACoAH), acyl-Coenzyme A:cholesterol acyltransfer (ACAT), and fatty acyl ethyl ester synthesis (FAEES). The structural basis for the ability of hCE1 to perform these catalytic actions involving large substrates and products has remained unclear. Here we present four crystal structures of the hCE1 glycoprotein in complexes with the following endogenous substrates or substrate analogues: Coenzyme A, the fatty acid palmitate, and the bile acids cholate and taurocholate. While the active site of hCE1 was known to be promiscuous and capable of interacting with a variety of chemically distinct ligands, these structures reveal that the enzyme contains two additional ligand-binding sites and that each site also exhibits relatively non-specific ligand-binding properties. Using this multisite promiscuity, hCE1 appears structurally capable of assembling several catalytic events depending, apparently, on the physiological state of the cellular environment. These results expand our understanding of enzyme promiscuity and indicate that, in the case of hCE1, multiple non-specific sites are employed to perform distinct catalytic actions.

Detection of Foot and Mouth Disease and Porcine Reproductive and Respiratory Syndrome Viral Genes Using Microarray Chip

Two viral pathogens, namely, porcine reproductive and respiratory syndrome virus (PRRSV) and foot and mouth disease virus (FMDV), were selected as models for multiple pathogen detection in a cDNA microarray. Two signature regions selected from ORF2 (around 500 bp) and ORF5 (around 600 bp) of PRRVS (America serotype), and one signature region from structural genes VP1 (around 500 bp) of FMDV type O were designed and spotted on a nylon membrane. For PCR sensitivity study, the cloned FMDV-VP1 template could be diluted to near one copy and its PCR product was still detectable in gel electrophoresis. In the microarray detection, the labelling FMDV probes (3 mg/ml) could be diluted 320 times and still maintained a visible colour when hybridized with the chip. Using the mixing primers, the microarray chip demonstrated rapid and accurate detection of the specific genes. To our knowledge, this preliminary study is the first example reported applying the long signature sequences to the multiple pathogen detection in cDNA microarray.

Cholesterol loading augments oxidative stress in macrophages

To investigate the molecular consequence of loading free cholesterol into macrophages, we conducted a large-scale gene expression study to analyze acetylated-LDL-laden foam cells (AFC) and oxidized-LDL-laden foam cells (OFC) induced from human THP-1 cell lines. Cluster analysis was performed using 9600-gene microarray datasets from time course experiment. AFC and OFC shared common expression profiles; however, there were sufficient differences between these two treatments that AFC and OFC appealed as two separate entities. We identified 80 commonly upregulated genes and 48 commonly downregulated genes in AFC and OFC. Functional annotation of the differentially expressed genes indicated that apoptosis, extracellular matrix, oxidative stress, and cell proliferation was deregulated. We also identified 87 differentially expressed genes unique for AFC and 31 genes for OFC. The uniquely expressed genes of AFC are associated with kinase activity, ATP binding activity, and transporter activity, while unique genes for OFC are associated with cell signaling and adhesion. To validate the hypothesis that oxidative stress is a common feature for AFC and OFC, we performed a cluster analysis employing the genes related to oxidative stress, but we were unable to distinguish AFC from OFC in this manner. We performed real-time RT-PCR and ELISA on foam cells to examine the transcripts and secreted protein of interleukin 1 beta (IL1beta). IL1beta was rapidly induced in foam cells, but for AFC both RNA level and protein level dropped immediately and was attenuated. To detect levels of reactive oxygen species in foam cells we conducted hydroethidine staining and observed high levels of superoxide anion. We conclude that loading free cholesterol induces high levels of superoxide anion, increases oxidative stress, and triggers a transient inflammatory response in macrophages.

Gene expression in rats with Barrett’s esophagus and esophageal adenocarcinoma induced by gastroduodenoesophageal reflux

AIM: To study the different gene expression profiles in rats with Barrett’s esophagus (BE) and esophageal adenocarcinoma (EA) induced by gastro-duodeno-esophageal reflux.

METHODS: Esophagoduodenostomy was performed in 8-wk old Sprague-Dawley rats to induce gastro-duodeno-esophageal reflux, and a group of rats that received sham operation served as control. Esophageal epithelial pathological tissues were dissected and frozen in liquid nitrogen immediately. The expression profiles of 4 096 genes in EA and BE tissues were compared to normal esophagus epithelium in normal control (NC) by cDNA microarray.

