DNA microarrays in neuropsychopharmacology

Three-dimensional protein microarrays fabricated on reactive microsphere modified COC substrates

Fabrication of three-dimensional (3D) surface structures for the high density immobilization of biomolecules is an effective way to prepare highly sensitive biochips. In this work, a strategy to attach polymeric microspheres on a cyclic olefin copolymer (COC) substrate for the preparation of a 3D protein chip was developed. The COC surface was firstly functionalized by the photograft technique with epoxy groups, which were subsequently converted to amine groups. Then monodisperse poly(styrene-alt-maleic anhydride) (PSM) copolymer microspheres were prepared by self-stabilized precipitation polymerization and deposited as a single layer on a modified COC surface to form a 3D surface texture. The surface roughness of the COC support undergoes a significant increase from 1.4 nm to 37.1 nm after deposition of PSM microspheres with a size of 460 nm, and the modified COC still maintains a transmittance of more than 63% at the fluorescence excitation wavelengths (555 nm and 647 nm). The immobilization efficiency of immunoglobulin G (IgG) on the 3D surface reached 75.6% and the immobilization density was calculated to be 0.255 μg cm^-2, at a probe protein concentration of 200 μg mL^-1. The 3D protein microarray can be rapidly blocked by gaseous ethylenediamine within 10 minutes due to the high reactivity of anhydride groups in PSM microspheres. Immunoassay results show that the 3D protein microarray achieved specific identification of the target protein with a linear detection range from 6.25 ng mL^-1 to 250 ng mL^-1 (R² > 0.99) and a limit of detection of 8.87 ng mL^-1. This strategy offers a novel way to develop high performance polymer-based 3D protein chips.

Genomics and proteomics in solving brain complexity

The human brain is extraordinarily complex, composed of billions of neurons and trillions of synaptic connections. Neurons are organized into circuit assemblies that are modulated by specific interneurons and non-neuronal cells, such as glia and astrocytes. Data on human genome sequences predicts that each of these cells in the human brain has the potential of expressing ∼20 000 protein coding genes and tens of thousands of noncoding RNAs. A major challenge in neuroscience is to determine (1) how individual neurons and circuitry utilize this potential during development and maturation of the nervous system, and for higher brain functions such as cognition, and (2) how this potential is altered in neurological and psychiatric disorders. In this review, we will discuss how recent advances in next generation sequencing, proteomics and bioinformatics have transformed our understanding of gene expression and the functions of neural circuitry, memory storage, and disorders of cognition.

Is brain banking of psychiatric cases valuable for neurobiological research?

It is widely accepted that neurobiological abnormalities underlie the symptoms of psychiatric disorders such as schizophrenia and unipolar or bipolar affective disorders. New molecular methods, computer-assisted quantification techniques and neurobiological investigation methods that can be applied to the human brain are all used in post-mortem investigations of psychiatric disorders. The following article describes modern quantitative methods and recent post-mortem findings in schizophrenia and affective disorders. Using our brain bank as an example, necessary considerations of modern brain banking are addressed such as ethical considerations, clinical work-up, preparation techniques and the organization of a brain bank, the value of modern brain banking for investigations of psychiatric disorders is summarized.

How a neuropsychiatric brain bank should be run: a consensus paper of Brainnet Europe II

The development of new molecular and neurobiological methods, computer-assisted quantification techniques and neurobiological investigation methods which can be applied to the human brain, all have evoked an increased demand for post-mortem tissue in research. Psychiatric disorders are considered to be of neurobiological origin. Thus far, however, the etiology and pathophysiology of schizophrenia, depression and dementias are not well understood at the cellular and molecular level. The following will outline the consensus of the working group for neuropsychiatric brain banking organized in the Brainnet Europe II, on ethical guidelines for brain banking, clinical diagnostic criteria, the minimal clinical data set of retrospectively analyzed cases as well as neuropathological standard investigations to perform stageing for neurodegenerative disorders in brain tissue. We will list regions of interest for assessments in psychiatric disorder, propose a dissection scheme and describe preservation and storage conditions of tissue. These guidelines may be of value for future implementations of additional neuropsychiatric brain banks world-wide.

