1
|
Lötsch J, Doehring A, Mogil JS, Arndt T, Geisslinger G, Ultsch A. Functional genomics of pain in analgesic drug development and therapy. Pharmacol Ther 2013; 139:60-70. [PMID: 23567662 DOI: 10.1016/j.pharmthera.2013.04.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 03/19/2013] [Indexed: 12/28/2022]
Abstract
Advances in genomic research have led to the clarification of the detailed involvement of gene products in biological pathways and these are being increasingly exploited in strategies for drug discovery and repurposing. Concomitant developments in informatics have resulted in the acquisition of complex gene information through the application of computational analysis of molecular interaction networks. This approach enables the acquired knowledge on hundreds of genes to be used to view molecular disease mechanisms from a genetic point of view. By analyzing 410 genes which control the complex process of pain, we show by computational analysis, based on functional annotations to pain-related genes, that 12 clearly circumscribed functional areas are essential for pain perception and thus for analgesic drug development. The genetics perspective revealed that future development strategies should focus on substances modulating intracellular signal transduction, ion transport and anatomical structure development. These processes are involved in the genetic-based absence of pain and therefore, provide promising fields for curative or preventive treatments. In contrast, interactions with G-protein coupled receptor pathways seem merely to provide symptomatic, not preventative relief of pain. In addition, biological functions accessed either by analgesic drugs or microRNAs suggest that synergistic therapies may be a future direction for drug development. With modern computational functional genomics, it is possible to exploit genetic information from increasingly available data sets on complex diseases, such as pain, and offers a new insight into drug development and therapy which is complementary to pathway-centered approaches.
Collapse
Affiliation(s)
- Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe-University Hospital, Theodor Stern Kai 7, D-60590 Frankfurt am Main, Germany
| | | | | | | | | | | |
Collapse
|
2
|
Ruaño G, Thompson PD, Kane JP, Pullinger CR, Windemuth A, Seip RL, Kocherla M, Holford TR, Wu AHB. Physiogenomic analysis of statin-treated patients: domain-specific counter effects within the ACACB gene on low-density lipoprotein cholesterol? Pharmacogenomics 2011; 11:959-71. [PMID: 20602615 DOI: 10.2217/pgs.10.58] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIM Administered at maximal dosages, the most common statins--atorvastatin, simvastatin and rosuvastatin--lower low-density lipoprotein cholesterol (LDLC) by an average of 37-57% in patients with primary hypercholesterolemia. We hypothesized novel genetic underpinnings for variation in LDLC levels in the context of statin therapy. MATERIALS & METHODS Genotyping of 384 SNPs in 202 volunteers from a lipid outpatient clinic was accomplished and LDLC levels obtained from chart records. The SNPs were distributed across 222 genes representing physiological pathways such as general metabolism, cholesterol biochemistry, cardiovascular function, inflammation, neurobiology and cell proliferation. We discovered significant associations with LDLC levels for the rs34274 SNP (p < 0.0002) and for rs2241220 (p < 0.008) in the acetyl-coenzyme A carboxylase beta (ACACB) gene. When corrected for multiple testing, the false-discovery rate associated with rs34274 was 0.076 (significance threshold: 0.10) and for rs2241220 the false-discovery rate was 0.93 (not significant). The acetyl coenzyme A carboxylase beta enzyme synthesizes malonyl coenzyme A, an essential substrate for hepatic fatty acid synthesis and an inhibitor of fatty acid oxidation. RESULTS The SNPs were in weak linkage disequilibrium (D = 0.302). Minor alleles at these sites demonstrate opposing influences on LDLC; the C>T substitution at rs34724 is a risk marker and the C>T substitution at rs2241220 a protective marker for LDLC levels. These SNPs hypothetically influence enzymatic activity through different mechanisms, rs34274 through the PII promoter and rs2241220 via alteration of the protein's responsiveness to allosteric influence. CONCLUSION Physiogenomic evidence suggests a novel link between LDLC levels and the regulation of fatty acid metabolism. The findings complement previously discovered novel SNP relationships to myalgia (pain) and myositis (serum creatine kinase activity). By genotyping for myositis, myalgia and LDLC levels, a physiogenomic model may be developed to help clinicians maximize effectiveness and minimize side effects in prescribing statins.