RESULTS: Four hundred and forty-eight genes in BE were more than three times different from those in NC, including 312 upregulated and 136 downregulated genes. Three hundred and seventy-seven genes in EA were more than three times different from those in NC, including 255 upregulated and 142 downregulated genes. Compared to BE, there were 122 upregulated and 156 downregulated genes in EA. In the present study, the interested genes were those involved in carcinogenesis. Among them, the upregulated genes included cathepsin C, aminopeptidase M, arachidonic acid epoxygenase, tryptophan-2,3-dioxygenase, ubiquitin-conjugating enzyme, cyclic GMP-stimulated phosphodiesterase, tissue inhibitor of metalloproteinase-1, betaine-homocysteine methyltra-nsferase, lysozyme, complement 4b binding protein, complement 9 protein, insulin-like growth factor binding protein, UDP-glucuronosyltransferase, tissue inhibitor of metalloproteinase-3, aldolase B, retinoid X receptor gamma, carboxylesterase and testicular cell adhesion molecule 1. The downregulated genes included glutathione synthetase, lecithin-cholesterol acyltransferase, p55CDC, heart fatty acid binding protein, cell adhesion regulator and endothelial cell selectin ligand.

CONCLUSION: Esophageal epithelium exposed excessively to harmful ingredients of duodenal and gastric reflux may develop into BE and even EA gradually. The gene expression level is different between EA and BE, and may be related to the occurrence and progression of EA.

Gene expression in rats with Barrett's esophagus and esophageal adenocarcinoma induced by gastroduodenoesophageal reflux

AIM

To study the different gene expression profiles in rats with Barrett's esophagus (BE) and esophageal adenocarcinoma (EA) induced by gastro-duodeno-esophageal reflux.

METHODS

Esophagoduodenostomy was performed in 8-wk old Sprague-Dawley rats to induce gastro-duodeno-esophageal reflux, and a group of rats that received sham operation served as control. Esophageal epithelial pathological tissues were dissected and frozen in liquid nitrogen immediately. The expression profiles of 4096 genes in EA and BE tissues were compared to normal esophagus epithelium in normal control (NC) by cDNA microarray.

RESULTS

Four hundred and forty-eight genes in BE were more than three times different from those in NC, including 312 upregulated and 136 downregulated genes. Three hundred and seventy-seven genes in EA were more than three times different from those in NC, including 255 upregulated and 142 downregulated genes. Compared to BE, there were 122 upregulated and 156 downregulated genes in EA. In the present study, the interested genes were those involved in carcinogenesis. Among them, the upregulated genes included cathepsin C, aminopeptidase M, arachidonic acid epoxygenase, tryptophan-2,3-dioxygenase, ubiquitin-conjugating enzyme, cyclic GMP-stimulated phosphodiesterase, tissue inhibitor of metalloproteinase-1, betaine-homocysteine methyltransferase, lysozyme, complement 4b binding protein, complement 9 protein, insulin-like growth factor binding protein, UDP-glucuronosyltransferase, tissue inhibitor of metalloproteinase-3, aldolase B, retinoid X receptor gamma, carboxylesterase and testicular cell adhesion molecule 1. The downregulated genes included glutathione synthetase, lecithin-cholesterol acyltransferase, p55CDC, heart fatty acid binding protein, cell adhesion regulator and endothelial cell selectin ligand.

CONCLUSION

Esophageal epithelium exposed excessively to harmful ingredients of duodenal and gastric reflux may develop into BE and even EA gradually. The gene expression level is different between EA and BE, and may be related to the occurrence and progression of EA.

Gene expression in Barrett’s esophagus and reflux esophagitis induced by gastroduodenoesophageal reflux in rats

AIM: To investigate the difference of gene expression profiles between Barrett’s esophagus and reflux eso-phagitis induced by gastroduodenoesophageal reflux in rats.

METHODS: Eight-week-old Sprague-Dawley rats were treated esophagoduodenostomy to produce gastroduode-noesophageal reflux, and another group received sham operation as control. Esophageal epithelial tissues were dissected and frozen in liquid nitrogen immediately for pathology 40 wk after surgery. The expression profiles of 4096 genes in reflux esophagitis and Barrett’s esophagus tissues were compared with normal esophageal epithelium by cDNA microarray.