DNA microarray analysis of striatal gene expression in symptomatic transgenic Huntington's mice (R6/2) reveals neuroinflammation and insulin associations

Huntington's disease (HD) is an inherited, progressive neurodegenerative disorder caused by CAG repeat expansion in the gene that codes for the protein huntingtin. The underlying neuropathological events leading to the selectivity of striatal neuronal loss are unknown. However, the huntingtin mutation interferes at several levels of normal cell function. The complexity of this disease makes microarray analysis an appealing technique to begin the identification of common pathways that may contribute to the pathology. In this study, striatal tissue was extracted for gene expression profiling from wild-type and symptomatic transgenic Huntington mice (R6/2) expressing part of the human Huntington's disease gene. We interrogated a 15 K high-density mouse EST array not previously used for HD and identified 170 significantly differentially expressed ESTs in symptomatic R6/2 mice. Of the 80 genes with known function, 9 genes had previously been identified as altered in HD. 71 known genes were associated with HD for the first time. The data obtained from this study confirm and extend previous observations using DNA microarray techniques on genetic models for HD, revealing novel changes in expression in a number of genes not previously associated with HD. Further bioinformatic analysis, using software to construct biological association maps, focused attention on proteins such as insulin and TH1-mediated cytokines, suggesting that they may be important regulators of affected genes. These results may provide insight into the regulation and interaction of genes that contribute to adaptive and pathological processes involved in HD.

Analysis of microarray studies performed in the neurosciences

The application of microarray technology to basic and applied fields of science has been progressing rapidly and broadly since its initial description. The field of neuroscience stands to benefit particularly, as nervous tissue is the most transcriptionally active system within most biological organisms. Moreover, large numbers of cell and animal models have been created that mimic many biochemical and behavioral features of neurological states and diseases. In the present study, data on study designs, tissue sources, technology platforms, bioinformatic tools, and results obtained from 448 published microarray studies were collected. The data were then summarized to determine overall usage statistics of microarrays. Future directions and applications for microarrays in the neurosciences were then inferred from the data analyzed.

Functional Genomics meets neurodegenerative disorders

Transcriptomics and proteomics are increasingly applied to gain a mechanistic insight into neurodegenerative disorders. These techniques not only identify distinct, differentially expressed mRNAs and proteins but are also employed to dissect signaling pathways and reveal networks by using an integrated approach. In part I of this back-to-back review, technical aspects are discussed: in the transcriptomics section, which includes enrichment by laser microcapture dissection, we comment on qRT-PCR, SAGE, subtractive hybridization, differential display and microarrays, including software packages. In the proteomics section we discuss two-dimensional (2D) gel electrophoresis, liquid chromatography, methods to label and enrich specific proteins or peptides, and different types of mass spectrometers. These tools have been applied to a range of neurodegenerative disorders and are discussed and integrated in part II (Functional Genomics meets neurodegenerative disorders. Part II: application and data integration).

Microarray studies of psychostimulant-induced changes in gene expression

Alterations in the expression of multiple genes in many brain regions are likely to contribute to psychostimulant-induced behaviours. Microarray technology provides a powerful tool for the simultaneous interrogation of gene expression levels of a large number of genes. Several recent experimental studies, reviewed here, demonstrate the power, limitations and progress of microarray technology in the field of psychostimulant addiction. These studies vary in the paradigms of cocaine or amphetamine administration, drug doses, route and also mode of administration, duration of treatment, animal species, brain regions studied and time of tissue collection after final drug administration. The studies also utilize different microarray platforms and statistical techniques for analysis of differentially expressed genes. These variables influence substantially the results of these studies. It is clear that current microarray techniques cannot detect small changes reliably in gene expression of genes with low expression levels, including functionally significant changes in components of major neurotransmission systems such as glutamate, dopamine, opioid and GABA receptors, especially those that may occur after chronic drug administration or drug withdrawal. However, the microarray studies reviewed here showed cocaine- or amphetamine-induced alterations in the expression of numerous genes involved in the modulation of neuronal growth, cytoskeletal structures, synaptogenesis, signal transduction, apoptosis and cell metabolism. Application of laser capture microdissection and single-cell cDNA amplification may greatly enhance microarray studies of gene expression profiling. The combination of rapidly evolving microarray technology with established methods of neuroscience, molecular biology and genetics, as well as appropriate behavioural models of drug reinforcement, may provide a productive approach for delineating the neurobiological underpinnings of drug responses that lead to addiction.

