Gene expression analysis in schizophrenia: reproducible up-regulation of several members of the apolipoprotein L family located in a high-susceptibility locus for schizophrenia on chromosome 22

Progress in the use of microarray technology to study the neurobiology of disease

The diverse functions of the brain are mediated by neurons and glia whose phenotype is defined by a dynamically maintained set of gene transcripts, or 'transcriptome'. Large-scale analysis of gene expression in postmortem brain using microarray technology has the potential to elucidate molecular changes that occur in disease states. There are unique challenges associated with studies of postmortem brain, including limited sample sizes and variable clinical phenotypes that are typical of complex disorders. Nevertheless, recent microarray-based studies have implicated both individual dysregulated genes and abnormal patterns of gene expression in brain disorders.

Molecular characterization of bipolar disorder by comparing gene expression profiles of postmortem brains of major mental disorders

We performed the oligonucleotide microarray analysis in bipolar disorder, major depression, schizophrenia, and control subjects using postmortem prefrontal cortices provided by the Stanley Foundation Brain Collection. By comparing the gene expression profiles of similar but distinctive mental disorders, we explored the uniqueness of bipolar disorder and its similarity to other mental disorders at the molecular level. Notably, most of the altered gene expressions in each disease were not shared by one another, suggesting the molecular distinctiveness of these mental disorders. We found a tendency of downregulation of the genes encoding receptor, channels or transporters, and upregulation of the genes encoding stress response proteins or molecular chaperons in bipolar disorder. Altered expressions in bipolar disorder shared by other mental disorders mainly consisted of upregulation of the genes encoding proteins for transcription or translation. The genes identified in this study would be useful for the understanding of the pathophysiology of bipolar disorder, as well as the common pathophysiological background in major mental disorders at the molecular level. In addition, we found the altered expression of LIM and HSPF1 both in the brains and lymphoblastoid cells in bipolar disorder. These genes may have pathophysiological importance and would be novel candidate genes for bipolar disorder.

Functional genomics and proteomics: application in neurosciences

The sequencing of the complete genome for many organisms, including man, has opened the door to the systematic understanding of how complex structures such as the brain integrate and function, not only in health but also in disease. This blueprint, however, means that the piecemeal analysis regimes of the past are being rapidly superseded by new methods that analyse not just tens of genes or proteins at any one time, but thousands, if not the entire repertoire of a cell population or tissue under investigation. Using the most appropriate method of analysis to maximise the available data therefore becomes vital if a complete picture is to be obtained of how a system or individual cell is affected by a treatment or disease. This review examines what methods are currently available for the large scale analysis of gene and protein expression, and what are their limitations.

Expression of nNOS and soluble guanylate cyclase in schizophrenic brain

Recent evidence suggests that nitric oxide (NO) systems are affected in the pathophysiology of schizophrenia. We quantified levels of neuronal NO synthase (nNOS) and soluble guanylate cyclase (sGC) subunit mRNAs in the prefrontal cortex of post-mortem brains from individuals with schizophrenia and controls using real-time quantitative PCR, to determine whether levels of nNOS and sGC subunits are altered in 'schizophrenic' brains. Neuronal NOS expression in the prefrontal cortex was significantly higher in individuals with schizophrenia, whereas no significant changes were found in sGC subunit mRNAs in people with schizophrenia or in controls. Abnormalities of nNOS expression in the brain might contribute to the development of schizophrenia.

Quantitative polymerase chain reaction: validation of microarray results from postmortem brain studies

Quantitative polymerase chain reaction (Q-PCR) is now considered the "technique of choice" for validating gene expression changes identified with ribonucleic acid-based expression profiling technologies (especially micro- and macroarray techniques). The identification of altered gene expression profiles with microarrays is best viewed as the first step in the determination of potential disease-associated genes; however, the false-positive rate can be high, particularly with small sample sets and in view of the typically small differences observed in brain expression studies. Quantitative PCR is a rapid and highly sensitive technique for accurate quantification of microarray results; however, careful consideration of experimental design, quality of primer/probe design, internal standards, and normalization procedures are pivotal, particularly when the work involves postmortem tissue.

