1
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Gentry AE, Alexander JC, Ahangari M, Peterson RE, Miles MF, Bettinger JC, Davies AG, Groteweil M, Bacanu SA, Kendler KS, Riley BP, Webb BT. Case-only exome variation analysis of severe alcohol dependence using a multivariate hierarchical gene clustering approach. PLoS One 2023; 18:e0283985. [PMID: 37098020 PMCID: PMC10128939 DOI: 10.1371/journal.pone.0283985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/21/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Variation in genes involved in ethanol metabolism has been shown to influence risk for alcohol dependence (AD) including protective loss of function alleles in ethanol metabolizing genes. We therefore hypothesized that people with severe AD would exhibit different patterns of rare functional variation in genes with strong prior evidence for influencing ethanol metabolism and response when compared to genes not meeting these criteria. OBJECTIVE Leverage a novel case only design and Whole Exome Sequencing (WES) of severe AD cases from the island of Ireland to quantify differences in functional variation between genes associated with ethanol metabolism and/or response and their matched control genes. METHODS First, three sets of ethanol related genes were identified including those a) involved in alcohol metabolism in humans b) showing altered expression in mouse brain after alcohol exposure, and altering ethanol behavioral responses in invertebrate models. These genes of interest (GOI) sets were matched to control gene sets using multivariate hierarchical clustering of gene-level summary features from gnomAD. Using WES data from 190 individuals with severe AD, GOI were compared to matched control genes using logistic regression to detect aggregate differences in abundance of loss of function, missense, and synonymous variants, respectively. RESULTS Three non-independent sets of 10, 117, and 359 genes were queried against control gene sets of 139, 1522, and 3360 matched genes, respectively. Significant differences were not detected in the number of functional variants in the primary set of ethanol-metabolizing genes. In both the mouse expression and invertebrate sets, we observed an increased number of synonymous variants in GOI over matched control genes. Post-hoc simulations showed the estimated effects sizes observed are unlikely to be under-estimated. CONCLUSION The proposed method demonstrates a computationally viable and statistically appropriate approach for genetic analysis of case-only data for hypothesized gene sets supported by empirical evidence.
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Affiliation(s)
- Amanda Elswick Gentry
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Jeffry C Alexander
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Mohammad Ahangari
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Integrative Life Sciences Ph.D. Program, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Roseann E Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Psychiatry and Behavioral Sciences, Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, New York, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael F Miles
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Jill C Bettinger
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Andrew G Davies
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Mike Groteweil
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Silviu A Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Brien P Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Bradley T Webb
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, North Caroline, United States of America
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2
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Bogenpohl JW, Weston RM, Foreman TN, Kitchen KE, Miles MF. Chloride intracellular channel 4 (CLIC4) expression profile in the mouse medial prefrontal cortex and its regulation by ethanol. Alcohol Clin Exp Res 2022; 46:29-39. [PMID: 34839533 PMCID: PMC8799520 DOI: 10.1111/acer.14754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/12/2021] [Accepted: 11/22/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Chloride intracellular channel 4 (CLIC4) is a multifunctional metamorphic protein for which a growing body of evidence supports a major role in the brain's molecular and behavioral responses to ethanol (EtOH). Although key to understanding the functional biology underlying this role, little is known about the cellular and subcellular expression patterns of CLIC4 in brain and how they are affected by EtOH. METHODS We used qRT-PCR to assess Clic4 mRNA expression in the medial prefrontal cortex (mPFC) of C57BL/6J mice in the absence and presence of acute EtOH exposure. Two complementary immunohistochemical techniques were employed to assess the subcellular localization of the CLIC4 protein and its pattern of expression across brain cell types in the mPFC in the absence and presence of acute EtOH. RESULTS Through immunohistochemical and stereological techniques, we show that CLIC4 protein is robustly expressed by oligodendrocytes (most abundant), microglia, and astrocytes, with minimal expression in neurons. Following acute EtOH exposure, we observed a rapid increase in Clic4 mRNA expression in female but not male mice and an overall increase in the number of oligodendrocytes and astrocytes expressing the CLIC4 protein. CONCLUSIONS These findings suggest that Clic4 functions as an early response gene for acute EtOH in brain, which likely underlies its ability to modulate EtOH behavior. Our results also suggest that the role of CLIC4 in the brain's response to EtOH is mediated through oligodendrocytes.
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Affiliation(s)
- James W. Bogenpohl
- Department of Molecular Biology and Chemistry, Christopher
Newport University, Newport News, VA, USA,Corresponding author: Correspondence:
James Bogenpohl PhD; Christopher Newport University; Department of Molecular
Biology and Chemistry; 1 Avenue of the Arts, Newport News, VA 23606;
757-594-8289;
| | - Rory M. Weston
- Department of Pharmacology and Toxicology, Virginia
Commonwealth University, Richmond, VA, USA
| | - Taylor N. Foreman
- Department of Molecular Biology and Chemistry, Christopher
Newport University, Newport News, VA, USA
| | - Kaitlyn E. Kitchen
- Department of Molecular Biology and Chemistry, Christopher
Newport University, Newport News, VA, USA
| | - Michael F. Miles
- Department of Pharmacology and Toxicology, Virginia
Commonwealth University, Richmond, VA, USA,VCU Alcohol Research Center, Virginia Commonwealth
University, Richmond, VA, USA
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3
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Weston RM, Schmitt RE, Grotewiel M, Miles MF. Transcriptome analysis of chloride intracellular channel knockdown in Drosophila identifies oxidation-reduction function as possible mechanism of altered sensitivity to ethanol sedation. PLoS One 2021; 16:e0246224. [PMID: 34228751 PMCID: PMC8259981 DOI: 10.1371/journal.pone.0246224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/18/2021] [Indexed: 01/22/2023] Open
Abstract
Chloride intracellular channels (CLICs) are a unique family of evolutionarily conserved metamorphic proteins, switching between stable conformations based on redox conditions. CLICs have been implicated in a wide variety biological processes including ion channel activity, apoptosis, membrane trafficking, and enzymatic oxidoreductase activity. Understanding the molecular mechanisms by which CLICs engage in these activities is an area of active research. Here, the sole Drosophila melanogaster ortholog, Clic, was targeted for RNAi knockdown to identify genes and biological processes associated with Clic expression. Clic knockdown had a substantial impact on global transcription, altering expression of over 7% of transcribed Drosophila genes. Overrepresentation analysis of differentially expressed genes identified enrichment of Gene Ontology terms including Cytoplasmic Translation, Oxidation-Reduction Process, Heme Binding, Membrane, Cell Junction, and Nucleolus. The top term, Cytoplasmic Translation, was enriched almost exclusively with downregulated genes. Drosophila Clic and vertebrate ortholog Clic4 have previously been tied to ethanol sensitivity and ethanol-regulated expression. Clic knockdown-responsive genes from the present study were found to overlap significantly with gene sets from 4 independently published studies related to ethanol exposure and sensitivity in Drosophila. Bioinformatic analysis of genes shared between these studies revealed an enrichment of genes related to amino acid metabolism, protein processing, oxidation-reduction processes, and lipid particles among others. To determine whether the modulation of ethanol sensitivity by Clic may be related to co-regulated oxidation-reduction processes, we evaluated the effect of hyperoxia on ethanol sedation in Clic knockdown flies. Consistent with previous findings, Clic knockdown reduced acute ethanol sedation sensitivity in flies housed under normoxia. However, this effect was reversed by exposure to hyperoxia, suggesting a common set of molecular-genetic mechanism may modulate each of these processes. This study suggests that Drosophila Clic has a major influence on regulation of oxidative stress signaling and that this function overlaps with the molecular mechanisms of acute ethanol sensitivity in the fly.
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Affiliation(s)
- Rory M. Weston
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Rebecca E. Schmitt
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Mike Grotewiel
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael F. Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
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4
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Francisco MA, Wanggou S, Fan JJ, Dong W, Chen X, Momin A, Abeysundara N, Min HK, Chan J, McAdam R, Sia M, Pusong RJ, Liu S, Patel N, Ramaswamy V, Kijima N, Wang LY, Song Y, Kafri R, Taylor MD, Li X, Huang X. Chloride intracellular channel 1 cooperates with potassium channel EAG2 to promote medulloblastoma growth. J Exp Med 2020; 217:133839. [PMID: 32097463 PMCID: PMC7201926 DOI: 10.1084/jem.20190971] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/27/2019] [Accepted: 01/16/2020] [Indexed: 01/13/2023] Open
Abstract
Ion channels represent a large class of drug targets, but their role in brain cancer is underexplored. Here, we identify that chloride intracellular channel 1 (CLIC1) is overexpressed in human central nervous system malignancies, including medulloblastoma, a common pediatric brain cancer. While global knockout does not overtly affect mouse development, genetic deletion of CLIC1 suppresses medulloblastoma growth in xenograft and genetically engineered mouse models. Mechanistically, CLIC1 enriches to the plasma membrane during mitosis and cooperates with potassium channel EAG2 at lipid rafts to regulate cell volume homeostasis. CLIC1 deficiency is associated with elevation of cell/nuclear volume ratio, uncoupling between RNA biosynthesis and cell size increase, and activation of the p38 MAPK pathway that suppresses proliferation. Concurrent knockdown of CLIC1/EAG2 and their evolutionarily conserved channels synergistically suppressed the growth of human medulloblastoma cells and Drosophila melanogaster brain tumors, respectively. These findings establish CLIC1 as a molecular dependency in rapidly dividing medulloblastoma cells, provide insights into the mechanism by which CLIC1 regulates tumorigenesis, and reveal that targeting CLIC1 and its functionally cooperative potassium channel is a disease-intervention strategy.
