Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis. Serial Analysis of Gene Expression

Investigation of gene expression profiles in a rat adjuvant arthritis model suggests an effective role of triptolide via PI3K-AKT signaling

Rheumatoid arthritis (RA) is a common systemic autoimmune disease mainly involving the formation of a synovial pannus, for which no effective treatment is available. In order to study the molecular biological mechanisms underlying the inhibition of RA synovial pannus by triptolide, differentially expressed genes in synovial tissues from an adjuvant arthritis (AA) rat model with and without triptolide treatment were detected in an mRNA microarray profile produced by Agilent Technologies and verified by reverse transcription-quantitative polymerase chain reaction analysis (RT-qPCR). An AA model was established by subcutaneously injecting 0.1 ml Freund's complete adjuvant daily for 18 days and scored by arthritis index assessment. Subsequently, triptolide (0.4 mg/kg) or an equivalent amount of saline was administered daily for 14 days. At the end of the experiment, synovial tissues were obtained from the ankle joints of the rats' hind legs. Total RNA was extracted and purified, and microarray hybridization was used to obtain the gene expression profile for RA with and without triptolide treatment. A total of 48 genes were identified to be differentially expressed between the treatment and model groups, including 32 upregulated and 16 downregulated genes. The possible signaling pathways associated with the effect of triptolide were investigated by Gene Ontology and pathway analysis, revealing that the phosphoinositide-3 kinase (PI3K)/AKT signaling pathway has a key role in the proliferation and apoptosis of synovial cells in RA joints. Reverse transcription-quantitative polymerase chain reaction analysis was applied to confirm the aberrant expression of key mRNAs and revealed that vascular endothelial growth factor (VEGF) A and C1q and tumor necrosis factor related protein 3 (C1QTNF3) were downregulated in the treatment group compared with the model group (P<0.05). In conclusion, triptolide may exert its effects against RA via the PI3K/AKT pathway and has an inhibitory effect on the expression of VEGFA and C1QTNF3, thus are potentially associated with the occurrence and development of RA.

Experience and the ever-changing brain: what the transcriptome can reveal

The brain is an ever-changing organ that encodes memories and directs behavior. Neuroanatomical studies have revealed structural plasticity of neural architecture, and advances in gene expression technology and epigenetics have demonstrated new mechanisms underlying the brain's dynamic nature. Stressful experiences challenge the plasticity of the brain, and prolonged exposure to environmental stress redefines the normative transcriptional profile of both neurons and glia, and can lead to the onset of mental illness. A more thorough understanding of normal and abnormal gene expression is needed to define the diseased brain and improve current treatments for psychiatric disorders. The efforts to describe gene expression networks have been bolstered by microarray and RNA-sequencing technologies. The heterogeneity of neural cell populations and their unique microenvironments, coupled with broad ranging interconnectivity, makes resolving this complexity exceedingly challenging and requires the combined efforts of single cell and systems level expression profiling to identify targets for therapeutic intervention.

Lifetime achievement from a brain-adrenal perspective: on the CRF-urocortin-glucocorticoid balance

This contribution dedicated to Wylie Vale is focused on the action of the glucocorticoid hormone aimed to counterbalance the stress response orchestrated by the corticotrophin releasing factor (CRF) and urocortin (Ucn) family of peptides. It appears that the release and action of these stress hormones themselves are subjected to intrinsic self-regulatory feedback loops that operate as checks and balances in stress adaptation. One of these feedback loops is operated by the mineralocorticoid (MR) and glucocorticoid receptors (GR) that mediate in complementary fashion the action of endogenous cortisol/corticosterone in brain circuits underlying the onset and termination of the stress response. By affecting appraisal processes MR has an important role in coordinating emotional expression and cognitive flexibility with the onset of the stress response, while GR's role is prominent in the management of behavioral and physiological adaptations during the recovery phase. Genetic variation in interaction with environmental input and experience-related factors can modulate this balance between susceptibility and recovery governed by a balanced MR:GR signaling. Thanks to the Wylie Vale School of scientists a parallel balanced regulation between the CRF/CRF-1 and Ucn/CRF-2 receptor systems is being uncovered, leading inexorably to the question: how do the CRF/Ucn and glucocorticoid systems interact in multiple brain sites to maintain homeostasis and health?

Gestational age-dependent changes in gene expression of metabolic enzymes and transporters in pregnant mice

Pregnancy-induced changes in drug pharmacokinetics can be explained by changes in expression of drug-metabolizing enzymes and transporters and/or normal physiology. In this study, we determined gestational age-dependent expression profiles for all metabolic enzyme and transporter genes in the maternal liver, kidney, small intestine, and placenta of pregnant mice by microarray analysis. We specifically examined the expression of genes important for xenobiotic, bile acid, and steroid hormone metabolism and disposition, namely, cytochrome P450s (Cyp), UDP-glucuronosyltranserases (Ugt), sulfotransferases (Sult), and ATP-binding cassette (Abc), solute carrier (Slc), and solute carrier organic anion (Slco) transporters. Few Ugt and Sult genes were affected by pregnancy. Cyp17a1 expression in the maternal liver increased 3- to 10-fold during pregnancy, which was the largest observed change in the maternal tissues. Cyp1a2, most Cyp2 isoforms, Cyp3a11, and Cyp3a13 expression in the liver decreased on gestation days (gd) 15 and 19 compared with nonpregnant controls (gd 0). In contrast, Cyp2d40, Cyp3a16, Cyp3a41a, Cyp3a41b, and Cyp3a44 in the liver were induced throughout pregnancy. In the placenta, Cyp expression on gd 10 and 15 was upregulated compared with gd 19. Notable changes were also observed in Abc and Slc transporters. Abcc3 expression in the liver and Abcb1a, Abcc4, and Slco4c1 expression in the kidney were downregulated on gd 15 and 19. In the placenta, Slc22a3 (Oct3) expression on gd 10 was 90% lower than that on gd 15 and 19. This study demonstrates important gestational age-dependent expression of metabolic enzyme and transporter genes, which may have mechanistic relevance to drug disposition in human pregnancy.

Evaluation of sensitivity, performance and reproducibility of microarray technology in neuronal tissue

Microarray technology is a powerful technique that allows the simultaneous study of thousands of gene transcripts. During the past two years there has been an explosion of publications describing experiments utilizing microarray technology that range from original research findings from biological paradigms to mathematically modeled systems. However, neuroscientists using microarray technology face significant challenges due to high tissue complexity, low abundance transcripts, and small magnitude changes in transcript levels that have significant biological impact. This manuscript describes a series of studies designed to address issues regarding microarray sensitivity, ability of microarrays to detect subtle changes, and reproducibility of microarray experiments, all in the context of neuronal tissue. From the presentation of these studies, the authors argue that although microarray technology is limited with regards to sensitivity, the outcome of these experiments, if approached with appropriate skepticism, can be fruitful in the generation of hypotheses and seeding of future experiments.