Collapse
|
3
|
Dmitrieva RI, Hinojos CA, Grove ML, Bell RJ, Boerwinkle E, Fornage M, Doris PA. Genome-wide identification of allelic expression in hypertensive rats. ACTA ACUST UNITED AC 2009; 2:106-15. [PMID: 20031574 DOI: 10.1161/circgenetics.108.809509] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Identification of genes involved in complex cardiovascular disease traits has proven challenging. Inbred animal models can facilitate genetic studies of disease traits. The spontaneously hypertensive rat (SHR) is an inbred model of hypertension that exists in several closely related but genetically distinct lines. METHODS AND RESULTS We used renal gene-expression profiling across 3 distinct SHR lines to identify genes that show different expression in SHR than in the genetically related normotensive control strain, Wistar-Kyoto. To ensure robust discovery of genes showing SHR-specific expression differences, we considered only those genes in which differential expression is replicated in multiple animals of each of multiple hypertensive rat lines at multiple time points during the ontogeny of hypertension. Mutation analysis was performed on the identified genes to uncover allelic variation. We identified those genes in which all SHR lines share a single allele of the gene when normotensive controls (Wistar-Kyoto) have fixed the alternative allele. We then identified which of the differentially expressed genes show expression that is controlled by the alleleic variation present in and around the gene. Allelic expression was demonstrated by observing the effect on gene expression of alleles inherited in the freely segregating F(2) progeny of a cross between SHR and Wistar-Kyoto animals. CONCLUSIONS The result of these studies is the identification of several genes (Ptprj, Ela1, Dapk-2, and Gstt2) in which each of 4 SHR lines examined have fixed the same allele and in which each of 2 Wistar-Kyoto lines have a contrasting allele for which the inherited allele influences the level of gene expression. We further show that alleles of these genes lie in extensive haplotype blocks that have been inherited identical by descent in the hypertensive lines.
Collapse
Affiliation(s)
- Renata I Dmitrieva
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center, 2121 Holcombe Blvd., Houston, TX 77030, USA
| | | | | | | | | | | | | |
Collapse
|
4
|
Ruaño G, Bernene J, Windemuth A, Bower B, Wencker D, Seip RL, Kocherla M, Holford TR, Petit WA, Hanks S. Physiogenomic comparison of edema and BMI in patients receiving rosiglitazone or pioglitazone. Clin Chim Acta 2009; 400:48-55. [DOI: 10.1016/j.cca.2008.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 09/16/2008] [Accepted: 10/07/2008] [Indexed: 12/15/2022]
|
5
|
Szewczyk N, Tillman J, Conley C, Granger L, Segalat L, Higashitani A, Honda S, Honda Y, Kagawa H, Adachi R, Higashibata A, Fujimoto N, Kuriyama K, Ishioka N, Fukui K, Baillie D, Rose A, Gasset G, Eche B, Chaput D, Viso M. Description of International Caenorhabditis elegans Experiment first flight (ICE-FIRST). ADVANCES IN SPACE RESEARCH : THE OFFICIAL JOURNAL OF THE COMMITTEE ON SPACE RESEARCH (COSPAR) 2008; 42:1072-1079. [PMID: 22146801 PMCID: PMC2493420 DOI: 10.1016/j.asr.2008.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Traveling, living and working in space is now a reality. The number of people and length of time in space is increasing. With new horizons for exploration it becomes more important to fully understand and provide countermeasures to the effects of the space environment on the human body. In addition, space provides a unique laboratory to study how life and physiologic functions adapt from the cellular level to that of the entire organism. Caenorhabditis elegans is a genetic model organism used to study physiology on Earth. Here we provide a description of the rationale, design, methods, and space culture validation of the ICE-FIRST payload, which engaged C. elegans researchers from four nations. Here we also show C. elegans growth and development proceeds essentially normally in a chemically defined liquid medium on board the International Space Station (10.9 day round trip). By setting flight constraints first and bringing together established C. elegans researchers second, we were able to use minimal stowage space to successfully return a total of 53 independent samples, each containing more than a hundred individual animals, to investigators within one year of experiment concept. We believe that in the future, bringing together individuals with knowledge of flight experiment operations, flight hardware, space biology, and genetic model organisms should yield similarly successful payloads.
