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PubMed2006

ArrayExpress--a public database of microarray experiments and gene expression profiles.

UNLABELLED: ArrayExpress is a public database for high throughput functional genomics data. ArrayExpress consists of two parts--the ArrayExpress Repository, which is a MIAME supportive public archive of microarray data, and the ArrayExpress Data Warehouse, which is a database of gene expression profiles selected from the repository and consistently re-annotated. Archived experiments can be queried by experiment attributes, such as keywords, species, array platform, authors, journals or accession numbers. Gene expression profiles can be queried by gene names and properties, such as Gene Ontology terms and gene expression profiles can be visualized. ArrayExpress is a rapidly growing database, currently it contains data from >50,000 hybridizations and >1,500,000 individual expression profiles. ArrayExpress supports community standards, including MIAME, MAGE-ML and more recently the proposal for a spreadsheet based data exchange format: MAGE-TAB. AVAILABILITY: www.ebi.ac.uk/arrayexpress.

Animals↗
PubMed2002

Gene expression profile induced by 17alpha-ethynyl estradiol, bisphenol A, and genistein in the developing female reproductive system of the rat.

Exposure to some compounds with estrogenic activity, during fetal development, has been shown to alter development of reproductive organs, leading to abnormal function and disease either after birth or during adulthood. In order to understand the molecular events associated with the estrogenicity of different chemicals and to determine whether common sets of gene expression changes can be predictive of estrogenic activity, we have used microarray technology to determine the transcriptional program influenced by exposure to this class of compounds during organogenesis and development. Changes in patterns of gene expression were determined in the developing uterus and ovaries of Sprague-Dawley rats on GD 20, exposed to graded dosages (sc) of 17alpha-ethynyl estradiol (EE), genistein, or bisphenol A (BPA) from GD 11 to GD 20. Dose levels were roughly equipotent in estrogenic activity. We compared the transcript profiles between treatment groups and controls, using oligonucleotide arrays to determine the expression level of approximately 7000 rat genes and over 1000 expressed squence tags (ESTs). At the highest tested doses of EE, BPA, or genistein, we determined that less than 2% of the mRNA detected by the array showed a 2-fold or greater change in their expression level (increase or decrease). A dose-dependent analysis of the transcript profile revealed a common set of genes whose expression is significantly and reproducibly modified in the same way by each of the 3 chemicals tested. Additionally, each compound induces changes in the expression of other transcripts that are not in common with the others, which indicated not all compounds with estrogenic activity act alike. The results of this study demonstrate that transplacental exposure to chemicals with estrogenic activity changes the gene expression profile of estrogen-sensitive tissues, and that the analysis of the transcript profile of these tissues could be a valuable approach to determining the estrogenicity of different compounds.

Animals↗
PubMed2003

Gestational exposure to persistent organic pollutants: maternal liver residues, pregnancy outcome, and effects on hepatic gene expression profiles in the dam and fetus.

Dietary exposure of Inuit people to a mixture of pesticides and polychlorinated biphenyls, or persistent organic pollutants (POPs), during pregnancy is a public health concern. We examined the consequences of administering the mixture of 28 POPs found in the Inuit diet (at doses representing 10-1000 times dietary levels) by gavage to pregnant Sprague-Dawley rats either during gestation days 0-19 or 8-19. The levels of individual components of the POPs mixture in the maternal liver were measured by high-resolution mass spectrometry. On gestation day 20, dams were sacrificed and pregnancy outcome determined. RNA isolated from maternal and fetal livers was 32P-labeled for gene expression profiling. The concentrations of individual POPs were increased in maternal livers of dams gavaged with the 1000x POPs mixture by 10- to 500-fold. While exposure to POPs had no significant effects on pregnancy outcome, dramatic changes were observed in the gene expression profiles of both the maternal and fetal livers. The gene expression profiles of maternal and fetal female and male liver were distinct with respect to the numbers of transcripts detected, the genes expressed exclusively in control or POPs-exposed livers, and those for which expression was up- or downregulated. While different genes were affected in each group, the overall consequence of POPs exposure on hepatic gene expression profiles was to decrease both the numbers of genes expressed and the relative intensity of expression. Thus, in utero exposure to POPs alters hepatic gene expression in the dam and the fetus; these changes may have functional implications.

Animals↗
PubMed2006

Within-tree transcriptome profiling in wood-forming tissues of a fast-growing Eucalyptus tree.