RESULTS: Four hundred and forty-eight genes in Barrett’s esophagus were more than three times different from those in normal esophageal epithelium, including 312 up-regulated and 136 down-regulated genes. Two hundred and thirty-two genes in RE were more than three times different from those in normal esophageal epithelium, 90 up-regulated and 142 down-regulated genes. Compared to reflux esophagitis, there were 214 up-regulated and 142 down-regulated genes in Barrett’s esophagus.

CONCLUSION: Esophageal epithelium exposed excessively to harmful ingredients of duodenal and gastric reflux can develop esophagitis and Barrett’s esophagus gradually. The gene expression level is different between reflux esophagitis and Barrett’s esophagus and the differentially expressed genes might be related to the occurrence and development of Barrett’s esophagus and the promotion or progression in adenocarcinoma.

Differential gene expression in recombinant Pichia pastoris analysed by heterologous DNA microarray hybridisation

Background

Pichia pastoris is a well established yeast host for heterologous protein expression, however, the physiological and genetic information about this yeast remains scanty. The lack of a published genome sequence renders DNA arrays unavailable, thereby hampering more global investigations of P. pastoris from the beginning. Here, we examine the suitability of Saccharomyces cerevisiae DNA microarrays for heterologous hybridisation with P. pastoris cDNA.

Results

We could show that it is possible to obtain new and valuable information about transcriptomic regulation in P. pastoris by probing S. cerevisiae DNA microarrays. The number of positive signals was about 66 % as compared to homologous S. cerevisiae hybridisation, and both the signal intensities and gene regulations correlated with high significance between data obtained from P. pastoris and S. cerevisiae samples. The differential gene expression patterns upon shift from glycerol to methanol as carbon source were investigated in more detail. Downregulation of TCA cycle genes and a decrease of genes related to ribonucleotide and ribosome synthesis were among the major effects identified.

Conclusions

We could successfully demonstrate that heterologous microarray hybridisations allow deep insights into the transcriptomic regulation processes of P. pastoris. The observed downregulation of TCA cycle and ribosomal synthesis genes correlates to a significantly lower specific growth rate during the methanol feed phase.

Cross-species hybridization: characterization of gene expression in woodchuck liver using human membrane arrays

Total RNA from normal adult woodchucks was analyzed using membrane arrays containing human cDNA clones, and the gene expression patterns were compared to human liver. Various hybridization and wash conditions were examined. In both the woodchuck and human livers, 352 genes were identified as highly expressed (Z-scores > or =1.96). These genes represented numerous liver functions: transcription, RNA processing, signal transduction, protein synthesis and degradation, as well as enzymes. Several genes were selected and expression was verified by Northern blots for woodchuck liver. There were no false positives but 29 genes were identified as false negatives, expressed only in human liver. Possible reasons for these false negatives were the length and percentage of homology between the two species, differences in the distribution and types of mismatches, and the sequence region spotted on the array. These were assessed by examining expression of the transferrin gene in both species. A 200-fold range of RNA concentration (0.1-20 microg total RNA) was also examined and the optimal RNA concentration was determined to be 5 microg. Membranes were capable of being hybridized and reprobed at least five times. The study demonstrates that cross-species hybridization is a valid method for identifying gene expression in woodchuck liver.

Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays

BACKGROUND

Cross-species gene-expression comparison is a powerful tool for the discovery of evolutionarily conserved mechanisms and pathways of expression control. The usefulness of cDNA microarrays in this context is that broad areas of homology are compared and hybridization probes are sufficiently large that small inter-species differences in nucleotide sequence would not affect the analytical results. This comparative genomics approach would allow a common set of genes within a specific developmental, metabolic, or disease-related gene pathway to be evaluated in experimental models of human diseases. The objective of this study was to investigate the feasibility and reproducibility of cross-species analysis employing a human cDNA microarray as probe.

RESULTS

As a proof of principle, total RNA derived from human and bovine fetal brains was used as a source of labelled targets for hybridisation onto a human cDNA microarray composed of 349 characterised genes. Each gene was spotted 20 times representing 6,980 data points thus enabling highly reproducible spot quantification. Employing high stringency hybridisation and washing conditions, followed by data analysis, revealed slight differences in the expression levels and reproducibility of the signals between the two species. We also assigned each of the genes into three expression level categories- i.e. high, medium and low. The correlation co-efficient of cross hybridisation between the orthologous genes was 0.94. Verification of the array data by semi-quantitative RT-PCR using common primer sequences enabled co-amplification of both human and bovine transcripts. Finally, we were able to assign gene names to previously uncharacterised bovine ESTs.

