Toxicogenomic analysis of N-nitrosomorpholine induced changes in rat liver: comparison of genomic and proteomic responses and anchoring to histopathological parameters.

A common animal model of chemical hepatocarcinogenesis was used to examine the utility of transcriptomic and proteomic data to identify early biomarkers related to chemically induced carcinogenesis. N-nitrosomorpholine, a frequently used genotoxic model carcinogen, was applied via drinking water at 120 mg/L to male Wistar rats for 7 weeks followed by an exposure-free period of 43 weeks. Seven specimens of each treatment group (untreated control and 120 mg/L N-nitrosomorpholine in drinking water) were sacrificed at nine time points during and after N-nitrosomorpholine treatment. Individual samples from the liver were prepared for histological and toxicogenomic analyses. For histological detection of preneoplastic and neoplastic tissue areas, sections were stained using antibodies against the placental form of glutathione-S-transferase (GST-P). Gene and protein expression profiles of liver tissue homogenates were analyzed using RG-U34A Affymetrix rat gene chips and two-dimensional gel electrophoresis-based proteomics, respectively. In order to compare results obtained by histopathology, transcriptomics and proteomics, GST-P-stained liver sections were evaluated morphometrically, which revealed a parallel time course of the area fraction of preneoplastic lesions and gene plus protein expression patterns. On the transcriptional level, an increase of hepatic GST-P expression was detectable as early as 3 weeks after study onset. Comparing deregulated genes and proteins, eight species were identified which showed a corresponding expression profile on both expression levels. Functional analysis suggests that these genes and corresponding proteins may be useful as biomarkers of early hepatocarcinogenesis.

Cell cycle arrest and reversion of Ras-induced transformation by a conditionally activated form of mitogen-activated protein kinase kinase kinase 3.

Signal-induced proliferation, differentiation, or stress responses of cells depend on mitogen-activated protein kinase (MAPK) cascades, the core modules of which consist of members of three successively acting kinase families (MAPK kinase kinase [MAP3K], MAPK kinase, and MAPK). It is demonstrated here that the MEKK3 kinase inhibits cell proliferation, a biologic response not commonly associated with members of the MAP3K family of kinases. A conditionally activated form of MEKK3 stably expressed in fibroblasts arrests these cells in early G1. MEKK3 critically blocks mitogen-driven expression of cyclin D1, a cyclin which is essential for progression of fibroblasts through G1. The MEKK3-induced block of cyclin D1 expression and of cell cycle progression may be mediated via p38 MAPK, a downstream effector of MEKK3. The MEKK3-mediated block of proliferation also reverses Ras-induced cellular transformation, suggesting possible tumor-suppressing functions for this kinase. Together, these results suggest an involvement of the MEKK3 kinase in negative regulation of cell cycle progression, and they provide the first insights into biologic activities of this kinase.

FTZ-F1-related orphan receptors in Xenopus laevis: transcriptional regulators differentially expressed during early embryogenesis.

Orphan receptors of the FTZ-F1-related group of nuclear receptors (xFF1r) were identified in Xenopus laevis by isolation of cDNAs from a neurula stage library. Two cDNAs were found, which encode full length, highly related receptor proteins, xFF1rA and B, whose closet relative known so far is the murine LRH-1 orphan receptor. xFF1rA protein expressed by a recombinant vaccinia virus system specifically binds to FTZ-F1 response elements (FRE; PyCAAGGPyCPu). In cotransfection studies, xFF1rA constitutively activates transcription, in a manner dependent on the number of FREs. The amounts of at least four mRNAs encoding full-length receptors greatly increase between gastrula and early tailbud stages and decrease at later stages. At early tailbud stages, xFTZ-F1-related antigens are found in all nuclei of the embryo.

Evaluation of the rodent Hershberger bioassay: testing of coded chemicals and supplementary molecular-biological and biochemical investigations.

