Biological response genes after single dose administration of interferon beta-1b to healthy male volunteers.

Treatment with interferon beta-1b (IFNB-1b) is clinically effective in multiple sclerosis patients. However, the mechanism of action is only partially understood, and validated biological response markers are lacking. We assessed IFNB-1b-induced transcriptional changes by microarray technology. Healthy male volunteers received 250 mug IFNB-1b or placebo in a double-blind, randomized controlled trial (n=5 per group). Most transcripts demonstrated peak levels after 6-12 h and returned to baseline after 48 h. We identified 227 differentially regulated genes including novel and previously described markers. This panel may become a valuable tool for development of new IFNB-1b formulations and assessment of clinical drug effects.

Gene expression analysis of the hepatotoxicant methapyrilene in primary rat hepatocytes: an interlaboratory study.

Genomics technologies are used in several disciplines, including toxicology. However, these technologies are relatively new, and their applications require further investigations. When investigators apply these technologies to in vitro experiments, two major issues need to be clarified: a) can in vitro toxicity studies, in combination with genomics analyses, be used to predict the toxicity of a compound; and b) are the generated toxicogenomics data reproducible between laboratories? These questions were addressed by an interlaboratory study with laboratories of four pharmaceutical companies. We evaluated gene expression patterns from cultured rat primary hepatocytes after a 24-hr incubation with methapyrilene (MP). Extensive data analysis showed that comparison of genomics data from different sources is complex because both experimental and statistical variability are important confounding factors. However, appropriate statistical tools allowed us to use gene expression profiles to distinguish high-dose-treated cells from vehicle-treated cells. Moreover, we correctly identified MP in an independently generated in vitro database, underlining that in vitro toxicogenomics could be a predictive tool for toxicity. From a mechanistic point of view, despite the observed site-to-site variability, there was good concordance regarding the affected biologic processes. Several subsets of regulated genes were obtained by analyzing the data sets with one method or using different statistical analysis methods. The identified genes are involved in cellular processes that are associated to the exposure of primary hepatocytes to MP. Whether they are specific for MP and are cause or consequence of the toxicity requires further investigations.

Interlaboratory evaluation of rat hepatic gene expression changes induced by methapyrilene.

Several studies using microarrays have shown that changes in gene expression provide information about the mechanism of toxicity induced by xenobiotic agents. Nevertheless, the issue of whether gene expression profiles are reproducible across different laboratories remains to be determined. To address this question, several members of the Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute evaluated the liver gene expression profiles of rats treated with methapyrilene (MP). Animals were treated at one facility, and RNA was distributed to five different sites for gene expression analysis. A preliminary evaluation of the number of modulated genes uncovered striking differences between the five different sites. However, additional data analysis demonstrated that these differences had an effect on the absolute gene expression results but not on the outcome of the study. For all users, unsupervised algorithms showed that gene expression allows the distinction of the high dose of MP from controls and low dose. In addition, the use of a supervised analysis method (support vector machines) made it possible to correctly classify samples. In conclusion, the results show that, despite some variability, robust gene expression changes were consistent between sites. In addition, key expression changes related to the mechanism of MP-induced hepatotoxicity were identified. These results provide critical information regarding the consistency of microarray results across different laboratories and shed light on the strengths and limitations of expression profiling in drug safety analysis.

Comparison of progestin transcriptional profiles in rat mammary gland using Laser Capture Microdissection and whole tissue-sampling.

INTRODUCTION: Investigation of molecular mechanisms by gene expression profiling gains increasingly importance in preclinical safety evaluation. However, assigning expressed genes to specific cell populations is nearly impossible if the investigated RNA originates from whole tissue extracts. In this regard, Laser Capture Microdissection (LCM) can be used to detect changes specific to individual cell types. The objective of this study was to investigate the use of LCM for characterisation of progestin-related gene expression changes in the mammary gland. Thus, transcriptional profiles of the mammary gland of rats treated with a non-steroidal progesterone-receptor ligand, promegestone, medroxyprogesterone acetate, progesterone or vehicle were compared using whole tissue homogenates or LCM-captured epithelial cells. METHODS: Total RNA from 30 mammary glands was isolated from snap-frozen specimen of the whole tissue and from approximately 25.000-30.000 cells of cresyl violet stained frozen sections employing LCM. After amplification of averaged 0.2µg total RNA of LCM-captured samples, RNA was labelled, hybridised to Affymetrix GeneChips and analysed. RESULTS: LCM-captured samples showed up to 3-fold more differentially expressed probe sets (progesterone) and up to 10-fold more downregulated (promegestone) probe sets than whole tissue samples implying high cell specificity. Moreover, mammary gland specific differentiation markers like whey acidic protein, alpha lactalbumin, casein alpha s1 and casein kappa showed up to 3.4-fold (alpha lactalbumin, vehicle) higher expression values. Multivariate data analyses revealed a clear separation of gene expression profiles according to the method used, suggesting an amplification dependent bias. DISCUSSION: LCM transcriptional profiling provides highly cell-specific information. An amplification dependent bias was observed. The technical variability was shown to be smaller than the biological variability. For progestin-related transcriptional profiling of the mammary gland, whole tissue-sampling proved to yield more informative results. Therefore LCM should only be considered when cell-type specific gene expression profiles are necessary for an in depth evaluation.