SpliceAid 2: a database of human splicing factors expression data and RNA target motifs

Splicing is the most frequently altered biological process by mutations within gene regions. Information for splicing is recognized by several factors that bind pre-mRNA sequence and, through coordinated interaction, yield mature transcripts. Some in silico methods have been developed to predict if a mutation leads to aberrant splicing patterns. We previously created SpliceAid tool that is able to minimize false positive predictions because it adopts strictly experimental RNA target motifs bound by splicing proteins in humans. In order to improve prediction accuracy and better understand the splicing outcome, the tissue specificity of each splicing regulatory factor has to be taken into account. Here, we have developed SpliceAid 2 by adding the expression data related to the splicing factors extracted from the main proteomic and transcriptomic databases, true 5' and 3' splice sites, polypyrimidine tracts, and branch point sequences. The new version collects 2,220 target sites of 62 human splicing proteins and their expression data in 320 tissues per cell. SpliceAid 2 can be useful to foresee the splicing pattern alteration, to guide the identification of the molecular effect due to the mutations and to understand the tissue-specific alternative splicing. SpliceAid 2 is freely accessible at www.introni.it/spliceaid.html.

Alterations in the transcriptome of porcine oocytes derived from prepubertal and cyclic females is associated with developmental potential

The developmental competence of oocytes is progressively attained as females approach puberty. The poor quality of prepubertally derived oocytes suggests that essential processes during cytoplasmic maturation have not been completed. The objective of this experiment was to identify genes in oocytes that are associated with good (cyclic females) and poor (prepubertal females) developmental competence. Development to the blastocyst stage in vitro was significantly decreased in oocytes derived from prepubertal females compared with cyclic females (5.26 and 12.86%, respectively). Approximately 10% of the oocyte transcriptome was differentially expressed between in vitro-matured oocytes derived from cyclic and prepubertal females (P < 0.05); 58% of differentially expressed genes had increased transcript abundance in oocytes derived from cyclic females. Genes involved in the metabolism and regulation of biological processes had increased transcript abundance in oocytes derived from cyclic females, whereas genes involved in translation were increased in prepubertally derived oocytes. Quantitative PCR confirmed differential expression (P < 0.05) for 6 out of 11 selected genes [DPYD (dihydropyrimidine dehydrogenase), RDH11 (retinol dehydrogenase 11), SFRS4 (serine/arginine-rich splicing factor 4), SFRS7 (serine/arginine-rich splicing factor 7), TL4 (transcribed loci 4), and TOP2B (topoisomerase II β)] that were differentially expressed with greater than a 2-fold change by microarray, although 3 of these genes, DPYD, TL4, and TOP2B, were in opposing directions by the 2 methods. In conclusion, expression of multiple genes involved in metabolism and translation was significantly altered in oocytes from prepubertal females compared with cyclic females, which was associated with reduced in vitro development to the blastocyst stage. These genes may represent important cellular mechanisms that regulate oocyte quality.

Digital multiplexed gene expression analysis using the NanoString nCounter system

This unit presents the protocol for the NanoString nCounter Gene Expression Assay, a robust and highly reproducible method for detecting the expression of up to 800 genes in a single reaction with high sensitivity and linearity across a broad range of expression levels. The methodology serves to bridge the gap between genome-wide (microarrays) and targeted (real-time quantitative PCR) expression profiling. The nCounter assay is based on direct digital detection of mRNA molecules of interest using target-specific, color-coded probe pairs. It does not require the conversion of mRNA to cDNA by reverse transcription or the amplification of the resulting cDNA by PCR. Each target gene of interest is detected using a pair of reporter and capture probes carrying 35- to 50-base target-specific sequences. In addition, each reporter probe carries a unique color code at the 5' end that enables the molecular barcoding of the genes of interest, while the capture probes all carry a biotin label at the 3' end that provides a molecular handle for attachment of target genes to facilitate downstream digital detection. After solution-phase hybridization between target mRNA and reporter-capture probe pairs, excess probes are removed and the probe/target complexes are aligned and immobilized in the nCounter cartridge, which is then placed in a digital analyzer for image acquisition and data processing. Hundreds of thousands of color codes designating mRNA targets of interest are directly imaged on the surface of the cartridge. The expression level of a gene is measured by counting the number of times the color-coded barcode for that gene is detected, and the barcode counts are then tabulated.

Gene regulation in the rat prefrontal cortex after learning with or without cholinergic insult

The prefrontal cortex is essential for a wide variety of higher functions, including attention and memory. Cholinergic neurons are thought to be of prime importance in the modulation of these processes. Degeneration of forebrain cholinergic neurons has been linked to several neurological disorders. The present study was designed to identify genes and networks in rat prefrontal cortex that are associated with learning and cholinergic-loss-memory deficit. Affymetrix microarray technology was used to screen gene expression changes in rats submitted or not to 192 IgG-saporin immunolesion of cholinergic basal forebrain and trained in spatial/object novelty tasks. Results showed learning processes were associated with significant expression of genes, which were organized in several clusters of highly correlated genes and would be involved in biological processes such as intracellular signaling process, transcription regulation, and filament organization and axon guidance. Memory loss following cortical cholinergic deafferentation was associated with significant expression of genes belonging to only one clearly delineated cluster and would be involved in biological processes related to cytoskeleton organization and proliferation, and glial and vascular remodeling, i.e., in processes associated with brain repair after injury.

A single dose of dihydrotestosterone induced a myogenic transcriptional program in female intra-abdominal adipose tissue

Sex steroids are key regulators of adipose tissue (AT) mass, determining gender-specific differences in fat distribution and accumulation. With the aim of exploring the relevance and peculiarities of androgen action in female intra-abdominal AT, we used the serial analysis of gene expression (SAGE) method to analyze the AT transcriptome in four groups of female mice: intact, ovariectomized (OVX), OVX plus dihydrotestosterone (DHT) injection at 3h or 24h before sacrifice (DHT3h, DHT24h). An average of 19555 transcript species was examined in retroperitoneal fat. We found a total of 321 transcripts differentially modulated by DHT and OVX, including 125 novel genes. Several genes involved in energy metabolism/ATP production were up-regulated by DHT, whereas important regulators of lipid metabolism were reduced. Transcripts involved in Ca(2+) uptake/release, cell signalling, cell defence and protein expression were differentially modulated by DHT. A surprising number of myogenic genes were up-regulated, including myosin light and heavy polypeptides, troponins, as well as several actin-binding proteins. These results suggest that DHT24h may have induced a myogenic-like transcriptional program in adipocytes. The present study sheds light on the distinctive female transcriptional pattern acutely induced by androgens in intra-abdominal fat, and may add new insights into the global understanding of menopausal endocrinology and its association to intra-abdominal obesity.