Erythropoietin: a candidate compound for neuroprotection in schizophrenia

Erythropoietin (EPO) is a candidate compound for neuroprotection in human brain disease capable of combating a spectrum of pathophysiological processes operational during the progression of schizophrenic psychosis. The purpose of the present study was to prepare the ground for its application in a first neuroprotective add-on strategy in schizophrenia, aiming at improvement of cognitive brain function as well as prevention/slowing of degenerative processes. Using rodent studies, primary hippocampal neurons in culture, immunohistochemical analysis of human post-mortem brain tissue and nuclear imaging technology in man, we demonstrate that: (1) peripherally applied recombinant human (rh) EPO penetrates into the brain efficiently both in rat and humans, (2) rhEPO is enriched intracranially in healthy men and more distinctly in schizophrenic patients, (3) EPO receptors are densely expressed in hippocampus and cortex of schizophrenic subjects but distinctly less in controls, (4) rhEPO attenuates the haloperidol-induced neuronal death in vitro, and (4) peripherally administered rhEPO enhances cognitive functioning in mice in the context of an aversion task involving cortical and subcortical pathways presumably affected in schizophrenia. These observations, together with the known safety of rhEPO, render it an interesting compound for neuroprotective add-on strategies in schizophrenia and other human diseases characterized by a progressive decline in cognitive performance.

Increased levels of apolipoprotein E in the frontal cortex of subjects with schizophrenia

BACKGROUND

It is unclear whether altered expression of a specific isoform of apolipoprotein E (apoE) is associated with the pathology of schizophrenia.

METHODS

To address whether apoE may be involved in the pathology of schizophrenia, we measured the genotypic and allelic frequency of polymorphisms in its gene and transcriptional regulatory region in DNA from Brodmann's area (BA) 9 obtained postmortem from schizophrenic and control subjects as well as its levels in the same tissue using Western blot analysis.

RESULTS

The genotypic or allelic frequencies of any polymorphism studied did not vary between diagnostic cohorts. There was a significant increase in the levels of apoE protein in BA 9 from the schizophrenic subjects (Mean +/- SEM: 270 +/- 8.3 vs. 238 +/- 7.1 ng apoE/mg protein, p =.008) and a decrease in tissue from an analogous cortical region from rats treated with haloperidol compared with vehicle-treated animals (50 +/- 6.4 vs. 116 +/- 9.2 ng apoE/mg protein; p =.0002).

CONCLUSIONS

These data support the hypothesis that increased levels of apoE may be associated with the pathology of schizophrenia and that antipsychotic drugs decrease apoE levels as part of their therapeutic actions.

Oligodendrocyte dysfunction in schizophrenia and bipolar disorder

BACKGROUND

Results of array studies have suggested abnormalities in expression of lipid and myelin-related genes in schizophrenia. Here, we investigated oligodendrocyte-specific and myelination-associated gene expression in schizophrenia and bipolar affective disorder.

METHODS

We used samples from the Stanley brain collection, consisting of 15 schizophrenia, 15 bipolar affective disorder, and 15 control brains. Indexing-based differential display PCR was done to screen for differences in gene expression in schizophrenia patients versus controls. Results were cross-validated with quantitative PCR, which was also used to investigate expression profiles of 16 other oligodendrocyte and myelin genes in schizophrenia and bipolar disorder. These genes were further investigated with an ongoing microarray analysis.

FINDINGS

Results of differential display and quantitative PCR analysis showed a reduction of key oligodendrocyte-related and myelin-related genes in schizophrenia and bipolar patients; expression changes for both disorders showed a high degree of overlap. Microarray results of the same genes investigated by quantitative PCR correlated well overall.