Under the auspices of the Organization for Economic Cooperation and Development (OECD) the Hershberger assay is being validated as an in vivo screen for compounds with (anti)androgenic potential. We participated in the final activity, the testing of coded chemicals. Test compounds included trenbolone (TREN; 1.5, 40 mg/kg), testosterone propionate (TP; 0.4 mg/kg), flutamide (FLUT; 3mg/kg), linuron (LIN; 10, 100mg/kg), 1,1-bis-(4-chlorophenyl)-2,2-dichloroethylene (p,p'-DDE; 16, 160 mg/kg), and two negative reference substances, i.e., compounds not considered to affect androgen-sensitive tissue weights (ASTWs) in the Hershberger assay, namely 4-nonylphenol (NP; 160 mg/kg) and 2,4-dinitrophenol (DNP; 10mg/kg); TREN, LIN, p,p'-DDE, NP, and DNP being used under code. Compounds were administered for 10 days by oral intubation or subcutaneous injection (TP). Additional investigations not mandatorily requested by OECD included organ gravimetry of the liver, gene expression analysis in prostate using quantitative RT PCR for prostate specific binding protein polypeptide C3 (PBPC3) and ornithine decarboxylase 1 (ODC1) and determination of testosterone metabolizing and phase II conjugating enzymes in the liver. After submission of all study reports to OECD by participants uncoding revealed the following results: (A) When assessing androgenic potential in castrated rats, administration of TREN increased the weights of ventral prostate (VP), seminal vesicles (SV), glans penis, levator ani and bulbocavernosus muscles, and Cowper's glands at the high dose. A similar or stronger (VP, SV) increase of ASTWs was observed for TP; NP and DNP were ineffective. TREN dose-dependently increased gene expression of ODC1 and PBPC3, TP induced expression of these genes even more strongly (almost) to the level of untreated intact animals, whereas NP and DNP were inactive. Liver enzyme activities depending on physiological androgen levels were lower in castrated than in intact rats and could not be restored by androgen treatment. (B) When assessing antiandrogenic potential in TP-supplemented castrated rats, administration of LIN and p,p'-DDE decreased ASTWs only at the high dose. FLUT even more effectively decreased ASTWs, NP and DNP were again without effect. Decreases in androgen-responsive gene expression in the prostate corresponding to the organ weight changes were only observed for p,p'-DDE (high dose) and flutamide (PBPC3 only). p,p'-DDE dose-dependently induced liver weights and most liver enzyme activities including androgen-dependent ones. Our study accurately reproduced ASTW changes obtained in previous studies also under code suggesting that the Hershberger assay is a robust tool to screen for an (anti)androgenic potential. Assessment of ODC1 and PBPC3 gene expression in prostate, however, may only represent a sensitive tool for the detection of an androgenic potential. Finally, p,p'-DDE may affect ASTWs by several mechanisms including enhanced testosterone metabolism.

Characterization of primary rat proximal tubular cells by gene expression analysis.

The kidney plays a major role in excretory and reabsorptive processes. The kidney cortex consists primarily of proximal tubular cells, which are epithelial cells that are often involved in the induction and progression of various kidney diseases. Therefore primary proximal tubular cells are widely used as a renal cell model. To further characterize this kidney in vitro model different time points in culture after isolation of the cells were compared to the cortex in vivo using gene expression analysis based on microarrays. This study revealed that many metabolic pathways and some kidney-specific functions are lacking in the in vitro model. Furthermore genes involved in RNA and protein synthesis, intracellular transport, extracellular matrix and cytoskeletal organization were upregulated in culture compared to in vivo, indicating proliferation of the cells and differentiation into a cell culture phenotype. The data represented here may help to evaluate the in vivo relevance of results obtained with this in vitro model.

The pattern of retinoic acid receptor gamma (RAR gamma) expression in normal development of Xenopus laevis and after manipulation of the main body axis.

Nuclear receptors are a prerequisite for the transduction of retinoid signals in vertebrate embryogenesis. We have raised an antiserum against the X. laevis retinoic acid receptor gamma (xRAR gamma), which specifically detects a polypeptide with an M(r) of 54 x 10(3) in embryos at gastrula and neurula stages. The antiserum reveals xRAR gamma as a nuclear protein in the head endomesoderm, the neuroectoderm of the hindbrain region, and the entire posterior region during neurula stages. Explanted animal caps express low amounts of xRAR gamma in the absence of mesoderm induction. Treatment of animal caps with activin leads to an increase of the amount and to a regionalization of the xRAR gamma expression. In exogastrulae and in Keller sandwiches, the pattern of expression in the endomesoderm is as expected by analogy to the normal embryo and therefore independent of the vertical contact between the germ layers. A planar signal coming from the dorsal mesoderm is sufficient to impose region-specific expression of xRAR gamma in the neuroectoderm of Keller sandwiches.