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Affiliation(s)
- Michelle A Francisco
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Siyi Wanggou
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jerry J Fan
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Weifan Dong
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Xin Chen
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ali Momin
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Namal Abeysundara
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hyun-Kee Min
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jade Chan
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Rochelle McAdam
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Marian Sia
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ronwell J Pusong
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shixuan Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nish Patel
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Vijay Ramaswamy
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Noriyuki Kijima
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lu-Yang Wang
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Canada.,Department of Physiology, University of Toronto, Toronto, Canada
| | - Yuanquan Song
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ran Kafri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Surgery, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xi Huang
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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5
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Lathen DR, Merrill CB, Rothenfluh A. Flying Together: Drosophila as a Tool to Understand the Genetics of Human Alcoholism. Int J Mol Sci 2020; 21:E6649. [PMID: 32932795 PMCID: PMC7555299 DOI: 10.3390/ijms21186649] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
Alcohol use disorder (AUD) exacts an immense toll on individuals, families, and society. Genetic factors determine up to 60% of an individual's risk of developing problematic alcohol habits. Effective AUD prevention and treatment requires knowledge of the genes that predispose people to alcoholism, play a role in alcohol responses, and/or contribute to the development of addiction. As a highly tractable and translatable genetic and behavioral model organism, Drosophila melanogaster has proven valuable to uncover important genes and mechanistic pathways that have obvious orthologs in humans and that help explain the complexities of addiction. Vinegar flies exhibit remarkably strong face and mechanistic validity as a model for AUDs, permitting many advancements in the quest to understand human genetic involvement in this disease. These advancements occur via approaches that essentially fall into one of two categories: (1) discovering candidate genes via human genome-wide association studies (GWAS), transcriptomics on post-mortem tissue from AUD patients, or relevant physiological connections, then using reverse genetics in flies to validate candidate genes' roles and investigate their molecular function in the context of alcohol. (2) Utilizing flies to discover candidate genes through unbiased screens, GWAS, quantitative trait locus analyses, transcriptomics, or single-gene studies, then validating their translational role in human genetic surveys. In this review, we highlight the utility of Drosophila as a model for alcoholism by surveying recent advances in our understanding of human AUDs that resulted from these various approaches. We summarize the genes that are conserved in alcohol-related function between humans and flies. We also provide insight into some advantages and limitations of these approaches. Overall, this review demonstrates how Drosophila have and can be used to answer important genetic questions about alcohol addiction.
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Affiliation(s)
- Daniel R. Lathen
- Department of Psychiatry and Neuroscience Ph.D. Program, University of Utah, Salt Lake City, UT 84108, USA;
| | - Collin B. Merrill
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA;
| | - Adrian Rothenfluh
- Department of Psychiatry and Neuroscience Ph.D. Program, University of Utah, Salt Lake City, UT 84108, USA;
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA;
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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6
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Schmitt RE, Messick MR, Shell BC, Dunbar EK, Fang H, Shelton KL, Venton BJ, Pletcher SD, Grotewiel M. Dietary yeast influences ethanol sedation in Drosophila via serotonergic neuron function. Addict Biol 2020; 25:e12779. [PMID: 31169340 DOI: 10.1111/adb.12779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 03/23/2019] [Accepted: 05/02/2019] [Indexed: 01/10/2023]
Abstract
Abuse of alcohol is a major clinical problem with far-reaching health consequences. Understanding the environmental and genetic factors that contribute to alcohol-related behaviors is a potential gateway for developing novel therapeutic approaches for patients that abuse the drug. To this end, we have used Drosophila melanogaster as a model to investigate the effect of diet, an environmental factor, on ethanol sedation. Providing flies with diets high in yeast, a routinely used component of fly media, increased their resistance to ethanol sedation. The yeast-induced resistance to ethanol sedation occurred in several different genetic backgrounds, was observed in males and females, was elicited by yeast from different sources, was readily reversible, and was associated with increased nutrient intake as well as decreased internal ethanol levels. Inhibition of serotonergic neuron function using multiple independent genetic manipulations blocked the effect of yeast supplementation on ethanol sedation, nutrient intake, and internal ethanol levels. Our results demonstrate that yeast is a critical dietary component that influences ethanol sedation in flies and that serotonergic signaling is required for the effect of dietary yeast on nutrient intake, ethanol uptake/elimination, and ethanol sedation. Our studies establish the fly as a model for diet-induced changes in ethanol sedation and raise the possibility that serotonin might mediate the effect of diet on alcohol-related behavior in other species.
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Affiliation(s)
- Rebecca E. Schmitt
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA USA
| | - Monica R. Messick
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA USA
| | - Brandon C. Shell
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA USA
| | - Ellyn K. Dunbar
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA USA
| | - Huai‐Fang Fang
- Department of Chemistry and Neuroscience Graduate Program University of Virginia Charlottesville VA USA
| | - Keith L. Shelton
- Department of Pharmacology and Toxicology Virginia Commonwealth University Richmond VA USA
| | - B. Jill Venton
- Department of Chemistry and Neuroscience Graduate Program University of Virginia Charlottesville VA USA
| | - Scott D. Pletcher
- Department of Molecular and Integrative Physiology and Geriatrics Center University of Michigan Ann Arbor MI USA
| | - Mike Grotewiel
- Department of Human and Molecular Genetics Virginia Commonwealth University Richmond VA USA
- Virginia Commonwealth University Alcohol Research Center Richmond VA USA
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7
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Smith ML, Lopez MF, Wolen AR, Becker HC, Miles MF. Brain regional gene expression network analysis identifies unique interactions between chronic ethanol exposure and consumption. PLoS One 2020; 15:e0233319. [PMID: 32469986 PMCID: PMC7259766 DOI: 10.1371/journal.pone.0233319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/01/2020] [Indexed: 11/28/2022] Open
Abstract
Progressive increases in ethanol consumption is a hallmark of alcohol use disorder (AUD). Persistent changes in brain gene expression are hypothesized to underlie the altered neural signaling producing abusive consumption in AUD. To identify brain regional gene expression networks contributing to progressive ethanol consumption, we performed microarray and scale-free network analysis of expression responses in a C57BL/6J mouse model utilizing chronic intermittent ethanol by vapor chamber (CIE) in combination with limited access oral ethanol consumption. This model has previously been shown to produce long-lasting increased ethanol consumption, particularly when combining oral ethanol access with repeated cycles of intermittent vapor exposure. The interaction of CIE and oral consumption was studied by expression profiling and network analysis in medial prefrontal cortex, nucleus accumbens, hippocampus, bed nucleus of the stria terminalis, and central nucleus of the amygdala. Brain region expression networks were analyzed for ethanol-responsive gene expression, correlation with ethanol consumption and functional content using extensive bioinformatics studies. In all brain-regions studied the largest number of changes in gene expression were seen when comparing ethanol naïve mice to those exposed to CIE and drinking. In the prefrontal cortex, however, unique patterns of gene expression were seen compared to other brain-regions. Network analysis identified modules of co-expressed genes in all brain regions. The prefrontal cortex and nucleus accumbens showed the greatest number of modules with significant correlation to drinking behavior. Across brain-regions, however, many modules with strong correlations to drinking, both baseline intake and amount consumed after CIE, showed functional enrichment for synaptic transmission and synaptic plasticity.
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Affiliation(s)
- Maren L. Smith
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Marcelo F. Lopez
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Aaron R. Wolen
- Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Howard C. Becker
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina, United States of America
- RHJ Department of Veterans Affairs Medical Center, Charleston, South Carolina, United States of America
| | - Michael F. Miles
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
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8
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Salvatore JE, Han S, Farris SP, Mignogna KM, Miles MF, Agrawal A. Beyond genome-wide significance: integrative approaches to the interpretation and extension of GWAS findings for alcohol use disorder. Addict Biol 2019; 24:275-289. [PMID: 29316088 PMCID: PMC6037617 DOI: 10.1111/adb.12591] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 11/20/2017] [Accepted: 11/26/2017] [Indexed: 12/16/2022]
Abstract
Alcohol use disorder (AUD) is a heritable complex behavior. Due to the highly polygenic nature of AUD, identifying genetic variants that comprise this heritable variation has proved to be challenging. With the exception of functional variants in alcohol metabolizing genes (e.g. ADH1B and ALDH2), few other candidate loci have been confidently linked to AUD. Genome-wide association studies (GWAS) of AUD and other alcohol-related phenotypes have either produced few hits with genome-wide significance or have failed to replicate on further study. These issues reinforce the complex nature of the genetic underpinnings for AUD and suggest that both GWAS studies with larger samples and additional analysis approaches that better harness the nominally significant loci in existing GWAS are needed. Here, we review approaches of interest in the post-GWAS era, including in silico functional analyses; functional partitioning of single nucleotide polymorphism heritability; aggregation of signal into genes and gene networks; and validation of identified loci, genes and gene networks in postmortem brain tissue and across species. These integrative approaches hold promise to illuminate our understanding of the biological basis of AUD; however, we recognize that the main challenge continues to be the extremely polygenic nature of AUD, which necessitates large samples to identify multiple loci associated with AUD liability.
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Affiliation(s)
- Jessica E. Salvatore
- Department of Psychology; Virginia Commonwealth University; Richmond VA USA
- Virginia Institute for Psychiatric and Behavioral Genetics; Virginia Commonwealth University; Richmond VA USA
| | - Shizhong Han
- Department of Psychiatry; University of Iowa; Iowa City IA USA
- Department of Psychiatry and Behavioral Sciences; Johns Hopkins School of Medicine; Baltimore MD USA
| | - Sean P. Farris
- Waggoner Center for Alcohol and Addiction Research; The University of Texas at Austin; Austin TX USA
| | - Kristin M. Mignogna
- Virginia Institute for Psychiatric and Behavioral Genetics; Virginia Commonwealth University; Richmond VA USA
| | - Michael F. Miles
- Department of Pharmacology and Toxicology; Virginia Commonwealth University; Richmond VA USA
| | - Arpana Agrawal
- Department of Psychiatry; Washington University School of Medicine; Saint Louis MO USA
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9
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Blednov YA, Bajo M, Roberts AJ, Da Costa AJ, Black M, Edmunds S, Mayfield J, Roberto M, Homanics GE, Lasek AW, Hitzemann RJ, Harris RA. Scn4b regulates the hypnotic effects of ethanol and other sedative drugs. GENES BRAIN AND BEHAVIOR 2019; 18:e12562. [PMID: 30817077 PMCID: PMC6612599 DOI: 10.1111/gbb.12562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/23/2019] [Accepted: 02/27/2019] [Indexed: 11/28/2022]
Abstract
The voltage-gated sodium channel subunit β4 (SCN4B) regulates neuronal activity by modulating channel gating and has been implicated in ethanol consumption in rodent models and human alcoholics. However, the functional role for Scn4b in ethanol-mediated behaviors is unknown. We determined if genetic global knockout (KO) or targeted knockdown of Scn4b in the central nucleus of the amygdala (CeA) altered ethanol drinking or related behaviors. We used four different ethanol consumption procedures (continuous and intermittent two-bottle choice (2BC), drinking-in-the dark and chronic intermittent ethanol vapor) and found that male and female Scn4b KO mice did not differ from their wild-type (WT) littermates in ethanol consumption in any of the tests. Knockdown of Scn4b mRNA in the CeA also did not alter 2BC ethanol drinking. However, Scn4b KO mice showed longer duration of the loss of righting reflex induced by ethanol, gaboxadol, pentobarbital and ketamine. KO mice showed slower recovery to basal levels of handling-induced convulsions after ethanol injection, which is consistent with the increased sedative effects observed in these mice. However, Scn4b KO mice did not differ in the severity of acute ethanol withdrawal. Acoustic startle responses, ethanol-induced hypothermia and clearance of blood ethanol also did not differ between the genotypes. There were also no functional differences in the membrane properties or excitability of CeA neurons from Scn4b KO and WT mice. Although we found no evidence that Scn4b regulates ethanol consumption in mice, it was involved in the acute hypnotic effects of ethanol and other sedatives.