INTERPRETATION

Schizophrenia and bipolar brains showed downregulation of key oligodendrocyte and myelination genes, including transcription factors that regulate these genes, compared with control brains. These results lend support to and extend observations from other microarray investigations. Our study also showed similar expression changes to the schizophrenia group in bipolar brains, which thus lends support to the notion that the disorders share common causative and pathophysiological pathways.

Subtraction libraries for the molecular characterization of gene-environmental interactions in bipolar disorder

OBJECTIVES

We endeavoured to identify gene-environmental interactions related to bipolar disorder.

METHODS

We generated subtraction libraries from the frontal cortex of brains obtained postmortem from individuals with bipolar disorder and age- and sex-matched unaffected controls.

RESULTS

There are a number of RNA transcripts which are apparently up-regulated or down-regulated in the frontal cortex of individuals with bipolar disorder as compared with the controls. Many of these transcripts are involved in processes crucial to brain function. Several are also related to pathways involved in infections or the inflammatory response in environmental stimuli.

CONCLUSIONS

Bipolar disorder may involve a complex set of interactions between genes which affect brain function and infections which control the expression of these genes.

Antipsychotic drug treatment induces differential gene expression in the rat cortex

Antipsychotic drug treatment is known to modulate gene expression in experimental animals. In this study, candidate target genes for antipsychotic drug action were searched using microarrays after acute clozapine treatment (1, 6 and 24 h) in the rat prefrontal cortex. Microarray data clustering with a self-organizing map algorithm revealed differential expression of genes involved in presynaptic function following acute clozapine treatment. The differential expression of 35 genes most profoundly regulated in expression arrays was further examined using in situ hybridization following acute clozapine, and chronic clozapine and haloperidol treatments. Acute administration of clozapine regulated the expression of chromogranin A, synaptotagmin V and calcineurin A mRNAs in the cortex. Chronic clozapine treatment induced differential cortical expression of chromogranin A, son of sevenless (SoS) and Sec-1. Chronic treatment with haloperidol regulated the mRNA expression of inhibitor of DNA-binding 2 (ID-2) and Rab-12. Furthermore, the expression of visinin-like proteins-1, -2 and -3 was regulated by chronic drug treatments in various brain regions. Our data suggest that acute and chronic treatments with haloperidol and clozapine modulate the expression of genes involved in synaptic function and in regulation of intracellular Ca2+ in cortex.

Yellow pages to the transcriptome

Transcriptomics has become an important tool for the large-scale analysis of biological processes. This review aims to provide sufficient criteria to make an appropriate choice among the variety of 'closed' systems, represented by DNA microarrays, and 'open' systems like fragment display, tag sequencing and subtractive hybridization, depending on the biological system under investigation. The most important technologies currently available are presented, their strengths and weaknesses are discussed and companies active in the field are listed. The potential of transcriptomics in the pharmaceutical research and development process is highlighted by applications in oncology, research on neurological diseases, and predictive toxicology. Finally, a prognosis for future developments of the technologies is given.

RNA amplification in brain tissues

Recent developments in gene array technologies, specifically cDNA microarray platforms, have made it easier to try to understand the constellation of gene alterations that occur within the CNS. Unlike an organ that is comprised of one principal cell type, the brain contains a multiplicity of both neuronal (e.g., pyramidal neurons, interneurons, and others) and noneuronal (e.g., astrocytes, microglia, oligodendrocytes, and others) populations of cells. An emerging goal of modern molecular neuroscience is to sample gene expression from similar cell types within a defined region without potential contamination by expression profiles of adjacent neuronal subtypes and noneuronal cells. At present, an optimal methodology to assess gene expression is to evaluate single cells, either identified physiologically in living preparations, or by immunocytochemical or histochemical procedures in fixed cells in vitro or in vivo. Unfortunately, the quantity of RNA harvested from a single cell is not sufficient for standard RNA extraction methods. Therefore, exponential polymerase-chain reaction (PCR) based analyses and linear RNA amplifications, including a newly developed terminal continuation (TC) RNA amplification methodology, have been used in combination with single cell microdissection procedures to enable the use of cDNA microarray analysis within individual populations of cells obtained from postmortem brain samples as well as the brains of animal models of neurodegeneration.

