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A digital atlas to characterize the mouse brain transcriptome.

Massive amounts of data are being generated in an effort to represent for the brain the expression of all genes at cellular resolution. Critical to exploiting this effort is the ability to place these data into a common frame of reference. Here we have developed a computational method for annotating gene expression patterns in the context of a digital atlas to facilitate custom user queries and comparisons of this type of data. This procedure has been applied to 200 genes in the postnatal mouse brain. As an illustration of utility, we identify candidate genes that may be related to Parkinson disease by using the expression of a dopamine transporter in the substantia nigra as a search query pattern. In addition, we discover that transcription factor Rorb is down-regulated in the barrelless mutant relative to control mice by quantitative comparison of expression patterns in layer IV somatosensory cortex. The semi-automated annotation method developed here is applicable to a broad spectrum of complex tissues and data modalities.

Anatomy, Artistic↗

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.

BACKGROUND: The differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD), Crohn disease (CD), and ulcerative colitis (UC) are only partially understood. cDNA microarrays can be used to decipher gene regulation events at a genome-wide level and to identify novel unknown genes that might be involved in perpetuating inflammatory disease progression. METHODS AND FINDINGS: High-density cDNA microarrays representing 33,792 UniGene clusters were prepared. Biopsies were taken from the sigmoid colon of normal controls (n = 11), CD patients (n = 10) and UC patients (n = 10). 33P-radiolabeled cDNA from purified poly(A)+ RNA extracted from biopsies (unpooled) was hybridized to the arrays. We identified 500 and 272 transcripts differentially regulated in CD and UC, respectively. Interesting hits were independently verified by real-time PCR in a second sample of 100 individuals, and immunohistochemistry was used for exemplary localization. The main findings point to novel molecules important in abnormal immune regulation and the highly disturbed cell biology of colonic epithelial cells in IBD pathogenesis, e.g., CYLD (cylindromatosis, turban tumor syndrome) and CDH11 (cadherin 11, type 2). By the nature of the array setup, many of the genes identified were to our knowledge previously uncharacterized, and prediction of the putative function of a subsection of these genes indicate that some could be involved in early events in disease pathophysiology. CONCLUSION: A comprehensive set of candidate genes not previously associated with IBD was revealed, which underlines the polygenic and complex nature of the disease. It points out substantial differences in pathophysiology between CD and UC. The multiple unknown genes identified may stimulate new research in the fields of barrier mechanisms and cell signalling in the context of IBD, and ultimately new therapeutic approaches.

Adolescent↗

Open architecture expression profiling of plant transcriptomes and gene discovery using GeneCalling technology.

The recent rapid developments in genomics tools, technologies, and bioinformatics have revolutionized gene expression analysis. It is now routine to measure gene expression modulation at the genomic level. GeneCalling technology is an open architecture system capable of assaying more than 95% of genes expressed in a tissue. Unlike the closed systems, GeneCalling is not dependent upon an existing sequence or clone database. GeneCalling uses as low as 50 pg of the cDNA from samples and identifies cDNA fragments that are differentially modulated within a set of samples. With the use of 96 pairs of restriction enzymes, more than 30,000 cDNA fragments are routinely assayed to identify those that are differentially modulated. Specific processes, such as SeqCalling, Trace Poisoning, and GeneCall Poisoning, are set up to not only confirm the known genes, but also to clone and analyze unknown and novel genes that have an interesting expression profile. GeneCalling has been successfully applied to expression profiling of several plant and fungal species, and resulted in identification and characterization of genes that are useful in commercial applications towards improving agriculturally important traits in plants.

DNA, Complementary↗

Noncontact laser microdissection and pressure catapulting: sample preparation for genomic, transcriptomic, and proteomic analysis.