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Affiliation(s)
- Yuri A Blednov
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas
| | - Michal Bajo
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Amanda J Roberts
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Adriana J Da Costa
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas
| | - Mendy Black
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas
| | - Stephanie Edmunds
- Department of Behavioral Neuroscience, Oregon Health & Science University, Oregon, Portland
| | - Jody Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas
| | - Marisa Roberto
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Gregg E Homanics
- Department of Anesthesiology & Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Neurobiology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Amy W Lasek
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois
| | - Robert J Hitzemann
- Department of Behavioral Neuroscience, Oregon Health & Science University, Oregon, Portland
| | - Robert A Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas
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10
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Farris SP, Riley BP, Williams RW, Mulligan MK, Miles MF, Lopez MF, Hitzemann R, Iancu OD, Colville A, Walter NAR, Darakjian P, Oberbeck DL, Daunais JB, Zheng CL, Searles RP, McWeeney SK, Grant KA, Mayfield RD. Cross-species molecular dissection across alcohol behavioral domains. Alcohol 2018; 72:19-31. [PMID: 30213503 PMCID: PMC6309876 DOI: 10.1016/j.alcohol.2017.11.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/14/2022]
Abstract
This review summarizes the proceedings of a symposium presented at the "Alcoholism and Stress: A Framework for Future Treatment Strategies" conference held in Volterra, Italy on May 9-12, 2017. Psychiatric diseases, including alcohol-use disorders (AUDs), are influenced through complex interactions of genes, neurobiological pathways, and environmental influences. A better understanding of the common neurobiological mechanisms underlying an AUD necessitates an integrative approach, involving a systematic assessment of diverse species and phenotype measures. As part of the World Congress on Stress and Alcoholism, this symposium provided a detailed account of current strategies to identify mechanisms underlying the development and progression of AUDs. Dr. Sean Farris discussed the integration and organization of transcriptome and postmortem human brain data to identify brain regional- and cell type-specific differences related to excessive alcohol consumption that are conserved across species. Dr. Brien Riley presented the results of a genome-wide association study of DSM-IV alcohol dependence; although replication of genetic associations with alcohol phenotypes in humans remains challenging, model organism studies show that COL6A3, KLF12, and RYR3 affect behavioral responses to ethanol, and provide substantial evidence for their role in human alcohol-related traits. Dr. Rob Williams expanded upon the systematic characterization of extensive genetic-genomic resources for quantifying and clarifying phenotypes across species that are relevant to precision medicine in human disease. The symposium concluded with Dr. Robert Hitzemann's description of transcriptome studies in a mouse model selectively bred for high alcohol ("binge-like") consumption and a non-human primate model of long-term alcohol consumption. Together, the different components of this session provided an overview of systems-based approaches that are pioneering the experimental prioritization and validation of novel genes and gene networks linked with a range of behavioral phenotypes associated with stress and AUDs.
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Affiliation(s)
- Sean P Farris
- University of Texas at Austin, Austin, TX, United States
| | - Brien P Riley
- Virginia Commonwealth University, Richmond, VA, United States
| | - Robert W Williams
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Megan K Mulligan
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Michael F Miles
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Marcelo F Lopez
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Robert Hitzemann
- Oregon Health and Science University, Portland, OR, United States
| | - Ovidiu D Iancu
- Oregon Health and Science University, Portland, OR, United States
| | | | | | | | | | - James B Daunais
- Wake Forest School of Medicine, Winston-Salem, NC, United States
| | | | - Robert P Searles
- Oregon Health and Science University, Portland, OR, United States
| | | | - Kathleen A Grant
- Oregon Health and Science University, Portland, OR, United States
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11
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Ethanol Stimulates Locomotion via a G αs-Signaling Pathway in IL2 Neurons in Caenorhabditis elegans. Genetics 2017; 207:1023-1039. [PMID: 28951527 PMCID: PMC5676223 DOI: 10.1534/genetics.117.300119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/23/2017] [Indexed: 01/21/2023] Open
Abstract
Alcohol abuse is among the top causes of preventable death, generating considerable financial, health, and societal burdens. Paradoxically, alcohol... Alcohol is a potent pharmacological agent when consumed acutely at sufficient quantities and repeated overuse can lead to addiction and deleterious effects on health. Alcohol is thought to modulate neuronal function through low-affinity interactions with proteins, in particular with membrane channels and receptors. Paradoxically, alcohol acts as both a stimulant and a sedative. The exact molecular mechanisms for the acute effects of ethanol on neurons, as either a stimulant or a sedative, however remain unclear. We investigated the role that the heat shock transcription factor HSF-1 played in determining a stimulatory phenotype of Caenorhabditis elegans in response to physiologically relevant concentrations of ethanol (17 mM; 0.1% v/v). Using genetic techniques, we demonstrate that either RNA interference of hsf-1 or use of an hsf-1(sy441) mutant lacked the enhancement of locomotion in response to acute ethanol exposure evident in wild-type animals. We identify that the requirement for HSF-1 in this phenotype was IL2 neuron-specific and required the downstream expression of the α-crystallin ortholog HSP-16.48. Using a combination of pharmacology, optogenetics, and phenotypic analyses we determine that ethanol activates a Gαs-cAMP-protein kinase A signaling pathway in IL2 neurons to stimulate nematode locomotion. We further implicate the phosphorylation of a specific serine residue (Ser322) on the synaptic protein UNC-18 as an end point for the Gαs-dependent signaling pathway. These findings establish and characterize a distinct neurosensory cell signaling pathway that determines the stimulatory action of ethanol and identifies HSP-16.48 and HSF-1 as novel regulators of this pathway.
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12
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Liang J, Shaulov Y, Savage-Dunn C, Boissinot S, Hoque T. Chloride intracellular channel proteins respond to heat stress in Caenorhabditis elegans. PLoS One 2017; 12:e0184308. [PMID: 28886120 PMCID: PMC5590911 DOI: 10.1371/journal.pone.0184308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/21/2017] [Indexed: 01/05/2023] Open
Abstract
Chloride intracellular channel proteins (CLICs) are multi-functional proteins that are expressed in various cell types and differ in their subcellular location. Two CLIC homologs, EXL-1 (excretory canal abnormal like-1) and EXC-4 (excretory canal abnormal- 4), are encoded in the Caenorhabditis elegans genome, providing an excellent model to study the functional diversification of CLIC proteins. EXC-4 functions in excretory canal formation during normal animal development. However, to date, the physiological function of EXL-1 remains largely unknown. In this study, we demonstrate that EXL-1 responds specifically to heat stress and translocates from the cytoplasm to the nucleus in intestinal cells and body wall muscle cells under heat shock. In contrast, we do not observe EXC-4 nuclear translocation under heat shock. Full protein sequence analysis shows that EXL-1 bears a non-classic nuclear localization signal (NLS) that EXC-4 is lacking. All mammalian CLIC members have a nuclear localization signal, with the exception of CLIC3. Our phylogenetic analysis of the CLIC gene families across various animal species demonstrates that the duplication of CLICs in protostomes and deuterostomes occurred independently and that the NLS was subsequently lost in amniotes and nematodes, suggesting convergent evolution. We also observe that EXL-1 nuclear translocation occurs in a timely ordered manner in the intestine, from posterior to anterior regions. Finally, we find that exl-1 loss of function mutants are more susceptible to heat stress than wild-type animals, demonstrating functional relevance of the nuclear translocation. This research provides the first link between CLICs and environmental heat stress. We propose that C. elegans CLICs evolved to achieve different physiological functions through subcellular localization change and spatial separation in response to external or internal signals.
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Affiliation(s)
- Jun Liang
- Department of Science, Borough of Manhattan Community College / CUNY, New York, New York, United States of America
- * E-mail:
| | - Yakov Shaulov
- Department of Biology, Queens College, CUNY, Flushing, New York, United States of America
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, CUNY, Flushing, New York, United States of America
- Biology PhD Program and Biochemistry PhD Program, the Graduate Center, New York, New York, United States of America
| | - Stephane Boissinot
- New York University Abu Dhabi, Saadiyat Island campus, Abu Dhabi, United Arab Emirates
| | - Tasmia Hoque
- Department of Science, Borough of Manhattan Community College / CUNY, New York, New York, United States of America
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13
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Adkins AE, Hack LM, Bigdeli TB, Williamson VS, McMichael GO, Mamdani M, Edwards A, Aliev F, Chan RF, Bhandari P, Raabe RC, Alaimo JT, Blackwell GG, Moscati AA, Poland RS, Rood B, Patterson DG, Walsh D, Whitfield JB, Zhu G, Montgomery GW, Henders AK, Martin NG, Heath AC, Madden PA, Frank J, Ridinger M, Wodarz N, Soyka M, Zill P, Ising M, Nöthen MM, Kiefer F, Rietschel M, Gelernter J, Sherva R, Koesterer R, Almasy L, Zhao H, Kranzler HR, Farrer LA, Maher BS, Prescott CA, Dick DM, Bacanu SA, Mathies LD, Davies AG, Vladimirov VI, Grotewiel M, Bowers MS, Bettinger JC, Webb BT, Miles MF, Kendler KS, Riley BP. Genomewide Association Study of Alcohol Dependence Identifies Risk Loci Altering Ethanol-Response Behaviors in Model Organisms. Alcohol Clin Exp Res 2017; 41:911-928. [PMID: 28226201 PMCID: PMC5404949 DOI: 10.1111/acer.13362] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 02/16/2017] [Indexed: 01/23/2023]
Abstract
BACKGROUND Alcohol dependence (AD) shows evidence for genetic liability, but genes influencing risk remain largely unidentified. METHODS We conducted a genomewide association study in 706 related AD cases and 1,748 unscreened population controls from Ireland. We sought replication in 15,496 samples of European descent. We used model organisms (MOs) to assess the role of orthologous genes in ethanol (EtOH)-response behaviors. We tested 1 primate-specific gene for expression differences in case/control postmortem brain tissue. RESULTS We detected significant association in COL6A3 and suggestive association in 2 previously implicated loci, KLF12 and RYR3. None of these signals are significant in replication. A suggestive signal in the long noncoding RNA LOC339975 is significant in case:control meta-analysis, but not in a population sample. Knockdown of a COL6A3 ortholog in Caenorhabditis elegans reduced EtOH sensitivity. Col6a3 expression correlated with handling-induced convulsions in mice. Loss of function of the KLF12 ortholog in C. elegans impaired development of acute functional tolerance (AFT). Klf12 expression correlated with locomotor activation following EtOH injection in mice. Loss of function of the RYR3 ortholog reduced EtOH sensitivity in C. elegans and rapid tolerance in Drosophila. The ryanodine receptor antagonist dantrolene reduced motivation to self-administer EtOH in rats. Expression of LOC339975 does not differ between cases and controls but is reduced in carriers of the associated rs11726136 allele in nucleus accumbens (NAc). CONCLUSIONS We detect association between AD and COL6A3, KLF12, RYR3, and LOC339975. Despite nonreplication of COL6A3, KLF12, and RYR3 signals, orthologs of these genes influence behavioral response to EtOH in MOs, suggesting potential involvement in human EtOH response and AD liability. The associated LOC339975 allele may influence gene expression in human NAc. Although the functions of long noncoding RNAs are poorly understood, there is mounting evidence implicating these genes in multiple brain functions and disorders.