A naturally occurring short variant of the FTZ-F1-related nuclear orphan receptor xFF1rA and interactions between domains of xFF1rA.

The FTZ-F1-related nuclear orphan receptors xFF1rA and B were identified previously in Xenopus laevis by cDNA cloning. In addition to two cDNAs that encode full-length receptor proteins, a third cDNA encodes a form of xFF1rA truncated at the C terminus. Transcripts encoding the short form of the receptor are present at much lower levels than mRNAs encoding the full-length receptors. Significant activation of reporter genes in xFF1rA-transfected HeLa cells requires two or more copies of a FTZ-F1-responsive element (FRE). However, in vitro, recombinant xFF1rA protein binds FRE monomers and dimers with apparently equal affinity. In cotransfection studies, full-length xFF1rA activates transcription, in contrast to xFF1rAshort. In vitro, xFF1rAshort binds to FRE with a lower efficiency than xFF1rA. A partial truncation of the E domain reduces the DNA-binding activity of domain C, suggesting that parts of the E domain might interact with the DNA-binding domain C. In parallel with the loss of DNA-binding efficiency, such truncations lead to loss of transcriptional activation. For transcriptional activation, either the A/B domain or the complete E domain is required, as shown by recombination of different domains of xFF1rA with the DNA-binding domain of Gal4. Coexpression of the truncated form xFF1rAshort decreases transcriptional activation by xFF1rA, but not by the active Gal4-xFF1rA fusion protein that contains domain E. This indicates that xFF1rAshort interferes with xFF1A by competition for FRE binding. An excess of xFF1rAshort is required, presumably due to its poor FRE-binding activity. The function of the E domain in regulating DNA-binding and transcriptional activation is discussed.

Retinoic acid receptors and nuclear orphan receptors in the development of Xenopus laevis.

Nuclear hormone receptors are ligand-activated transcription factors that regulate the expression of target genes by binding to hormone responsive elements (HRE) in their 5' upstream region. Retinoids which are known for their teratogenicity and which have a potential role in the specification of the anteroposterior axis of vertebrate embryos regulate transcription via a hormone-like mechanism by activating nuclear retinoic acid receptors, designated RAR and RXR. Of the several isoforms of RAR found in embryos of Xenopus laevis, xRAR gamma 2 appears to be the most abundant. During the early retinoic acid-sensitive period of development, the total amount of xRAR gamma 2 transcript and protein is increased and a highly specific pattern of expression emerges. During neurulation, the receptor is predominantly found in the dorsal posterior region, in the head endomesoderm, and in the rostral hindbrain. The dependence of this pattern on mesoderm induction and on neural induction is discussed. Contrasting with the elaborate pattern of xRAR gamma 2, the FTZ-F1-related nuclear orphan receptors (xFF1rA/B) are ubiquitous nuclear proteins in Xenopus embryos, as are the peroxisome proliferator-activated receptors xPPAR alpha and beta. PPARs are activated by polyunsaturated fatty acids and regulate the synthesis of enzymes involved in lipid metabolism. Later in development, the isoforms xPPAR alpha, beta, and gamma attain different tissue specificities.

Application of RNA interference to improve mechanistic understanding of omics responses to a hepatotoxic drug in primary rat hepatocytes.