The understanding of the molecular mechanisms of cellular metabolism and proliferation necessitates accurate identification, isolation, and finally characterization of a specific cell or a population of cells and subsequently their subsets of biomolecules. For the simultaneous analysis of thousands of molecular parameters within a single experiment, as realized by DNA, RNA, and protein microarray technologies, a defined number of homogeneous cells derived from a distinct morphological origin is required. Sample preparation is therefore a very crucial step for high-resolution downstream applications. Laser microdissection and laser pressure catapulting (LMPC) enables such pure and homogeneous sample preparation, resulting in an eminent increase in the specificity of molecular analyses. For microdissection, the force of focused laser light is used to excise selected cells or large tissue areas from object slides or from living cell culture down to a resolution of individual single cells and subcellular components like organelles or chromosomes, respectively. After microdissection this sample is directly catapulted into an appropriate collection device. As the entire process works without any mechanical contact, it enables pure sample retrieval from morphologically defined origin without cross contamination. Wherever homogenous samples are required for subsequent analysis of, e.g., cell areas, single cells, or chromosomes, the PALM MicroBeam system is an indispensable tool. The integration of image analysis platforms fully automates screening, identification, and finally subsequent high-throughput sample handling. These samples can be directly linked into versatile downstream applications, such as single-cell mRNA-extraction, different PCR methods, microarray techniques, and many others. Acceleration in sample generation vastly increases the throughput in molecular laboratories and leads to an increasing knowledge about differentially regulated mRNAs and expressed proteins, providing new insights into cellular mechanisms and therefore enabling the development of systems for tumor biomarker identification, early detection of disease-causing alterations, therapeutic targeting and/or patient-tailored therapy.

Animals↗

Ovarian transcriptomes as a tool for a global approach of genes modulated by gonadotropic hormones in human ovarian granulosa cells.

Follicle-stimulating hormone (FSH) is a key stimulant for the development of the ovarian follicle, while luteinizing hormone (LH) plays a major role in triggering ovulation and luteinization. Both FSH and LH are glycoprotein hormones that share the same alpha subunit but bind to specific seven transmembrane-domain G coupled receptors located on the cell membrane of the granulosa cells, which comprise the main somatic population of the ovarian follicle. These hormone-receptor complexes may trigger different signaling cascades, but the entire repertoire of genes modulated by these hormones is far from being understood, in particular on the transcriptional level. The development of DNA micro-arrays technique, using the entire genome profile of some mammalian species, allows a global approach and screening of multiple signal transduction pathways. This method opened new insights into the cellular and molecular events that control ovulation and desensitization of the corpus luteum to hyperstimulation by gonadotropic hormones. In addition, this technique permitted the discovery of novel members of the EGF family, such as epiregulin and amphiregulin, that were found to be expressed in the gonadotropin-stimulated cells and were discovered to play a crucial role in the mechanism of ovulation. However, because of the pitfalls in interpreting the data other approaches, for example, Northern blots and RT-PCR must be conducted in parallel to verify the validity of the data.

Corpus Luteum↗

Graves' disease and Hashimoto's thyroiditis in monozygotic twins: case study as well as transcriptomic and immunohistological analysis of thyroid tissues.

OBJECTIVE: To report on the rare simultaneous occurrence of Graves' disease (GD) and Hashimoto's thyroiditis (HT) in monozygotic twins. DESIGN: We compared the pattern of thyroid tissue-derived cDNAs to gain insight into previous and ongoing immune destruction and reconstruction processes using microarrays. The results were confirmed by immunohistology and real-time PCR. RESULTS: Destruction of thyroid tissue in HT reduced levels of thyrocyte-related cDNAs and cDNAs encoding extracellular matrix components, but increased levels of proteases involved in extracellular matrix degradation compared with GD. Lymphocytic infiltrates forming ectopic follicles replaced the thyroid tissue almost completely in HT. Thus, lymphocyte-related cDNA levels were higher in HT than in GD. The same was true for many chemokines and their receptors, which not only enable migration towards the thyroid but also maintain the lymphocytic infiltrate. HT also showed increased levels of cDNAs encoding molecules related to apoptosis than did GD. Surprisingly, the Th1- and Th2-specific cytokine profiles suggested for HT and GD respectively could not be confirmed. cDNAs encoding factors and receptors involved in angiogenesis were increased in GD compared with HT. CONCLUSIONS: Comparison of gene expression reflects the cellular differences between the two types of autoimmune thyroid disease in twins with identical genetic and similar environmental background.