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Affiliation(s)
- Amy E. Adkins
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Laura M. Hack
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Tim B. Bigdeli
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Vernell S. Williamson
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - G. Omari McMichael
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Mohammed Mamdani
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Alexis Edwards
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Fazil Aliev
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Robin F. Chan
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Poonam Bhandari
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Richard C. Raabe
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Joseph T. Alaimo
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - GinaMari G. Blackwell
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Arden A. Moscati
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Ryan S. Poland
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Benjamin Rood
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Diana G. Patterson
- Shaftesbury Square Hospital, 116-120 Great Victoria Street, Belfast,
BT2 7BG, United Kingdom
| | - Dermot Walsh
- Health Research Board, 67-72 Lower Mount Street, Dublin 2,
Ireland
| | | | - John B. Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Gu Zhu
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Grant W. Montgomery
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Anjali K. Henders
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Nicholas G. Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute,
Royal Brisbane and Women’s Hospital, 300 Herston Road, Brisbane, QLD 4006,
Australia
| | - Andrew C. Heath
- Department of Psychiatry, Washington University School of Medicine,
4560 Clayton Ave., Suite 1000, St. Louis, MO, 63110, USA
| | - Pamela A.F. Madden
- Department of Psychiatry, Washington University School of Medicine,
4560 Clayton Ave., Suite 1000, St. Louis, MO, 63110, USA
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute
of Mental Health, Medical Faculty Mannheim/Heidelberg University, J 5, 68159
Mannheim, Germany
| | - Monika Ridinger
- Department of Psychiatry, University Hospital Regensburg,
University of Regensburg, 93042 Regensburg, Germany
| | - Norbert Wodarz
- Department of Psychiatry, University Hospital Regensburg,
University of Regensburg, 93042 Regensburg, Germany
| | - Michael Soyka
- Privatklinik Meiringen, Willigen, 3860 Meiringen, Switzerland
- Department of Psychiatry and Psychotherapy, University of Munich,
Nussbaumstrasse 7, 80336 Munich, Germany
| | - Peter Zill
- Department of Psychiatry and Psychotherapy, University of Munich,
Nussbaumstrasse 7, 80336 Munich, Germany
| | - Marcus Ising
- Department of Molecular Psychology, Max-Planck-Institute of
Psychiatry, Kraepelinstrasse 2–10, 80804 Munich, Germany
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of
Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
- Department of Institute of Human Genetics, University of Bonn,
Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of
Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
| | - Falk Kiefer
- Department of Addictive Behavior and Addiction Medicine, Central
Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, J 5,
68159 Mannheim, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute
of Mental Health, Medical Faculty Mannheim/Heidelberg University, J 5, 68159
Mannheim, Germany
| | | | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, 333
Cedar Street, New Haven, CT, 06510, USA
- Department of Neurobiology, Yale University School of Medicine, 333
Cedar Street, New Haven, CT, 06510, USA
- Department of Genetics, Yale University School of Medicine, 333
Cedar Street, New Haven, CT, 06510, USA
- Department of Psychiatry, VA CT Healthcare Center, 950 Campbell
Avenue, West Haven, CT, 06516, USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University
School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Ryan Koesterer
- Department of Medicine (Biomedical Genetics), Boston University
School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Laura Almasy
- Texas Biomedical Research Institute, Department of Genetics, P.O.
Box 760549, San Antonio, TX, 78245-0549, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, 333
Cedar Street, New Haven, CT, 06510, USA
- Department of Biostatistics, Yale University School of Medicine,
333 Cedar Street, New Haven, CT, 06510, USA
| | - Henry R. Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman
School of Medicine, Treatment Research Center, 3900 Chestnut Street, Philadelphia,
PA 19104, USA
- VISN 4 MIRECC, Philadelphia VA Medical Center, 3900 Woodland
Avenue, Philadelphia, PA, 19104, USA
| | - Lindsay A. Farrer
- Department of Psychiatry, VA CT Healthcare Center, 950 Campbell
Avenue, West Haven, CT, 06516, USA
- Department of Neurology, Boston University School of Medicine, 72
East Concord Street, Boston, MA, 02118, USA
- Department of Ophthalmology, Boston University School of Medicine,
72 East Concord Street, Boston, MA, 02118, USA
- Department of Genetics and Genomics, Boston University School of
Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Department of Epidemiology and Biostatistics, Boston University
School of Public Health, 715 Albany Street, Boston, MA, 02118, USA
| | - Brion S. Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of
Public Health, 624 N. Broadway, 8th Floor, Baltimore, MD, 21205, USA
| | - Carol A. Prescott
- Department of Psychology, University of Southern California, SGM
501, 3620 South McClintock Ave., Los Angeles, CA, 90089-1061, USA
| | - Danielle M. Dick
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Silviu A. Bacanu
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Laura D. Mathies
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Andrew G. Davies
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Vladimir I. Vladimirov
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Lieber Institute for Brain Development, Johns Hopkins University,
855 North Wolfe Street Suite 300, Baltimore, MD, 21205, USA
- Center for Biomarker Research and Personalized Medicine, School of
Pharmacy, PO Box 980533, Virginia Commonwealth University, Richmond, VA 23298-0533,
USA
| | - Mike Grotewiel
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - M. Scott Bowers
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Jill C. Bettinger
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Bradley T. Webb
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
| | - Michael F. Miles
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Pharmacology & Toxicology, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Kenneth S. Kendler
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
| | - Brien P. Riley
- Virginia Commonwealth University Alcohol Research Center, PO Box
980424, Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
- Department of Psychiatry, PO Box 980424, Virginia Commonwealth
University, Richmond, VA, 23298-0424, USA
- Department of Human & Molecular Genetics, PO Box 980424,
Virginia Commonwealth University, Richmond, VA, 23298-0424, USA
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14
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Park A, Ghezzi A, Wijesekera TP, Atkinson NS. Genetics and genomics of alcohol responses in Drosophila. Neuropharmacology 2017; 122:22-35. [PMID: 28161376 DOI: 10.1016/j.neuropharm.2017.01.032] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/24/2017] [Accepted: 01/29/2017] [Indexed: 02/07/2023]
Abstract
Drosophila melanogaster has become a significant model organism for alcohol research. In flies, a rich variety of behaviors can be leveraged for identifying genes affecting alcohol responses and adaptations. Furthermore, almost all genes can be easily genetically manipulated. Despite the great evolutionary distance between flies and mammals, many of the same genes have been implicated in strikingly similar alcohol-induced behaviors. A major problem in medical research today is that it is difficult to extrapolate from any single model system to humans. Strong evolutionary conservation of a mechanistic response between distantly related organisms, such as flies and mammals, is a powerful predictor that conservation will continue all the way to humans. This review describes the state of the Drosophila alcohol research field. It describes common alcohol behavioral assays, the independent origins of resistance and tolerance, the results of classical genetic screens and candidate gene analysis, and the outcomes of recent genomics studies employing GWAS, transcriptome, miRNA, and genome-wide histone acetylation surveys. This article is part of the Special Issue entitled "Alcoholism".
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Affiliation(s)
- Annie Park
- Department of Neuroscience and The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, United States
| | - Alfredo Ghezzi
- Department of Biology, University of Puerto Rico, Rio Piedras. San Juan, PR, United States
| | - Thilini P Wijesekera
- Department of Neuroscience and The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, United States
| | - Nigel S Atkinson
- Department of Neuroscience and The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, United States.
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Xu Y, Zhu J, Hu X, Wang C, Lu D, Gong C, Yang J, Zong L. CLIC1 Inhibition Attenuates Vascular Inflammation, Oxidative Stress, and Endothelial Injury. PLoS One 2016; 11:e0166790. [PMID: 27861612 PMCID: PMC5115793 DOI: 10.1371/journal.pone.0166790] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 11/03/2016] [Indexed: 01/26/2023] Open
Abstract
Endothelial dysfunction, which includes endothelial oxidative damage and vascular inflammation, is a key initiating step in the pathogenesis of atherosclerosis (AS) and an independent risk factor for this disorder. Intracellular chloride channel 1 (CLIC1), a novel metamorphic protein, acts as a sensor of cell oxidation and is involved in inflammation. In this study, we hypothesize that CLIC1 plays an important role in AS. Apolipoprotein E-deficient mice were supplied with a normal diet or a high-fat and high-cholesterol diet for 8 weeks. Overexpressed CLIC1 was associated with the accelerated atherosclerotic plaque development, amplified oxidative stress, and in vivo release of inflammatory cytokines. We subsequently examined the underlying molecular mechanisms through in vitro experiments. Treatment of cultured human umbilical vein endothelial cells (HUVECs) with H2O2 induced endothelial oxidative damage and enhanced CLIC1 expression. Suppressing CLIC1 expression through gene knocked-out (CLIC1-/-) or using the specific inhibitor indanyloxyacetic acid-94 (IAA94) reduced ROS production, increased SOD enzyme activity, and significantly decreased MDA level. CLIC1-/- HUVECs exhibited significantly reduced expression of TNF-α and IL-1β as well as ICAM-1 and VCAM-1 at the protein levels. In addition, H2O2 promoted CLIC1 translocation to the cell membrane and insertion into lipid membranes, whereas IAA94 inhibited CLIC1 membrane translocation induced by H2O2. By contrast, the majority of CLIC1 did not aggregate on the cell membrane in normal HUVECs, and this finding is consistent with the changes in cytoplasmic chloride ion concentration. This study demonstrates for the first time that CLIC1 is overexpressed during AS development both in vitro and in vivo and can regulate the accumulation of inflammatory cytokines and production of oxidative stress. Our results also highlight that deregulation of endothelial functions may be associated with the membrane translocation of CLIC1 and active chloride-selective ion channels in endothelial cells.