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.

Genetics and etiopathophysiology of schizophrenia

Schizophrenia is one of the most common, devastating, and least understood neuropsychiatric illnesses present in the human population. Despite decades of research involving neurochemical, neuroanatomical, neuropathologic, neurodevelopmental, neuropsychological, and genetic approaches, no clear etiopathophysiology has been elucidated. Among the most robust findings, however, is the contribution of genetics to disease development. Statistical models suggest that susceptibility to the disorder is governed by the effects of multiple genes, coupled with environmental and stochastic factors. This review briefly summarizes recent etiopathologic findings and hypotheses, with special attention to genetics.

Molecular and cellular evidence for an oligodendrocyte abnormality in schizophrenia

Our previous analyses in postmortem prefrontal cortex samples from a well-characterized cohort of severely affected schizophrenics and in matched controls demonstrated decreased expression of myelin and oligodendrocyte-related genes in the disease state. This decreased expression, now replicated in independent studies, suggests that there is a disruption of oligodendrocyte function and/or a loss of oligodendrocytes in schizophrenia. In the current report, we review expression studies in schizophrenia and present data demonstrating consistently fewer oligodendrocytes in schizophrenics compared to controls. The decrease in density reached 22% (p < 0.01) in layer III of area 9 and 20% (p < 0.02) in the white matter of the superior frontal gyrus. These data, when taken together with expression studies carried out by us and by other groups, and by imaging and other microscopic studies, point to a major involvement of oligodendrocyte abnormalities in schizophrenia. Therapies modulating oligodendrocyte survival and differentiation may therefore be beneficial in schizophrenia.

The neurobiology of apolipoproteins in psychiatric disorders

A genetic contribution to the transmission of psychiatric disorders has been established and it is now accepted that several genes confer susceptibility to schizophrenia, and similar disorders, giving rise to a complex polygenic mode of inheritance. With the high-throughput molecular profiling techniques available, apolipoproteins have emerged as being important factors in psychiatric disorders. This review will focus on three apolipoproteins that have recently been shown to be elevated in neuropsychiatric disorders: apoD, apoE, and apoL. Furthermore, the authors discuss the role of apoD in the pathology and pharmacotherapy of schizophrenia and bipolar disorder.

Optimizing gene expression analysis in archival brain tissue

Analysis of gene expression in the brain is a valuable tool to study the function of the brain under normal and pathological conditions. Although there are many techniques used to measure gene expression the validity of any such experiment is directly related to the quality of the RNA in the samples. The most readily available source of human brain tissue is post-mortem and while frozen tissue is sometimes available, most archived tissue is fixed and paraffin-embedded. The use of fixed tissue for expression analysis introduces variables, which must be considered in the experimental design. In addition, factors associated with clinical variability of the patient and with tissue procurement can affect RNA transcript levels. In order to illustrate the effects of two common tissue fixatives, formalin and ethanol, on the quality of RNA for expression analysis we compare RNA extracted from these fixed tissues to the gold standard, flash-frozen tissue. We describe RNA extraction from fixed tissue and ways to assess the quality or intactness of the RNA using reverse transcription combined with polymerase chain reaction amplification. An advantage of using archived tissue is the ease with which single cells or subpopulations of cells can be obtained by laser microdissection. The successful isolation of RNA from microdissected cells is also presented. From our results and a review of the literature we conclude that RNA from fixed tissues is a viable source of RNA for expression analysis which should enable new experimental approaches and discoveries as long as attention is given to variables that can affect RNA at all levels of analysis.

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.