CONCLUSIONS

Results of our study demonstrate the harnessing and utilisation power of comparative genomics and prove the feasibility of using human microarrays to facilitate the identification of co-expressed orthologous genes in common tissues derived from different species.

A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis

Microarrays have great potential for the study of developmental biology. As a model system Xenopus is well suited for making the most of this potential. However, Xenopus laevis has undergone a genome wide duplication meaning that most genes are represented by two paralogues. This causes a number of problems. Most importantly the presence of duplicated genes mean that a X. laevis microarray will have less or even half the coverage of a similar sized microarray from the closely related but diploid frog Xenopus tropicalis. However, to date, X. laevis is the most commonly used amphibian system for experimental embryology. Therefore, we have tested if a microarray based on sequences from X. tropicalis will work across species using RNA from X. laevis. We produced a pilot oligonucleotide microarray based on sequences from X. tropicalis. The microarray was used to identify genes whose expression levels changed during early X. tropicalis development. The same assay was then carried out using RNA from X. laevis. The cross species experiments gave similar results to those using X. tropicalis RNA. This was true at the whole microarray level and for individual genes, with most genes giving similar results using RNA from X. laevis and X. tropicalis. Furthermore, the overlap in genes identified between a X. laevis and a X. tropicalis set of experiments was only 12% less than the overlap between two sets of X. tropicalis experiments. Therefore researchers can work with X. laevis and still make use of the advantages offered by X. tropicalis microarrays.

The S-adenosyl homocysteine hydrolase inhibitor 3-deaza-adenosine prevents oxidative damage and cognitive impairment following folate and vitamin E deprivation in a murine model of age-related, oxidative stress-induced neurodegeneration

Deficiencies in folate promote neurodegeneration and potentiate the influence of other risk factors for neurodegeneration. This is accomplished at least in part by increasing levels of the neurotoxin homocysteine (HC). The S-adenosyl homocysteine (SAH) hydrolase inhibitor 3-deaza-adenosine (DZA) prevents HC accumulation following folate deprivation. We tested the ability of dietary supplementation with DZA to counteract the deleterious influence of folate deprivation. Folate deficiency has previously been shown to potentiate the impact of apolipoprotein E (ApoE); ApoE-/- mice deprived of folate demonstrated increased oxidative damage in brain tissue and impaired cognitive performance as compared to normal mice or to ApoE-/- mice receiving folate. Herein, we demonstrate that dietary supplementation with DZA prevented both the increase in oxidative damage and impaired cognition characteristic of ApoE-/- mice following folate deprivation. These findings suggest that manipulation of the methionine cycle by DZA can counteract folate deficiency. Because folate deprivation, increased HC, and apolipoprotein E deficiency are all risk factors for Alzheimer's disease, these findings also underscore that DZA might be useful in a therapeutic approach to delay neurodegeneration in Alzheimer's disease.

Increased transcription and activity of glutathione synthase in response to deficiencies in folate, vitamin E, and apolipoprotein E

Oxidative stress is a major contributing factor in neurodegeneration and can arise from dietary, environmental, and genetic sources. Here we examine the separate and combined impact of deprivation of folate and vitamin E, coupled with dietary iron as a prooxidant, on normal mice and transgenic mice lacking apolipoprotein E (ApoE-/- mice). Both mouse strains exhibited increased levels of glutathione when deprived of folate and vitamin E, but a substantial further increase was observed in ApoE-/- mice. To determine the mechanism(s) underlying this increase, we quantified transcription and activity of glutathione synthase (GS). Both normal and ApoE-/- mice demonstrated increased GS activity when deprived of folate and vitamin E. However, transcription was increased only in ApoE-/- mice deprived of folate and vitamin E. These findings demonstrate that deficiency in one gene can result in compensatory up-regulation in a second relevant gene and, furthermore, indicate that compensation for oxidative stress can occur in brain tissue at epigenetic and genetic levels depending on the nature and/or extent of oxidative stress.