Heat shock protein 12A shows reduced expression in the prefrontal cortex of subjects with schizophrenia

BACKGROUND

Deoxyribonucleic acid microarray analyses of dorsolateral prefrontal cortex (DLPFC) area 9 from 10 matched pairs of schizophrenic and control subjects revealed a consistent and significant decrease (p = .001; mean log2 signal difference = -.58) in transcript expression for a gene clone KIAA0417. This database entry has been recently annotated as two highly homologous members of a heat-shock protein family (HSPA12A and HSPA12B).

METHODS

We followed up our initial results by in situ hybridization in subjects with schizophrenia, major depression, and a chronic haloperidol-treated nonhuman primate model. Furthermore, we investigated the distribution of HSPA12A and HSPA12B transcripts across the human and nonhuman primate brain.

RESULTS

We found that HSPA12A (but not HSPA12B) is highly expressed in the human brain and shows a neuron- and region-specific transcript distribution, with strongest expression in the frontal and occipital cortical regions. HSPA12A messenger ribonucleic acid was significantly reduced (p < .01; mean log2 optical density difference = -.84) across subjects with schizophrenia but not in the DLPFC of subjects with major depression or in monkeys chronically treated with haloperidol.

CONCLUSIONS

The data are consistent with metabolic alterations in schizophrenia, reflected in selective changes in the expression of certain genes encoding proteins involved in cellular metabolism or metabolic responsiveness.

DNA microarray for discrimination between pathogenic 0157:H7 EDL933 and non-pathogenic Escherichia coli strains

The primary technique currently used to detect biological agents is based on immunoassays. Although sensitive and specific, currently employed immunoassays generally rely on the detection of a single epitope, and therefore often cannot discriminate subtle strain-specific differences. Since DNA microarrays can hybridize hundreds to thousands of genomic targets simultaneously and do not rely on phenotypic expression of these genetic features for identification purposes, they have enormous potential to provide inexpensive, flexible and specific strain-specific detection and identification of pathogens. In this study, pathogenic Escherichia coli O157:H7-specific genes, non-pathogenic K12-specific genes, common E. coli genes, and negative control genes were polymerase chain reaction-amplified and spotted onto the surface of treated glass slides. After labeled bacterial cDNA samples were hybridized with probes on the microarray, specific fluorescence patterns were obtained, enabling identification of pathogenic E. coli O157:H7 and non-pathogenic E. coli K12. To test the utility of this microarray device to detect genetically engineered bacteria, E. coli BL21 (a B strain derivative with antibiotic resistance gene, ampR) and E. coli JM107 (a K12 strain derivative lacking the gene ompT) were also employed. The array successfully confirmed the strain genotypes and demonstrated that antibiotic resistance can also be detected. The ability to assess multiple data points makes this array method more efficient and accurate than a typical immunoassay, which detects a single protein product.

Identification of lithium-regulated genes in cultured lymphoblasts of lithium responsive subjects with bipolar disorder

Lithium, a common drug for the treatment of bipolar disorder (BD), requires chronic administration to prevent recurrences of the illness. The necessity for long-term treatment suggests that changes in genes expression are involved in the mechanism of its action. We studied effects of lithium on gene expression in lymphoblasts from BD patients, all excellent responders to lithium prophylaxis. Gene expression was analyzed using cDNA arrays that included a total of 2400 cDNAs. We found that chronic lithium treatment at a therapeutically relevant concentration decreased the expression of seven genes in lymphoblasts from lithium responders. Five of these candidate lithium-regulated genes, including alpha1B-adrenoceptor (alpha1B-AR), acetylcholine receptor protein alpha chain precursor (ACHR), cAMP-dependent 3',5'-cyclic phosphodiesterase 4D (PDE4D), substance-P receptor (SPR), and ras-related protein RAB7, were verified by Northern blotting analysis in lithium responders. None of these genes were regulated by lithium in healthy control subjects. When we compared the expression of these five genes between bipolar subjects and healthy control subjects at baseline, prior to lithium administration, we found that alpha1B-AR gene expression was higher in bipolar subjects than in healthy control subjects. Our findings indicate that alpha1B-AR may play an important role in the mechanism of action of lithium treatment.