Collapse
Affiliation(s)
- N.J. Szewczyk
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
- School of Graduate Entry Medicine and Health, University of Nottingham, Derby City Hospital, Derby DE22 3DT, UK
- Corresponding author. Address: School of Graduate Entry Medicine and Health, University of Nottingham, Derby City Hospital, Derby DE22 3DT, UK. Tel.: +44 1332 724615. E-mail address: (N.J. Szewczyk)
| | - J. Tillman
- Lockheed Martin, Moffett Field, CA 94035, USA
| | - C.A. Conley
- National Aeronautics and Space Administration, Moffett Field, CA 94035, USA
| | - L. Granger
- CGMC, CNRS-UMR 5534, Universite Lyon1, 43 bld du 11 Novembre, 69622 Villeurbanne Cedex, France
| | - L. Segalat
- CGMC, CNRS-UMR 5534, Universite Lyon1, 43 bld du 11 Novembre, 69622 Villeurbanne Cedex, France
| | - A. Higashitani
- Graduate School of Life Sciences, Tohoku University, Sendai 980−8557, Japan
| | - S. Honda
- Tokyo Metropolitan Institute of Gerontology, Tokyo 173−0015, Japan
| | - Y. Honda
- Tokyo Metropolitan Institute of Gerontology, Tokyo 173−0015, Japan
| | - H. Kagawa
- Graduate School of Natural Science and Technology, Okayama University, 3−1−1, Tsushima Naka, Okayama City 700−8530, Japan
| | - R. Adachi
- Graduate School of Natural Science and Technology, Okayama University, 3−1−1, Tsushima Naka, Okayama City 700−8530, Japan
| | - A. Higashibata
- Japan Aerospace Exploration Agency, Tsukuba 305−8505, Japan
| | - N. Fujimoto
- Japan Aerospace Exploration Agency, Tsukuba 305−8505, Japan
| | - K. Kuriyama
- Japan Aerospace Exploration Agency, Tsukuba 305−8505, Japan
| | - N. Ishioka
- Japan Aerospace Exploration Agency, Tsukuba 305−8505, Japan
| | - K. Fukui
- Japan Space Forum, Tokyo 100−0004, Japan
| | - D. Baillie
- University of British Columbia, Vancouver, BC, Canada
| | - A. Rose
- University of British Columbia, Vancouver, BC, Canada
| | - G. Gasset
- Groupement Scientifique en Biologie et Medecine Spatiales, Universite Paul Sabatier, 31062 Toulouse Cedex, France
| | - B. Eche
- Groupement Scientifique en Biologie et Medecine Spatiales, Universite Paul Sabatier, 31062 Toulouse Cedex, France
| | - D. Chaput
- Centre National d'Estudes Spatiales, Paris Cedex 01, France
| | - M. Viso
- Centre National d'Estudes Spatiales, Paris Cedex 01, France
| |
Collapse
|
6
|
Abstract
Enhancing survival to hemorrhage of both civilian and military patients is a major emphasis for trauma research. Previous observations in humans and outbred rats show differential survival to similar levels of hemorrhage. In an initial attempt to determine potential genetic components of such differential outcomes, survival time after a controlled hemorrhage was measured in 15 inbred strains of rats. Anesthetized rats were catheterized, and approximately 24 h later, 55% of the calculated blood volume was removed during a 26-min period from conscious unrestrained animals. Rats were observed for a maximum of 6 h. Survival time was 7.7-fold longer in the longest-lived strain (Brown Norway/Medical College of Wisconsin; 306 +/- 36 min; mean +/- SEM) than in the shortest-lived strain (DA; 40 +/- 5 min; P < or = 0.01). Mean survival times for the remaining inbred strains ranged from 273 +/- 44 to 49 +/- 4 min (Dahl-Salt Sensitive > Brown Norway > Munich Wistar Fromter> Dahl-Salt Resistant > Copenhagen > Noble > Spontaneous-hypertensive > Lewis > BDIX > Fawn Hooded Hypertensive > FISCHER 344 > Black agouti > PVG). The variance in the hazard of death attributable to different strains was estimated to be 1.22 log-hazard units, corresponding to a heritability of approximately 48%. Graded and divergent survival times to hemorrhage in inbred rat strains are remarkable and suggest multiple genetic components for this characteristic. However, this interpretation of differential responses to hemorrhage may be confounded by potential strain-associated differences related to the surgical preparation. Identification of inbred strains divergent in survival time to hemorrhage provides the opportunity for future use of these strains to identify genes associated with this complex response.