Despite the availability of high-throughput transcript profiling technology, little is known about tissue-specific gene expression patterns in the wood-forming tissues of Eucalyptus plantation tree species. We used cDNA-amplified fragment length polymorphism (AFLP) analysis in combination with infrared fragment detection and semi-automated band quantification to profile gene expression in a 6-year-old, fast- growing Eucalyptus tree. The expression profiles of 6385 transcript-derived fragments (TDFs) were analyzed across four major woody tissues (mature xylem, immature xylem, phloem and cork) collected from two stem positions, to provide a global view of transcript abundance and variability in the Eucalyptus stem. About 21% of the TDFs were differentially expressed and could be grouped into clusters representing co- expressed genes. A total of 71 TDFs representing different gene clusters were isolated and characterized. These included genes implicated in cell fate, signal transduction and cell wall biosynthesis, processes closely associated with xylogenesis. Analysis of the expression levels of selected TDFs by quantitative RT-PCR corroborated the TDF quantification and confirmed that cDNA-AFLP analysis is a highly efficient and accurate tool for transcript profiling and gene discovery in wood-forming tissues of tree species.

Cluster Analysis↗
PubMed2003

Monitoring human radiation exposure by gene expression profiling: possibilities and pitfalls.

Advances in high throughput analysis of mRNA expression have made it possible to establish gene expression profiles for different cells, tissues, diseases and exposure states. For instance, recent studies have demonstrated the utility of such an approach to classify sub-types of cancers with more detail than was previously possible. In addition, gene expression studies of ionizing radiation exposure both in vitro and in vivo are affording insight into the molecular mechanisms of mammalian radiation response. We have demonstrated that radiation expression profiles are a good predictor of p53 function in cell lines, and such profiles also indicate a major role for p53-regulated genes in the in vivo radiation response. Gene expression can be a sensitive indicator of radiation response as we have shown linear dose-responses for induction of several genes down to doses as low as 2 cGy. As profiles are established from radiation studies, it is hoped that they may be useful for identifying individuals with specific exposures or predisposition to negative outcome of exposure. Although this technology holds great promise, some obstacles remain to be overcome before it can be successfully applied to population studies.

Cyclin-Dependent Kinase Inhibitor p21↗
PubMed2002

Cytokine expression profiling in human leukocytes after exposure to hypertonic and isotonic fluids.

BACKGROUND: Resuscitation from hemorrhagic shock causes profound immunologic changes. The tonicity of fluids used for resuscitation clearly influences the immune response. Our study was designed to determine whether isotonic and hypertonic fluids exert their differential effects on immune response by altering the cytokine gene profile of human leukocytes. The cDNA array method was used to profile transcriptional responses after exposure to hypertonic and isotonic fluids. METHODS: Blood from seven healthy volunteers was incubated for 30 minutes with isotonic (10% dextran-40 and lactated Ringer's [LR] solution) and hypertonic (7.5% hypertonic saline and hypertonic dextran [HTD]) fluids. The volumes of isotonic fluids used were equal to the volume of blood, whereas the volumes of hypertonic fluids were adjusted to keep the salt load identical to the LR group. The cDNA array technique was used to measure the gene expression of 23 common cytokines. RESULTS: Increased gene transcription of proinflammatory cytokines (interleukin [IL]-1alpha, IL-6, IL-10, and tumor necrosis factor-alpha) as well as others (IL-5, IL-7, and IL-16) was found after incubation with resuscitation fluids. Variances were noted depending on the type of fluid: HTD and LR solution did not induce expression of IL-5, and HTD also did not induce IL-1beta expression. Genes encoding IL-1alpha, IL-6, IL-9, and tumor necrosis factor-alpha had low level baseline expression in leukocytes isolated from unstimulated blood, and their expression increased markedly after exposure to resuscitation fluids. The inducible transcripts included IL-1beta, IL-7, IL-10, and IL-16. However, there was no difference in cytokine expression profile between isotonic and hypertonic fluids. CONCLUSION: Exposure of human leukocytes to resuscitation fluids causes an increase in cytokine gene expressions compared with undiluted blood. This expression profile is largely independent of the type of fluid used.

Adult↗
PubMed1999

An international comparison of the reliability and responsiveness of the Duke Health Profile for measuring health-related quality of life of patients treated with alprostadil for erectile dysfunction.