Inhibition of the glucagon receptor (GCGR) has been identified as a potential therapeutic approach for the treatment of type 2 diabetes. However, a small molecule drug candidate antagonizing GCGR (BAY16) failed during preclinical drug development, in part due to drug induced hepatotoxicity in animals. Since there is evidence to suggest that endogenous GCGR signaling might be important for hepatocyte survival, we hypothesized that on-target effects, i.e., modulation of GCGR activity by BAY16, may contribute to BAY16 hepatotoxicity and associated gene expression changes in rats. To understand the role of GCGR inhibition in BAY16 toxicity, we analyzed cell viability and gene expression profiles in non-silenced and GCGR-targeting siRNA transfected primary rat hepatocytes with and without exposure to BAY16 to discriminate between on- and off-target effects of BAY16. siRNA-mediated silencing of the GCGR did not affect cell viability in primary rat hepatocytes, indicating that cytotoxicity of BAY16 occurs independent of its pharmacological effects. In support of this, gene expression analysis of GCGR silenced hepatocytes revealed no transcriptional alterations relevant to toxicity. In contrast, BAY16 caused a concentration-dependent decrease in cell viability, along with changes in the expression of genes associated with altered xenobiotic metabolism, oxidative stress, increased fatty acid synthesis, and alterations in cholesterol and bile acid metabolic processes. Based on gene expression data, it appears that hepatocytes inhibit cholesterol synthesis and increase detoxifying and eliminating processes in order to protect themselves from accumulation of bile acids, cholesterol or drug intermediates. Importantly, comparison of transcriptional changes in the absence and presence of GCGR revealed that the same pathways were affected in both silenced and non-silenced hepatocytes, indicating that BAY16 toxicity occurs independent of the GCGR receptor.

In vitro - in vivo correlation of gene expression alterations induced by liver carcinogens.

Although cultivated hepatocytes are widely used in the studies of drug metabolism, their application in toxicogenomics is considered as problematic, because previous studies have reported only little overlap between chemically induced gene expression alterations in liver in vivo and in cultivated hepatocytes. Here, we identified 22 genes that were altered in livers of rats after oral administration of the liver carcinogens aflatoxin B1 (AB1), 2-nitrofluorene (2-NF), methapyrilene (MP) or piperonyl-butoxide (PBO). The functions of the 22 genes have been classified into two groups. Genes related to stress response, DNA repair or metabolism and genes associated with cell proliferation, respectively. Next, rat hepatocyte sandwich cultures were exposed to AB1, 2-NF, MP or PBO for 24h and expression of the above mentioned genes was determined by RT-qPCR. Significant correlations between the degree of gene expression alterations in vivo and in vitro were obtained for the stress, DNA repair and metabolism associated genes at concentrations covering a range from cytotoxic concentrations to non-toxic/in vivo relevant concentrations. In contrast to the stress associated genes, no significant in vivo/in vitro correlation was obtained for the genes associated with cell proliferation. To understand the reason of this discrepancy, we compared replacement proliferation in vivo and in vitro. While hepatocytes in vivo, killed after administration of hepatotoxic compounds, are rapidly replaced by proliferating surviving cells, in vitro no replacement proliferation as evidenced by BrdU incorporation was observed after washing out hepatotoxic concentrations of MP. In conclusion, there is a good correlation between gene expression alterations induced by liver carcinogens in vivo and in cultivated hepatocytes. However, it should be considered that cultivated primary hepatocytes do not show replacement proliferation explaining the in vivo/in vitro discrepancy concerning proliferation associated genes.

Testosterone response of hepatic gene expression in female mice having acquired testosterone-unresponsive immunity to Plasmodium chabaudi malaria.

Blood-stage malaria of Plasmodium chabaudi is characterized by its responsiveness to testosterone (T): T suppresses development of protective immunity, whereas once acquired immunity is T-unresponsive. Here, we have analyzed the liver, a T target and lymphoid organ with anti-malaria activity, for its T-responsiveness of gene expression in immune mice. Using Affymetrix microarray technology, in combination with quantitative RT-PCR, we have identified (i) T-unresponsive expression of newly acquired mRNAs encoding diverse sequences of IgG- and IgM-antibodies, (ii) 24 genes whose expression has become T-unresponsive including those encoding the T(H)2 response promoting EHMT2 and the erythrocyte membrane protein band 7.2 STOM, (iii) T-unresponsive expression of mRNAs for the cytokines IL-1ß, IL-6, TNFα, and IFNγ, as well as iNOS, which are even not inducible by infection, and (iv) 35 genes retaining their T-responsiveness, which include those encoding the infection-inducible acute phase proteins SAA1, SAA2, and ORM2 as well as those of liver metabolism which encode the T-downregulated female-prevalent enzymes CYP2B9, CYP2B13, CYP3A41, CYP7A1, and SULT2A2 and the T-upregulated male-prevalent enzymes CYP2D9, CYP7B1, UGT2B1, HSD3B2, HSD3B5, respectively. The mRNA of the latter T-metabolizing enzyme is even 5-fold increased by T, suggesting a decrease in the effective T concentrations in the liver of immune mice. Collectively, our data suggest that the liver, which has acquired a selective T-unresponsiveness of gene expression, contributes to the acquired T-unresponsive, antibody-mediated protective immunity to blood-stage malaria of P. chabaudi.

