Paul Thompson

Cytochrome P450 1B1 mRNA untranslated regions interact to inhibit protein translation

CYP1B1 mRNA is expressed constitutively in all normal extrahepatic human tissues, though the protein is usually undetectable. In contrast, CYP1B1 protein is expressed at high levels in tumors. In this study CYP1B1 mRNA and protein expression was measured in a panel of cell lines indicating that CYP1B1 regulation is altered in tumor cell lines in vitro. Interrogation of ONCOMINE revealed that CYP1B1 mRNA is not significantly overexpressed in tumors compared to normal tissues, suggesting CYP1B1 is subject to posttranscriptional control. Analysis of the CYP1B1 mRNA revealed a complex 5′ untranslated region (UTR) containing a small upstream open‐reading frame (uORF). These features are present in mRNAs subject to translational control so the effect of the 5′UTR was tested using in vitro translation in CHO‐K1 cells. The 5′UTR significantly inhibited luciferase reporter gene translation, and mutation of the uORF start codon abolished the inhibitory effect. The 5′UTR also interacted with the microRNA‐27b recognition element in the CYP1B1 mRNA 3′UTR to almost completely inhibit translation. CYP1B1 is subject to a high degree of translational control, which may explain the absence of protein expression in normal cells. Alterations in translational control during malignant transformation may help to explain the tumor‐specific expression of CYP1B1 protein.

Effect of prototypical inducers on ligand activated nuclear receptor regulated drug disposition genes in rodent hepatic and intestinal cells

AbstractAim:The aim of this study was to investigate the impact on expression of mRNA and protein by paradigm inducers/activators of nuclear receptors and their target genes in rat hepatic and intestinal cells. Furthermore, assess marked inter laboratory conflicting reports regarding species and tissue differences in expression to gain further insight and rationalise previously observed species differences between rodent and human based systems.Methods:Quantitative real time-polymerase chain reaction (QRT-PCR) and immunoblots were used to assess messenger RNA (mRNA) and protein expression for CYP2B2, CYP3A1, CYP3A2, CYP3A9, ABCB1a, ABCB1b, ABCC1, ABCC2, pregnane X receptor (PXR), farnesoid X receptor (FXR) and constituitive androstane receptor (CAR) in rat hepatoma cell line H411E, intestinal cells, Iec-6, and rat primary hepatocytes, in response to exposure for 18 h with prototypical inducers.Results:Dexamethasone (DEX) and pregnenolone 16α carbonitrile (PCN) significantly induced PXR, CYP3A9, ABCB1a and ABCB1b. However, when co-incubated, DEX appeared to restrict PCN-dependent induction. Chenodeoxycholic acid (CDCA) was the only ligand to induce FXR in all three cell types. Despite previously reported species differences between PCN and rifampicin (RIF), both compounds exhibited a similar profile of induction.Conclusion:Data presented herein may explain some of the discrepancies previously reported with respect to species differences from different laboratories and have important implications for study design.

Sentrin/SUMO specific proteases as novel tissue-selective modulators of vitamin D receptor-mediated signaling.

Vitamin D receptor (VDR) is a substrate for modification with small ubiquitin-like modifier (SUMO). To further assess the role of reversible SUMOylation within the vitamin D hormonal response, we evaluated the effects of sentrin/SUMO-specific proteases (SENPs) that can function to remove small ubiquitin-like modifier (SUMO) from target proteins upon the activities of VDR and related receptors. We report that SENP1 and SENP2 strikingly potentiate ligand-mediated transactivation of VDR and also its heterodimeric partner, retinoid X receptor (RXRα) with depletion of cellular SENP1 significantly diminishing the hormonal responsiveness of the endogenous vitamin D target gene CYP24A1. We find that SENP-directed modulation of VDR activity is cell line-dependent, achieving potent modulatory effects in Caco-2 and HEK-293 cells, while in MCF-7 cells the vitamin D signal is unaffected by any tested SENP. In support of their function as novel modulators of the vitamin D hormonal pathway we demonstrate that both SENP1 and SENP2 can interact with VDR and reverse its modification with SUMO2. In a preliminary analysis we identify lysine 91, a residue known to be critical for formation and DNA binding of the VDR-RXR heterodimer, as a minor SUMO acceptor site within VDR. In combination, our results support a repressor function for SUMOylation of VDR and reveal SENPs as a novel class of VDR/RXR co-regulatory protein that significantly modulate the vitamin D response and which could also have important impact upon the functionality of both RXR-containing homo and heterodimers.

Reverse engineering of gene regulation models from multi-condition experiments

Reverse-engineering of quantitative, dynamic gene-regulatory network (GRN) models from time-series gene expression data is becoming important as such data are increasingly generated for research and other purposes. A key problem in the reverse-engineering process is the under-determined nature of these data. Because of this, the reverse-engineered GRN models often lack robustness and perform poorly when used to simulate system responses to new conditions. In this study, we present a novel method capable of inferring robust GRN models from multi-condition GRN experiments. This study uses two important computational intelligence methods: artificial neural networks and particle swarm optimization.

Vitamin D receptor agonist EB1089 is a potent regulator of prostatic "intracrine" metabolism.