Adolescent↗

Transcriptome analysis and physical mapping of barley genes in wheat-barley chromosome addition lines.

Wheat-barley chromosome addition lines are useful genetic resources for a variety of studies. In this study, transcript accumulation patterns in Betzes barley, Chinese Spring wheat, and Chinese Spring-Betzes chromosome addition lines were examined with the Barley1 Affymetrix GeneChip probe array. Of the 4014 transcripts detected in Betzes but not in Chinese Spring, 365, 271, 265, 323, 194, and 369 were detected in wheat-barley disomic chromosome addition lines 2(2H), 3(3H), 4(4H), 7(5H), 6(6H), and 1(7H), respectively. Thus, 1787 barley transcripts were detected in a wheat genetic background and, by virtue of the addition line in which they were detected, were physically mapped to barley chromosomes. We validated and extended our approach to physically map barley genes to the long and short arms of chromosome 6(6H). Our physical map data exhibited a high level of synteny with homologous sequences on the wheat and/or rice syntenous chromosomes, indicating that our barley physical maps are robust. Our results show that barley transcript detection in wheat-barley chromosome addition lines is an efficient approach for large-scale physical mapping of genes.

Chromosomes, Plant↗

Segregating variation in the transcriptome: cis regulation and additivity of effects.

Properties of genes underlying variation in complex traits are largely unknown, especially for variation that segregates within populations. Here, we evaluate allelic effects, cis and trans regulation, and dominance patterns of transcripts that are genetically variable in a natural population of Drosophila melanogaster. Our results indicate that genetic variation due to the third chromosome causes mainly additive and nearly additive effects on gene expression, that cis and trans effects on gene expression are numerically about equal, and that cis effects account for more genetic variation than do trans effects. We also evaluated patterns of variation in different functional categories and determined that genes involved in metabolic processes are overrepresented among variable transcripts, but those involved in development, transcription regulation, and signal transduction are underrepresented. However, transcripts for proteins known to be involved in protein-protein interactions are proportionally represented among variable transcripts.

Animals↗

In silico study of transcriptome genetic variation in outbred populations.

Dissecting the genetic architecture of regulatory elements on a genome-wide basis is now technically feasible. The potential medical and genetical implications of this kind of experiment being very large, it is paramount to assess the reliability and repeatability of the results. This is especially relevant in outbred populations, such as humans, where the genetic architecture is necessarily more complex than in crosses between inbred lines. Here we simulated a chromosome-wide SNP association study using real human microarray data. Our model predicted, as observed, a highly significant clustering of quantitative trait loci (QTL) for gene expression. Importantly, the estimates of QTL positions were often unstable, and a decrease in the number of individuals of 16% resulted in a loss of power of approximately 30% and a large shift in the position estimate in approximately 30-40% of the remaining significant QTL. We also found that the analysis of two repeated measures of the same mRNA can also result in two QTL that are located far apart. The intrinsic difficulties of analyzing outbred populations should not be underestimated. We anticipate that (many) conflicting results may be collected in the future if whole-genome association studies for mRNA levels are carried out in outbred populations.

Alleles↗

The biological effects of high-pressure gas on the yeast transcriptome.

