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Wu W, Kaminski N. Chronic lung diseases. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 1:298-308. [PMID: 20835999 DOI: 10.1002/wsbm.23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chronic lung diseases often have high morbidity and mortality rate and have posed a serious threat to human health. The incidence of many chronic lung diseases such as asthma has been on the rise in the past decade, which causes serious economic burden. Despite many efforts which employed traditional experimental approaches to elucidate the mechanisms of the diseases have been made, little is known about the pathogenesis of complex lung diseases. Systems biology approaches which aim to integrate and analyze information gathered from multiple sources offer a great opportunity to examine complex human diseases from a new angle. Many attempts have been made using high-throughput technologies such as microarrays to study chronic lung diseases; although compared with the full-fledged systems biology approach, research strategies employed in most of these investigations still have much room to improve, promising findings have already emerged from these efforts, which demonstrates the potential of implementing systems biology in pulmonary biomedical research.
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Affiliation(s)
- Wei Wu
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Naftali Kaminski
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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52
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Minor RAC, Limmon GV, Miller-DeGraff L, Dixon D, Andrews DMK, Kaufman RJ, Imani F. Double-stranded RNA-activated protein kinase regulates early innate immune responses during respiratory syncytial virus infection. J Interferon Cytokine Res 2010; 30:263-72. [PMID: 20038207 DOI: 10.1089/jir.2009.0051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of childhood viral bronchiolitis and lung injury. Inflammatory responses significantly contribute to lung pathologies during RSV infections and bronchiolitis but the exact mechanisms have not been completely defined. The double-stranded RNA-activated protein kinase (PKR) functions to inhibit viral replication and participates in several signaling pathways associated with innate inflammatory immune responses. Using a functionally defective PKR (PKR(-/-)) mouse model, we investigated the role of this kinase in early events of RSV-induced inflammation. Our data showed that bronchoalveolar lavage (BAL) fluid from infected PKR(-/-) mice had significantly lower levels of several innate inflammatory cytokines and chemokines. Histological examinations revealed that there was less lung injury in infected PKR(-/-) mice as compared to the wild type. A genome-wide analysis showed that several early antiviral and immune regulatory genes were affected by PKR activation. These data suggest that PKR is a signaling molecule for immune responses during RSV infections.
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53
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Sukumaran S, Almon RR, DuBois DC, Jusko WJ. Circadian rhythms in gene expression: Relationship to physiology, disease, drug disposition and drug action. Adv Drug Deliv Rev 2010; 62:904-17. [PMID: 20542067 PMCID: PMC2922481 DOI: 10.1016/j.addr.2010.05.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 05/10/2010] [Accepted: 05/26/2010] [Indexed: 12/26/2022]
Abstract
Circadian rhythms (24h cycles) are observed in virtually all aspects of mammalian function from expression of genes to complex physiological processes. The master clock is present in the suprachiasmatic nucleus (SCN) in the anterior part of the hypothalamus and controls peripheral clocks present in other parts of the body. Components of this core clock mechanism regulate the circadian rhythms in genome-wide mRNA expression, which in turn regulate various biological processes. Disruption of circadian rhythms can be either the cause or the effect of various disorders including metabolic syndrome, inflammatory diseases and cancer. Furthermore, circadian rhythms in gene expression regulate both the action and disposition of various drugs and affect therapeutic efficacy and toxicity based on dosing time. Understanding the regulation of circadian rhythms in gene expression plays an important role in both optimizing the dosing time for existing drugs and in the development of new therapeutics targeting the molecular clock.