Identification of a novel marker for dendritic cell maturation, mouse transmembrane protein 123

Dendritic cells (DCs) are a group of professional antigen-presenting cells, and many genes are known to be associated with their maturation. We compared the transcriptional profiles of immature and mature mouse Langerhans cells using the suppressive, subtractive hybridization method and identified a novel gene of unknown function, termed herein transmembrane protein 123 (Tmem123), of which mRNA expression was enhanced in mature but not in immature Langerhans cells. Its expression was also enhanced in other mature DCs such as bone marrow-derived DCs (BMDCs) and splenic DCs. Interestingly, CD40 expression was up-regulated on mature BMDCs cultured with colchicine concurrently with the enhanced expression of Tmem123 compared with that of fresh BMDCs. Furthermore, the expression of CD40 was enhanced on Tmem123-transfected DC2.4 cells, a mouse BMDC-derived cell line, compared with that on mock-transfected DC2.4 cells. This enhancement of CD40 expression did not occur after deletion of lysosome/endosome targeting YXXϕ motifs (where X is any amino acid and ϕ is a bulky hydrophobic amino acid) in the Tmem123 cytoplasmic tail. By stimulation with anti-CD40 monoclonal antibody, these transfectants secreted an increased amount of IL-12/23 p40 compared with mock-transfected DC2.4 cells. Thus, our study demonstrates that Tmem123 may be used as a new maturation marker in DCs and that this molecule may be closely associated with the cell surface expression of CD40.

Identification of follicular marker genes as pregnancy predictors for human IVF: new evidence for the involvement of luteinization process

Multiple pregnancy represents an important health risk to both mother and child in fertility treatment. To reduce a high twin rate, restriction to one embryo transfer is needed. Morphological evaluation methods for predicting embryo viability has significant limitations. Tight communication exists between the follicular cells (FCs) and the oocyte; therefore, developmental competence may be determined by markers expressed in the surrounding FCs. In this study, cells were recovered on a per-follicle basis by individual follicle puncture. Hybridization analysis using a custom-made complementary DNA microarray containing FC transcripts was performed. Genes expressed in FCs associated with good morphological transferred embryos were identified from follicles associated with a pregnancy outcome (pregnancy group) or no pregnancy (non-pregnancy group). Ten candidates from the Pregnancy group and three from the Non-pregnancy group were validated by quantitative RT-PCR. The best predictors associated with pregnancy were UDP-glucose pyrophosphorylase-2 and pleckstrin homology-like domain, family A, member 1. Genes assessment showed no significant candidate genes associated with non-pregnancy outcome, but GA-binding protein transcription factor beta1 showed a tendency to be potentially more expressed in the non-pregnancy group. These markers could be related to granulosa luteinization process and could be used to improve embryo selection for successful single embryo transfer.

Identification of genes involved in stem rust resistance from wheat mutant D51 with the cDNA-AFLP technique

Wheat (Triticum aestivum L.) stem rust caused by Puccinia graminis f. sp. tritici is one of the main diseases of wheat worldwide. Wheat mutant line D51, which was derived from the highly susceptible cultivar L6239, shows resistance to the prevailing races 21C3CPH, 21C3CKH, and 21C3CTR of P. graminis f. sp. tritici in China. In this study, we used the cDNA-AFLP technology to identify the genes that are likely involved in the stem rust resistance. EcoRI/MseI selective primers were used to generate approximately 1920 DNA fragments. Seventy five differentially transcribed fragments (3.91%) were identified by comparing the samples of 21C3CPH infected D51 with infected L6239 or uninfected D51. Eleven amplified cDNA fragments were sequenced. Eight showed significant similarity to known genes, including TaLr1 (leaf rust resistance gene), wlm24 (wheat powdery mildew resistance gene), stress response genes and ESTs of environment stress of tall fescue. These identified genes are involved in plant defense response and stem rust resistance and need further research to determine their usefulness in breeding new resistance cultivars.

Global expression profiling in epileptogenesis: does it add to the confusion?

Since the inception of global gene expression profiling platforms in the mid-1990s, there has been a significant increase in publications of differentially expressed genes in the process of epileptogenesis. In particular for mesial temporal lobe epilepsy, the presence of a latency period between the first manifestation of seizures to chronic epilepsy provides the opportunity for therapeutic interventions at the molecular biology level. Using global expression profiling techniques, approximately 2000 genes have been published demonstrating differential expression in mesial temporal epilepsy. The majority of these changes, however, are specific to laboratory or experimental conditions with only 53 genes demonstrating changes in more than two publications. To this end, we review the current status of gene expression profiling in epileptogenesis and suggest standard guidelines to be followed for greater accuracy and reproducibility of results.

Profiling microRNA expression in Arabidopsis pollen using microRNA array and real-time PCR

BACKGROUND

MicroRNAs (miRNAs) are approximately 22-nt small non-coding RNAs that regulate the expression of specific target genes in many eukaryotes. In higher plants, miRNAs are involved in developmental processes and stress responses. Sexual reproduction in flowering plants relies on pollen, the male gametophyte, to deliver sperm cells to fertilize the egg cell hidden in the embryo sac. Studies indicated that post-transcriptional processes are important for regulating gene expression during pollen function. However, we still have very limited knowledge on the involved gene regulatory mechanisms. Especially, the function of miRNAs in pollen remains unknown.

RESULTS

Using miRCURY LNA array technology, we have profiled the expression of 70 known miRNAs (representing 121 miRBase IDs) in Arabidopsis mature pollen, and compared the expression of these miRNAs in pollen and young inflorescence. Thirty-seven probes on the array were identified using RNAs isolated from mature pollen, 26 of which showed significant differences in expression between mature pollen and inflorescence. Real-time PCR based on TaqMan miRNA assays confirmed the expression of 22 miRNAs in mature pollen, and identified 8 additional miRNAs that were expressed at low level in mature pollen. However, the expression of 11 miRNA that were identified on the array could not be confirmed by the Taqman miRNA assays. Analyses of transcriptome data for some miRNA target genes indicated that miRNAs are functional in pollen.

CONCLUSION

In summary, our results showed that some known miRNAs were expressed in Arabidopsis mature pollen, with most of them being low abundant. The results can be utilized in future research to study post-transcriptional gene regulation in pollen function.

Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies

Background

The recent development within high-throughput technologies for expression profiling has allowed for parallel analysis of transcriptomes and proteomes in biological systems such as comparative analysis of transcript and protein levels of tissue regulated genes. Until now, such studies of have only included microarray or short length sequence tags for transcript profiling. Furthermore, most comparisons of transcript and protein levels have been based on absolute expression values from within the same tissue and not relative expression values based on tissue ratios.

Results

Presented here is a novel study of two porcine tissues based on integrative analysis of data from expression profiling of identical samples using cDNA microarray, 454-sequencing and iTRAQ-based proteomics. Sequence homology identified 2.541 unique transcripts that are detectable by both microarray hybridizations and 454-sequencing of 1.2 million cDNA tags. Both transcript-based technologies showed high reproducibility between sample replicates of the same tissue, but the correlation across these two technologies was modest. Thousands of genes being differentially expressed were identified with microarray. Out of the 306 differentially expressed genes, identified by 454-sequencing, 198 (65%) were also found by microarray. The relationship between the regulation of transcript and protein levels was analyzed by integrating iTRAQ-based proteomics data. Protein expression ratios were determined for 354 genes, of which 148 could be mapped to both microarray and 454-sequencing data. A comparison of the expression ratios from the three technologies revealed that differences in transcript and protein levels across heart and muscle tissues are positively correlated.

Conclusion

We show that the reproducibility within cDNA microarray and 454-sequencing is high, but that the agreement across these two technologies is modest. We demonstrate that the regulation of transcript and protein levels across identical tissue samples is positively correlated when the tissue expression ratios are used for comparison. The results presented are of interest in systems biology research in terms of integration and analysis of high-throughput expression data from mammalian tissues.

Climbing Mount Efficiency--small steps, not giant leaps towards higher cloning success in farm animals

Despite more than a decade of research efforts, farm animal cloning by somatic cell nuclear transfer (SCNT) is still frustratingly inefficient. Inefficiency manifests itself at different levels, which are currently not well integrated. At the molecular level, it leads to widespread genetic, epigenetic and transcriptional aberrations in cloned embryos. At the organismal level, these genome-wide abnormalities compromise development of cloned foetuses and offspring. Specific molecular defects need to be causally linked to specific cloned phenotypes, in order to design specific treatments to correct them. Cloning efficiency depends on the ability of the nuclear donor cell to be fully reprogrammed into an embryonic state and the ability of the enucleated recipient cell to carry out the reprogramming reactions. It has been postulated that reprogrammability of the somatic donor cell epigenome is influenced by its differentiation status. However, direct comparisons between cells of divergent differentiation status within several somatic lineages have found no conclusive evidence for this. Choosing somatic stem cells as donors has not improved cloning efficiency, indicating that donor cell type may be less critical for cloning success. Different recipient cells, on the other hand, vary in their reprogramming ability. In bovine, using zygotes instead of oocytes has increased cloning success. Other improvements in livestock cloning efficiency include better coordinating donor cell type with cell cycle stage and aggregating cloned embryos. In the future, it will be important to demonstrate if these small increases at every step are cumulative, adding up to an integrated cloning protocol with greatly improved efficiency.

Microarray evaluation of endometrial receptivity in Chinese women with polycystic ovary syndrome

Patients with polycystic ovary syndrome (PCOS) have lower pregnancy and higher miscarriage rates, possibly due to decreased endometrial receptivity. In this study, endometrium was processed for RNA extraction and hybridization of chemically fragmented, biotinylated, complementary RNA on high-density oligonucleotide microarrays, and screened for 21,571 genes. Real-time polymerase chain reaction (PCR) was used to verify the result. Genes found to be down-regulated in the endometrium during the implantation window in PCOS patients included those whose activity was integral to membrane function, adhesion, invasive growth and the cytoskeleton. Among these genes, some have previously been associated with endometrial receptivity (by microarray research or other methods) and some have never previously been associated with endometrial receptivity. Using real-time PCR, expression of transmembrane 4 superfamily member 4 (TM4SF4) and matrix metalloproteinase 26 (MMP26) was found to be significantly decreased during the implantation window in patients with PCOS (P= 0.003). TM4SF4 has been demonstrated to be associated with adhesion; MMP26 has been shown to be related to degradation of extracellular matrix. It is suggested the down-regulated gene expression during the implantation window in patients with PCOS indicates differential gene expression in the endometrium between PCOS and normal women during the implantation window. This might affect endometrial receptivity.

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

The hippocampal expression profiles of wild-type mice and mice transgenic for δC-doublecortin-like kinase were compared with Solexa/Illumina deep sequencing technology and five different microarray platforms. With Illumina's digital gene expression assay, we obtained ∼2.4 million sequence tags per sample, their abundance spanning four orders of magnitude. Results were highly reproducible, even across laboratories. With a dedicated Bayesian model, we found differential expression of 3179 transcripts with an estimated false-discovery rate of 8.5%. This is a much higher figure than found for microarrays. The overlap in differentially expressed transcripts found with deep sequencing and microarrays was most significant for Affymetrix. The changes in expression observed by deep sequencing were larger than observed by microarrays or quantitative PCR. Relevant processes such as calmodulin-dependent protein kinase activity and vesicle transport along microtubules were found affected by deep sequencing but not by microarrays. While undetectable by microarrays, antisense transcription was found for 51% of all genes and alternative polyadenylation for 47%. We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies.

Identification of differentially expressed markers in human follicular cells associated with competent oocytes

BACKGROUND

The development of an accurate method for selection of high-quality embryos is essential to achieve high pregnancy rates with single embryo transfer in human IVF. The developmental competence of the oocyte is acquired during follicle maturation and strong communication also exists between the follicular cells (FCs) and the oocytes; thus oocyte developmental competence may be determined by markers expressed in the surrounding FCs.

METHODS

From consenting patients (n = 40), FCs were recovered on a per follicle basis by individual follicle puncture. Hybridization analyses using a custom-made complementary DNA microarray containing granulosa/cumulus expressed sequence tags (ESTs) from subtracted libraries and an Affymetrix GeneChip were performed to identify specific genes expressed in follicles leading to a pregnancy. The selected candidate genes were validated by quantitative-PCR (Q-PCR).

RESULTS

Subtractive libraries prepared from pooled samples representing pregnant versus non-pregnant patients produced 1694 ESTs. Hybridization data analysis discriminated 115 genes associated with competent follicles. Selected candidates were confirmed by Q-PCR: 3-beta-hydroxysteroid dehydrogenase 1 (P = 0.0078), Ferredoxin 1 (P = 0.0203), Serine (or cysteine) proteinase inhibitor clade E member 2 (P = 0.0499), Cytochrome P450 aromatase (P = 0.0359) and Cell division cycle 42 (P = 0.0396).