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Affiliation(s)
- Yingling Xu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ji Zhu
- Clinical Laboratory, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiao Hu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Cui Wang
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Dezhao Lu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
- * E-mail:
| | - Chenxue Gong
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinhuan Yang
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Lei Zong
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
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16
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Marballi K, Genabai NK, Blednov YA, Harris RA, Ponomarev I. Alcohol consumption induces global gene expression changes in VTA dopaminergic neurons. GENES BRAIN AND BEHAVIOR 2015; 15:318-26. [PMID: 26482798 DOI: 10.1111/gbb.12266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/28/2015] [Accepted: 10/16/2015] [Indexed: 12/22/2022]
Abstract
Alcoholism is associated with dysregulation in the neural circuitry that mediates motivated and goal-directed behaviors. The dopaminergic (DA) connection between the ventral tegmental area (VTA) and the nucleus accumbens is viewed as a critical component of the neurocircuitry mediating alcohol's rewarding and behavioral effects. We sought to determine the effects of binge alcohol drinking on global gene expression in VTA DA neurons. Alcohol-preferring C57BL/6J × FVB/NJ F1 hybrid female mice were exposed to a modified drinking in the dark (DID) procedure for 3 weeks, while control animals had access to water only. Global gene expression of laser-captured tyrosine hydroxylase (TH)-positive VTA DA neurons was measured using microarrays. A total of 644 transcripts were differentially expressed between the drinking and nondrinking mice, and 930 transcripts correlated with alcohol intake during the last 2 days of drinking in the alcohol group. Bioinformatics analysis of alcohol-responsive genes identified molecular pathways and networks perturbed in DA neurons by alcohol consumption, which included neuroimmune and epigenetic functions, alcohol metabolism and brain disorders. The majority of genes with high and specific expression in DA neurons were downregulated by or negatively correlated with alcohol consumption, suggesting a decreased activity of DA neurons in high drinking animals. These changes in the DA transcriptome provide a foundation for alcohol-induced neuroadaptations that may play a crucial role in the transition to addiction.
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Affiliation(s)
- K Marballi
- Waggoner Center for Alcohol and Addiction Research and The College of Pharmacy, The University of Texas at Austin, Austin
| | - N K Genabai
- Waggoner Center for Alcohol and Addiction Research and The College of Pharmacy, The University of Texas at Austin, Austin.,Center of Emphasis in Neurosciences, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Y A Blednov
- Waggoner Center for Alcohol and Addiction Research and The College of Pharmacy, The University of Texas at Austin, Austin
| | - R A Harris
- Waggoner Center for Alcohol and Addiction Research and The College of Pharmacy, The University of Texas at Austin, Austin
| | - I Ponomarev
- Waggoner Center for Alcohol and Addiction Research and The College of Pharmacy, The University of Texas at Austin, Austin
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Caenorhabditis elegans as a Model to Study the Molecular and Genetic Mechanisms of Drug Addiction. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 137:229-52. [PMID: 26810004 DOI: 10.1016/bs.pmbts.2015.10.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug addiction takes a massive toll on society. Novel animal models are needed to test new treatments and understand the basic mechanisms underlying addiction. Rodent models have identified the neurocircuitry involved in addictive behavior and indicate that rodents possess some of the same neurobiologic mechanisms that mediate addiction in humans. Recent studies indicate that addiction is mechanistically and phylogenetically ancient and many mechanisms that underlie human addiction are also present in invertebrates. The nematode Caenorhabditis elegans has conserved neurobiologic systems with powerful molecular and genetic tools and a rapid rate of development that enables cost-effective translational discovery. Emerging evidence suggests that C. elegans is an excellent model to identify molecular mechanisms that mediate drug-induced behavior and potential targets for medications development for various addictive compounds. C. elegans emit many behaviors that can be easily quantitated including some that involve interactions with the environment. Ethanol (EtOH) is the best-studied drug-of-abuse in C. elegans and at least 50 different genes/targets have been identified as mediating EtOH's effects and polymorphisms in some orthologs in humans are associated with alcohol use disorders. C. elegans has also been shown to display dopamine and cholinergic system-dependent attraction to nicotine and demonstrate preference for cues previously associated with nicotine. Cocaine and methamphetamine have been found to produce dopamine-dependent reward-like behaviors in C. elegans. These behavioral tests in combination with genetic/molecular manipulations have led to the identification of dozens of target genes/systems in C. elegans that mediate drug effects. The one target/gene identified as essential for drug-induced behavioral responses across all drugs of abuse was the cat-2 gene coding for tyrosine hydroxylase, which is consistent with the role of dopamine neurotransmission in human addiction. Overall, C. elegans can be used to model aspects of drug addiction and identify systems and molecular mechanisms that mediate drug effects. The findings are surprisingly consistent with analogous findings in higher-level organisms. Further, model refinement is warranted to improve model validity and increase utility for medications development.
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Grotewiel M, Bettinger JC. Drosophila and Caenorhabditis elegans as Discovery Platforms for Genes Involved in Human Alcohol Use Disorder. Alcohol Clin Exp Res 2015; 39:1292-311. [PMID: 26173477 PMCID: PMC4656040 DOI: 10.1111/acer.12785] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/18/2015] [Indexed: 01/08/2023]
Abstract
BACKGROUND Despite the profound clinical significance and strong heritability of alcohol use disorder (AUD), we do not yet have a comprehensive understanding of the naturally occurring genetic variance within the human genome that drives its development. This lack of understanding is likely to be due in part to the large phenotypic and genetic heterogeneities that underlie human AUD. As a complement to genetic studies in humans, many laboratories are using the invertebrate model organisms (iMOs) Drosophila melanogaster (fruit fly) and Caenorhabditis elegans (nematode worm) to identify genetic mechanisms that influence the effects of alcohol (ethanol) on behavior. While these extremely powerful models have identified many genes that influence the behavioral responses to alcohol, in most cases it has remained unclear whether results from behavioral-genetic studies in iMOs are directly applicable to understanding the genetic basis of human AUD. METHODS In this review, we critically evaluate the utility of the fly and worm models for identifying genes that influence AUD in humans. RESULTS Based on results published through early 2015, studies in flies and worms have identified 91 and 50 genes, respectively, that influence 1 or more aspects of behavioral responses to alcohol. Collectively, these fly and worm genes correspond to 293 orthologous genes in humans. Intriguingly, 51 of these 293 human genes have been implicated in AUD by at least 1 study in human populations. CONCLUSIONS Our analyses strongly suggest that the Drosophila and C. elegans models have considerable utility for identifying orthologs of genes that influence human AUD.
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Affiliation(s)
- Mike Grotewiel
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
- Virginia Commonwealth University Alcohol Research Center, Richmond, Virginia
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology , Virginia Commonwealth University, Richmond, Virginia
- Virginia Commonwealth University Alcohol Research Center, Richmond, Virginia
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Bubier JA, Phillips CA, Langston MA, Baker EJ, Chesler EJ. GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data. Mamm Genome 2015; 26:556-66. [PMID: 26092690 PMCID: PMC4602068 DOI: 10.1007/s00335-015-9575-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/03/2015] [Indexed: 01/20/2023]
Abstract
A persistent challenge lies in the interpretation of consensus and discord from functional genomics experimentation. Harmonizing and analyzing this data will enable investigators to discover relations of many genes to many diseases, and from many phenotypes and experimental paradigms to many diseases through their genomic substrates. The GeneWeaver.org system provides a platform for cross-species integration and interrogation of heterogeneous curated and experimentally derived functional genomics data. GeneWeaver enables researchers to store, share, analyze, and compare results of their own genome-wide functional genomics experiments in an environment containing rich companion data obtained from major curated repositories, including the Mouse Genome Database and other model organism databases, along with derived data from highly specialized resources, publications, and user submissions. The data, largely consisting of gene sets and putative biological networks, are mapped onto one another through gene identifiers and homology across species. A versatile suite of interactive tools enables investigators to perform a variety of set analysis operations to find consilience among these often noisy experimental results. Fast algorithms enable real-time analysis of large queries. Specific applications include prioritizing candidate genes for quantitative trait loci, identifying biologically valid mouse models and phenotypic assays for human disease, finding the common biological substrates of related diseases, classifying experiments and the biological concepts they represent from empirical data, and applying patterns of genomic evidence to implicate novel genes in disease. These results illustrate an alternative to strict emphasis on replicability, whereby researchers classify experimental results to identify the conditions that lead to their similarity.
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Affiliation(s)
| | - Charles A Phillips
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Michael A Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Erich J Baker
- Computer Science Department, Baylor University, Waco, TX, 76798, USA
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20
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Farris SP, Harris RA, Ponomarev I. Epigenetic modulation of brain gene networks for cocaine and alcohol abuse. Front Neurosci 2015; 9:176. [PMID: 26041984 PMCID: PMC4438259 DOI: 10.3389/fnins.2015.00176] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/30/2015] [Indexed: 12/19/2022] Open
Abstract
Cocaine and alcohol are two substances of abuse that prominently affect the central nervous system (CNS). Repeated exposure to cocaine and alcohol leads to longstanding changes in gene expression, and subsequent functional CNS plasticity, throughout multiple brain regions. Epigenetic modifications of histones are one proposed mechanism guiding these enduring changes to the transcriptome. Characterizing the large number of available biological relationships as network models can reveal unexpected biochemical relationships. Clustering analysis of variation from whole-genome sequencing of gene expression (RNA-Seq) and histone H3 lysine 4 trimethylation (H3K4me3) events (ChIP-Seq) revealed the underlying structure of the transcriptional and epigenomic landscape within hippocampal postmortem brain tissue of drug abusers and control cases. Distinct sets of interrelated networks for cocaine and alcohol abuse were determined for each abusive substance. The network approach identified subsets of functionally related genes that are regulated in agreement with H3K4me3 changes, suggesting cause and effect relationships between this epigenetic mark and gene expression. Gene expression networks consisted of recognized substrates for addiction, such as the dopamine- and cAMP-regulated neuronal phosphoprotein PPP1R1B/DARPP-32 and the vesicular glutamate transporter SLC17A7/VGLUT1 as well as potentially novel molecular targets for substance abuse. Through a systems biology based approach our results illustrate the utility of integrating epigenetic and transcript expression to establish relevant biological networks in the human brain for addiction. Future work with laboratory models may clarify the functional relevance of these gene networks for cocaine and alcohol, and provide a framework for the development of medications for the treatment of addiction.