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Affiliation(s)
- Siddharth Sukumaran
- Department of Biological Sciences, State University of New York at Buffalo, 14260, United States
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54
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Circadian dysfunction in disease. Trends Pharmacol Sci 2010; 31:191-8. [PMID: 20171747 DOI: 10.1016/j.tips.2010.01.002] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/14/2010] [Accepted: 01/19/2010] [Indexed: 02/06/2023]
Abstract
The classic view of circadian timing in mammals emphasizes a light-responsive 'master clock' within the hypothalamus which imparts temporal information to the organism. Recent work indicates that such a unicentric model of the clock is inadequate. Autonomous circadian timers have now been demonstrated in numerous brain regions and peripheral tissues in which molecular-clock machinery drives rhythmic transcriptional cascades in a tissue-specific manner. Clock genes also participate in reciprocal regulatory feedback with key signalling pathways (including many nuclear hormone receptors), thereby rendering the clock responsive to the internal environment of the body. This implies that circadian-clock genes can directly affect previously unforeseen physiological processes, and that amid such a network of body clocks, internal desynchronisation may be a key aspect to circadian dysfunction in humans. Here we consider the implications of decentralised and internally responsive clockwork to disease, with a focus on energy metabolism and the immune response.
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55
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Pershouse MA, Smartt AM, Schwanke C, Putnam EA. Differences in gene expression profiles from asbestos-treated SPARC-null and wild-type mouse lungs. Genomics 2009; 94:101-9. [PMID: 19446018 DOI: 10.1016/j.ygeno.2009.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 04/28/2009] [Accepted: 04/30/2009] [Indexed: 01/07/2023]
Abstract
The role of SPARC in the in vivo lung response to crocidolite asbestos was addressed by instillation of crocidolite asbestos in a series of wild-type or SPARC-null mice. Animals were sacrificed at one week, one month, and three months post-instillation to assess the impact of SPARC on multiple stages in the development of fibrosis. RNA was harvested from 10 animals/time point, pooled, and used to probe a mouse array containing approximately 10,000 probes. Gene expression data were analyzed for fold change, and for broader functional group alterations. As expected, the one-week time point displayed alterations in genes involved in immune recognition, energy utilization, and growth factor production. Later time points showed expression alterations for genes involved in protein degradation, Wnt receptor signaling, membrane protein activity, and transport. Molecules in the Wnt pathway have been implicated in bone growth, mediation of fibroblast activity, and have been directly linked to SPARC regulation.
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Affiliation(s)
- Mark A Pershouse
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, MT 59812-1552, USA
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56
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Jetten AM. Retinoid-related orphan receptors (RORs): critical roles in development, immunity, circadian rhythm, and cellular metabolism. NUCLEAR RECEPTOR SIGNALING 2009; 7:e003. [PMID: 19381306 PMCID: PMC2670432 DOI: 10.1621/nrs.07003] [Citation(s) in RCA: 499] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 03/18/2009] [Indexed: 12/11/2022]
Abstract
The last few years have witnessed a rapid increase in our knowledge of the retinoid-related orphan receptors RORα, -β, and -γ (NR1F1-3), their mechanism of action, physiological functions, and their potential role in several pathologies. The characterization of ROR-deficient mice and gene expression profiling in particular have provided great insights into the critical functions of RORs in the regulation of a variety of physiological processes. These studies revealed that RORα plays a critical role in the development of the cerebellum, that both RORα and RORβ are required for the maturation of photoreceptors in the retina, and that RORγ is essential for the development of several secondary lymphoid tissues, including lymph nodes. RORs have been further implicated in the regulation of various metabolic pathways, energy homeostasis, and thymopoiesis. Recent studies identified a critical role for RORγ in lineage specification of uncommitted CD4+ T helper cells into Th17 cells. In addition, RORs regulate the expression of several components of the circadian clock and may play a role in integrating the circadian clock and the rhythmic pattern of expression of downstream (metabolic) genes. Study of ROR target genes has provided insights into the mechanisms by which RORs control these processes. Moreover, several reports have presented evidence for a potential role of RORs in several pathologies, including osteoporosis, several autoimmune diseases, asthma, cancer, and obesity, and raised the possibility that RORs may serve as potential targets for chemotherapeutic intervention. This prospect was strengthened by recent evidence showing that RORs can function as ligand-dependent transcription factors.