CONCLUSIONS

Microarray technologies are useful to mine the transcriptome of FCs expressed in follicles associated with competent oocytes and could be used to improve embryo selection with the objective of successful single embryo transfer.

Central corticosteroid actions: Search for gene targets

Although many of the physiological effects of corticosteroid stress hormones on neuronal function are well recognised, the underlying genomic mechanisms are only starting to be elucidated. Linking physiology and genomics has proven to be a complicated task, despite the emergence of large-scale gene expression profiling technology in the last decade. This is in part due to the complexity of glucocorticoid-signaling, in part due to the complexity of the brain itself. The presence of a binary receptor system for glucocorticoid hormones in limbic brain structures, the coexistence of membrane and intracellular receptors and the highly contextual action of glucocorticoids contribute to this complexity. In addition, the anatomical complexity, extensive cellular heterogeneity of brain and the modest changes in gene expression (mostly in the range of 10-30%) hamper detection of responsive genes, in particular of low abundant transcripts, such as many neurotransmitter receptors and growth factors. Nonetheless, ongoing research into central targets of glucocorticoids has identified many different functional gene classes that underlie the diverse effects of glucocorticoids on brain function. These functional classes include genes involved in energy metabolism, signal transduction, neuronal structure, vesicle dynamics, neurotransmitter catabolism, cell adhesion, genes encoding neurotrophic factors and their receptors and genes involved in regulating glucocorticoid-signalling. The aim of this review is to give an overview of the current status of the field on identification of central corticosteroid targets, discuss the opportunities and pitfalls and highlight new developments in understanding central corticosteroid action.

Methodological considerations for gene expression profiling of human brain

Gene expression profiles of postmortem brain tissue represent important resources for understanding neuropsychiatric illnesses. The impact(s) of quality covariables on the analysis and results of gene expression studies are important questions. This paper addressed critical variables which might affect gene expression in two brain regions. Four broad groups of quality indicators in gene expression profiling studies (clinical, tissue, RNA, and microarray quality) were identified. These quality control indicators were significantly correlated, however one quality variable did not account for the total variance in microarray gene expression. The data showed that agonal factors and low pH correlated with decreased integrity of extracted RNA in two brain regions. These three parameters also modulated the significance of alterations in mitochondrial-related genes. The average F-ratio summaries across all transcripts showed that RNA degradation from the AffyRNAdeg program accounted for higher variation than all other quality factors. Taken together, these findings confirmed prior studies, which indicated that quality parameters including RNA integrity, agonal factors, and pH are related to differences in gene expression profiles in postmortem brain. Individual candidate genes can be evaluated with these quality parameters in post hoc analysis to help strengthen the relevance to psychiatric disorders. We find that clinical, tissue, RNA, and microarray quality are all useful variables for collection and consideration in study design, analysis, and interpretation of gene expression results in human postmortem studies.

A SAGE study of apolipoprotein E3/3, E3/4 and E4/4 allele-specific gene expression in hippocampus in Alzheimer disease

APOE4 allele is a major risk factor for late-onset Alzheimer disease (AD). The mechanism of action of APOE in AD remains unclear. To study the effects of APOE alleles on gene expression in AD, we have analyzed the gene transcription patterns of human hippocampus from APOE3/3, APOE3/4, APOE4/4 AD patients and normal control using Serial Analysis of Gene Expression (SAGE). Using SAGE, we found gene expression patterns in hippocampus of APOE3/4 and APOE4/4 AD patients differ substantially from those of APOE3/3 AD patients. APOE3/4 and APOE4/4 allele expression may activate similar genes or gene pools with associated functions. APOE4 AD alleles activate multiple tumor suppressors, tumor inducers and negative regulator of cell growth or repressors that may lead to increased cell arrest, senescence and apoptosis. In contrast, there is decreased expression of large clusters of genes associated with synaptic plasticity, synaptic vesicle docking and fusing and axonal/neuronal outgrowth. In addition, reduction of neurotransmitter receptors and Ca2+ homeostasis, disruption of multiple signal transduction pathways, loss of cell protection, and perhaps most notably, mitochondrial oxidative phosphorylation/energy metabolism are associated with APOE3/4 and APOE4/4 AD alleles. These findings may help define the mechanisms that APOE4 contribute that increase risk for AD and identify new candidate genes conferring susceptibility to AD.

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates

Background

High-throughput systems for gene expression profiling have been developed and have matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing-based approaches. With data from different technologies being accumulated, concerns and challenges are raised about the level of agreement across technologies. As part of an ongoing large-scale cross-platform data comparison framework, we report here a comparison based on identical samples between one-dye DNA microarray platforms and MPSS (Massively Parallel Signature Sequencing).

Results

The DNA microarray platforms generally provided highly correlated data, while moderate correlations between microarrays and MPSS were obtained. Disagreements between the two types of technologies can be attributed to limitations inherent to both technologies. The variation found between pooled biological replicates underlines the importance of exercising caution in identification of differential expression, especially for the purposes of biomarker discovery.

Conclusion

Based on different principles, hybridization-based and sequencing-based technologies should be considered complementary to each other, rather than competitive alternatives for measuring gene expression, and currently, both are important tools for transcriptome profiling.

Single molecule transcription profiling with AFM

Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

Exploring host-pathogen interactions at the epithelial surface: application of transcriptomics in lung biology

The epithelial surface of the airways is the largest barrier-forming interface between the human body and the outside world. It is now well recognized that, at this strategic position, airway epithelial cells play an eminent role in host defense by recognizing and responding to microbial exposure. Conversely, inhaled microorganisms also respond to contact with epithelial cells. Our understanding of this cross talk is limited, requiring sophisticated experimental approaches to analyze these complex interactions. High-throughput technologies, such as DNA microarray analysis and serial analysis of gene expression (SAGE), have been developed to screen for gene expression levels at large scale within single experiments. Since their introduction, these hypothesis-generating technologies have been widely used in diverse areas such as oncology and brain research. Successful application of these genomics-based technologies has also revealed novel insights in host-pathogen interactions in both the host and pathogen. This review aims to provide an overview of the SAGE and microarray technology illustrated by their application in the analysis of host-pathogen interactions. In particular, the interactions between epithelial cells in the human lungs and clinically relevant microorganisms are the central focus of this review.