OBJECTIVES: It is important that health measures are both reliable and responsive to clinical change. The aim of this study was to assess the reliability and responsiveness of the physical, mental, and social health scales of the Duke Health Profile (DUKE). METHODS: Impotent males self-administered the Duke Health Profile before and during treatment with alprostadil for erectile dysfunction during a 19-month period. Subjects were 490 patients in the United States and 583 patients in 12 other countries. Each of the three basic Duke Health Profile scales has only five items, and each is heterogeneous because each measures more than one health concept. RESULTS: Cronbach's alpha reliability estimates were: physical health, 0.68 for United States and 0.64 for other countries; mental health, 0.62 and 0.52, respectively; and social health, 0.53 and 0.47, respectively. Alprostadil was expected to improve mental health primarily, and results of the study were consistent with this hypothesis. For example, at approximately 14 months from therapy onset, mental health improved for patients both in the United States (standardized response mean, SRM, = 0.17) and other countries (mean SRM = 0.30), whereas physical health worsened in the United States and was unchanged in other countries, and social health was unchanged in the United States and improved in other countries. Maximum responsiveness was shown for mental health in the other countries, where the mean standardized response means at four follow-ups during a 19-month period were 0.11, 0.21, 0.30, and 0.36. CONCLUSIONS: This study provides support for the responsiveness of the Duke Health Profile mental health scale.

Adult↗
PubMed2002

Molecular diagnosis of lymphoid malignancies by gene expression profiling.

Gene expression profiling using DNA microarrays has great potential to improve the understanding, diagnosis, and management of lymphomas, leukemias, and other malignancies. Gene expression profiling studies of diffuse large B-cell lymphoma (DLBCL) have shown that this diagnostic category encompasses at least two molecularly distinct diseases, differing in differentiation stage (cell of origin), oncogenic mechanisms, and clinical outcome. Gene expression profiling revealed that the antiapoptotic NF-kappaB pathway is constitutively active in one DLBCL subgroup, termed activated B cell-like DLBCL, and subsequent studies validated NF-kappaB as a therapeutic target in this type of lymphoma. DNA microarray studies of chronic lymphocytic leukemia (CLL) have led to a gene expression-based predictor that identifies two subtypes of CLL that differ with respect to clinical course and presence of immunoglobulin gene mutations in the CLL cells. These findings underscore the value of gene expression profiling in defining subtypes within the lymphoid malignancies that are molecularly and clinically distinct and argue that this genomic technology should become an integral part of prospective clinical trials.

DNA, Neoplasm↗
PubMed2005

Expression profiling of colon cancer cell lines and colon biopsies: towards a screening system for potential cancer-preventive compounds.

Interest in mechanisms of colon cancer prevention by food compounds is strong and research in this area is often performed with cultured colon cancer cells. In order to assess utility for screening of potential cancer-preventive (food) compounds, expression profiles of 14 human cell lines derived from colonic tissue were measured using cDNA microarrays with 4000 genes and compared with expression profiles in biopsies of human colon tumours and normal tissue. Differences and similarities in the gene expression profiles of the cell lines were analysed by clustering and principal component analysis (PCA). Cytoskeleton genes and immune response genes are two functional classes of genes that contributed to the differences between the cell lines. A subset of 72 colon cancer-specific genes was identified by comparing expression profiles in human colon biopsies of tumour tissue and normal tissue. A separation of the cell lines based on the tumour stage of the original adenocarcinoma was observed after PCA of expression data of the subset of colon cancer-specific genes in the cell lines. The results of this study may be useful in the ongoing research into mechanisms of cancer prevention by dietary components.

Adenocarcinoma↗
PubMed2006

Molecular profiling of breast cancer.

PURPOSE OF REVIEW: This review is a comprehensive survey of molecular-profiling literature published since 2004. RECENT FINDINGS: More microarray-based gene-expression profiles that are prognostic for breast cancer have been published, strengthening the possibility that the microarray gene-expression profile may indeed provide clinically meaningful results. Requirement for snap-frozen tissue, however, will continue to be a limiting factor in clinical application. Results from a multicenter validation study were less spectacular than the original findings. A prognostic model based on classical markers performed well in a comparative study. Further clinical validation, with a large sample size, is needed. A prognostic gene-expression profile of 21 genes, which can be assayed using routinely processed formalin-fixed paraffin-embedded tumor tissue, has been introduced and this assay has also been shown to correlate with degree of benefit from chemotherapy. Two large clinical trials to validate gene-expression-based assays are to be launched in North America (TAILORx) and the European Union (MINDACCT). The usefulness of these genomic tools is still being debated, because clinicopathologic factors also are still important. SUMMARY: Gene-expression-based prognostic tests are now available as commercial reference laboratory tests. Their successful implementation will depend on the seamless integration with existing clinicopathologic markers.