Collapse
|
7
|
Moreno C, Lazar J, Jacob HJ, Kwitek AE. Comparative genomics for detecting human disease genes. ADVANCES IN GENETICS 2008; 60:655-97. [PMID: 18358336 DOI: 10.1016/s0065-2660(07)00423-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Originally, comparative genomics was geared toward defining the synteny of genes between species. As the human genome project accelerated, there was an increase in the number of tools and means to make comparisons culminating in having the genomic sequence for a large number of organisms spanning the evolutionary tree. With this level of resolution and a long history of comparative biology and comparative genetics, it is now possible to use comparative genomics to build or select better animal models and to facilitate gene discovery. Comparative genomics takes advantage of the functional genetic information from other organisms, (vertebrates and invertebrates), to apply it to the study of human physiology and disease. It allows for the identification of genes and regulatory regions, and for acquiring knowledge about gene function. In this chapter, the current state of comparative genomics and the available tools are discussed in the context of developing animal model systems that reflect the clinical picture.
Collapse
Affiliation(s)
- Carol Moreno
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | | | | |
Collapse
|
8
|
Lee NH. Physiogenomic strategies and resources to associate genes with rat models of heart, lung and blood disorders. Exp Physiol 2007; 92:992-1002. [PMID: 17591683 DOI: 10.1113/expphysiol.2006.036350] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As is the case for many human disorders, cardiovascular disease is a complex ailment exhibiting a multifactorial mode of transmission. Rat models have been developed to aid in the analysis of this complex genetic and phenotypic disorder. The purpose of this brief review is to describe current gene expression profiling strategies that have been implemented to search for candidate causative genes of disease phenotypes in animal models. Strategies include integrating gene expression information with linkage analysis, expression profiling chromosome-substituted and/or congenic rat strains, correlating gene expression with physiological data across a panel of rodent strains, and linking expression quantitative trait loci to physiological quantitative trait loci. A primary goal of these strategies is to narrow and prioritize the search for causal genes of physiological interest. Also discussed are ways to harness two recent publicly available resources that have been created to investigate the role of genes and environment on cardiovascular physiology and pathophysiology.
Collapse
Affiliation(s)
- Norman H Lee
- Department of Pharmacology and Physiology, The George Washington University Medical Center, 2300 Eye Street NW, Washington, DC 20037, USA.
| |
Collapse
|
9
|
Pitiot A, Pausova Z, Prior M, Perrin J, Loyse N, Paus T. Magnetic resonance imaging as a tool for in vivo and ex vivo anatomical phenotyping in experimental genetic models. Hum Brain Mapp 2007; 28:555-66. [PMID: 17437283 PMCID: PMC6871449 DOI: 10.1002/hbm.20399] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 03/06/2007] [Accepted: 03/09/2007] [Indexed: 11/08/2022] Open
Abstract
This article describes a suite of computational approaches suitable for deriving various quantitative phenotypes from structural magnetic resonance (MR) images obtained in rodents and used subsequently in genetic studies of complex traits. We begin by introducing the basic principles of genetic studies of complex traits in experimental models. We then illustrate the use of MR-based computational anatomy in vivo and ex vivo, and in combination with histology. This work was carried out in two inbred strains of rats, namely spontaneously hypertensive rats and Brown Norway rats; these are parental strains of the only existing panel of recombinant inbred strains of rats. The rats were scanned in vivo at two time points (at 8 and 12 weeks of age) and ex vivo (at 12 weeks of age). We describe between-strain differences and across-time changes in brain and kidney volumes, as well as regional variations in brain structure using surface- and deformation-based approaches. We conclude by discussing the power of the population-based computational analysis of MR images, and their fusion with histology, in studies of complex traits.