Regulation of triacylglycerol hydrolase expression by dietary fatty acids and peroxisomal proliferator-activated receptors

Triacylglycerol hydrolase (TGH) is an enzyme that catalyzes the lipolysis of intracellular stored triacylglycerol (TG). Peroxisomal proliferator-activated receptors (PPAR) regulate a multitude of genes involved in lipid homeostasis. Polyunsaturated fatty acids (PUFA) are PPAR ligands and fatty acids are produced via TGH activity, so we studied whether dietary fats and PPAR agonists could regulate TGH expression. In 3T3-L1 adipocytes, TGH expression was increased 10-fold upon differentiation, compared to pre-adipocytes. 3T3-L1 cells incubated with a PPARgamma agonist during the differentiation process resulted in a 5-fold increase in TGH expression compared to control cells. Evidence for direct regulation of TGH expression by PPARgamma could not be demonstrated as TGH expression was not affected by a 24-h incubation of mature 3T3-L1 adipocytes with the PPARgamma agonist. Feeding mice diets enriched in fatty acids for 3 weeks did not affect hepatic TGH expression, though a 3-week diet enriched in fatty acids and cholesterol increased hepatic TGH expression 2-fold. Two weeks of clofibrate feeding did not significantly affect hepatic TGH expression or microsomal lipolytic activities in wild-type or PPARalpha-null mice, indicating that PPARalpha does not regulate hepatic TGH expression. Therefore, TGH expression does not appear to be directly regulated by PPARs or fatty acids in the liver or adipocytes.

Differential gene expression of scopolamine-treated rat hippocampus-application of cDNA microarray technology

The molecular study of learning and memory has been concentrated at muscarinic acetylcholine receptors and their associating signaling molecules. To explore alternative pathways we applied human cDNA microarray and searched for differentially expressed genes in the hippocampus of scopolamine-treated rat. Interspecies hybridization using human cDNA microarray to analyze scopolamine-treated rat hippocampus exhibited a minor difference for the expression profile compared to normal control with standard deviation of 0.08-fold in ratio. Based on differential expression, forty-two genes were selected for further analysis from 9,600 candidate genes on the array. Twenty-eight genes were validated by semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) using primer pairs against rat orthologs. The broad spectrum of the differentially expressed genes indicated an overall cellular response upon scopolamine treatment. In addition to genes associated with muscarinic receptor signaling pathways, we have disclosed genes associated with novel pathways such as apoptosis, cytoskeleton reconstruction, protein trafficking, cell differentiation, and genes without a clear role. Our result should provide an insight into the molecular study of scopolamine-induced memory impairment.

Quantification of antioxidant activity in brain tissue homogenates using the 'total equivalent antioxidant capacity'

We demonstrate herein that the standard 'Trolox equivalent antioxidant capacity' (TEAC) assay, typically utilized to quantify total antioxidant levels within plasma, can also be utilized for tissue homogenates. Normal mice and transgenic mice lacking apolipoprotein E were subjected to a diet including iron as a generic pro-oxidant for 1 month (which has been shown to induce oxidative damage in our prior studies) and homogenates of brain tissue were subjected to the TEAC assay. Levels of the endogenous antioxidant glutathione levels were also monitored by HPLC. As described previously, ApoE-deficient mice expressed increased levels of glutathione; total antioxidant levels, as determined by TEAC, were increased to a similar extent. The increase in total antioxidant levels, as determined by TEAC, following dietary iron challenge paralleled the increase in glutathione levels, as determined by HPLC. These findings indicate that the TEAC assay may be useful for tissue homogenates. The rapid nature of this assay compared to HPLC, coupled with its lack of requirement for sophisticated equipment, makes it well suited for analyses of multiple tissue samples.

Apolipoprotein E deficiency promotes increased oxidative stress and compensatory increases in antioxidants in brain tissue

The epsilon 4 allele of the apolipoprotein E gene (ApoE) is associated with Alzheimer's disease (AD). The extent of oxidative damage in AD brains correlates with the presence of the E4 allele of ApoE, suggesting an association between the ApoE4 genotype and oxygen-mediated damage in AD. We tested this hypothesis by subjecting normal and transgenic mice lacking ApoE to oxidative stress by folate deprivation and/or excess dietary iron. Brain tissue of ApoE-deficient mice displayed increased glutathione and antioxidant levels, consistent with attempts to compensate for the lack of ApoE. Folate deprivation and iron challenge individually increased glutathione and antioxidant levels in both normal and ApoE-deficient brain tissue. However, combined treatment with folate deprivation and dietary iron depleted antioxidant capacity and induced oxidative damage in ApoE-deficient brains despite increased glutathione, indicating an inability to compensate for the lack of ApoE under these conditions. These data support the hypothesis that ApoE deficiency is associated with oxidative damage, and demonstrate a combinatorial influence of genetic predisposition, dietary deficiency, and oxidative stress on oxidative damage relevant to AD.

