Gene expression studies using microarrays

Gene Expression Measurement Module (GEMM) for space application: Design and validation

In order to facilitate studies on the impact of the space environment on biological systems, we have developed a prototype of GEMM (Gene Expression Measurement Module) - an automated, miniaturized, integrated fluidic system for in-situ measurements of gene expression in microbial samples. The GEMM instrument is capable of (1) lysing bacterial cell walls, (2) extracting and purifying RNA released from cells, (3) hybridizing the RNA to probes attached to a microarray and (4) providing electrochemical readout, all in a microfluidics cartridge. To function on small, uncrewed spacecraft, the conventional, laboratory protocols for both sample preparation and hybridization required significant modifications. Biological validation of the instrument was carried out on Synechococcus elongatus, a photosynthetic cyanobacterium known for its metabolic diversity and resilience to adverse conditions. It was demonstrated that GEMM yielded reliable, reproducible gene expression profiles. GEMM is the only high throughput instrument that can be deployed in near future on space platforms other than the ISS to advance biological research in space. It can also prove useful for numerous terrestrial applications in the field.

Identification of low Ca(2+) stress-induced embryo apoptosis response genes in Arachis hypogaea by SSH-associated library lift (SSHaLL)

Calcium is a universal signal in the regulation of wide aspects in biology, but few are known about the function of calcium in the control of early embryo development. Ca(2+) deficiency in soil induces early embryo abortion in peanut, producing empty pods, which is a general problem; however, the underlying mechanism remains unclear. In this study, embryo abortion was characterized to be caused by apoptosis marked with cell wall degradation. Using a method of SSH cDNA libraries associated with library lift (SSHaLL), 62 differentially expressed genes were isolated from young peanut embryos. These genes were classified to be stress responses, catabolic process, carbohydrate and lipid metabolism, embryo morphogenesis, regulation, etc. The cell retardation with cell wall degradation was caused by up-regulated cell wall hydrolases and down-regulated cellular synthases genes. HsfA4a, which was characterized to be important to embryo development, was significantly down-regulated under Ca(2+) -deficient conditions from 15 days after pegging (DAP) to 30 DAP. Two AhCYP707A4 genes, encoding abscisic acid (ABA) 8'-hydroxylases, key enzymes for ABA catabolism, were up-regulated by 21-fold under Ca(2+) -deficient conditions upstream of HsfA4a, reducing the ABA level in early embryos. Over-expression of AhCYP707A4 in Nicotiana benthamiana showed a phenotype of low ABA content with high numbers of aborted embryos, small pods and less seeds, which confirms that AhCYP707A4 is a key player in regulation of Ca(2+) deficiency-induced embryo abortion via ABA-mediated apoptosis. The results elucidated the mechanism of low Ca(2+) -induced embryo abortion and described the method for other fields of study.

Oligonucleotide Immobilization and Hybridization on Aldehyde-Functionalized Poly(2-hydroxyethyl methacrylate) Brushes

DNA biosensing requires high oligonucleotide binding capacity interface chemistries that can be tuned to maximize probe presentation as well as hybridization efficiency. This contribution investigates the feasibility of aldehyde-functionalized poly(2-hydroxyethyl methacrylate) (PHEMA) brush-based interfaces for oligonucleotide binding and hybridization. These polymer brushes, which allow covalent immobilization of oligonucleotides, are prepared by surface-initiated atom transfer radical polymerization (SI-ATRP) of HEMA followed by a postpolymerization oxidation step to generate side chain aldehyde groups. A series of polymer brushes covering a range of film thicknesses and grafting densities was investigated with regard to their oligonucleotide binding capacity as well as their ability to support oligonucleotide hybridization. Densely grafted brushes were found to have probe oligonucleotide binding capacities of up to ∼30 pmol/cm(2). Increasing the thickness of these densely grafted brush films, however, resulted in a decrease in the oligonucleotide binding capacity. Less densely grafted brushes possess binding capacities of ∼10 pmol/cm(2), which did not significantly depend on film thickness. The oligonucleotide hybridization efficiencies, however, were highest (93%) on those brushes that present the lowest surface concentration of the probe oligonucleotide. These results highlight the importance of optimizing the probe oligonucleotide surface concentration and binding interface chemistry. The versatility and tunability of the PHEMA-based brushes presented herein makes these films a very attractive platform for the immobilization and hybridization of oligonucleotides.