Antineoplastic Agents↗
PubMed2003

Genetic profiling of Gleason grade 4/5 prostate cancer: which is the best prostatic control tissue?

PURPOSE: We examined the variation in gene expression profiles of prostate cancer caused by zone specific genes. MATERIALS AND METHODS: Ten normal central zone, 10 transition zone (benign prostatic hyperplasia) and 6 normal peripheral zone tissues from radical retropubic prostatectomies were compared to each other and to 12 peripheral zone Gleason grade 4/5 cancers. Test chips and HuGeneFL6800 (Affymetrix, Inc., Santa Clara, California) chips were used to assay the transcribed genes. Data were obtained with the Microarray Suite Version 4.0.1 (Affymetrix, Inc.) and analyzed statistically. RESULTS: Substantially different gene expression profiles were found depending upon which of the 3 zonal tissues were used as a control. All 3 profiles were compared for efficiency (ability to locate genes) and for robustness (the magnitude of difference between the control and the Gleason grade 4/5 tissue). Microscopically normal appearing peripheral zone tissue at the gene level shows many characteristics of Gleason grade 4/5 cancer. CONCLUSIONS: Gene expression profiles of prostate cancer are affected by the zonal location of the control tissue and the cancer.

Down-Regulation↗
PubMed2006

Recent developments in molecular profiling of bladder cancer.

PURPOSE OF REVIEW: Profiling bladder tumors using high-density microarrays has recently become possible. We review recent reports on the use of profiling for the prediction of various clinical courses in bladder cancer. We also stress the methods and materials needed to translate such molecular profiles into clinically useful tests. RECENT FINDINGS: Using gene expression microarrays, it has been possible to identify signatures that predict various properties of bladder cancer such as stage, grade, progression, and likelihood of metastases. Using arrays for genomic instability, similar properties have been examined, but the effectiveness seems to be less than that of gene expression. Some of genes identified also work as predictors using immunohistochemistry. SUMMARY: The signatures or molecular profiles for some of these arrays are now being tested in multicenter studies with the purpose of introducing these into the clinic, for planning of follow-up and treatment selection.

Biomarkers, Tumor↗
PubMed2001

An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles.

We have developed a statistical regression modeling approach to discover genes that are differentially expressed between two predefined sample groups in DNA microarray experiments. Our model is based on well-defined assumptions, uses rigorous and well-characterized statistical measures, and accounts for the heterogeneity and genomic complexity of the data. In contrast to cluster analysis, which attempts to define groups of genes and/or samples that share common overall expression profiles, our modeling approach uses known sample group membership to focus on expression profiles of individual genes in a sensitive and robust manner. Further, this approach can be used to test statistical hypotheses about gene expression. To demonstrate this methodology, we compared the expression profiles of 11 acute myeloid leukemia (AML) and 27 acute lymphoblastic leukemia (ALL) samples from a previous study (Golub et al. 1999) and found 141 genes differentially expressed between AML and ALL with a 1% significance at the genomic level. Using this modeling approach to compare different sample groups within the AML samples, we identified a group of genes whose expression profiles correlated with that of thrombopoietin and found that genes whose expression associated with AML treatment outcome lie in recurrent chromosomal locations. Our results are compared with those obtained using t-tests or Wilcoxon rank sum statistics.

Acute Disease↗
PubMed2004

A versatile assay for high-throughput gene expression profiling on universal array matrices.

We report a flexible, sensitive, and quantitative gene-expression profiling system for assaying more than 400 genes, with three probes per gene, for 96 samples in parallel. The cDNA-mediated annealing, selection, extension and ligation (DASL) assay targets specific transcripts, using oligonucleotides containing unique address sequences that can hybridize to universal arrays. Cell-specific gene expression profiles were obtained using this assay for hormone-treated cell lines and laser-capture microdissected cancer tissues. Gene expression profiles derived from this assay were consistent with those determined by qRT-PCR. The DASL assay has been automated for use with a bead-based 96-array matrix system. The combined high-throughput assay and readout system is accurate and efficient, and can cost-effectively profile the expression of hundreds of genes in thousands of samples.

Androgens↗
PubMed2002

Transcript profiling of functionally related groups of genes during conditional differentiation of a mammalian cochlear hair cell line.