A contributing factor to the emergence of castrate resistant prostate cancer (CRPC) is the ability of the tumor to circumvent low circulating levels of testosterone during androgen deprivation therapy (ADT), through the production of “intracrine” tumoral androgens from precursors including cholesterol and dehydroepiandrosterone (DHEA). As these processes promote AR signaling and prostate cancer progression their modulation is required for disease prevention and treatment.

MultiGrain/MAPPER: A distributed multiscale computing approach to modeling and simulating gene regulation networks

Abstract Modeling and simulation of gene-regulatory networks (GRNs) has become an important aspect of modern systems biology investigations into mechanisms underlying gene regulation. A key task in this area is the automated inference or reverse-engineering of dynamic mechanistic GRN models from gene expression time-course data. Besides a lack of suitable data (in particular multi-condition data from the same system), one of the key challenges of this task is the computational complexity involved. The more genes in the GRN system and the more parameters a GRN model has, the higher the computational load. The computational challenge is likely to increase substantially in the near future when we tackle larger GRN systems. The goal of this study was to develop a distributed computing framework and system for reverse-engineering of GRN models. We present the resulting software called MultiGrain/MAPPER. This software is based on a new architecture and tools supporting multiscale computing in a distributed computing environment. A key feature of MultiGrain/MAPPER is the realization of GRN reverse-engineering based on the underlying distributed computing framework and multi-swarm particle swarm optimization. We demonstrate some of the features of MultiGrain/MAPPER and evaluate its performance using both real and artificial gene expression data.

PIAS4 represses vitamin D receptor-mediated signaling and acts as an E3-SUMO ligase towards vitamin D receptor.

The present study investigated the potential for members of the protein inhibitors of activated STAT (PIAS) family to function as co-regulators of the vitamin D signal pathway. Among the PIAS proteins evaluated, we establish PIAS4 as a potent inhibitor of the transcriptional responses of the CYP3A4 and CYP24A1 target genes to the active hormonal form of vitamin D, a repression that was observed to be dependent upon an intact SUMO-ligase function of PIAS4. We report that PIAS4 represents a direct binding partner for vitamin D receptor (VDR) and also facilitates its modification with SUMO2, a process that preferentially occurs on the apo-form of VDR and which is reversed upon binding of ligand. Our results implicate PIAS4 and the process of SUMOylation as important modulators of VDR-mediated signaling which may both represent flexible mechanistic components as to how vitamin D achieves its pleiotropic effects.

The influence of network topology on reverse-engineering of gene-regulatory networks

Modeling and simulation of gene-regulatory networks (GRNs) has become an important aspect of modern computational biology investigations into gene regulation. A key challenge in this area is the automated inference (reverse-engineering) of dynamic, mechanistic GRN models from time-course gene expression data. Common mathematical formalisms used to represent such models capture both the relative weight or strength of a regulator gene and the type of the regulator (activator, repressor) with a single model parameter. The goal of this study is to quantify the role this parameter plays in terms of the computational performance of the reverse-engineering process and the predictive power of the inferred GRN models. We carried out three sets of computational experiments on a GRN system consisting of 22 genes. While more comprehensive studies of this kind are ultimately required, this computational study demonstrates that models with similar training (reverse-engineering) error that have been inferred under varying degrees of a priori known topology information, exhibit considerably different predictive performance. This study was performed with a newly developed multiscale modeling and simulation tool called MultiGrain/MAPPER.

Bisociative exploration of biological and financial literature using clustering

The bile acid and xenobiotic system describes a biological network or system that facilitates detoxification and removal from the body of harmful xenobiotic and endobiotic compounds. While life scientists have developed a relatively comprehensive understanding of this system, many mechanistic details are yet to be discovered. Critical mechanisms are those which are likely to significantly further our understanding of the fundamental components and the interaction patterns that govern this systems gene expression and the identification of potential regulatory nodes. Our working assumption is that a creative information exploration of available bile acid and xenobiotic system information could support the development (and testing) of novel hypotheses about this system. To explore this we have set up an information space consisting of information from biology and finance, which we consider to be two semantically distant knowledge domains and therefore have a high potential for interesting bisociations. Using a cross-context clustering approach and outlier detection, we identify bisociations and evaluate their value in terms of their potential as novel biological hypotheses.

Distinct functional modes of SUMOylation for retinoid X receptor alpha.

The present study investigated human retinoid X receptor alpha (hRXRα) as a substrate for modification with small ubiquitin like modifier (SUMO) and how members of the protein inhibitor of activated STAT (PIAS) family may impact upon this process. In agreement with a previous study, we validate Ubc9 to facilitate SUMOylation of hRXRα at lysine 108 but note this modification to occur for all isoforms rather than specifically with SUMO1 and to preferentially occur with the unliganded form of hRXRα. SUMOylation of hRXRα is significantly enhanced through PIAS4-mediated activity with lysine 245 identified as a specific SUMO2 acceptor site modified in a PIAS4-dependent fashion. While individual mutations at lysine 108 or 245 modestly increase receptor activity, the combined loss of SUMOylation at both sites significantly potentiates the transcriptional responsiveness of hRXRα suggesting both sites may cooperate in a DNA element-dependent context. Our findings highlight combinatorial effects of SUMOylation may regulate RXRα-directed signalling in a gene-specific fashion.