cDNA microarray and proteomic approaches in the study of brain diseases: focus on schizophrenia and Alzheimer's disease

Recent advances in experimental genomics and proteomics, coupled with the wealth of sequence information available for a variety of organisms, have tremendous implications for how biomedical research is performed. Genomic techniques, such as complementary DNA (cDNA) microarrays, currently allow researchers to quickly and accurately quantify vast numbers of potential gene expression changes simultaneously. Modern proteomic techniques allow for the detection and elucidation of protein-protein interactions on a scale and at a speed never before possible. Although hurdles remain, together, these tools open the possibility of enormous change in our ability to analyze and interpret complex biological processes. The field of neuroscience is particularly well suited to analysis with these new techniques, given the complexity of neuronal signaling and the diversity of cellular responses. This review summarizes the major cDNA microarray and proteomic findings of relevance to schizophrenia and Alzheimer's disease (AD) as 2 representative areas of neuroscience research. The potential for these techniques to help unravel the underlying pathology of complex neurological and neuropsychiatric conditions is considerable and warrants continued investigation.

Gene expression profiling following chronic NMDA receptor blockade-induced learning deficits in rats

Acute treatments with MK-801, a noncompetitive antagonist of the NMDA glutamate receptor, induce spatial memory deficits in rodents. In the present study, we developed a low-dose chronic MK-801 treatment regimen that induced persistent learning deficits (determined by the Morris water maze task) after administration of the drug (0.2 mg/kg) every 12 h for 14 days. To determine the impact of such a treatment, changes in mRNA expression were investigated in the hippocampi and striata of treated animals using a cDNA membrane array followed by Western blots. Genes whose expression levels were found to be most altered included preprolactin (downregulated) and mitogen-activated protein kinase (MAP kinase 1; upregulated) in the hippocampus, and acyl-CoA synthetase (downregulated) and apolipoprotein D (upregulated) in the striatum. Furthermore, MAP kinase 1 and proteosome subunit beta precursor was found to meet selection criteria for upregulation in both the hippocampus and striatum. Among other genes found to be most changed in the hippocampus were protein kinase C beta I and II, protein tyrosine phosphatase 1beta, neuropilin I and II, adenosine receptor A1, and metabotropic glutamate receptor 2/3. The impact of some gene expression alterations on their corresponding protein levels was studied next. In the hippocampus, protein kinase C beta I and II, protein tyrosine phosphatase, neuropilin I and II, adenosine receptor A, metabotropic glutamate receptor 2/3, and in the striatum phosphatidyl inositol 4 kinase, mitogen-activated protein kinase 1, adenylyl cyclase II, dopamine receptors 1A and 2, and cytochrome C oxidase subunit Va gene and protein expression levels were found to be highly correlated. These results suggest the potential involvement of several genes and proteins in the neuropharmacological effects of MK-801 and possibly the persisting cognitive deficits induced by this repeated drug treatment.

Overview of microarrays in drug discovery and development

With the sequencing of the human genome, new tools and technologies have been developed to identify and quantify global gene-expression changes occurring in the cell. One of the main tools being utilized is microarray technology, which allows one to quantitate expression changes of thousands of genes in a single experiment. Microarrays allow researchers to gain an unprecedented understanding of the function and regulation of genes, and are transforming virtually all areas of biological research. In the drug-discovery process, microarrays have the potential to play a role in all stages, from new target discovery through compound profiling and safety assessment. This overview highlights some of these studies and discusses how this technology is transforming the field of drug discovery and development.