We have used Affymetrix high-density gene arrays to generate a temporal profile of gene expression during differentiation of UB/OC-1, a conditionally immortal cell line derived from the mouse cochlea. Gene expression was assessed daily for 14 days under differentiating conditions. The experiment was replicated in two separate populations of cells. Profiles for selected genes were correlated with those obtained by RT-PCR, TaqMan analysis, immunoblotting, and immunofluorescence. The results suggest that UB/OC-1 is derived from a population of nonsensory epithelial cells in the greater epithelial ridge that have the potential to differentiate into a hair-cell-like phenotype, without the intervention of Math1. Elements of the Notch signaling cascade were identified, including the receptor Notch3, with a transient up-regulation that suggests a role in hair cell differentiation. Several genes showed a profile similar to Notch3, including the transcriptional co-repressor Groucho1. UB/OC-1 also expressed Me1, a putative partner of Math1 that may confer competence to differentiate into hair cells. Cluster analysis revealed expression profiles for neural guidance genes associated with Gata3. The temporal dimension of this analysis provides a powerful tool to study genetic mechanisms that underlie the conversion of nonsensory epithelial cells into hair cells.

Animals↗
PubMed2004

Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse.

To examine the process by which duplicated genes diverge in function, we studied how the gene expression profiles of orthologous gene sets in human and mouse are affected by the presence of additional recent species-specific paralogs. Gene expression profiles were compared across 16 homologous tissues in human and mouse using microarray data from the Gene Expression Atlas for 1575 sets of orthologs including 250 with species-specific paralogs. We find that orthologs that have undergone recent duplication are less likely to have strongly correlated expression profiles than those that remain in a one-to-one relationship between human and mouse. There is a general trend for paralogous genes to become more specialized in their expression patterns, with decreased breadth and increased specificity of expression as gene family size increases. Despite this trend, detailed examination of some particular gene families where species-specific duplications have occurred indicated several examples of apparent neofunctionalization of duplicated genes, but only one case of subfunctionalization. Often, the expression of both copies of a duplicated gene appears to have changed relative to the ancestral state. Our results suggest that gene expression profiles are surprisingly labile and that expression in a particular tissue may be gained or lost repeatedly during the evolution of even small gene families. We conclude that gene duplication is a major driving force behind the emergence of divergent gene expression patterns.

Animals↗
PubMed2006

Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon.

Farmed salmon strains have been selected to improve growth rates as well as other traits of commercial interest but the 2 million farmed salmon escaping annually may enhance the risk of extinction of wild populations through genetic and ecological interactions. Here, we compare the transcription profiles of 3557 genes in the progeny of farmed and wild Atlantic salmon from Norway and Canada grown in controlled conditions, and demonstrate that five to seven generations of artificial selection led to heritable changes in gene transcription profiles, the average magnitude of the differences being 25% and 18% for at least 1.4% and 1.7% of the expressed genes in juvenile salmon from Norway and Canada, respectively. Moreover, genes showing significant transcription profile differences in both farmed strains (16%) all exhibited parallel changes. These findings, along with the identification of several genes whose expression profiles were modified through artificial selection, provide new insights into the molecular basis of parallel evolution, and suggest how gene flow from farmed escapees may affect the genetic integrity of wild populations.

Analysis of Variance↗
PubMed2004

Gene expression profiles associated with survival of individual rat dentate cells after endogenous corticosteroid deprivation.

Removal of circulating corticosterone by adrenalectomy (ADX) leads to apoptosis after 3 days in a small population of rat dentate granule neurons, whereas most surrounding cells remain viable. Interestingly, a specific expression profile is triggered in surviving granule cells that may enhance their survival. Hippocampal slices prepared 1, 2 or 3 days after ADX or sham operation were stained ex vivo with Hoechst 33258, which serves to identify apoptotic neurons. After electrophysiological analysis, multiple gene expression in surviving individual granule cells was assessed by linear antisense RNA amplification and hybridization to slot blots containing various neuronal cDNAs. Hierarchical clustering and principal component analysis was performed on two physiological variables and 14 mRNA ratios from ADX cells from every time point. Our results indicate that surviving 3-day ADX granule cells display lower membrane capacitance, lower relative N-methyl-d-aspartate (NMDA) R1 mRNA expression and higher relative mineralocorticoid receptor (MR), alpha1A voltage-gated Ca-channel, Bcl-2 and NMDA R2C mRNA expression. Some 1- and 2-day ADX cells cluster with these 3-day survivors; therefore, one or more components of their mRNA expression profile may represent predictive markers for apoptosis resistance. The functional relevance of two candidate genes was tested by in vivo local over-expression in the same model system; of these, Bcl-2 conferred partial protection when induced shortly before ADX. Therefore, removal of corticosteroids triggers a specific gene expression profile in surviving dentate granule cells; key components of this profile may be associated with their survival.

Adrenalectomy↗