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Affiliation(s)
- Anton M Jetten
- Cell Biology Section, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
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57
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Wada T, Kang HS, Jetten AM, Xie W. The emerging role of nuclear receptor RORalpha and its crosstalk with LXR in xeno- and endobiotic gene regulation. Exp Biol Med (Maywood) 2008; 233:1191-201. [PMID: 18535165 PMCID: PMC2658633 DOI: 10.3181/0802-mr-50] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Retinoid-related orphan receptors (RORs), including the alpha, beta and gamma isoforms (NR1F1-3), are orphan nuclear receptors that have been implicated in tissue development, immune responses, and circadian rhythm. Although RORalpha and RORgamma have been shown to be expressed in the liver, the hepatic function of these two RORs remains unknown. We have recently shown that loss of RORalpha and/or RORgamma can positively or negatively influence the expression of multiple Phase I and Phase II drug metabolizing enzymes and transporters in the liver. Among ROR responsive genes, we identified oxysterol 7alpha-hydroxylase (Cyp7b1), which plays a critical role in the homeostasis of cholesterol, as a RORalpha target gene. We showed that RORalpha is both necessary and sufficient for Cyp7b1 activation. Studies of mice deficient of RORalpha or liver X receptors (LXRs) revealed an interesting and potentially important functional crosstalk between RORalpha and LXR. The respective activation of LXR target genes and ROR target genes in RORalpha null mice and LXR null mice led to our hypothesis that these two receptors are mutually suppressive in vivo. LXRs have been shown to regulate a battery of metabolic genes. We conclude that RORs participate in the xeno- and endobiotic regulatory network by regulating gene expression directly or through crosstalk with LXR, which may have broad implications in metabolic homeostasis.
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Affiliation(s)
- Taira Wada
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261
| | - Hong Soon Kang
- Cell Biology Section, Division of Intramural Research, The National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Anton M. Jetten
- Cell Biology Section, Division of Intramural Research, The National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Wen Xie
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261
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58
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Smoak K, Madenspacher J, Jeyaseelan S, Williams B, Dixon D, Poch KR, Nick JA, Worthen GS, Fessler MB. Effects of liver X receptor agonist treatment on pulmonary inflammation and host defense. THE JOURNAL OF IMMUNOLOGY 2008; 180:3305-12. [PMID: 18292555 DOI: 10.4049/jimmunol.180.5.3305] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Liver X receptor (LXR) alpha and beta are members of the nuclear receptor superfamily of ligand-activated transcription factors. Best known for triggering "reverse cholesterol transport" gene programs upon their activation by endogenous oxysterols, LXRs have recently also been implicated in regulation of innate immunity. In this study, we define a role for LXRs in regulation of pulmonary inflammation and host defense and identify the lung and neutrophil as novel in vivo targets for pharmacologic LXR activation. LXR is expressed in murine alveolar macrophages, alveolar epithelial type II cells, and neutrophils. Treatment of mice with TO-901317, a synthetic LXR agonist, reduces influx of neutrophils to the lung triggered by inhaled LPS, intratracheal KC chemokine, and intratracheal Klebsiella pneumoniae and impairs pulmonary host defense against this bacterium. Pharmacologic LXR activation selectively modulates airspace cytokine expression induced by both LPS and K. pneumoniae. Moreover, we report for the first time that LXR activation impairs neutrophil motility and identify inhibition of chemokine-induced RhoA activation as a putative underlying mechanism. Taken together, these data define a novel role for LXR in lung pathophysiology and neutrophil biology and identify pharmacologic activation of LXR as a potential tool for modulation of innate immunity in the lung.
