Identification of genes controlled by the pregnane X receptor by microarray analysis of mRNAs from pregnenolone 16alpha-carbonitrile-treated rats.

Mammalian liver contains a pregnane X receptor (PXR, NR1I2), which binds drugs and other xenobiotics, and stimulates (or suppresses) expression of numerous genes involved in the metabolic elimination of foreign compounds and some toxic endogenous substances. In the present study, we used microarray analysis to identify genes whose expression in rat liver was significantly altered by pregnenolone 16alpha-carbonitrile (PCN) treatment. PCN is a synthetic steroid that induces cytochrome P4503A expression and is hepatoprotective by increasing resistance to subsequent stressful insults. Significant induction was seen for 138 genes while expression of 82 genes was significantly repressed. We found induction of genes known to be induced by PCN, such as enzymes involved in drug metabolism and transport. In addition, many genes were differentially expressed whose functions concerned intracellular metabolism, transport of essential small molecules, cell cycle, and redox balance. Our results support the idea that the domain of PXR-controlled gene networks may be even more extensive than currently thought and may extend to functions apart from xenobiotic metabolism.

Evidence-based toxicology: a comprehensive framework for causation.

This paper identifies deficiencies in some current practices of causation and risk evaluation by toxicologists and formulates an evidence-based solution. The practice of toxicology focuses on adverse health events caused by physical or chemical agents. Some relations between agents and events are identified risks, meaning unwanted events known to occur at some frequency. However, other relations that are only possibilities--not known to occur (and may never be realized)--also are sometimes called risks and are even expressed quantitatively. The seemingly slight differences in connotation among various uses of the word 'risk' conceal deeply philosophic differences in the epistemology of harm. We label as 'nomological possibilities' (not as risks) all predictions of harm that are known not to be physically or logically impossible. Some of these nomological possibilities are known to be causal. We term them 'epistemic'. Epistemic possibilities are risks. The remaining nomological possibilities are called 'uncertainties'. Distinguishing risks (epistemic relationships) from among all nomological possibilities requires knowledge of causation. Causality becomes knowable when scientific experiments demonstrate, in a strong, consistent (repeatable), specific, dose-dependent, coherent, temporal and predictive manner that a change in a stimulus determines an asymmetric, directional change in the effect. Many believe that a similar set of characteristics, popularly called the 'Hill Criteria', make it possible, if knowledge is robust, to infer causation from only observational (nonexperimental) studies, where allocation of test subjects or items is not under the control of the investigator. Until the 1980s, medical decisions about diagnosis, prevention, treatment or harm were often made authoritatively. Rather than employing a rigorous evaluation of causal relationships and applying these criteria to the published knowledge, the field of medicine was dominated by authority-based opinions, expressed by experts (or consensus groups of experts) relying on their education, training, experience, wisdom, prestige, intuition, skill and improvisation. In response, evidence-based medicine (EBM) was developed, to make a conscientious, explicit and judicious use of current best evidence in deciding about the care of individual patients. Now globally embraced, EBM employs a structured, 'transparent' protocol for carrying out a deliberate, objective, unbiased and systematic review of the evidence about a formally framed question. Not only in medicine, but now in dentistry, engineering and other fields that have adapted the methods of EBM, it is the quality of the evidence and the rigor of the analysis through evidence-based logic (EBL), rather than the professional standing of the reviewer, that leads to evidence-based conclusions about what is known. Recent studies have disclosed that toxicologists (individually or in expert groups), not unlike their medical counterparts prior to EBM, show distressing variations in their biases with regard to data selection, data interpretation and data evaluation when performing reviews for causation analyses. Moreover, toxicologists often fail to acknowledge explicitly (particularly in regulatory and policy-making arenas) when shortcomings in the evidence necessitate reliance upon authority-based opinions, rather than evidence-based conclusions (Guzelian PS, Guzelian CP. Authority-based explanation. Science 2004; 303: 1468-69). Accordingly, for answering questions about general and specific causation, we have constructed a framework for evidence-based toxicology (EBT), derived from the accepted principles of EBM and expressed succinctly as three stages, comprising 12 total steps. These are: 1) collecting and evaluating the relevant data (Source, Exposure, Dose, Diagnosis); 2) collecting and evaluating the relevant knowledge (Frame the question, Assemble the relevant (delimited) literature, Assess and critique the literature); and 3) Joining data with knowledge to arrive at a conclusion (General causation--answer to the framed question, Dose-response, Timing, Alternative cause, Coherence). The second of these stages (which amounts to an analysis of general causation), is addressed by an EBM-styled approach (adapted for the infrequent availability of human experimental studies in environmental toxicology). This involves assembling literature (through documented algorithms for database queries), excluding irrelevancies by use of delimiters as filters, and ranking and rating the remaining articles for strength of study design and for quality of execution gauged by application of either a ready-made quality assessment instrument or a custom designed checklist or scale. The results of this systematic review (including a structured review of relevant animal and in vitro studies) are then themselves systematically used to determine which causation criteria are fulfilled. Toxicology is maturing from a derivative science largely devoted to routinized performance and interpretation of safety tests, to a discipline deeply enmeshed in the remarkable advances in biochemistry and molecular biology to better understanding the nature and mechanism of adverse effects caused by chemicals. It is time for toxicologists, like scientists in other fields, to formalize a method for differentiating settled toxicological knowledge of risk from mere nomological possibility, and for communicating their conclusions to other scientists and the public. It is time for EBT.