Assessment of candidate biomarkers of drug-induced hepatobiliary injury in preclinical toxicity studies.

This study was designed to assess the value of a set of potential markers for improved detection of liver injury in preclinical toxicity studies. Male Wistar rats were treated with drug candidates (BAY16, EMD335823, BI-3) that previously failed during development, in part due to hepatotoxicity, at two dose levels for 1, 3 and 14 days. Concentrations of lipocalin-2/NGAL and clusterin, which are frequently overexpressed and released from damaged tissues, and thiostatin, recently identified within PredTox as being elevated in urine in response to liver injury, were determined in rat urine and serum by ELISA. This was supplemented by confirmatory qRT-PCR and immunohistochemical analyses in the target organ. Serum paraoxonase-1 activity (PON1), which has been suggested as a marker of hepatotoxicity, was determined using a fluorometric assay. Clusterin and PON1 were not consistently altered in response to liver injury. In contrast, thiostatin and NGAL were increased in serum and urine of treated animals in a time- and dose-dependent manner. These changes correlated well with mRNA expression in the target organ and generally reflected the onset and degree of drug-induced liver injury. Receiver-operating characteristics (ROC) analyses supported serum thiostatin, but not NGAL, as a better indicator of drug-induced hepatobiliary injury than conventional clinical chemistry parameters, i.e. ALP, ALT and AST. Although thiostatin, an acute phase protein expressed in a range of tissues, may not be specific for liver injury, our results indicate that thiostatin may serve as a sensitive, minimally-invasive diagnostic marker of inflammation and tissue damage in preclinical safety assessment.

A retinoic acid receptor expressed in the early development of Xenopus laevis.

We have isolated cDNAs coding for a putative retinoic acid receptor (RAR) of the gamma-type from a Xenopus laevis neurula cDNA library. By transient cotransfection of COS cells with an expression vector and a reporter plasmid, this cDNA is shown to direct the synthesis of a retinoic acid-dependent transcription factor. In embryos of X. laevis, transcription of the corresponding gene is greatly enhanced during gastrulation and early neurulation. Two distinct areas with high abundance of RAR gamma mRNA are located at the anterior and at the posterior end of the neurula. The two maxima have emerged by the end of gastrulation and they become more pronounced during neurulation. At tailbud and early tadpole stages, the RAR transcripts are found mainly in the head mesenchyme and in the tailbud. The expression of this RAR is region-specific but not germ-layer-specific. The strong and stage-specific activation of zygotic transcription of this RAR gene, and the specific localization of the mRNA are consistent with the temporal and spatial pattern of retinoic acid sensitivity of X. laevis embryos. Therefore it is likely that the gene product mediates the effects of endogenous and of exogenous retinoic acid on early embryogenesis of Xenopus. The significance of these findings for the specification of the anteroposterior axis is discussed.

Direct activation of the stress-activated protein kinase (SAPK) and extracellular signal-regulated protein kinase (ERK) pathways by an inducible mitogen-activated protein Kinase/ERK kinase kinase 3 (MEKK) derivative.