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Affiliation(s)
- Kathleen Smoak
- Laboratory of Respiratory Biology, Department of Health and Human Services, Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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59
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Kang HS, Angers M, Beak JY, Wu X, Gimble JM, Wada T, Xie W, Collins JB, Grissom SF, Jetten AM. Gene expression profiling reveals a regulatory role for ROR alpha and ROR gamma in phase I and phase II metabolism. Physiol Genomics 2007; 31:281-94. [PMID: 17666523 DOI: 10.1152/physiolgenomics.00098.2007] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Retinoid-related orphan receptors alpha (ROR alpha) and gamma (ROR gamma) are both expressed in liver; however, their physiological functions in this tissue have not yet been clearly defined. The ROR alpha1 and ROR gamma 1 isoforms, but not ROR alpha 4, show an oscillatory pattern of expression during circadian rhythm. To obtain insight into the physiological functions of ROR receptors in liver, we analyzed the gene expression profiles of livers from WT, ROR alpha-deficient staggerer (sg) mice (ROR alpha(sg/sg)), ROR gamma(-/-), and ROR alpha(sg/sg)ROR gamma(-/-) double knockout (DKO) mice by microarray analysis. DKO mice were generated to study functional redundancy between ROR alpha and ROR gamma. These analyses demonstrated that ROR alpha and ROR gamma affect the expression of a number of genes. ROR alpha and ROR gamma are particularly important in the regulation of genes encoding several phase I and phase II metabolic enzymes, including several 3beta-hydroxysteroid dehydrogenases, cytochrome P450 enzymes, and sulfotransferases. In addition, our results indicate that ROR alpha and ROR gamma each affect the expression of a specific set of genes but also exhibit functional redundancy. Our study shows that ROR alpha and ROR gamma receptors influence the regulation of several metabolic pathways, including those involved in the metabolism of steroids, bile acids, and xenobiotics, suggesting that RORs are important in the control of metabolic homeostasis.
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MESH Headings
- Animals
- Bile Acids and Salts/metabolism
- Cells, Cultured/metabolism
- Circadian Rhythm/genetics
- Cytochrome P-450 Enzyme System/metabolism
- Female
- Gene Expression Profiling
- Hepatocytes/metabolism
- Lipid Metabolism/genetics
- Liver/metabolism
- Metabolic Networks and Pathways/genetics
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Neurologic Mutants
- Nuclear Receptor Subfamily 1, Group F, Member 1
- Nuclear Receptor Subfamily 1, Group F, Member 3
- Receptors, Cytoplasmic and Nuclear/deficiency
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/physiology
- Receptors, Retinoic Acid/deficiency
- Receptors, Retinoic Acid/genetics
- Receptors, Retinoic Acid/physiology
- Receptors, Thyroid Hormone/deficiency
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/physiology
- Recombinant Fusion Proteins/metabolism
- Steroids/metabolism
- Trans-Activators/deficiency
- Trans-Activators/genetics
- Trans-Activators/physiology
- Transfection
- Xenobiotics/metabolism
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Affiliation(s)
- Hong Soon Kang
- Cell Biology Section, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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60
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Affiliation(s)
- Wendy C Moore
- Center for Human Genomics and Department of Internal Medicine, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
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61
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Lechtken A, Hörnig M, Werz O, Corvey N, Zündorf I, Dingermann T, Brandes R, Steinhilber D. Extracellular signal-regulated kinase-2 phosphorylates RORalpha4 in vitro. Biochem Biophys Res Commun 2007; 358:890-6. [PMID: 17512500 DOI: 10.1016/j.bbrc.2007.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 05/03/2007] [Indexed: 11/19/2022]
Abstract
The retinoic acid related orphan receptor RORalpha activates transcription of genes that play an important role in cerebellar development, the protection against age-related degenerative processes, the regulation of inflammatory responses, and is one of the pivotal participants that control the circadian rhythmicity in the core-clock of mammals. We identified the extracellular signal-regulated kinase 2 (ERK-2) as RORalpha4 phosphorylating kinase in vitro. The primary sequence of RORalpha4 contains an ERK-2 recognition motif (P-L-T(128)-P) within the hinge domain, and mutation of Thr-128 to Ala prevents RORalpha4 phosphorylation by ERK. The RORalpha4-T128A mutant exhibits an increased DNA-binding affinity, an increased transcriptional activity and, in the interplay with the opponent RevErbalpha, acts as a stronger competitor at ROR response elements than RORalpha4-WT.
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Affiliation(s)
- Adriane Lechtken
- Institute of Pharmaceutical Chemistry/ZAFES, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
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