Spinal cord transcriptional profile analysis reveals protein trafficking and RNA processing as prominent processes regulated by tactile allodynia

Since partial peripheral injury does not necessarily lead to the development of neuropathic pain it is possible that a set of genes is directly regulated by the development of neuropathic pain independent of the genes regulated by nerve injury. This study identifies the genes expressed within the spinal cord that are uniquely regulated by tactile allodynia in rats. Using subtractive methods, genes regulated by allodynia were differentiated from those of nerve injury. Gene ontology analysis identified that allodynic genes are involved in a variety of processes including myelination, actin cytoskeleton reorganization, dephosphorylation, phosphorylation, response to stress, as well as protein trafficking and RNA processing. The processes of protein trafficking and RNA processing were found to be as statistically significant as other processes that have been associated with neuropathic pain development such as response to stress, phosphorylation, and cell migration. Trafficking and transcription are linked and undergo activity dependent regulation which results in both rapid and gradual synaptic changes (plasticity). The data presented here greatly expand the list of genes regulated by the development of tactile allodynia and reveal protein trafficking and RNA processing as prominent biological processes that may be involved in synaptic plasticity changes within the spinal cord in response to allodynia.

Understanding SAGE data

Serial analysis of gene expression (SAGE) is a method for identifying and quantifying transcripts from eukaryotic genomes. Since its invention, SAGE has been widely applied to analyzing gene expression in many biological and medical studies. Vast amounts of SAGE data have been collected and more than a thousand SAGE-related studies have been published since the mid-1990s. The principle of SAGE has been developed to address specific issues such as determination of normal gene structure and identification of abnormal genome structural changes. This review focuses on the general features of SAGE data, including the specificity of SAGE tags with respect to their original transcripts, the quantitative nature of SAGE data for differentially expressed genes, the reproducibility, the comparability of SAGE with microarray and the future potential of SAGE. Understanding these basic features should aid the proper interpretation of SAGE data to address biological and medical questions.

Differentially expressed genes in the rat cochlear nucleus

The cochlear nucleus is the first central pathway involved in the processing of peripheral auditory activity. The anterior ventral cochlear nucleus (AVCN), posterior ventral cochlear nucleus (PVCN) and dorsal cochlear nucleus (DCN) each contain predominant populations of neurons that have been well characterized regarding their morphological and electrophysiological properties. Little is known, however, of the underlying genetic factors that contribute to these properties and the initial steps in auditory processing. Serial analysis of gene expression (SAGE), supported by microarray experiments, was performed on each subdivision of the rat cochlear nucleus to identify genes that may sub-serve specialized roles in the central auditory system. Pair-wise comparisons between SAGE libraries from the AVCN, PVCN and DCN were correlated with microarray experiments to identify individual transcripts with significant differential expression. Twelve highly correlated genes were identified representing cytoskeletal, vesicular, metabolic and g-protein regulating proteins. Among these were Rgs4 which showed higher expression in the DCN, Sst and Cyp11b1 with very high expression in the AVCN and Calb2 with preferential expression in the PVCN. The differential expression of these genes was validated with real-time reverse transcriptase-polymerase chain reaction. These experiments provide a basis for understanding normal auditory processing on a molecular level and a template for investigating changes that may occur in the cochlear nucleus with hearing loss, the generation and percept of tinnitus, and central auditory processing disorders.

Effect of brief corticosterone administration on SGK1 and RGS4 mRNA expression in rat hippocampus

Acute stress and corticosterone enhance 5-HT1A receptor-mediated responses in rat hippocampal CA1 cells within 1-2 h, through a process involving transcriptional regulation of unknown genes. Earlier studies showed that regulation of the 5-HT1A receptor gene cannot explain the functional effects. We here tested the hypothesis that corticosterone targets genes encoding RGS4 or SGK1, which can both affect the 5-HT1A receptor associated Kir channel, thus affecting 5-HT1A receptor function. To this end, the effect of a single corticosterone injection on hippocampal expression of RGS4 and SGK1 mRNAs, measured by in situ hybridization, was studied. Expression of RGS4 or SGK1 mRNA was not affected by the corticosterone injection, neither in the CA1 area nor in other hippocampal subregions. Strikingly, SGK1 mRNA expression was strongly up-regulated in the corpus callosum. We reject, however, the hypothesis that the effect of corticosterone on 5-HT1A responsiveness is mediated via altered RGS4 or SGK1 mRNA expression.

Nedd4-WW domain-binding protein 5 (Ndfip1) is associated with neuronal survival after acute cortical brain injury

Understanding the transcriptional response to neuronal injury after trauma is a necessary prelude to formulation of therapeutic strategies. We used Serial Analysis of Gene Expression (SAGE) to identify 50,000 sequence tags representing 18,000 expressed genes in the cortex 2 h after traumatic brain injury (TBI). A similar tag library was obtained from sham-operated cortex. The SAGE data were validated on biological replicates using quantitative real-time-PCR on multiple samples at 2, 6, 12, and 24 h after TBI. This analysis revealed that the vast majority of genes showed a downward trend in their pattern of expression over 24 h. This was confirmed for a subset of genes using in situ hybridization and immunocytochemistry on brain sections. Of the overexpressed genes in the trauma library, Nedd4-WW (neural precursor cell expressed, developmentally downregulated) domain-binding protein 5 (N4WBP5) (also known as Ndfip1) is strongly expressed in surviving neurons around the site of injury. Overexpression of N4WBP5 in cultured cortical neurons increased the number of surviving neurons after gene transfection and growth factor starvation compared with control transfections. These results identify N4WBP5 as a neuroprotective protein and, based on its known interaction with the ubiquitin ligase Nedd4, would suggest protein ubiquitination as a possible survival strategy in neuronal injury.

Changes in transcription within the CA1 field of the hippocampus are associated with age-related spatial learning impairments

Aged rats display a broad range of behavioral performance in spatial learning. The aim of this study was to identify candidate genes that are associated with learning and memory impairments. We first categorized aged-superior learners and age learning-impaired rats based on their performance in the Morris water maze (MWM) and then isolated messenger RNA from the CA1 hippocampal region of each animal to interrogate Affymetrix microarrays. Microarray analysis identified a set of 50 genes that was transcribed differently in aged-superior learners that had successfully learned the spatial strategy in the MWM compared to aged learning-impaired animals that were unable to learn and a variety of groups designed to control for all non-learning aspects of exposure to the water maze paradigm. A detailed analysis of the navigation patterns of the different groups of animals during acquisition and probe trials of the MWM task was performed. Young animals used predominantly an allocentric (spatial) search strategy and aged-superior learners appeared to use a combination of allocentric and egocentric (response) strategies, whereas aged-learning impaired animals displayed thigmotactic behavior. The significant 50 genes that we identified were tentatively classified into four groups based on their putative role in learning: transcription, synaptic morphology, ion conductivity and protein modification. Thus, this study has potentially identified a set of genes that are responsible for the learning impairments in aged rats. The role of these genes in the learning impairments associated with aging will ultimately have to be validated by manipulating gene expression in aged rats. Finally, these 50 genes were functioning in the context of an aging CA1 region where over 200 genes was found to be differentially expressed compared to a young CA1.