The aim of the present study was to examine the feasibility of DNA microarray technology in an attempt to construct an evaluation system for determining gas toxicity using high-pressure conditions, as it is well known that pressure increases the concentration of a gas. As a first step, we used yeast (Saccharomyces cerevisiae) as the indicator organism and analyzed the mRNA expression profiles after exposure of yeast cells to nitrogen gas. Nitrogen gas was selected as a negative control since this gas has low toxicity. Yeast DNA microarray analysis revealed induction of genes whose products were localized to the membranes, and of genes that are involved in or contribute to energy production. Furthermore, we found that nitrogen gas significantly affected the transport system in the cells. Interestingly, nitrogen gas also resulted in induction of cold-shock responsive genes. These results suggest the possibility of applying yeast DNA microarray to gas bioassays up to 40 MPa. We therefore think that "bioassays" are ideal for use in environmental control and protection studies.

Feasibility Studies↗

Effects of dihydrotestosterone on skeletal muscle transcriptome in mice measured by serial analysis of gene expression.

In order to characterize the action of androgen in skeletal muscle, we have investigated the effects of castration (GDX) and dihydrotestosterone (DHT) on global gene expression in mice. The serial analysis of gene expression method was performed in the muscle of male mice in six experimental groups: intact, GDX and GDX+DHT injection 1, 3, 6 or 24 h before they were killed. A total of 780 822 sequenced tags quantified the expression level of 80 142 tag species. Thirteen and seventy-nine transcripts were differentially expressed in GDX and DHT respectively (P < 0.05), including eight partially characterized and 21 potential novel transcripts. The induced transcripts within 3 h after DHT injection were involved in the following functions: transcription, protein synthesis, modification and degradation, muscle contraction and relaxation, cell signaling, polyamine biosynthesis, cell cycle progression and arrest, angiogenesis, energy metabolism and immunity. However, the inductions of transcripts related to cell cycle arrest and angiogenesis were no longer significant 24 h after DHT injection. The current study might suggest that DHT promotes protein synthesis, cell signaling, cell proliferation and ATP production, as well as muscle contraction and relaxation at the transcriptional level in skeletal muscle in vivo.

Animals↗

Evaluation of methods for duration of preservation of RNA quality in rat liver used for transcriptome analysis.

In The Toxicogenomics Project, about 150 chemicals are administered to rats, and gene expression in the liver analyzed by Affymetrix GeneChip and stored in the database. As the quality of RNA greatly influences the accuracy of gene expression data, conditions of the storage of the sample are very important. Recently, an RNA stabilization solution, RNAlater, has become commercially available. In this study, the new storage method was compared with the traditional storage method (stored in freezer or liquid nitrogen) under various conditions by looking at the degradation of RNA assessed by its total yield, OD260/280 ratio, 28S/18S ratio, and quantity of beta-actin. It was confirmed that RNAlater preserved the liver tissue sample by maintaining the quality of RNA for one year (in liquid N(2) or -80 degrees C), for 3 days (4 degrees C), or for 2 hr (room temperature) without degradation of RNA. Quality of RNA samples dissolved in buffer RLT and stored at -20 degrees C tended to decrease, but samples stored at -80 degrees C were almost equivalent to those stored in liquid nitrogen. In conclusion, we recommend the following procedure for preservation of liver tissue for extraction of RNA: 1) tissues removed should be put into chilled RNAlater as soon as possible; 2) samples in RNAlater must be stored overnight or longer at 4 degrees C and can be left for as long as 2 weeks without freezing; 3) samples in RNAlater can be stored for at least one year under less than -20 degrees C and 4) samples dissolved in buffer RLT can be preserved at least for one year under -80 degrees C.

Actins↗

The transcriptome in blood: challenges and solutions for robust expression profiling.

Peripheral blood may be the most feasible tissue source in clinical assessment of differences in gene expression between diseases and drug treatments due to accessibility. Yet, gene expression profiling from blood remains a challenge. Blood is a complicated biological system consisting of a variety of cell types at different stages of development. In addition, blood is also one of the most variable tissue types for gene expression analysis. The success of a blood microarray study depends on the choice of cell isolation method and preparation technique. In this review, we give a brief overview of the current status of using blood as a source for expression profiling and discuss potential applications of this method in the practices of clinical research.

Animals↗