Dual isotope labeling: conjugation of 32P-oligonucleotides with 18F-aryltrifluoroborate via copper(I) catalyzed cycloaddition

A one-pot-two-step labeling of an oligonucleotide with an (18)F-ArBF3(-)(aryltrifluoroborate) radioprosthetic is reported herein. In order to characterize labeling in terms of radiochemistry, phosphorus-32 was also introduced to the 5'-terminus of the oligonucleotide via enzymatic phosphorylation. A pendant azide group was subsequently conjugated to the 5'-phosphate of the oligonucleotide. Copper(I) catalyzed [2+3] cycloaddition was undertaken to conjugate an alkyne-bearing(18)F-ArBF3(-) to the oligonucleotide. Following polyacrylamide gel electrophoresis, this doubly-labeled bioconjugate exhibited decay properties of both the phosphorus-32 and fluorine-18, that were confirmed by autoradiography at selected lengths of time, which in turn provided concrete evidence of successful conjugation. These results are corroborated by HPLC analysis of the labeled material. Taken together this work demonstrates viable use of (18)F-ArBF3(-) prosthetics for labeling oligonucleotides for use in PET imaging.

How can microarrays unlock asthma?

Asthma is a complex disease regulated by the interplay of a large number of underlying mechanisms which contribute to the overall pathology. Despite various breakthroughs identifying genes related to asthma, our understanding of the importance of the genetic background remains limited. Although current therapies for asthma are relatively effective, subpopulations of asthmatics do not respond to these regimens. By unlocking the role of these underlying mechanisms, a source of novel and more effective treatments may be identified. In the new age of high-throughput technologies, gene-expression microarrays provide a quick and effective method of identifying novel genes and pathways, which would be impossible to discover using an individual gene screening approach. In this review we follow the history of expression microarray technologies and describe their contributions to advancing our current knowledge and understanding of asthma pathology.

Multiplex cytokine analysis technologies

Multiplex technologies at both the mRNA and protein level have given researchers the ability to determine the co-ordinated cellular response to any given stimuli, in both biological and laboratory-derived fluids. This article examines some of the different mRNA and protein multiplex platforms available and how they may be used in assessing vaccine immunity.

cDNA microarray analysis of cyclosporin A (CsA)-treated human peripheral blood mononuclear cells reveal modulation of genes associated with apoptosis, cell-cycle regulation and DNA repair

Cyclosporin A (CsA) is a potent immunosuppressant that has been extensively used to attenuate patient immune response following organ transplantation. The molecular biological mechanism of CsA has been extensively investigated in human T cells, and it has been shown to involve modulation of the intracellular calcineurin pathway. However, it is plausible that this chemical immunosuppressant certainly up- or down-regulate many other biochemical pathways of immune cells. In the present study, we used the cDNA microarray method to characterize the gene expression profile of human peripheral blood mononuclear cells (PBMC) treated in vitro with CsA and controls. The CsA treated PBMC displayed statistically significant induction of genes involved in the control of cell-cycle regulation (TRRAP), apoptosis/DNA repair (PRKDC, MAEA, TIA1), DNA metabolism/response to DNA damage stimulus (PRKDC, FEN1), transcription (NR4A2, THRA) and cell proliferation (FEN1, BIN1), whose data have permitted identification of target genes involved in CsA immunosuppression.

Pharmacogenetics and pharmacogenomics: origin, status, and the hope for personalized medicine

Pharmacogenetics arose with studies of single genes, which had major effects on the action of particular drugs. It turned into pharmacogenomics through realization that the controls of most drug responses are multifactorial. Then, variable gene expression posed new problems, for example what do drugs do to genes, or how useful is any genetic pretesting of a person? A common disease may be caused by different groups of genes in different people, who therefore require different drugs for treatment. Personalized medicine is currently represented by a physician's attention to a patients age, sex, or ethnic background, that is groups showing smaller genetic variation than is typical for general humanity. Occasionally, there is also the use of single-gene pretesting of a patient before drug administration. Over time, improvements in multigenic testing promise to increase the role of personalized medicine. However, the many pharmacogenomic complexities, and particularly time-dependent changes of gene expression, will never allow personalized medicine to become an error-free entity.