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Affiliation(s)
- Sean P Farris
- Waggoner Center for Alcohol & Addiction Research and The College of Pharmacy, University of Texas at Austin Austin, TX, USA
| | - Robert A Harris
- Waggoner Center for Alcohol & Addiction Research and The College of Pharmacy, University of Texas at Austin Austin, TX, USA
| | - Igor Ponomarev
- Waggoner Center for Alcohol & Addiction Research and The College of Pharmacy, University of Texas at Austin Austin, TX, USA
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21
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Sandhu S, Kollah AP, Lewellyn L, Chan RF, Grotewiel M. An inexpensive, scalable behavioral assay for measuring ethanol sedation sensitivity and rapid tolerance in Drosophila. J Vis Exp 2015:52676. [PMID: 25939022 PMCID: PMC4423423 DOI: 10.3791/52676] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Alcohol use disorder (AUD) is a serious health challenge. Despite a large hereditary component to AUD, few genes have been unambiguously implicated in their etiology. The fruit fly, Drosophila melanogaster, is a powerful model for exploring molecular-genetic mechanisms underlying alcohol-related behaviors and therefore holds great promise for identifying and understanding the function of genes that influence AUD. The use of the Drosophila model for these types of studies depends on the availability of assays that reliably measure behavioral responses to ethanol. This report describes an assay suitable for assessing ethanol sensitivity and rapid tolerance in flies. Ethanol sensitivity measured in this assay is influenced by the volume and concentration of ethanol used, a variety of previously reported genetic manipulations, and also the length of time the flies are housed without food immediately prior to testing. In contrast, ethanol sensitivity measured in this assay is not affected by the vigor of fly handling, sex of the flies, and supplementation of growth medium with antibiotics or live yeast. Three different methods for quantitating ethanol sensitivity are described, all leading to essentially indistinguishable ethanol sensitivity results. The scalable nature of this assay, combined with its overall simplicity to set-up and relatively low expense, make it suitable for small and large scale genetic analysis of ethanol sensitivity and rapid tolerance in Drosophila.
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Affiliation(s)
- Simran Sandhu
- Department of Human and Molecular Genetics, Virginia Commonwealth University
| | - Arnavaz P Kollah
- Department of Human and Molecular Genetics, Virginia Commonwealth University
| | - Lara Lewellyn
- Department of Human and Molecular Genetics, Virginia Commonwealth University
| | - Robin F Chan
- Department of Human and Molecular Genetics, Virginia Commonwealth University
| | - Mike Grotewiel
- Department of Human and Molecular Genetics, Virginia Commonwealth University; VCU Alcohol Research Center, Virginia Commonwealth University;
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22
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Davies AG, Blackwell GG, Raabe RC, Bettinger JC. An Assay for Measuring the Effects of Ethanol on the Locomotion Speed of Caenorhabditis elegans. J Vis Exp 2015:52681. [PMID: 25938273 PMCID: PMC4476067 DOI: 10.3791/52681] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Alcohol use disorders are a significant public health concern, for which there are few effective treatment strategies. One difficulty that has delayed the development of more effective treatments is the relative lack of understanding of the molecular underpinnings of the effects of ethanol on behavior. The nematode, Caenorhabditis elegans (C. elegans), provides a useful model in which to generate and test hypotheses about the molecular effects of ethanol. Here, we describe an assay that has been developed and used to examine the roles of particular genes and environmental factors in behavioral responses to ethanol, in which locomotion is the behavioral output. Ethanol dose-dependently causes an acute depression of crawling on an agar surface. The effects are dynamic; animals exposed to a high concentration demonstrate an initial strong depression of crawling, referred to here as initial sensitivity, and then partially recover locomotion speed despite the continued presence of the drug. This ethanol-induced behavioral plasticity is referred to here as the development of acute functional tolerance. This assay has been used to demonstrate that these two phenotypes are distinct and genetically separable. The straightforward locomotion assay described here is suitable for examining the effects of both genetic and environmental manipulations on these acute behavioral responses to ethanol in C. elegans.
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Affiliation(s)
- Andrew G Davies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University; VCU Alcohol Research Center, Virginia Commonwealth University
| | - GinaMari G Blackwell
- Department of Pharmacology and Toxicology, Virginia Commonwealth University; VCU Alcohol Research Center, Virginia Commonwealth University
| | - Richard C Raabe
- Department of Pharmacology and Toxicology, Virginia Commonwealth University
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University; VCU Alcohol Research Center, Virginia Commonwealth University;
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SWI/SNF chromatin remodeling regulates alcohol response behaviors in Caenorhabditis elegans and is associated with alcohol dependence in humans. Proc Natl Acad Sci U S A 2015; 112:3032-7. [PMID: 25713357 DOI: 10.1073/pnas.1413451112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Alcohol abuse is a widespread and serious problem. Understanding the factors that influence the likelihood of abuse is important for the development of effective therapies. There are both genetic and environmental influences on the development of abuse, but it has been difficult to identify specific liability factors, in part because of both the complex genetic architecture of liability and the influences of environmental stimuli on the expression of that genetic liability. Epigenetic modification of gene expression can underlie both genetic and environmentally sensitive variation in expression, and epigenetic regulation has been implicated in the progression to addiction. Here, we identify a role for the switching defective/sucrose nonfermenting (SWI/SNF) chromatin-remodeling complex in regulating the behavioral response to alcohol in the nematode Caenorhabditis elegans. We found that SWI/SNF components are required in adults for the normal behavioral response to ethanol and that different SWI/SNF complexes regulate different aspects of the acute response to ethanol. We showed that the SWI/SNF subunits SWSN-9 and SWSN-7 are required in neurons and muscle for the development of acute functional tolerance to ethanol. Examination of the members of the SWI/SNF complex for association with a diagnosis of alcohol dependence in a human population identified allelic variation in a member of the SWI/SNF complex, suggesting that variation in the regulation of SWI/SNF targets may influence the propensity to develop abuse disorders. Together, these data strongly implicate the chromatin remodeling associated with SWI/SNF complex members in the behavioral responses to alcohol across phyla.
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24
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Batman AM. Translating Alcohol Research: Opportunities and Challenges. Alcohol Res 2015; 37:7-14. [PMID: 26259085 PMCID: PMC4476605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Alcohol use disorder (AUD) and its sequelae impose a major burden on the public health of the United States, and adequate long-term control of this disorder has not been achieved. Molecular and behavioral basic science research findings are providing the groundwork for understanding the mechanisms underlying AUD and have identified multiple candidate targets for ongoing clinical trials. However, the translation of basic research or clinical findings into improved therapeutic approaches for AUD must become more efficient. Translational research is a multistage process of stream-lining the movement of basic biomedical research findings into clinical research and then to the clinical target populations. This process demands efficient bidirectional communication across basic, applied, and clinical science as well as with clinical practitioners. Ongoing work suggests rapid progress is being made with an evolving translational framework within the alcohol research field. This is helped by multiple interdisciplinary collaborative research structures that have been developed to advance translational work on AUD. Moreover, the integration of systems biology approaches with collaborative clinical studies may yield novel insights for future translational success. Finally, appreciation of genetic variation in pharmacological or behavioral treatment responses and optimal communication from bench to bedside and back may strengthen the success of translational research applications to AUD.
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A novel cholinergic action of alcohol and the development of tolerance to that effect in Caenorhabditis elegans. Genetics 2014; 199:135-49. [PMID: 25342716 DOI: 10.1534/genetics.114.171884] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the genes and mechanisms involved in acute alcohol responses has the potential to allow us to predict an individual's predisposition to developing an alcohol use disorder. To better understand the molecular pathways involved in the activating effects of alcohol and the acute functional tolerance that can develop to such effects, we characterized a novel ethanol-induced hypercontraction response displayed by Caenorhabditis elegans. We compared body size of animals prior to and during ethanol treatment and showed that acute exposure to ethanol produced a concentration-dependent decrease in size followed by recovery to their untreated size by 40 min despite continuous treatment. An increase in cholinergic signaling, leading to muscle hypercontraction, is implicated in this effect because pretreatment with mecamylamine, a nicotinic acetylcholine receptor (nAChR) antagonist, blocked ethanol-induced hypercontraction, as did mutations causing defects in cholinergic signaling (cha-1 and unc-17). Analysis of mutations affecting specific subunits of nAChRs excluded a role for the ACR-2R, the ACR-16R, and the levamisole-sensitive AChR and indicated that this excitation effect is dependent on an uncharacterized nAChR that contains the UNC-63 α-subunit. We performed a forward genetic screen and identified eg200, a mutation that affects a conserved glycine in EAT-6, the α-subunit of the Na(+)/K(+) ATPase. The eat-6(eg200) mutant fails to develop tolerance to ethanol-induced hypercontraction and remains contracted for at least 3 hr of continuous ethanol exposure. These data suggest that cholinergic signaling through a specific α-subunit-containing nAChR is involved in ethanol-induced excitation and that tolerance to this ethanol effect is modulated by Na(+)/K(+) ATPase function.
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26
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Narayanasamy SK, Simpson DC, Martin I, Grotewiel M, Gronert S. Paraquat exposure and Sod2 knockdown have dissimilar impacts on the Drosophila melanogaster carbonylated protein proteome. Proteomics 2014; 14:2566-77. [PMID: 25091824 DOI: 10.1002/pmic.201400192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/07/2014] [Accepted: 07/30/2014] [Indexed: 12/15/2022]
Abstract
Exposure to Paraquat and RNA interference knockdown of mitochondrial superoxide dismutase (Sod2) are known to result in significant lifespan reduction, locomotor dysfunction, and mitochondrial degeneration in Drosophila melanogaster. Both perturbations increase the flux of the progenitor ROS, superoxide, but the molecular underpinnings of the resulting phenotypes are poorly understood. Improved understanding of such processes could lead to advances in the treatment of numerous age-related disorders. Superoxide toxicity can act through protein carbonylation. Analysis of carbonylated proteins is attractive since carbonyl groups are not present in the 20 canonical amino acids and are amenable to labeling and enrichment strategies. Here, carbonylated proteins were labeled with biotin hydrazide and enriched on streptavidin beads. On-bead digestion was used to release carbonylated protein peptides, with relative abundance ratios versus controls obtained using the iTRAQ MS-based proteomics approach. Western blotting and biotin quantitation assay approaches were also investigated. By both Western blotting and proteomics, Paraquat exposure, but not Sod2 knockdown, resulted in increased carbonylated protein relative abundance. For Paraquat exposure versus control, the median carbonylated protein relative abundance ratio (1.53) determined using MS-based proteomics was in good agreement with that obtained using a commercial biotin quantitation kit (1.36).
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27
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Raabe RC, Mathies LD, Davies AG, Bettinger JC. The omega-3 fatty acid eicosapentaenoic acid is required for normal alcohol response behaviors in C. elegans. PLoS One 2014; 9:e105999. [PMID: 25162400 PMCID: PMC4146551 DOI: 10.1371/journal.pone.0105999] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/01/2014] [Indexed: 12/18/2022] Open
Abstract
Alcohol addiction is a widespread societal problem, for which there are few treatments. There are significant genetic and environmental influences on abuse liability, and understanding these factors will be important for the identification of susceptible individuals and the development of effective pharmacotherapies. In humans, the level of response to alcohol is strongly predictive of subsequent alcohol abuse. Level of response is a combination of counteracting responses to alcohol, the level of sensitivity to the drug and the degree to which tolerance develops during the drug exposure, called acute functional tolerance. We use the simple and well-characterized nervous system of Caenorhabditis elegans to model the acute behavioral effects of ethanol to identify genetic and environmental factors that influence level of response to ethanol. Given the strong molecular conservation between the neurobiological machinery of worms and humans, cellular-level effects of ethanol are likely to be conserved. Increasingly, variation in long-chain polyunsaturated fatty acid levels has been implicated in complex neurobiological phenotypes in humans, and we recently found that fatty acid levels modify ethanol responses in worms. Here, we report that 1) eicosapentaenoic acid, an omega-3 polyunsaturated fatty acid, is required for the development of acute functional tolerance, 2) dietary supplementation of eicosapentaenoic acid is sufficient for acute tolerance, and 3) dietary eicosapentaenoic acid can alter the wild-type response to ethanol. These results suggest that genetic variation influencing long-chain polyunsaturated fatty acid levels may be important abuse liability loci, and that dietary polyunsaturated fatty acids may be an important environmental modulator of the behavioral response to ethanol.