In vitro characterization of ZK 230211--A type III progesterone receptor antagonist with enhanced antiproliferative properties.

The progesterone receptor (PR) is a key regulator of female reproductive functions. Compounds with progesterone inhibiting effects (PR antagonists) have found numerous utilities in female reproductive health, ranging from contraception to potential treatment of progesterone-dependent diseases like uterine leiomyomas. Based on in vitro characteristics such as DNA binding activity and partial agonistic transcriptional behavior in the presence of protein kinase A activators (cyclic-AMP), three types of PR modulators with antagonistic properties have been defined. In this study, we analyzed the in vitro characteristics of the PR antagonist ZK 230211 in comparison to the classical antagonists onapristone and mifepristone. We focused on PR actions in genomic signaling pathways, including DNA binding activity, nuclear localization and association with the nuclear receptor corepressor (NCoR) as well as actions in non-genomic signaling, such as the activation of c-Src kinase signaling and cyclin D1 gene promoter activity. ZK 230211 represents a type of PR antagonist with increased inhibitory properties in comparison to mifepristone and onapristone. When liganded to the progesterone receptor, ZK 230211 induces a strong and persistent binding to its target response element (PRE) and increases NCoR recruitment in CV-1 cells. Furthermore, ZK 230211 displays less agonistic properties with regard to the association of PR isoform B and the cytoplasmic c-Src kinase in HeLa cells. It represses T47D cell cycle progression, in particular estradiol-induced S phase entry. In summary, our studies demonstrate ZK 230211 to be a type III progesterone receptor antagonist which is characterized by very strong DNA binding activity and strong antiproliferative effects in the cancer cell lines HeLa and T47D.

Recovery of microarray-quality RNA from frozen EDTA blood samples.

INTRODUCTION: The availability of blood collection systems with RNA stabilizing additives (e.g. PAXgene) has opened the field for gene expression profiling in large multi-center clinical trials. Here, we investigated whether the PAXgene system also offers a method for extraction of RNA from frozen EDTA blood samples, which do not yield RNA of high enough quality for RNA expression profiling, when extracted with standard protocols. METHODS: Whole blood was obtained from six healthy volunteers in conventional EDTA tubes and frozen. The thawed EDTA blood was transferred into PAXgene tubes, and the RNA was extracted using the PAXgene RNA extraction kit. Microarray analysis was performed to asses the effect of RNA quality on gene expression profiles. RESULTS: The RNA yield of the transferred samples was 1.76+/-0.88 microg/ml. This yield was clearly lower than the yield from a PAXgene reference group (2.84+/-0.62 microg/ml), but considerably higher than the yield resulting from a standard protocol usually applied to fresh EDTA blood samples (0.07+/-0.06 microg/ml). The RNA integrity number (RIN) of the transferred samples was 6.1+/-0.8 as compared to 9.8+/-0.1 for the PAXgene reference. Microarray analysis of the extracted RNA suggested that samples with RIN values above 5 produce data that fulfill the quality criteria defined by the manufacturer. DISCUSSION: The transfer of thawed EDTA blood into PAXgene blood collection tubes offers a method to recover sufficient RNA of acceptable quality for microarray experiments.

Increased expression of Wnt5a in psoriatic plaques.

Psoriasis vulgaris is characterized by hyperproliferation and incomplete terminal differentiation of epidermal keratinocytes. Despite the established role of Wnt pathways in the regulation of stem cell proliferation and differentiation, they have not yet been associated with the pathophysiology of psoriasis. Here, we took biopsies from uninvolved and from lesional skin of 20 patients with plaque-type psoriasis. The biopsies were used for microarray RNA expression profiling. Based on paired samples from 13 patients, we defined 179 genes that were more than 2-fold differentially expressed in lesional skin. This list included 16 genes with known or possible association to the canonical Wnt/beta-catenin or the non-canonical Wnt/Ca2+ pathway. The expression of Wnt5a was 4-fold higher in lesional skin. Other Wnt molecules were largely unchanged (Wnt4 and Wnt16), or tended to be expressed at lower levels (Wnt7b). The mRNA expression levels of two inhibitory factors related to Wnt signaling, frizzled-related protein, and dickkopf homolog 2, were reduced in lesional skin, as was mRNA expression of cyclin D1. These findings were confirmed by quantitative reverse transcription-PCR experiments. We conclude that Wnt5a and other Wnt pathway genes are differentially expressed in psoriatic plaques. Their functional contribution to the pathophysiology of psoriasis needs to be elaborated.