Regulation of a xenobiotic sulfonation cascade by nuclear pregnane X receptor (PXR).

The nuclear receptor PXR (pregnane X receptor) protects the body from hepatotoxicity of secondary bile acids such as lithocholic acid (LCA) by inducing expression of the hydroxylating cytochrome P450 enzyme CYP3A and promoting detoxification. We found that activation of PXR also increases the activity and gene expression of the phase II conjugating enzyme dehydroepiandrosterone sulfotransferase (STD) known to sulfate LCA to facilitate its elimination. This activation is direct and appears to extend to other xenobiotic sulfotransferases as well as to 3'-phosphoadenosine 5'-phosphosulfate synthetase 2 (PAPSS2), an enzyme that generates the donor cofactor for the reaction. Because sulfation plays an important role in the metabolism of many xenobiotics, prescription drugs, and toxins, we propose that PXR serves as a master regulator of the phase I and II responses to facilitate rapid and efficient detoxification and elimination of foreign chemicals.

Ectopic expression of MHC class II genes (RT1.B(I) beta/alpha) in rat hepatocytes in vivo and in culture can be elicited by treatment with the pregnane X receptor agonists pregnenolone 16 alpha-carbonitrile and dexamethasone.

The synthetic steroid, pregnenolone-16-alpha-carbonitrile (PCN), has served for decades as a probe for a postulated series of hepatic defenses activated under situations of environmental "stress". PCN, an antiglucocorticoid, and also such glucocorticoids as dexamethasone (Dex) appear to stimulate hepatic metabolism and elimination of xenobiotics by binding to the nuclear pregnane X receptor (PXR) which then interacts with a distinct DNA response element associated with induction of cytochrome P450 3A genes. To explore the full domain of genes controlled by PCN/PXR, we used differential display to detect rat liver mRNA species selectively induced by PCN or by Dex. Sequence analysis identified one of many PCN induced cDNA fragments as RT1.B(I)beta, a member of the major histocompatability class II (MHC) gene family usually found only in antigen presenting cells. Northern blot analysis of RNA from rat liver or from cultured hepatocytes confirmed that amounts of RT1.B(I)beta mRNA and also of its companion gene, RT1.B(I)alpha mRNA, became readily detectable within 3-6 hours following treatment with PCN or Dex, whereas no induction was observed in spleen RNA. Induction by PCN of RT1.B(I)beta immunoreactive protein was localized to the hepatocytes as judged by immunofluorescence. We conclude that ectopic expression of MHC II genes, an unprecedented effect of steroids or drugs, is rapidly evoked by PCN acting on the liver, directly. The concept of a set of genes coordinately controlled to maintain homeostasis in parenchymal tissues during toxic stress must now be extended to include the immune system.