Collapse
Affiliation(s)
- Alain Pitiot
- Brain and Body Centre, University of Nottingham, Nottingham, United Kingdom
| | - Zdenka Pausova
- Brain and Body Centre, University of Nottingham, Nottingham, United Kingdom
- Centre hospitalier de l'Université de Montréal, Montreal, Canada
| | - Malcolm Prior
- Brain and Body Centre, University of Nottingham, Nottingham, United Kingdom
| | - Jennifer Perrin
- Brain and Body Centre, University of Nottingham, Nottingham, United Kingdom
| | - Naomi Loyse
- Brain and Body Centre, University of Nottingham, Nottingham, United Kingdom
| | - Tomáš Paus
- Brain and Body Centre, University of Nottingham, Nottingham, United Kingdom
- Montreal Neurological Institute, McGill University, Montreal, Canada
| |
Collapse
|
10
|
|
11
|
Sedová L, Seda O, Kazdová L, Chylíková B, Hamet P, Tremblay J, Kren V, Krenová D. Sucrose feeding during pregnancy and lactation elicits distinct metabolic response in offspring of an inbred genetic model of metabolic syndrome. Am J Physiol Endocrinol Metab 2007; 292:E1318-24. [PMID: 17213469 DOI: 10.1152/ajpendo.00526.2006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The importance of early environment, including maternal diet during pregnancy, is suspected to play a major role in pathogenesis of metabolic syndrome and related conditions. One of the proposed mechanisms is a mismatch between the prenatal and postnatal environments, leading to misprogramming of the metabolic and signaling pathways of the developing fetus. We assessed whether the exposure to high-sucrose diet (HSD) alleviates the detrimental effects of sucrose feeding in later life (predictive adaptive hypothesis) in a highly inbred model of metabolic syndrome, the PD/Cub rat. Rat dams were continuously fed either standard or HSD (70% calories as sucrose) starting 1 wk before breeding, throughout pregnancy, at birth, and until weaning of the offspring. After weaning, all male offspring were fed HSD until the age of 20 wk, when detailed metabolic and morphometric profiles were ascertained. The early life exposure to a sucrose-rich diet resulted in distinct responses to longtime postnatal HSD feeding. Offspring of the sucrose-fed mothers displayed higher adiposity and substantial increases in triglyceride liver content together with unfavorable distribution of cholesterol into lipoprotein subfractions. On the other hand, their adiponectin concentrations were significantly higher, and insulin sensitivity of skeletal muscle was enhanced compared with the offspring of standard diet-fed mothers. Triglycerides, free fatty acids, overall glucose tolerance, and the insulin sensitivity of adipose tissue were comparable in both groups. In the genetically identical animals, maternal HSD feeding elicited a variety of subtle effects but did not lead to predictive adaptive protection from most HSD-induced metabolic derangements.
Collapse
Affiliation(s)
- Lucie Sedová
- Institute of Biology and Medical Genetics of the First Faculty of Medicine of Charles University and the General Teaching Hospital,Prague, Czech Republic.