Gross, histologic, and gene expression characteristics of osteoarthritic articular cartilage of the metacarpal condyle of horses

OBJECTIVE

To identify patterns and correlations of gross, histologic, and gene expression characteristics of articular cartilage from horses with osteoarthritis.

ANIMALS

10 clinically normal horses and 11 horses with osteoarthritis of the metacarpal condyles.

PROCEDURES

Metacarpophalangeal joints were opened and digitally photographed, and gross lesions were scored and quantified. Representative cartilage specimens were stained for histologic scoring. Total RNA from dorsal and palmar articular surfaces was processed on an equine gene expression microarray.

RESULTS

Histologic scores were greater in both regions of osteoarthritic joints, compared with corresponding regions in control joints. Cartilage from the palmar aspect of diseased joints had the highest histologic scores of osteoarthritic sites or of either region in control joints. A different set of genes for dorsal and palmar osteoarthritis was identified for high and low gene expression. Articular cartilage from the dorsal region had surface fraying and greater expression of genes coding for collagen matrix components and proteins with anti-apoptotic function, compared with control specimens. Articular cartilage from the palmar region had greater fraying, deep fissures, and less expression of genes coding for glycosaminoglycan matrix formation and proteins with anti-apoptotic function, compared with cartilage from disease-free joints and the dorsal aspect of affected joints.

CONCLUSIONS AND CLINICAL RELEVANCE

Metacarpal condyles of horses with naturally occurring osteoarthritis had an identifiable and regional gene expression signature with typical morphologic features.

Generation and performance of an equine-specific large-scale gene expression microarray

OBJECTIVE

To create high-quality sequence data for the generation of an equine gene expression microarray and evaluate array performance by use of lipopolysaccharide (LPS) exposure of synoviocytes.

SAMPLE POPULATION

Public nucleotide sequence database from Equus caballus and synoviocytes from clinically normal adult horses.

PROCEDURE

Computer procurement of equine gene sequences, probe design, and manufacture of an oligomicroarray were performed. Array performance was evaluated by use of patterns for equine synoviocytes in response to LPS.

RESULTS

Starting with 18,924 equine gene sequences, 3,098 equine 3' sequences were annotated and met the inclusion criteria for an expression microarray. An equine oligonucleotide expression microarray was created by use of 68,266 of the 25-oligomer probes to uniquely identify each gene. Most genes in the array (68%) were expressed in equine synoviocytes. Repeatability of the array was high (r, > 0.99), and LPS upregulated (> 5-fold change) 84 genes, many of which were inflammatory mediators, and downregulated (> 5-fold change) 14 genes. An initial pattern of gene expression for effects of LPS on synoviocytes consisted of 102 genes.

CONCLUSIONS AND CLINICAL RELEVANCE

Use of a computer algorithm to curate an equine sequence database generated high-quality annotated species-specific gene sequences and probe sets for a gene expression oligomicroarray, which was used to document changes in gene expression associated with LPS exposure of equine synoviocytes. The equine public database was expanded from 290 annotated genes to > 3,000 provisionally annotated genes. Similar curation and annotation of public databases could be used to create other species-specific microarrays.

Independent component analysis of microarray data in the study of endometrial cancer

Gene microarray technology is highly effective in screening for differential gene expression and has hence become a popular tool in the molecular investigation of cancer. When applied to tumours, molecular characteristics may be correlated with clinical features such as response to chemotherapy. Exploitation of the huge amount of data generated by microarrays is difficult, however, and constitutes a major challenge in the advancement of this methodology. Independent component analysis (ICA), a modern statistical method, allows us to better understand data in such complex and noisy measurement environments. The technique has the potential to significantly increase the quality of the resulting data and improve the biological validity of subsequent analysis. We performed microarray experiments on 31 postmenopausal endometrial biopsies, comprising 11 benign and 20 malignant samples. We compared ICA to the established methods of principal component analysis (PCA), Cyber-T, and SAM. We show that ICA generated patterns that clearly characterized the malignant samples studied, in contrast to PCA. Moreover, ICA improved the biological validity of the genes identified as differentially expressed in endometrial carcinoma, compared to those found by Cyber-T and SAM. In particular, several genes involved in lipid metabolism that are differentially expressed in endometrial carcinoma were only found using this method. This report highlights the potential of ICA in the analysis of microarray data.