The extracellular signal-regulated kinase (ERK) pathway, the stress-activated protein kinase (SAPK) pathway, and the p38 pathway are three major mitogen-activated protein kinase (MAPK) cascades known to participate in the regulation of cellular responses to a variety of extracellular signals. Upstream regulatory components of these kinase cascades, the MAPK/ERK kinase kinases (MEKK), have been described in several systems. We have isolated a cDNA encoding human MEKK3. Transfected MEKK3 has the ability to activate both SAPK and ERK pathways, but does not induce p38 activity, in agreement with a previous report on murine MEKK3 (Blank, J. L., Gerwins, P., Elliott, E. M., Sather, S., and Johnson, G. L. (1996) J. Biol. Chem. 271, 5361-5368). We now demonstrate that MEKK3 activates SEK and MEK, the known kinases targeting SAPK and ERK, respectively. Utilizing an estrogen ligand-activated MEKK3 derivative, we furthermore demonstrate that MEKK3 regulates the SAPK and the ERK pathway directly. Consistent with the fact that several SAPK-inducing agents activate the transcription factor NFkappaB, we now show that MEKK3 also enhances transcription from an NFkappaB-dependent reporter gene in cotransfection assays. The ability of MEKK3 to simultaneously activate the SAPK and ERK pathways is remarkable, given that they have divergent roles in cellular homeostasis.

Beta 1-integrin is a maternal protein that is inserted into all newly formed plasma membranes during early Xenopus embryogenesis.

A monoclonal antibody (mAb 8C8) that recognizes the Xenopus beta 1-integrin chain was used to study the appearance, synthesis and distribution of this integrin subunit during the early development of Xenopus. Both the precursor and the mature form of beta 1-integrin are provided maternally. They do not increase significantly in amount until early gastrula when the level of both forms begins to rise gradually. Synthesis of beta 1-integrin from maternal mRNA is observed throughout the pregastrula phase, though it seems to add only little to the total beta 1-integrin of the embryo. Until late blastula only small amounts of precursor are processed into the mature form. Starting with the formation of the first cleavage membrane, mature beta 1-integrin is inserted into the newly formed plasma membranes of all cells. The membrane domains forming the outer surface of the embryo remain devoid of the antigen. The data suggest an as yet unknown function of beta 1-integrin during the cleavage phase.

Ste20-like kinase (SLK), a regulatory kinase for polo-like kinase (Plk) during the G2/M transition in somatic cells.

BACKGROUND: Activation of the cyclin-dependent kinase cdc2-cyclin B1 at the G2/M transition of the cell cycle requires dephosphorylation of threonine-14 and tyrosine-15 in cdc2, which in higher eukaryotes is brought about by the Cdc25C phosphatase. In Xenopus, there is evidence that a kinase cascade comprised of xPlkk1 and Plx1, the Xenopus polo-like kinase 1, plays a key role in the activation of Cdc25C during oocyte maturation. In the mammalian somatic cell cycle, a polo-like kinase homologue (Plk1) also functions during mitosis, but a kinase upstream of Plk is still unknown. RESULTS: We show here that human Ste20-like kinase (SLK), which is a ubiquitously expressed mammalian protein related to xPlkk1, can phosphorylate and activate murine Plk1. During progression through the G2 phase of the mammalian cell cycle, the activity of endogenous SLK is increased. The amount of SLK protein is decreased in quiescent and differentiating cells. Treatment with okadaic acid induces a phosphorylation-dependent enhancement of SLK activity. CONCLUSIONS: We propose that SLK has a role in the regulation of Plk1 activity in actively dividing cells during the somatic cell cycle. SLK itself is suggested to be regulated by phosphorylation.

Physical and functional interaction of filamin (actin-binding protein-280) and tumor necrosis factor receptor-associated factor 2.

Tumor necrosis factor (TNF) receptor-associated factor 2 (TRAF2) is an intracellular protein involved in signal transduction from TNF receptor I and II and related receptors. TRAF2 is required for TNF-induced activation of c-Jun N-terminal kinase/stress-activated protein kinase (JNK/SAPK), and TRAF2 can also mediate activation of NF-kappaB. Here we have identified the actin-binding protein Filamin (actin-binding protein-280) as a TRAF2-interacting protein. Filamin binds to the Ring zinc finger domain of TRAF2. Overexpressed Filamin inhibits TRAF2-induced activation of JNK/SAPK and of NF-kappaB. Furthermore, ectopically expressed Filamin inhibits NF-kappaB activation induced via TNF, interleukin-1, Toll receptors, and TRAF6 but not activation induced via overexpression of NIK, a downstream effector in these pathways. Importantly, TNF fails to activate SAPK or NF-kappaB in a human melanoma cell line deficient in Filamin. Reintroduction of Filamin into these cells restores the TNF response. The data imply a role for Filamin in inflammatory signal transduction pathways.