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Michalkiewicz M, Michalkiewicz T, Geurts AM, Roman RJ, Slocum GR, Singer O, Weihrauch D, Greene AS, Kaldunski M, Verma IM, Jacob HJ, Cowley AW. Efficient transgenic rat production by a lentiviral vector. Am J Physiol Heart Circ Physiol 2007; 293:H881-94. [PMID: 17322424 DOI: 10.1152/ajpheart.00060.2007] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A lentiviral construct for an enhanced green fluorescent protein (eGFP) driven by a chicken beta-actin promoter, cytomegalovirus enhancer, and intronic sequences from rabbit beta-globin (CAG) was used to produce transgenic lines of rats for evaluation of the usefulness of this approach in gene function studies. Fertilized eggs were collected from inbred Dahl S and outbred Sprague-Dawley rats, and approximately 100 pl of concentrated virus were microinjected into the perivitrelline space of one-cell embryos. Of 121 embryos injected, 60 pups (49.6%) were born. Transgenic rates averaged 22% in Dahl S and 14% in Sprague-Dawley rats. Copy number ranged from one to four in the founders, and the inheritance of the transgene in a subsequent F(1) population was 48.2%. The small number of insertion sites enabled us to derive inbred transgenic lines with a single copy of the transgene within one generation. Sequencing of each transgene insertion site revealed that they inserted as single copies with a preference for the introns of genes. The CAG promoter drove high levels of eGFP expression in brain, kidney, heart, and vasculature, making it very suitable for exploring the cardiovascular function of newly discovered genes. The pattern of eGFP expression was similar across five different F(1) transgenic lines, indicating that the expression of the transgene was independent of its chromosomal position. Thus lentiviral transgenesis provides a powerful tool for the production of transgenic inbred rats and will enhance the usefulness of this species in gene discovery and target validation studies.
Collapse
Affiliation(s)
- Mieczyslaw Michalkiewicz
- Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Vadasz C, Saito M, O'Brien D, Zavadil J, Morahan G, Chakraborty G, Wang R. Ventral Tegmental Transcriptome Response to Intermittent Nicotine Treatment and Withdrawal in BALB/cJ, C57BL/6ByJ, and Quasi-Congenic RQI Mice. Neurochem Res 2007; 32:457-80. [PMID: 17268848 DOI: 10.1007/s11064-006-9250-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Accepted: 10/05/2006] [Indexed: 10/23/2022]
Abstract
The aim of this study was to identify neurochemical pathways and candidate genes involved in adaptation to nicotine treatment and withdrawal. Locomotor sensitization was assessed in a nicotine challenge test after exposure to intermittent nicotine treatment and withdrawal. About 24 h after the challenge test the ventral tegmentum of the mesencephaion was dissected and processed using oligonucleotide microarrays with 22,690 probe sets (Affymetrix 430A 2.0). Quasi-congenic RQI, and donor BALB/cJ mice developed significant locomotor sensitization, while sensitization was not significant in the background partner, C57BL/6By. Comparing saline treated controls of C57BL/6ByJ and BALB/cJ by a rigorous statistical microarray analysis method we identified 238 differentially expressed transcripts. Quasi-congenic strains B6.Cb4i5-alpha4/Vad and B6.Ib5i7-beta25A/Vad significantly differed from the background strain in 11 and 11 transcripts, respectively. Identification of several cis- and trans-regulated genes indicates that further work with quasi-congenic strains can quickly lead to mapping of Quantitative Trait Loci for nicotine susceptibility because donor chromosome regions have been mapped in quasi-congenic strains. Nicotine treatment significantly altered the abundance of 41, 29, 54, and 14 ventral tegmental transcripts in strains C57BL/6ByJ, BALB/cJ, B6.Cb4i5-alpha4/Vad, and B6.Ib5i7-beta25A/Vad, respectively. Although transcript sets overlapped to some extent, each strain showed a distinct profile of nicotine sensitive genes, indicating genetic effects on nicotine-induced gene expression. Nicotine-responsive genes were related to processes including regulation of signal transduction, intracellular protein transport, proteasomal ubiquitin-dependent protein catabolism, and neuropeptide signaling pathway. Our results suggest that while there are common regulatory mechanisms across inbred strains, even relatively small differences in genetic constitution can significantly affect transcriptome response to nicotine.