Standardization of protocols in cDNA microarray analysis

Systematic variations can occur at various steps of a cDNA microarray experiment and affect the measurement of gene expression levels. Accepted standards integrated into every cDNA microarray analysis can assess these variabilities and aid the interpretation of cDNA microarray experiments from different sources. A universally applicable approach to evaluate parameters such as input and output ratios, signal linearity, hybridization specificity and consistency across an array, as well as normalization strategies, is the utilization of exogenous control genes as spike-in and negative controls. We suggest that the use of such control sets, together with a sufficient number of experimental repeats, in-depth statistical analysis and thorough data validation should be made mandatory for the publication of cDNA microarray data.

Analysis of ecstasy (MDMA)-induced transcriptional responses in the rat cortex

3,4-methylenedioxymethamphetamine (MDMA, ecstasy) is a popular drug of abuse. MDMA is pharmacologically classified as an entactogen because of its affinities to classical hallucinogens and stimulants. Oral ingestion of a single dose of the drug is associated with euphoria, elevated self-confidence, and heightened sensory awareness in humans. Evidence for neurotoxicity in the human serotonin (5-HT) system has been provided. In rats, a single injection of MDMA induces hyperthermia and formation of reactive oxygen species. These effects may cause MDMA-associated, long-term 5-HT depletion, with the cortex being quite sensitive to the biochemical effects of MDMA. It has been suggested that these MDMA effects may be associated with molecular changes in this brain region. To test these ideas, we have made use of the cDNA array analysis, which can provide a more global view of the molecular changes secondary to MDMA injections. Our results show that the genes regulated by MDMA encode proteins that belong to signaling pathways, transcription regulators, or xenobiotic metabolism. Our observations indicate that cortical cells respond to the acute administration of MDMA by modulating transcription of several genes that might lead to long-term changes in the brain.

Gene expression profiling with DNA microarrays: advancing our understanding of psychiatric disorders

DNA microarray transcriptome profiling of the postmortem brain opens novel horizons in understanding molecular changes associated with complex psychiatric disorders. With careful analysis and interpretation of microarray data we are uncovering previously unknown, expression patterns that maybe subject-specific and pivotal in understanding the disease process. In our recent studies, analyses of the prefrontal cortex of subjects with schizophrenia and matched controls uncovered complex changes in the expression of genes related to presynaptic secretory release, GABAergic and glutamatergic transmission, metabolic pathways, myelination, as well as cAMP and phosphoinositol second messenger systems. Our goal will be to integrate this expression data within the context of the relevant anatomical, biochemical, molecular, imaging and clinical findings.

Functional genomics in neuropsychiatric disorders and in neuropharmacology

The rapidly accumulating amount of information concerning gene and protein expression patterns produced by functional genomics, proteomics and bioinformatics is presently providing new targets for drug development. Furthermore, the analysis of gene expression in cells and tissues affected by a disease may reveal the underlying metabolic pathways and cellular processes affected. Finally, changes in gene expression may be used in either diagnostics or the monitoring of drug responses. This review focuses on advances in the use of functional genomics in neurological and neuropsychiatric diseases and neuropsychopharmacology. Although the number of published studies in this field is still limited, it already appears that this strategy may become a fruitful means in the analysis of the aetiology of neuropsychiatric disorders and the search for novel neuropharmacological drugs.

Functional genomics approaches to understanding brain disorders

The completed draft of the human genome sequence has facilitated a revolution in neuroscience research. This sequence information and the development of new technologies used to analyze gene expression on a genomic scale provides a new and powerful means to investigate brain disorders of unknown etiology and to isolate novel drug targets for these disorders. The term functional genomics broadly describes a set of technologies and strategies directed at the problem of determining the function of genes, and understanding how the genome works together to generate whole patterns of biological function. The most powerful of these functional genomics approaches, expression profiling or DNA microarrays, can be used to analyze the expression of thousands of genes simultaneously. The results to date from the application of DNA microarray methods to postmortem diseased human brain tissue, animal models and cell culture models of brain disorders provide an exciting glimpse into the future of this field.