Novel directions in antipsychotic target identification using gene arrays

Schizophrenia is a major health problem that affects 2 million individuals in the United States. Antipsychotics offer considerable symptomatic relief and, although commonly discovered by screening with single biological targets, most interact with multiple receptors and signaling pathways. Considerable evidence from family and twin studies demonstrates genetic components and multiple chromosomal regions associated with schizophrenia. The polygenic nature of schizophrenia and multiple mechanisms for most effective agents indicate the need for broader approaches to target identification. Gene expression profiling of post-mortem human brain tissue simultaneously reveals the expression of many thousands of genes. A comparison of tissue from normals and patients provides a 'disease signature' of aberrantly expressed genes. 'Drug signatures' are the gene expression changes of cultured human or animal neurons treated with psychiatric drugs, and from animals chronically treated with these drugs. A selection of genes from disease and drug signatures can create a set of targets whose changes may better predict disease and its treatment by effective agents. This multi-parameter high throughput screening (MPHTS(SM)) approach evaluates the mRNA expression pattern of cultured cells exposed to candidate compounds. Compounds that normalize genes altered in schizophrenia may better address its underlying causes. Drugs that mimic gene expression changes that are consistently altered by effective antipsychotic agents provide a drug improvement strategy if efficacy is enhanced or side effects are attenuated.     

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.     

Growth plate cartilage as developmental model in osteoarthritis research--potentials and limitations

Gene expression analysis including large scale gene expression profiling has become a very basic tool for investigating the pathogenesis of degenerative joint diseases as well as for the search of new drug targets. However, gene expression analysis so far revealed very complex expression patterns rather than a clear picture of molecular changes occurring during the initiation and progression of the disease. To elucidate the molecular changes in osteoarthritis the analysis of the fetal growth plate as a developmental model for phenotypic changes in chondrocytes occurring in osteoarthritis can help in three ways: it allows to interpret gene expression patterns in the context of disease-relevant processes also occurring in developing cartilage (e.g. cell differentiation, proliferation, matrix synthesis, catabolism and calcification), it offers the chance to investigate gene function in these functional contexts by knocking out or overexpressing genes in animals, and it provides a suitable model for testing the effect of therapeutic compounds on these processes within the growing cartilage.     

Virogenomics: a novel approach to antiviral drug discovery

Target discovery in virology has been limited to the few open-reading frames encoded by viral genomes. However, several recent examples show that inhibiting host-cell proteins can prevent viral infection. The human genome sequence should, therefore, contain many more genes that are essential for viral propagation than viral genomes. A systematic approach to find these potential cellular antiviral targets is global host gene expression analysis using DNA microarrays. Several recent studies reveal both unique and common strategies by which viruses change the gene expression profile of the host cell. Moreover, work in progress shows that some of the host pathways discovered by expression profiling are important for viral replication. Thus, human genomics tools have the potential to deliver novel antiviral drugs.     

The Role of in Vitro Gene Expression Profiling in Particulate Matter Health Research

Exposure to particulate matter (PM) is consistently associated with increased morbidity and mortality rate. The mechanisms for these adverse health effects have been vigorously investigated for many years, but remain uncertain, in part due to the complex interactions between host and exposure. Over the past decade, the use of global gene expression profiling has increased to investigate molecular changes in an attempt to gain more insight into the complex mechanisms that underlie the adverse health effects induced by PM. These experiments have been performed mostly in cell cultures, in part due to the easy availability and maneuverability of different cell types. Whether or not the results obtained from these in vitro experiments are relevant to human exposure is unclear. In this study, cell culture studies were reviewed that used microarray technology to measure global gene expression in response to PM and the findings discussed in the context of global gene expression results obtained from animal and human exposure studies. Ten in vitro studies were identified from PubMed that reported global gene expression results in response to PM exposure. Despite difference in cell types, microarray platforms, incubation time, and PM sources and doses, these experiments showed commonality in the expression of genes and pathways, especially xenobiotic metabolism, oxidative stress, and inflammation. These gene expression profiles were consistent with results from animal and human controlled exposure experiments. The in vitro experiments also uncovered novel biological mechanisms that may be important in PM-induced health effects reported in epidemiological studies. Data indicate that in vitro microarray experiments complement animal and human exposure studies and allow the PM-associated health research to focus on the “toxic” components in PM and novel mechanisms, and may enhance risk assessment beyond the current mass-based standards.     

