Do in vitro assays in rat primary neurons predict drug-induced seizure liability in humans?

Drug-induced seizures contribute to the high attrition rate of pharmaceutical compounds in development. The assessment of drug-induced seizure liability generally occurs in later phases of development using low throughput and intensive in vivo assays. In the present study, we evaluated the potential of an in vitro assay for detecting drug-induced seizure risk compared to evaluation in rats in vivo. We investigated the effects of 8 reference drugs with a known seizurogenic risk using micro-electrode array (MEA) recordings from freshly-dissociated rat primary neurons cultured on 48-well dishes for 28 days, compared to their effects on the EEG in anesthetized rats. In addition, we evaluated functional responses and mRNA expression levels of different receptors in vitro to understand the potential mechanisms of drug-induced seizure risk. Combining the functional MEA in vitro data with concomitant gene expression allowed us to identify several potential molecular targets that might explain the drug-induced seizures occurring in both rats and humans. Our data 1) demonstrate the utility of a group of MEA parameters for detecting potential drug-induced seizure risk in vitro; 2) suggest that an in vitro MEA assay with rat primary neurons may have advantages over an in vivo rat model; and 3) identify potential mechanisms for the discordance between rat assays and human seizure risk for certain seizurogenic drugs.

Evaluation of established human iPSC-derived neurons to model neurodegenerative diseases.

Neurodegenerative diseases are difficult to study due to unavailability of human neurons. Cell culture systems and primary rodent cultures have shown to be indispensable to clarify disease mechanisms and provide insights into gene functions. Nevertheless, it is hard to translate new findings into new medicines. The discovery of human induced pluripotent stem cells (iPSC) might partially overcome this problem. Commercially available human iPSC-derived neurons, when thoroughly characterized and suitable for viral transduction, might represent a faster model for drugs screening than the time-consuming derivation and differentiation of iPSC from patient samples. In this study we show that iCell® neurons are primarily immature GABAergic neurons within the tested time frame. Addition of C6 glioma conditioned medium improved the bursting frequency of cells without further maturation or evidence for glutamatergic responses. Furthermore, cells were suitable for lentiviral transduction within the tested time frame. Altogether, iCell® neurons might be useful to model neurodegenerative diseases in which young GABAergic subtypes are affected.

An investigation on performance of Significance Analysis of Microarray (SAM) for the comparisons of several treatments with one control in the presence of small-variance genes.

One of multiple testing problems in drug finding experiments is the comparison of several treatments with one control. In this paper we discuss a particular situation of such an experiment, i.e., a microarray setting, where the many-to-one comparisons need to be addressed for thousands of genes simultaneously. For a gene-specific analysis, Dunnett's single step procedure is considered within gene tests, while the FDR controlling procedures such as Significance Analysis of Microarrays (SAM) and Benjamini and Hochberg (BH) False Discovery Rate (FDR) adjustment are applied to control the error rate across genes. The method is applied to a microarray experiment with four treatment groups (three microarrays in each group) and 16,998 genes. Simulation studies are conducted to investigate the performance of the SAM method and the BH-FDR procedure with regard to controlling the FDR, and to investigate the effect of small-variance genes on the FDR in the SAM procedure.

In vitro methylation of predetermined regions in recombinant DNA constructs.

DNA methylation at position 5 in the cytosine ring in the sequence CpG can be detrimental to the transcription of a variety of genes in higher eukaryotes (1,2). Although the significance of this transcriptional repression is currently under debate (3,4), there is little disagreement that it plays an important role in genomic imprinting and X-chromosome inactivation (5,6). To study the effects of DNA methylation on transcription in an experimental system, bacterial DNA methyltransferases have been used widely in order to mimic the DNA methylation pattern of eukaryotic genes. However, usually every target site in a given recombinant DNA molecule will be subject to DNA methylation by making use of those enzymes. This might result in an exaggeration of the effects of DNA methylation, as most recombinant DNA molecules contain a high degree of prokaryotic DNA, which is rich in CpGs. This methylated CpGrich DNA can contribute to the effects of DNA methylation by formation of a repressive chromatin structure (7,8). In addition, selective DNA methylation is required to distinguish the effects of DNA methylation on transcription initiation and transcript elongation (8,9). Thus, there is a requirement for a method to generate recombinant DNA molecules that are methylated in a predetermined region. The chapter following this one will describe a method that makes use of ligation of methylated DNA fragments into unmethylated vector DNA. This method relies on the availability of suitable restriction sites, which allow directional cloning of the fragment and, in addition, requires a highly efficient ligation reaction.

Cloning and characterization of human histone deacetylase 8.

To date, seven different human histone deacetylases (HDACs) have been identified, which fall into two distinct classes. We have isolated and characterized a cDNA encoding a novel human HDAC, which we name HDAC8. HDAC8 shows a high degree of sequence similarity to HDAC1 and HDAC2 and thus belongs to the class I of HDACs. HDAC8 is expressed in a variety of tissues. Human cells overexpressing HDAC8 localize the protein in sub-nuclear compartments whereas HDAC1 shows an even nuclear distribution. In addition, the HDAC8 gene is localized on the X chromosome at position q13, which is close to the XIST gene and chromosomal breakpoints associated with preleukemia.

Cloning and analysis of a novel human putative DNA methyltransferase.

DNA methylation is intricately involved in a variety of cellular processes, such as differentiation, cell cycle progression, X-chromosome inactivation and genomic imprinting. However, little is known about how specific DNA methylation patterns are established and maintained. Previously one mammalian DNA methyltransferase has been described, but there has been considerable speculation about the presence of a second activity capable of methylation. Here we report the identification and characterization of a novel human putative DNA methyltransferase. Using a bioinformatics screen we have identified several expressed sequence tags which show high sequence similarity to the Schizosaccharomyces pombe gene pmt1+. The cDNA for PuMet (for putative DNA methyltransferase) was cloned and the predicted amino acid sequence deduced. The gene is ubiquitously expressed, albeit at low levels. Like several other DNA methyltransferases, the bacterially overexpressed protein is not active in methylation assays.

Cloning and expression of a human serotonin 5-HT4 receptor cDNA.

Using a combination of library screening and nested PCR based on a partial human serotonin 5-HT4 receptor sequence, we have cloned the complete coding region for a human 5-HT4 receptor. The sequence shows extensive similarity to the published porcine 5-HT4A and rat 5-HT4L receptor cDNA; however, in comparison with the latter, we find an open reading frame corresponding to only 388 amino acids instead of 406 amino acids. This difference is due to a frame shift caused by an additional cytosine found in the human sequence after position 1,154. Moreover, we also found the same additional cytosine in the rat 5-HT4 sequence. We confirmed the occurrence of the sequence by examining this part of the sequence in genomic DNA of 10 human volunteers and in rat genomic DNA. Based on a part of the genomic 5-HT4 receptor sequence that was identified in the cloning process, there seem to be at least two possible splice sites in the coding region of the gene. The human 5-HT4 receptor, transiently expressed in COS-7 cells, showed radioligand binding properties similar to 5-HT4 receptors in guinea pig striatal tissue. [3H]GR 113808 revealed K(D) values of 0.15 +/- 0.01 nM for the human receptor and 0.3 +/- 0.1 nM in the guinea pig tissue. Binding constants were determined for four investigated 5-HT4 antagonists and three agonists, and appropriate binding inhibition constants were found in each case. Stimulation of transfected COS-7 cells with 5-HT4-specific agonists caused an increase in cyclic AMP levels.