Gene expression profiling reveals that peripheral nerve regeneration is a consequence of both novel injury-dependent and reactivated developmental processes

One of the most striking features of the injured mature peripheral nervous system is the ability to regenerate. The lesioned peripheral nervous system displays stereotypic histopathological reactions indicating the activation of a co-ordinated lesion-induced gene expression programme. Previous research has already identified molecular components of this axonal switch from a mature transmitting to a regenerative growth mode. The observed alterations in gene expression within the lesioned distal nerve stump were largely attributed to recapitulated developmental processes. However, to our knowledge, this hypothesis has not been proven systematically. Most of the stereotypic molecular and cellular reactions during nerve development and repair can be assigned to specific time windows. Consequently, we have compared gene expression profiles of both paradigms at six different time-points each by means of cDNA array hybridization. Our data identified injury-specific molecular reactions and revealed to what extent developmental mechanisms are reactivated in response to nerve lesion. Ninety-one genes (47% of the regeneration-associated genes) were found to be significantly regulated in both paradigms, suggesting that regeneration only partially recapitulates development and that approximately half of the regulated genes are part of a regeneration-dependent programme. Interestingly, mainly genes encoding signal transducers or factors involved in processes such as cell death, immune response, transport and transcriptional regulation showed injury-specific gene expression.

Gene expression profiling of primate neocortex: molecular neuroanatomy of cortical areas

One hundred years have passed since Brodmann's mapping of the mammalian neocortex. Solely on the basis of morphological observations, he envisaged the conservation and differentiation of cortical areal structures across various species. We now know that neurochemical, connectional and functional heterogeneity of the neocortex accompanies the morphological divergence observed in such cytoarchitectonic studies. Nevertheless, we are yet far from fully understanding the biological significance of this cortical heterogeneity. In this article, we review our past works on the gene expression profiling of the postnatal primate cortical areas, by quantitative real-time polymerase chain reaction (PCR), DNA array, differential display PCR and in situ hybridization analyses. These studies revealed both the overall homogeneity of gene expression across different cortical areas and the presence of a small number of genes that show markedly area-specific expression patterns. In situ hybridization showed that, among such genes, occ1 and retinol-binding protein (RBP) mRNAs are selectively expressed in the neuronal populations that seem to be involved in distinct neural processing such as sensory reception (for occ1) and associative function (for RBP). Such a molecular neuroanatomical approach has the promise to provide an important link between structure and function of the cerebral cortex.

Acute activation of hippocampal glucocorticoid receptors results in different waves of gene expression throughout time

Several aspects of hippocampal cell function are influenced by adrenal-secreted glucocorticoids in a delayed, genomic fashion. Previously, we used Serial Analysis of Gene Expression to identify glucocorticoid receptor (GR)-induced transcriptional changes in the hippocampus at a fixed time point. However, because changes in mRNA levels are transient and most likely precede the effects on hippocampal cell function, the aim of the current study was to assess the transcriptional changes in a broader time window by generating a time curve of GR-mediated gene expression changes. Therefore, we used rat hippocampal slices obtained from adrenalectomised rats, substituted in vivo with low corticosterone pellets, predominantly occupying the hippocampal mineralocorticoid receptors. To activate GR, slices were treated in vitro with a high (100 nM) dose of corticosterone and gene expression was profiled 1, 3 and 5 h after GR-activation. Using Affymetrix GeneChips, a striking pattern with different waves of gene expression was observed, shifting from exclusively down-regulated genes 1 h after GR-activation to both up and down regulated genes 3 h after GR-activation. After 5 h, the response was almost back to baseline. Additionally, real-time quantitative polymerase chain reaction was used for validation of a selection of responsive genes including genes involved in neurotransmission and synaptic plasticity such as the corticotropin releasing hormone receptor 1, monoamine oxidase A, LIMK1 and calmodulin 2. This permitted confirmation of GR-responsiveness of 15 out of 18 selected genes. In conclusion, direct activation of GR in hippocampal slices results in transient changes in gene expression. The pattern in which gene expression was modulated suggests that the fast genomic effects of glucocorticoids may be realised via transrepression, preceding a later wave of transactivation. Furthermore, we identified a number of interesting candidate genes which may underlie the glucocorticoid-mediated effects on hippocampal cell function.

Application of microarray technology in primate behavioral neuroscience research

Gene expression profiling of brain tissue samples applied to DNA microarrays promises to provide novel insights into the neurobiological bases of primate behavior. The strength of the microarray technology lies in the ability to simultaneously measure the expression levels of all genes in defined brain regions that are known to mediate behavior. The application of microarrays presents, however, various limitations and challenges for primate neuroscience research. Low RNA abundance, modest changes in gene expression, heterogeneous distribution of mRNA among cell subpopulations, and individual differences in behavior all mandate great care in the collection, processing, and analysis of brain tissue. A unique problem for nonhuman primate research is the limited availability of species-specific arrays. Arrays designed for humans are often used, but expression level differences are inevitably confounded by gene sequence differences in all cross-species array applications. Tools to deal with this problem are currently being developed. Here we review these methodological issues, and provide examples from our experiences using human arrays to examine brain tissue samples from squirrel monkeys. Until species-specific microarrays become more widely available, great caution must be taken in the assessment and interpretation of microarray data from nonhuman primates. Nevertheless, the application of human microarrays in nonhuman primate neuroscience research recovers useful information from thousands of genes, and represents an important new strategy for understanding the molecular complexity of behavior and mental health.

Serial analysis of gene expression in the hippocampus of patients with mesial temporal lobe epilepsy

Hippocampal sclerosis constitutes the most frequent neuropathological finding in patients with medically intractable mesial temporal lobe epilepsy. Serial analysis of gene expression was used to get a global view of the gene profile in human hippocampus in control condition and in epileptic condition associated with hippocampal sclerosis. Libraries were generated from control hippocampus, obtained by rapid autopsy, and from hippocampal surgical specimens of patients with mesial temporal lobe epilepsy and the classical pattern of hippocampal sclerosis. More than 50,000 tags were analyzed (28,282, control hippocampus; 25,953, hippocampal sclerosis) resulting in 9206 (control hippocampus) and 9599 (hippocampal sclerosis) unique tags (genes), each representing a specific mRNA transcript. Comparison of the two libraries resulted in the identification of 143 transcripts that were differentially expressed. These genes belong to a variety of functional classes, including basic metabolism, transcription regulation, protein synthesis and degradation, signal transduction, structural proteins, regeneration and synaptic plasticity and genes of unknown identity of function. The database generated by this study provides an extensive inventory of genes expressed in human control hippocampus, identifies new high-abundant genes associated with altered hippocampal morphology in patients with mesial temporal lobe epilepsy and serves as a reference for future studies aimed at detecting hippocampal transcriptional responses under various pathological conditions.

Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses

Large amounts of gene expression data from several different technologies are becoming available to the scientific community. A common practice is to use these data to calculate global gene coexpression for validation or integration of other "omic" data. To assess the utility of publicly available datasets for this purpose we have analyzed Homo sapiens data from 1202 cDNA microarray experiments, 242 SAGE libraries, and 667 Affymetrix oligonucleotide microarray experiments. The three datasets compared demonstrate significant but low levels of global concordance (rc<0.11). Assessment against Gene Ontology (GO) revealed that all three platforms identify more coexpressed gene pairs with common biological processes than expected by chance. As the Pearson correlation for a gene pair increased it was more likely to be confirmed by GO. The Affymetrix dataset performed best individually with gene pairs of correlation 0.9-1.0 confirmed by GO in 74% of cases. However, in all cases, gene pairs confirmed by multiple platforms were more likely to be confirmed by GO. We show that combining results from different expression platforms increases reliability of coexpression. A comparison with other recently published coexpression studies found similar results in terms of performance against GO but with each method producing distinctly different gene pair lists.

Overexpression of dopamine receptor genes and their products in the postnatal rat brain following maternal n-3 fatty acid dietary deficiency

A combination of PCR-Select cDNA subtraction and gene array hybridization was used to identify differentially expressed genomic markers in brains of rats fed for 3 weeks in utero and 2 weeks after birth on an n-3 polyunsaturated fatty acid (PUFA)-deficient diet supplied to dams. Total RNA was isolated, switch mechanism at 5'-end of the RNA transcripts (SMART) applied and used for PCR-Select subtraction of PUFA-deficient and adequately-fed control preparations. Subtracted and amplified ds-cDNA end-products were fragmented, terminally labeled with biotin-ddUTP and hybridized with a RN-U34A gene array. A 10-fold increase in potential genes with log2(Tester/Driver) = 1.4 was found compared with traditional gene array technology when the same chip was tested using non-subtracted targets. Reverse transcription-real-time relative PCR confirmed 30% of the transcripts. Among the validated transcripts, D1 and D2 receptors for dopamine (DA), were most prominent among a number of over-expressed neurotransmitter receptors and retinoic acid receptor (RXR alpha-2 and alpha-1). Immunohistochemical staining of brain sections from 2-week-old pups revealed a substantial enrichment of the D2 receptor in discrete regions of the mesolimbic and mesocortical pathways as well as in a large number of brain areas from the n-3 PUFA-deficient pups. Punches of the same areas run on western blots showed similar results. The overwhelming expression of D1 and D2 receptors may be attributed to a behavioral hypersensitivity caused by the possible impairment of DA production during brain development, which may have implications in certain disorders of the nervous system.

Identification of differentially expressed genes in hepatic HepG2 cells treated with acetaminophen using suppression subtractive hybridization

Acetaminophen (APAP) is widely used for the treatment of pain and fever. Although it is safe at therapeutic doses, APAP is toxic at higher doses and can cause severe damage to the liver. To clarify the mechanism of APAP-related liver damage, we attempted the identification of the differential gene expression in response to APAP treatment in hepatic HepG2 cells. In the present study, we used the technique of suppression subtractive hybridization (SSH) for the identification of the differentially expressed genes between untreated and treated cells and identified 14 candidate genes showing increased expression in response to APAP treatment. RT-PCR and real-time RT-PCR analysis confirmed that the expression of two genes was increased within 24 h following APAP treatment. Among them, only lysyl hydroxylase 2 expression was increased in a time- and dose-dependent manner. Furthermore, the expression of lysyl hydroxylase 2 was shown to be increased in the livers of APAP-treated mice compared to untreated controls. The increased expression of lysyl hydroxylase 2 was also observed when the cells were exposed to other hepatotoxins, ethanol and isoniazid. Since lysyl hydroxylase 2 is known to be a key enzyme of liver fibrosis, the increased expression of lysyl hydroxylase 2 may be involved in hepatotoxins-related liver fibrosis.

Large-scale genomic approaches to brain development and circuitry

Over the past two decades, molecular genetic studies have enabled a common conceptual framework for the development and basic function of the nervous system. These studies, and the pioneering efforts of mouse geneticists and neuroscientists to identify and clone genes for spontaneous mouse mutants, have provided a paradigm for understanding complex processes of the vertebrate brain. Gene cloning for human brain malformations and degenerative disorders identified other important central nervous system (CNS) genes. However, because many debilitating human disorders are genetically complex, phenotypic screens are difficult to design. This difficulty has led to large-scale, genomic approaches to discover genes that are uniquely expressed in brain circuits and regions that control complex behaviors. In this review, we summarize current phenotype- and genotype-driven approaches to discover novel CNS-expressed genes, as well as current approaches to carry out large-scale, gene-expression screens in the CNS.

Gene expression profiling of the rat hippocampus one month after focal cerebral ischemia followed by enriched environment

Functional recovery after experimental stroke in rats is enhanced by environmental enrichment by stimulating plastic changes in brain regions outside the lesion, but the molecular mechanisms are not known. We investigated the effect of environmental enrichment after focal cerebral ischemia on cognitive recovery and hippocampal gene expression using microarray analysis. Rats placed in enriched environment (EE) for 1 month after middle cerebral artery occlusion (MCAo) showed significantly improved spatial memory in the Morris water maze compared to rats housed alone after MCAo. Microarray analysis suggested several EE-induced differences in neuronal plasticity-related genes, but these changes could not be confirmed by quantitative real-time PCR. This study highlights some of the potential problems associated with gene expression profiling of brain tissues. Further studies at earlier time points and in additional subregions of the brain are of interest in the search for molecular mechanisms behind EE-induced neuronal plasticity after ischemic stroke.

Gene expression profiling in whole cerebral cortices of phencyclidine- or methamphetamine-treated rats

Both phencyclidine (PCP) and methamphetamine (MAP) can cause schizophrenia-like symptoms. To identify the molecules relating to the drug-induced psychotic state, we used serial analysis of gene expression in rodent cerebral cortices isolated 1 h after intraperitoneal injection of saline, PCP (10 mg/kg), or MAP (4 mg/kg). We analyzed a total of 150,000 tags and found significantly up- or down-regulated genes. The number of MAP-, PCP-, and MAP and PCP-reactive tags were 229, 215, and 41, respectively.