Microarray-based expression profiling in prostate tumors

High throughput gene expression profiling is increasingly becoming a desirable method for identifying genes differentially expressed in disease versus normal tissues. Microarrays and gene chips containing hundreds to thousands of genes of interest, both known and novel, can be used to establish the expression profile of numerous genes in a single experiment. In order to validate the hits emerging out of such an experiment it is necessary to use an appropriate panel of the cDNA repository. We investigated the usefulness of such a method to identify prostate cancer-specific genes. A microarray containing 588 known genes was analyzed using cDNA probes derived from normal and three independent prostate tumors. At least 19/588 genes were found to be differentially expressed in the tumors in comparison to the normal tissue. Among the nine test genes chosen, one gene, Glutathione-S-transferase theta 1 (GSTT1), showed a correlation with the microarray results when analyzed by RT-PCR. Using a comprehensive panel of normal and tumor tissues and cancer-derived cell lines, we have rapidly validated the expression relevance of GSTT1 in solid tumors. The microarray was also useful in the preliminary identification of androgen-regulated genes in the prostate tumor models. These results indicate that microarray in combination with a relevant cDNA repository can facilitate rapid identification of potential targets for therapy and diagnosis of prostate and other cancers.     

Exploring the tumour environment: cancer-associated fibroblasts as targets in cancer therapy

Stroma cells contribute to the microenvironment that is essential for cancer growth, invasion and metastatic progression. Fibroblasts, often termed myofibroblasts or cancer-associated fibroblasts (CAFs), represent the most abundant cell type in the tumour stroma. The demonstrated tumour-promoting capacities of CAFs has increased the interest to exploit them as drug targets for anticancer therapy. Although single factors, such as platelet-derived growth factor, transforming growth factor-beta1, hepatocyte growth factor and matrix metalloproteinases have been identified as mediators in the fibroblast tumour interaction, the morphological and functional differences of CAFs compared with their normal counterparts are only incompletely understood. Recently, novel global methods for gene expression profiling were applied to comprehensively characterise CAFs from breast, pancreas, colon and basal cell cancer in their in situ environment. The analysis of different CAF preparations revealed regulated genes that were previously not described in the tumour-stroma context. Additionally, besides a few striking overlaps, the comparison of the gene lists indicates a high level of heterogeneity in the expression pattern of CAFs from different tumour types. Together, these studies emphasise the importance of cross-talk between stromal and malignant cells of the tumour. It is likely that the continued characterisation of this interaction, and the molecular identification of key mediators, will provide insights into tumour biology and suggest novel therapeutic options.     

Genetic dissection of corticosterone receptor function in the rat hippocampus

The hippocampus, a brain structure with a crucial role in learning and memory and an involvement in stress-related neurological or psychiatric disorders, is extremely sensitive to aberrant levels of corticosteroid stress hormones (CORT). e hypothesized that CORT-affected brain disorders are the result of aberrant expression of specific CORT-responsive genes. In order to identify such genes, we have applied several gene expression profiling techniques such as differential display, DNA micro-arrays and in particular the highly sensitive serial analysis of gene expression (SAGE). Using SAGE, a total of 76,790 hippocampal tags were generated which together represent 28,748 unique mRNAs of which 4626 gave a hit with rat sequences in Genbank. By comparing SAGE profiles derived from rat hippocampi treated with different concentrations of corticosteroids, we have identified over 200 CORT-responsive genes with significant differential expression in hippocampus. The identified products include genes that are important for the plasticity of hippocampal neurones such as neural cell adhesion molecules, growth-promoting proteins, genes involved in axogenesis, synaptogenesis and signal-transduction. One novel corticosteroid-responsive gene, classified as Ca²⁺/calmodulin-dependent protein kinase (CaMK)-VI, exhibited structural resemblance with the family of CaMKs, in particular with that of CaMK-IV. We also identified an alternatively spliced mRNA of this gene encoding a peptide (CaMK-kinase related peptide or CARP) which may function in an autoregulatory feedback loop. These findings suggest a novel mode of operation of the CaMK pathway in control of Ca²⁺ homeostasis relevant for CORT-related brain disorders.     

Exploring the tumour environment: cancer-associated fibroblasts as targets in cancer therapy

Stroma cells contribute to the microenvironment that is essential for cancer growth, invasion and metastatic progression. Fibroblasts, often termed myofibroblasts or cancer-associated fibroblasts (CAFs), represent the most abundant cell type in the tumour stroma. The demonstrated tumour-promoting capacities of CAFs has increased the interest to exploit them as drug targets for anticancer therapy. Although single factors, such as platelet-derived growth factor, transforming growth factor-β1, hepatocyte growth factor and matrix metalloproteinases have been identified as mediators in the fibroblast tumour interaction, the morphological and functional differences of CAFs compared with their normal counterparts are only incompletely understood. Recently, novel global methods for gene expression profiling were applied to comprehensively characterise CAFs from breast, pancreas, colon and basal cell cancer in their in situ environment. The analysis of different CAF preparations revealed regulated genes that were previously not described in the tumour–stroma context. Additionally, besides a few striking overlaps, the comparison of the gene lists indicates a high level of heterogeneity in the expression pattern of CAFs from different tumour types. Together, these studies emphasise the importance of cross-talk between stromal and malignant cells of the tumour. It is likely that the continued characterisation of this interaction, and the molecular identification of key mediators, will provide insights into tumour biology and suggest novel therapeutic options.