Collapse
Affiliation(s)
- Csaba Vadasz
- Laboratory of Neurobehavioral Genetics, Nathan S. Kline Institute for Psychiatric Research, 140 Old Orangeburg Road, Orangeburg, NY 10962, USA.
| | | | | | | | | | | | | |
Collapse
|
14
|
Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ. The Rat Genome Database, update 2007--easing the path from disease to data and back again. Nucleic Acids Res 2007; 35:D658-62. [PMID: 17151068 PMCID: PMC1761441 DOI: 10.1093/nar/gkl988] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 10/24/2006] [Indexed: 11/14/2022] Open
Abstract
The Rat Genome Database (RGD, http://rgd.mcw.edu) is one of the core resources for rat genomics and recent developments have focused on providing support for disease-based research using the rat model. Recognizing the importance of the rat as a disease model we have employed targeted curation strategies to curate genes, QTL and strain data for neurological and cardiovascular disease areas. This work has centered on rat but also includes data for mouse and human to create 'disease portals' that provide a unified view of the genes, QTL and strain models for these diseases across the three species. The disease curation efforts combined with normal curation activities have served to greatly increase the content of the database, particularly for biological information, including gene ontology, disease, pathway and phenotype ontology annotations. In addition to improving the features and database content, community outreach has been expanded to demonstrate how investigators can leverage the resources at RGD to facilitate their research and to elicit suggestions and needs for future developments. We have published a number of papers that provide additional information on the ontology annotations and the tools at RGD for data mining and analysis to better enable researchers to fully utilize the database.
Collapse
Affiliation(s)
- Simon N Twigger
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
| | | | | | | | | |
Collapse
|
15
|
Abstract
This paper introduces a special issue of Animal Genetics, which is devoted to the recent symposium held at Iowa State University entitled 'Integration of Structural and Functional Genomics'. We describe issues and needs that confront the animal genomics community, and describe how this symposium was structured to address these issues by improving communication and collaboration across species and disciplines. The session topics and oral presentations are briefly described for all invited speakers.
Collapse
Affiliation(s)
- C K Tuggle
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA.
| | | | | |
Collapse
|
16
|
Seda O, Sedová L, Liska F, Krenová D, Prejzek V, Kazdová L, Tremblay J, Hamet P, Kren V. Novel double-congenic strain reveals effects of spontaneously hypertensive rat chromosome 2 on specific lipoprotein subfractions and adiposity. Physiol Genomics 2006; 27:95-102. [PMID: 16822831 DOI: 10.1152/physiolgenomics.00039.2006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have developed a new, double-congenic rat strain BN- Lx.SHR2, which carries two distinct segments of chromosome 2 introgressed from the spontaneously hypertensive rat strain (SHR) into the genetic background of congenic strain BN- Lx, which was previously shown to express variety of metabolic syndrome features. In 16-wk-old male rats of BN- Lx and BN- Lx.SHR2 strains, we compared their glucose tolerance and triacylglycerol and cholesterol concentrations in 20 lipoprotein subfractions and the lipoprotein particle sizes under conditions of feeding standard and high-sucrose diets. Introgression of two distinct SHR-derived chromosome 2 segments resulted in decreased adiposity together with aggravation of glucose intolerance in the double-congenic strain. The BN- Lx.SHR2 rats were more sensitive to sucrose-induced rise in triacylglycerolemia. Although the total cholesterol concentrations of the two strains were comparable after the standard diet and even lower in BN- Lx.SHR2 after sucrose feeding, detailed analysis revealed that under both dietary conditions, the double-congenic strain had significantly higher cholesterol concentrations in low-density lipoprotein fractions and lower high-density lipoprotein fractions. We established a new inbred model showing dyslipidemia and mild glucose intolerance without obesity, attributable to specific genomic regions. For the first time, the chromosome 2 segments of SHR origin are shown to influence other than blood pressure-related features of metabolic syndrome or to be involved in relevant nutrigenomic interactions.