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Affiliation(s)
- Richard C. Raabe
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Laura D. Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Andrew G. Davies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU-Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Jill C. Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU-Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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Dwyer DS, Aamodt E, Cohen B, Buttner EA. Drug elucidation: invertebrate genetics sheds new light on the molecular targets of CNS drugs. Front Pharmacol 2014; 5:177. [PMID: 25120487 PMCID: PMC4112795 DOI: 10.3389/fphar.2014.00177] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/09/2014] [Indexed: 02/02/2023] Open
Abstract
Many important drugs approved to treat common human diseases were discovered by serendipity, without a firm understanding of their modes of action. As a result, the side effects and interactions of these medications are often unpredictable, and there is limited guidance for improving the design of next-generation drugs. Here, we review the innovative use of simple model organisms, especially Caenorhabditis elegans, to gain fresh insights into the complex biological effects of approved CNS medications. Whereas drug discovery involves the identification of new drug targets and lead compounds/biologics, and drug development spans preclinical testing to FDA approval, drug elucidation refers to the process of understanding the mechanisms of action of marketed drugs by studying their novel effects in model organisms. Drug elucidation studies have revealed new pathways affected by antipsychotic drugs, e.g., the insulin signaling pathway, a trace amine receptor and a nicotinic acetylcholine receptor. Similarly, novel targets of antidepressant drugs and lithium have been identified in C. elegans, including lipid-binding/transport proteins and the SGK-1 signaling pathway, respectively. Elucidation of the mode of action of anesthetic agents has shown that anesthesia can involve mitochondrial targets, leak currents, and gap junctions. The general approach reviewed in this article has advanced our knowledge about important drugs for CNS disorders and can guide future drug discovery efforts.
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Affiliation(s)
- Donard S. Dwyer
- Department of Psychiatry–Department of Pharmacology, Toxicology and Neuroscience, Louisiana State University Health Sciences Center-ShreveportShreveport, LA, USA
| | - Eric Aamodt
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center-ShreveportShreveport, LA, USA
| | - Bruce Cohen
- Department of Psychiatry, Harvard Medical SchoolBoston, MA, USA
- Mailman Research Center, McLean HospitalBelmont, MA, USA
| | - Edgar A. Buttner
- Mailman Research Center, McLean HospitalBelmont, MA, USA
- Department of Neurology–Department of Psychiatry, McLean Hospital, Harvard Medical SchoolBelmont, MA, USA
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Identification of a QTL in Mus musculus for alcohol preference, withdrawal, and Ap3m2 expression using integrative functional genomics and precision genetics. Genetics 2014; 197:1377-93. [PMID: 24923803 DOI: 10.1534/genetics.114.166165] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Extensive genetic and genomic studies of the relationship between alcohol drinking preference and withdrawal severity have been performed using animal models. Data from multiple such publications and public data resources have been incorporated in the GeneWeaver database with >60,000 gene sets including 285 alcohol withdrawal and preference-related gene sets. Among these are evidence for positional candidates regulating these behaviors in overlapping quantitative trait loci (QTL) mapped in distinct mouse populations. Combinatorial integration of functional genomics experimental results revealed a single QTL positional candidate gene in one of the loci common to both preference and withdrawal. Functional validation studies in Ap3m2 knockout mice confirmed these relationships. Genetic validation involves confirming the existence of segregating polymorphisms that could account for the phenotypic effect. By exploiting recent advances in mouse genotyping, sequence, epigenetics, and phylogeny resources, we confirmed that Ap3m2 resides in an appropriately segregating genomic region. We have demonstrated genetic and alcohol-induced regulation of Ap3m2 expression. Although sequence analysis revealed no polymorphisms in the Ap3m2-coding region that could account for all phenotypic differences, there are several upstream SNPs that could. We have identified one of these to be an H3K4me3 site that exhibits strain differences in methylation. Thus, by making cross-species functional genomics readily computable we identified a common QTL candidate for two related bio-behavioral processes via functional evidence and demonstrate sufficiency of the genetic locus as a source of variation underlying two traits.
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Chan RF, Lewellyn L, DeLoyht JM, Sennett K, Coffman S, Hewitt M, Bettinger JC, Warrick JM, Grotewiel M. Contrasting influences of Drosophila white/mini-white on ethanol sensitivity in two different behavioral assays. Alcohol Clin Exp Res 2014; 38:1582-93. [PMID: 24890118 PMCID: PMC4049357 DOI: 10.1111/acer.12421] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 03/12/2014] [Indexed: 01/08/2023]
Abstract
BACKGROUND The fruit fly Drosophila melanogaster has been used extensively to investigate genetic mechanisms of ethanol (EtOH)-related behaviors. Many past studies in flies, including studies from our laboratory, have manipulated gene expression using transposons carrying the genetic-phenotypic marker mini-white(mini-w), a derivative of the endogenous gene white(w). Whether the mini-w transgenic marker or the endogenous w gene influences behavioral responses to acute EtOH exposure in flies has not been systematically investigated. METHODS We manipulated mini-w and w expression via (i) transposons marked with mini-w, (ii) RNAi against mini-w and w, and (iii) a null allele of w. We assessed EtOH sensitivity and tolerance using a previously described eRING assay (based on climbing in the presence of EtOH) and an assay based on EtOH-induced sedation. RESULTS In eRING assays, EtOH-induced impairment of climbing correlated inversely with expression of the mini-w marker from a series of transposon insertions. Additionally, flies harboring a null allele of w or flies with RNAi-mediated knockdown of mini-w were significantly more sensitive to EtOH in eRING assays than controls expressing endogenous w or the mini-w marker. In contrast, EtOH sensitivity and rapid tolerance measured in the EtOH sedation assay were not affected by decreased expression of mini-w or endogenous w in flies. CONCLUSIONS EtOH sensitivity measured in the eRING assay is noticeably influenced by w and mini-w, making eRING problematic for studies on EtOH-related behavior in Drosophila using transgenes marked with mini-w. In contrast, the EtOH sensitivity assay described here is a suitable behavioral paradigm for studies on EtOH sensitivity and rapid tolerance in Drosophila including those that use widely available transgenes marked with mini-w.
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Affiliation(s)
- Robin F. Chan
- Molecular Biology and Genetics Program, Virginia Commonwealth University, Richmond, VA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
| | - Lara Lewellyn
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
| | - Jacqueline M. DeLoyht
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
- Neuroscience Graduate Program, Virginia Commonwealth University, Richmond, VA
| | - Kristyn Sennett
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
| | - Scarlett Coffman
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
| | - Matthew Hewitt
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
| | - Jill C. Bettinger
- Molecular Biology and Genetics Program, Virginia Commonwealth University, Richmond, VA
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA
| | | | - Mike Grotewiel
- Molecular Biology and Genetics Program, Virginia Commonwealth University, Richmond, VA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
- Neuroscience Graduate Program, Virginia Commonwealth University, Richmond, VA
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, VA
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Padmakumar V, Masiuk KE, Luger D, Lee C, Coppola V, Tessarollo L, Hoover SB, Karavanova I, Buonanno A, Simpson RM, Yuspa SH. Detection of differential fetal and adult expression of chloride intracellular channel 4 (CLIC4) protein by analysis of a green fluorescent protein knock-in mouse line. BMC DEVELOPMENTAL BIOLOGY 2014; 14:24. [PMID: 24886590 PMCID: PMC4073518 DOI: 10.1186/1471-213x-14-24] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/13/2014] [Indexed: 01/17/2023]
Abstract
Background Chloride Intracellular Channel 4 (CLIC4) is one of seven members in the closely related CLIC protein family. CLIC4 is involved in multiple cellular processes including apoptosis, cellular differentiation, inflammation and endothelial tubulogenesis. Despite over a decade of research, no comprehensive in situ expression analysis of CLIC4 in a living organism has been reported. In order to fulfill this goal, we generated a knock-in mouse to express Green Fluorescent Protein (GFP) from the CLIC4 locus, thus substituting the GFP coding region for CLIC4. We used GFP protein expression to eliminate cross reaction with other CLIC family members. Results We analyzed CLIC4 expression during embryonic development and adult organs. During mid and late gestation, CLIC4 expression is modulated particularly in fetal brain, heart, thymus, liver and kidney as well as in developing brown adipose tissue and stratifying epidermis. In the adult mouse, CLIC4 is highly expressed globally in vascular endothelial cells as well as in liver, lung alveolar septae, pancreatic acini, spermatogonia, renal proximal tubules, cardiomyocytes and thymic epithelial cells. Neural expression included axonal tracks, olfactory bulb, Purkinje cell layer and dentate gyrus. Renal CLIC4 expression was most pronounced in proximal tubules, although altered renal function was not detected in the absence of CLIC4. Myeloid cells and B cells of the spleen are rich in CLIC4 expression as are CD4 and CD8 positive T cells. Conclusions In a comprehensive study detailing CLIC4 expression in situ in a mouse model that excludes cross reaction with other family members, we were able to document previously unreported expression for CLIC4 in developing fetus, particularly the brain. In addition, compartmentalized expression of CLIC4 in specific adult tissues and cells provides a focus to explore potential functions of this protein not addressed previously.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Stuart H Yuspa
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA.
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Abstract
This chapter provides an overview of current knowledge on the molecular and clinical aspects of chronic alcohol effects on the central nervous system. This drug is almost ubiquitous, widely enjoyed socially, but produces a diverse spectrum of neurologic disease when abused. Acutely, alcohol interacts predominantly with γ-aminobutyric acid-A (GABA-A) and N-methyl-d-aspartate (NMDA) receptors, but triggers diverse signaling events within well-defined neural pathways. These events result in adaptive changes in gene expression that ultimately produce two major states: addiction and toxicity. Epigenetic modifications of chromatin could lead to long-lived or even transgenerational changes in gene expression, thus producing aspects of the heritability of alcohol use disorders (AUD) and long-term behaviors such as recidivism. The diverse clinical syndromes produced by chronic alcohol actions in the central nervous system reflect the molecular pathology and predominantly involve aspects of tolerance/withdrawal, selective vulnerability (manifest as central pontine myelinolysis, Marchiafava-Bignami disease), and additional environmental factors (e.g., thiamine deficiency in Wernicke-Korsakoff's syndrome). Additionally, deleterious aspects of chronic alcohol on signaling, synaptic transmission, and cell toxicity lead to primary alcoholic dementia. Genetically determined aspects of myelin structure and alcohol actions on myelin gene expression may be a prominent molecular mechanism resulting in a predisposition to, or causation of, AUD and multiple other neurologic complications of chronic alcohol. The dramatic progress made in understanding molecular actions of alcohol holds great promise for our eventual treatment or prevention of AUD and neurologic complications resulting from chronic alcohol abuse.