Cross-species hybridisation of pig RNA to human nylon microarrays

BACKGROUND

The objective of this research was to investigate the reproducibility of cross-species microarray hybridisation. Comparisons between same- and cross-species hybridisations were also made. Nine hybridisations between a single pig skeletal muscle RNA sample and three human cDNA nylon microarrays were completed. Three replicate hybridisations of two different amounts of pig RNA, and of human skeletal muscle RNA were completed on three additional microarrays.

RESULTS

Reproducibility of microarray hybridisations of pig cDNA to human microarrays was high, as determined by Spearman and Pearson correlation coefficients and a Kappa statistic. Variability among replicate hybridisations was similar for human and pig data, indicating the reproducibility of results were not compromised in cross-species hybridisations. The concordance between data generated from hybridisations using pig and human skeletal muscle RNA was high, further supporting the use of human microarrays for the analysis of gene expression in the pig. No systematic effect of stripping and re-using nylon microarrays was found, and variability across microarrays was minimal.

CONCLUSION

The majority of genes generated highly reproducible data in cross-species microarray hybridisations, although approximately 6% were identified as highly variable. Experimental designs that include at least three replicate hybridisations for each experimental treatment will enable the variability of individual genes to be considered appropriately. The use of cross-species microarray analysis looks promising. However, additional validation is needed to determine the specificity of cross-species hybridisations, and the validity of results.

Challenges in dyslipidemia

Dyslipidemia is recognized as a significant risk factor for atherosclerotic disease. There has been a great deal of progress in the detection and management of dyslipidemia, but challenges remain, including whether to treat children, adolescents, and the elderly. Challenges include convincing physicians who tend to manage an outpatient disease with a single therapy that the management of cardiovascular risk and disease often requires multiple therapies, describing how we can combine therapies to provide an additive benefit without adding side effects or increasing morbidity, and determining whether a patient with one or more cardiovascular risk factors but a normal lipid should receive lipid-lowering therapy. Finally, there is the challenge of the Human Genome Project and predictive medicine. How will genetic information be integrated into the practice of medicine for disease prevention and management?

Analysis of gene expression with cDNA microarrays in rat brain after 7 and 42 days of oral lithium administration

The gene expression profile in rat brain was examined using microarrays in rats fed lithium chloride for 7 days (subacute) or 42 days (chronic). Brain lithium concentrations were 0.39 mM and 0.79 mM (therapeutically relevant), at 7 and 42 days, respectively. Of the 4132 genes represented in the microarrays, 25 genes were downregulated by at least twofold and none was upregulated after 7 days of treatment. Expression of 50 genes was downregulated by at least two-fold at 42 days, without any being upregulated. Lithium treatment for 7 days did not affect at a measurable extent expression of 37 of the 50 genes that were downregulated at 42 days. Genes whose expression was changed at 42 days coded for a number of receptors, protein kinases, transcription and translation factors, markers of energy metabolism, and signal transduction. Thus, chronic lithium at a therapeutically relevant concentration reduced expression of a large number of genes involved in multiple signaling and other pathways, without increasing expression at a comparable extent.

Project normal: defining normal variance in mouse gene expression

The mouse has become an indispensable and versatile model organism for the study of development, genetics, behavior, and disease. The application of comprehensive gene expression profiling technologies to compare normal and diseased tissues or to assess molecular alterations resulting from various experimental interventions has the potential to provide highly detailed qualitative and quantitative descriptions of these processes. Ideally, to interpret experimental data, the magnitude and diversity of gene expression for the system under study should be well characterized, yet little is known about the normal variation of mouse gene expression in vivo. To assess natural differences in murine gene expression, we used a 5406-clone spotted cDNA microarray to quantitate transcript levels in the kidney, liver, and testis from each of 6 normal male C57BL6 mice. We used ANOVA to compare the variance across the six mice to the variance among four replicate experiments performed for each mouse tissue. For the 6 kidney samples, 102 of 3,088 genes (3.3%) exhibited a statistically significant mouse variance at a level of 0.05. In the testis, 62 of 3,252 genes (1.9%) showed statistically significant variance, and in the liver, there were 21 of 2,514 (0.8%) genes with significantly variable expression. Immune-modulated, stress-induced, and hormonally regulated genes were highly represented among the transcripts that were most variable. The expression levels of several genes varied significantly in more than one tissue. These studies help to define the baseline level of variability in mouse gene expression and emphasize the importance of replicate microarray experiments.