Transcriptome analysis of endometrial cancer identifies peroxisome proliferator-activated receptors as potential therapeutic targets

Endometrial cancer is the most common gynecologic malignancy, frequently arising in association with obesity and diabetes mellitus. To identify gene pathways contributing to endometrial cancer development, we studied the transcriptome of 20 endometrial cancers and 11 benign endometrial tissues using cDNA microarrays. Among the transcript changes identified in endometrial cancer were up-regulation of the nuclear hormone receptors peroxisome proliferator-activated receptors (PPAR) α and γ, whereas retinoid X receptor β was down-regulated. To clarify the contribution of PPARα to endometrial carcinogenesis, we did experiments on cultured endometrial carcinoma cells expressing this transcript. Treatment with fenofibrate, an activating ligand for PPARα, significantly reduced proliferation and increased cell death, suggesting that altered expression of nuclear hormone receptors involved with fatty acid metabolism leads to deregulated cellular proliferation and apoptosis. These results support further investigation of members of the PPAR/retinoid X receptor pathway as novel therapeutic targets in endometrial cancer.

Genómica de la regulación del peso corporal: mecanismos moleculares que predisponen a la obesidad

Obesity has become a worldwide public health problem which affects millions of people. Substantial progress has been made in elucidating the pathogenesis of energy homeostasis over the past few years. The fact that obesity is under strong genetic control has been well established. Twin, adoption and family studies have shown that genetic factors play a significant role in the pathogenesis of obesity. Human monogenic obesity is rare in large populations. The most common form of obesity is considered to be a polygenic disorder. New treatments are currently required for this common metabolic disease and type 2 diabetes. The identification of physiological and biochemical factors that underlie the metabolic disturbances observed in obesity is a key step in developing better therapeutic outcomes. The discovery of new genes and pathways involved in the pathogenesis of such a disease is critical to this process. However, identification of genes that contribute to the risk of developing the disease represents a significant challenge since obesity is a complex disease with many genetic and environmental causes. A number of diverse approaches have been used to discover and validate potential new genes for obesity. To date, DNA-based approaches using candidate genes and genome-wide linkage analysis have not had a great success in identifying genomic regions or genes involved in the development of these diseases. Recent advances in the ability to evaluate linkage analysis data from large family pedigrees (using variance components-based linkage analysis) show great promise in robustly identifying genomic regions associated with the development of obesity. Studying rare mutations in humans and animal models has provided fundamental insight into a complex physiological process, and has complemented population-based studies that seek to reveal primary causes. Remarkable progress has been made in both fronts and the pace of advance is likely to accelerate as functional genomics and the human genome project expand and mature. Approaches based on Mendelian and quantitative genetics may well converge, and ultimately lead to more rational and selective therapies.

A spermatogenesis-related gene expression profile in human spermatozoa and its potential clinical applications

Spermatogenesis is an essential stage in the human reproductive process. In a previously study aiming to determine which genes might be involved in spermatogenesis, we compared the gene expression profiles of adult and fetal testes by hybridizing cDNA probes prepared from adult and fetal testes to membranes dotted with gene clones derived from a commercial human testis library. We identified 266 differentially expressed genes that showed higher expression levels in adult testes, indicating their potential roles in spermatogenesis. In the present study, we applied the same cDNA microarray technique to the analysis of gene expression in the spermatozoa of normal fertile men and found 149 genes that were expressed at higher levels in adult testis. A further study of five sperm motility-related genes selected from this profile by real-time PCR revealed that there was significant difference in the expression levels of two genes ( TPX-1, testis-specific protein 1 and LDHC, lactate dehydrogenase C, transcript variant 1) between normal ( n=29) and motility impaired ( n=24) semen samples, indicating that these genes are involved in sperm function. Our results demonstrated that spermatogenesis-related gene profiling could help to assess sperm quality in humans, and further study of these genes will help us to elucidate the mechanisms involved in spermatogenesis and diseases relating to human infertility.