Collapse
Affiliation(s)
- Ondrej Seda
- Institute of Biology and Medical Genetics of the First Faculty of Medicine of Charles University and the General Teaching Hospital, Prague, Czech Republic
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Cerutti C, Kurdi M, Bricca G, Hodroj W, Paultre C, Randon J, Gustin MP. Transcriptional alterations in the left ventricle of three hypertensive rat models. Physiol Genomics 2006; 27:295-308. [PMID: 16882881 DOI: 10.1152/physiolgenomics.00318.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Left ventricular hypertrophy (LVH) is commonly associated with hypertension and represents an independent cardiovascular risk factor. The aim of this study was to test the hypothesis that the cardiac overload related to hypertension is associated to a specific gene expression pattern independently of genetic background. Gene expression levels were obtained with microarrays for 15,866 transcripts from RNA of left ventricles from 12-wk-old rats of three hypertensive models [spontaneously hypertensive rat (SHR), Lyon hypertensive rat (LH), and heterozygous TGR(mRen2)27 rat] and their respective controls. More than 60% of the detected transcripts displayed significant changes between the three groups of normotensive rats, showing large interstrain variability. Expression data were analyzed with respect to hypertension, LVH, and chromosomal distribution. Only four genes had significantly modified expression in the three hypertensive models among which a single gene, coding for sialyltransferase 7A, was consistently overexpressed. Correlation analysis between expression data and left ventricular mass index (LVMI) over all rats identified a larger set of genes whose expression was continuously related with LVMI, including known genes associated with cardiac remodeling. Positioning the detected transcripts along the chromosomes pointed out high-density regions mostly located within blood pressure and cardiac mass quantitative trait loci. Although our study could not detect a unique reprogramming of cardiac cells involving specific genes at early stage of LVH, it allowed the identification of some genes associated with LVH regardless of genetic background. This study thus provides a set of potentially important genes contained within restricted chromosomal regions involved in cardiovascular diseases.
Collapse
Affiliation(s)
- Catherine Cerutti
- Equipe d'Accueil 3740 Génomique fonctionnelle dans l'athérothrombose, Université Lyon 1, Lyon, France.
| | | | | | | | | | | | | |
Collapse
|
18
|
N. Twigger S, S. Smith J, Zuniga-Meyer A, Bromberg SK. Exploring Phenotypic Data at the Rat Genome Database. ACTA ACUST UNITED AC 2006; Chapter 1:Unit 1.14. [DOI: 10.1002/0471250953.bi0114s14] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Simon N. Twigger
- Human and Molecular Genetics Center, Medical College of Wisconsin; Milwaukee Wisconsin
| | - Jennifer S. Smith
- Human and Molecular Genetics Center, Medical College of Wisconsin; Milwaukee Wisconsin
| | - Angela Zuniga-Meyer
- Human and Molecular Genetics Center, Medical College of Wisconsin; Milwaukee Wisconsin
| | - Susan K. Bromberg
- Human and Molecular Genetics Center, Medical College of Wisconsin; Milwaukee Wisconsin
| |
Collapse
|
19
|
Wright MW, Bruford EA. Human and orthologous gene nomenclature. Gene 2006; 369:1-6. [PMID: 16431039 DOI: 10.1016/j.gene.2005.10.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 10/24/2005] [Accepted: 10/24/2005] [Indexed: 10/25/2022]
Abstract
Standardised human gene nomenclature is an essential tool for all researchers, and applying this nomenclature to orthologous genes in other species greatly extends its utility. As more genomes are sequenced and annotated the wealth of information in the public domain concerning homologous genes and their products increases greatly. Here we review many of the resources currently available for identifying orthologs and paralogs, and viewing regions of synteny between genomes, and discuss how these can and are being used in the process of nomenclature assignment. Whilst synchronised gene naming has been actively pursued between human and mouse for many years, and continues apace, it is hoped that this nomenclature will eventually be extended to many other comparative genomes.
Collapse
Affiliation(s)
- Mathew W Wright
- HUGO Gene Nomenclature Committee, The Galton Laboratory, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London, NW1 2HE, UK.
| | | |
Collapse
|
20
|
Affiliation(s)
- Mingyu Liang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | |
Collapse
|
21
|
Abstract
The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to be combined with the years of physiological knowledge accumulated in numerous rat models, which is the subject of this perspective. Based on the successes to date and the research projects under way to further enhance the infrastructure of the rat, we also project where research in the rat will be in the near future. The impact of the rat genome project has just started, but it is an exciting time with tremendous progress.
Collapse
Affiliation(s)
- Jozef Lazar
- Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | | | | | | |
Collapse
|