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Affiliation(s)
- B N Costin
- Virginia Commonwealth University Alcohol Research Center and Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - M F Miles
- Virginia Commonwealth University Alcohol Research Center, Department of Pharmacology and Toxicology, Center for Study of Biological Complexity and Department of Neurology, Virginia Commonwealth University, Richmond, VA, USA.
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Farris SP, Miles MF. Fyn-dependent gene networks in acute ethanol sensitivity. PLoS One 2013; 8:e82435. [PMID: 24312422 PMCID: PMC3843713 DOI: 10.1371/journal.pone.0082435] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/23/2013] [Indexed: 12/26/2022] Open
Abstract
Studies in humans and animal models document that acute behavioral responses to ethanol are predisposing factor for the risk of long-term drinking behavior. Prior microarray data from our laboratory document strain- and brain region-specific variation in gene expression profile responses to acute ethanol that may be underlying regulators of ethanol behavioral phenotypes. The non-receptor tyrosine kinase Fyn has previously been mechanistically implicated in the sedative-hypnotic response to acute ethanol. To further understand how Fyn may modulate ethanol behaviors, we used whole-genome expression profiling. We characterized basal and acute ethanol-evoked (3 g/kg) gene expression patterns in nucleus accumbens (NAC), prefrontal cortex (PFC), and ventral midbrain (VMB) of control and Fyn knockout mice. Bioinformatics analysis identified a set of Fyn-related gene networks differently regulated by acute ethanol across the three brain regions. In particular, our analysis suggested a coordinate basal decrease in myelin-associated gene expression within NAC and PFC as an underlying factor in sensitivity of Fyn null animals to ethanol sedation. An in silico analysis across the BXD recombinant inbred (RI) strains of mice identified a significant correlation between Fyn expression and a previously published ethanol loss-of-righting-reflex (LORR) phenotype. By combining PFC gene expression correlates to Fyn and LORR across multiple genomic datasets, we identified robust Fyn-centric gene networks related to LORR. Our results thus suggest that multiple system-wide changes exist within specific brain regions of Fyn knockout mice, and that distinct Fyn-dependent expression networks within PFC may be important determinates of the LORR due to acute ethanol. These results add to the interpretation of acute ethanol behavioral sensitivity in Fyn kinase null animals, and identify Fyn-centric gene networks influencing variance in ethanol LORR. Such networks may also inform future design of pharmacotherapies for the treatment and prevention of alcohol use disorders.
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Affiliation(s)
- Sean P Farris
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
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Mustard JA. The buzz on caffeine in invertebrates: effects on behavior and molecular mechanisms. Cell Mol Life Sci 2013; 71:1375-82. [PMID: 24162934 DOI: 10.1007/s00018-013-1497-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/12/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
Abstract
A number of recent studies from as diverse fields as plant-pollinator interactions, analyses of caffeine as an environmental pollutant, and the ability of caffeine to provide protection against neurodegenerative diseases have generated interest in understanding the actions of caffeine in invertebrates. This review summarizes what is currently known about the effects of caffeine on behavior and its molecular mechanisms in invertebrates. Caffeine appears to have similar effects on locomotion and sleep in both invertebrates and mammals. Furthermore, as in mammals, caffeine appears to have complex effects on learning and memory. However, the underlying mechanisms for these effects may differ between invertebrates and vertebrates. While caffeine's ability to cause release of intracellular calcium stores via ryanodine receptors and its actions as a phosphodiesterase inhibitor have been clearly established in invertebrates, its ability to interact with invertebrate adenosine receptors remains an important open question. Initial studies in insects and mollusks suggest an interaction between caffeine and the dopamine signaling pathway; more work needs to be done to understand the mechanisms by which caffeine influences signaling via biogenic amines. As of yet, little is known about whether other actions of caffeine in vertebrates, such as its effects on GABAA and glycine receptors, are conserved. Furthermore, the pharmacokinetics of caffeine remains to be elucidated. Overall behavioral responses to caffeine appear to be conserved amongst organisms; however, we are just beginning to understand the mechanisms underlying its effects across animal phyla.
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Affiliation(s)
- Julie A Mustard
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA,
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Williams S, Zies D, Mullegama S, Grotewiel M, Elsea S. Smith-Magenis syndrome results in disruption of CLOCK gene transcription and reveals an integral role for RAI1 in the maintenance of circadian rhythmicity. Am J Hum Genet 2012; 90:941-9. [PMID: 22578325 DOI: 10.1016/j.ajhg.2012.04.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 03/27/2012] [Accepted: 04/06/2012] [Indexed: 12/11/2022] Open
Abstract
Haploinsufficiency of RAI1 results in Smith-Magenis syndrome (SMS), a disorder characterized by intellectual disability, multiple congenital anomalies, obesity, neurobehavioral abnormalities, and a disrupted circadian sleep-wake pattern. An inverted melatonin rhythm (i.e., melatonin peaks during the day instead of at night) and associated sleep-phase disturbances in individuals with SMS, as well as a short-period circadian rhythm in mice with a chromosomal deletion of Rai1, support SMS as a circadian-rhythm-dysfunction disorder. However, the molecular cause of the circadian defect in SMS has not been described. The circadian oscillator temporally orchestrates metabolism, physiology, and behavior largely through transcriptional modulation. Data support RAI1 as a transcriptional regulator, but the genes it might regulate are largely unknown. Investigation into the role that RAI1 plays in the regulation of gene transcription and circadian maintenance revealed that RAI1 regulates the transcription of circadian locomotor output cycles kaput (CLOCK), a key component of the mammalian circadian oscillator that transcriptionally regulates many critical circadian genes. Data further show that haploinsufficiency of RAI1 and Rai1 in SMS fibroblasts and the mouse hypothalamus, respectively, results in the transcriptional dysregulation of the circadian clock and causes altered expression and regulation of multiple circadian genes, including PER2, PER3, CRY1, BMAL1, and others. These data suggest that heterozygous mutation of RAI1 and Rai1 leads to a disrupted circadian rhythm and thus results in an abnormal sleep-wake cycle, which can contribute to an abnormal feeding pattern and dependent cognitive performance. Finally, we conclude that RAI1 is a positive transcriptional regulator of CLOCK, pinpointing a novel and important role for this gene in the circadian oscillator.
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Wang L, He S, Tu Y, Ji P, Zong J, Zhang J, Feng F, Zhao J, Zhang Y, Gao G. Elevated expression of chloride intracellular channel 1 is correlated with poor prognosis in human gliomas. J Exp Clin Cancer Res 2012; 31:44. [PMID: 22578365 PMCID: PMC3441274 DOI: 10.1186/1756-9966-31-44] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 05/05/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chloride intracellular channel 1 (CLIC1) is expressed ubiquitously in human tissues and is involved in the regulation of cell cycle, cell proliferation and differentiation. Recent studies have shown that CLIC1 is highly expressed in several human malignant tumors. However, its roles in human gliomas are still unclear. The aim of this study was to investigate the clinicopathological significance and prognostic value of CLIC1 expression in human gliomas. METHODS CLIC1 expression in human gliomas and nonneoplastic brain tissues was measured by real-time quantitative RT-PCR assay and immunohistochemistry. Its association with clinicopathological factors or prognosis in patients with gliomas was statistically analyzed. RESULTS The expression of CLIC1 at both mRNA and protein levels was significantly increased in high-grade (Grade III~IV) glioma tissues compared with that in low-grade (Grade I~II) and nonneoplastic brain tissues, and was up-regulated with ascending tumor World Health Organization (WHO) grades. The elevated expression of CLIC1 protein was also significantly correlated with low Karnofsky performance score (KPS) (P=0.008). Moreover, both univariate and multivariate analysis shown that high CLIC1 expression was significantly associated with poor prognosis in patients with gliomas (P<0.001 and P=0.01, respectively). In particular, the elevated CLIC1 expression also correlated with shorter overall survival in different glioma subgroups stratified according to the WHO grading. CONCLUSIONS Our data provide the first evidence that CLIC1 expression might play an important role in the regulation of aggressiveness in human gliomas. The elevated expression of CLIC1 might represent a valuable prognostic marker for this disease.
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Affiliation(s)
- Liang Wang
- Department of neurosurgery, Tangdu hospital, Fourth Military Medical University of PLA, No,569, Xinsi Road, Baqiao District, Xi'an City, 710038, China
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Jay JJ. Cross species integration of functional genomics experiments. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2012. [PMID: 23195309 DOI: 10.1016/b978-0-12-398323-7.00001-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
There is an increasing recognition of the value in integrating behavioral genomics data across species. The fragmentation of public resources, interoperability, and available representations present challenges due to the array of identifiers used to represent each genome feature. Once data are organized into a coherent collection, they can be integrated using a variety of methods to analyze convergent evidence for the roles of genes in behaviors. GeneWeaver.org is a web-based software system that employs many of these techniques and has been used in the study of complex behavior and addiction. These techniques will be increasingly necessary to understand global patterns emerging from experiments in behavioral genomics.
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Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2012. [PMID: 23195313 DOI: 10.1016/b978-0-12-398323-7.00005-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Postgenomic studies of the function of genes and their role in disease have now become an area of intense study since efforts to define the raw sequence material of the genome have largely been completed. The use of whole-genome approaches such as microarray expression profiling and, more recently, RNA-sequence analysis of transcript abundance has allowed an unprecedented look at the workings of the genome. However, the accurate derivation of such high-throughput data and their analysis in terms of biological function has been critical to truly leveraging the postgenomic revolution. This chapter will describe an approach that focuses on the use of gene networks to both organize and interpret genomic expression data. Such networks, derived from statistical analysis of large genomic datasets and the application of multiple bioinformatics data resources, potentially allow the identification of key control elements for networks associated with human disease, and thus may lead to derivation of novel therapeutic approaches. However, as discussed in this chapter, the leveraging of such networks cannot occur without a thorough understanding of the technical and statistical factors influencing the derivation of genomic expression data. Thus, while the catch phrase may be "it's the network … stupid," the understanding of factors extending from RNA isolation to genomic profiling technique, multivariate statistics, and bioinformatics are all critical to defining fully useful gene networks for study of complex biology.
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