Identification of calcium- and nitric oxide-regulated genes by differential analysis of library expression (DAzLE)

Using a method of expression profiling called differential analysis of cDNA library expression (DAzLE), we report the expression profile of late response genes in a model of activity-dependent neuronal survival and neurite outgrowth. Using DAzLE, we isolated differentially expressed genes from cultured rat embryonic cortical neurons after KCl (50 mM)-mediated membrane depolarization. We identified 469 activity-dependent regulated genes, of which 174 are genes of unknown function. The regulation of 63 genes was found to be nitric oxide (NO)-dependent. Identifiable genes fell into several major categories, including signal transduction pathways, neuronal development, DNA replication, gene transcription, protein metabolism, energy regulatory proteins, and antiapoptotic proteins. These genes may be important in activity-dependent neuron survival and development. Furthermore, these late response genes provide the tools to begin to investigate downstream events in activity-dependent neuronal survival and development. The major advantage of DAzLE is that it provides a nearly complete and relatively comprehensive differential screening profile that has the potential to be a powerful and useful tool in other fields of study.

Analysis of gene expression in carbon tetrachloride-treated rat livers using a novel bioarray technology

The present study successfully utilizes a new ADME Rat Expression Bioarray, containing 1040 metabolism- and toxicology-linked genes, to monitor gene expression from the livers of rats treated with carbon tetrachloride (CCl(4)). Histopathological analysis, hierarchical clustering methods, and gene expression profiling are compared between the control and CCl(4)-treated animals. A total of 44 transcripts were found to be altered in response to the hepatotoxin, 19 of which were upregulated and 25 were downregulated. Some of these gene expression changes were expected and concurred with previously published data while others were novel findings.

Gene expression profiling of human diseases by serial analysis of gene expression

Until recently, the approach to understanding the molecular basis of complex syndromes such as cancer, coronary artery disease, and diabetes was to study the behavior of individual genes. However, it is generally recognized that expression of a number of genes is coordinated both spatially and temporally and that this coordination changes during the development and progression of diseases. Newly developed functional genomic approaches, such as serial analysis of gene expression (SAGE) and DNA microarrays have enabled researchers to determine the expression pattern of thousands of genes simultaneously. One attractive feature of SAGE compared to microarrays is its ability to quantify gene expression without prior sequence information or information about genes that are thought to be expressed. SAGE has been successfully applied to the gene expression profiling of a number of human diseases. In this review, we will first discuss SAGE technique and contrast it to microarray. We will then highlight new biological insights that have emerged from its application to the study of human diseases.

Microarray, SAGE and their applications to cardiovascular diseases

The wealth of DNA data generated by the human genome project coupling with recently invented high-throughput gene expression profiling techniques has dramatically sped up the process for biomedical researchers on elucidating the role of genes in human diseases. One powerful method to reveal insight into gene functions is the systematic analysis of gene expression. Two popular high-throughput gene expression technologies, microarray and Serial Analysis of Gene Expression (SAGE) are capable of producing large amounts of gene expression data with the potential of providing novel insights into fundamental disease processes, especially complex syndromes such as cardiovascular disease, whose etiologies are due to multiple genetic factors and their interplay with the environment. Microarray and SAGE have already been used to examine gene expression patterns of cell-culture, animal and human tissues models of cardiovascular diseases. In this review, we will first give a brief introduction of microarray and SAGE technologies and point out their limitations. We will then discuss the major discoveries and the new biological insights that have emerged from their applications to cardiovascular diseases. Finally we will touch upon potential challenges and future developments in this area.

Understanding neonatal hyperbilirubinaemia in the era of genomics

The genomics revolution offers novel approaches to scientific investigation. Application of genomics technologies including microarray gene chips will provide a more complete picture of biological phenomena and help define the genetic contribution to disease by monitoring changes in expression across thousands of genes in physiological and clinical contexts. We briefly summarize identified genetic components that contribute to the genesis of neonatal hyperbilirubinaemia with a focus on inborn errors of hepatic bilirubin conjugation and discuss the potential use of microarray gene expression profiling technology to enhance our understanding of the pathogenesis of hyperbilirubinaemic neuronal cell injury. Expanded study using the tools of genomics will shed insights into the genetics of newborn jaundice and the pathogenesis of hyperbilirubinaemic encephalopathy.