Selection for drinking in the dark alters brain gene coexpression networks

Alcoholism: Clinical and Experimental Research

Volumn 37, Issue 8, 2013, Pages 1295-1303

  Iancu, Ovidiu D ^a   Oberbeck, Denesa ^a   Darakjian, Priscila ^a   Metten, Pamela ^a,b   Mcweeney, Shannon ^c   Crabbe, John C ^a,b   Hitzemann, Robert ^a,b  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b PORTLAND VA MEDICAL CENTER   (United States)

^c OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

Alcohol; Binge; Drinking in the Dark; Microarray; Mouse; Selection; Weighted Gene Coexpression Network Analysis

Indexed keywords

4 AMINOBUTYRIC ACID A RECEPTOR GAMMA1; 4 AMINOBUTYRIC ACID RECEPTOR; ALCOHOL; CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE II; CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE KINASE; DIACYLGLYCEROL KINASE; GLUTAMATE RECEPTOR 1; KAINIC ACID; NEUROPEPTIDE Y2 RECEPTOR; NEUROTENSIN; TRANSCRIPTOME;

ALCOHOL BLOOD LEVEL; ALCOHOL CONSUMPTION; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CHROMOSOME; CHROMOSOME 14; CHROMOSOME 16; CHROMOSOME 4; CONTROLLED STUDY; CORPUS STRIATUM; DARKNESS; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOTYPE; MOUSE; NEUROBIOLOGY; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS;

ALCOHOL; BINGE; DRINKING IN THE DARK; MICROARRAY; MOUSE; SELECTION; WEIGHTED GENE COEXPRESSION NETWORK ANALYSIS;

ALCOHOL DRINKING; ANIMALS; BASAL GANGLIA; BRAIN CHEMISTRY; DARKNESS; FEMALE; GENE REGULATORY NETWORKS; MALE; MICE; QUANTITATIVE TRAIT LOCI; SELECTION, GENETIC;

EID: 84880991359     PISSN: 01456008     EISSN: 15300277     Source Type: Journal    
DOI: 10.1111/acer.12100     Document Type: Article

References (55)

1. Belknap JK, Atkins AL (2001) The replicability of QTLs for murine alcohol preference drinking behavior across eight independent studies. Mamm Genome 12:893-899.
2. Belknap JK, Richards SP, O'Toole LA, Helms ML, Phillips TJ (1997) Short-term selective breeding as a tool for QTL mapping: ethanol preference drinking in mice. Behav Genet 27:55-66.
3. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57:289-300.
4. Bice PJ, Foroud T, Carr LG, Zhang L, Liu L, Grahame NJ, Lumeng L, Li TK, Belknap JK (2006) Identification of QTLs influencing alcohol preference in the high alcohol preferring (HAP) and low alcohol preferring (LAP) mouse lines. Behav Genet 36:248-260.
5. Blednov YA, Mayfield RD, Belknap J, Harris RA (2012) Behavioral actions of alcohol: phenotypic relations from multivariate analysis of mutant mouse data. Genes Brain Behav 11:424-435.
6. Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, Xing Y, Lubischer JL, Krieg PA, Krupenko SA, Thompson WJ, Barres BA (2008) A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci 28:264-278.
7. Carpenter-Hyland EP, Chandler LJ (2006) Homeostatic plasticity during alcohol exposure promotes enlargement of dendritic spines. Eur J Neurosci 24:3496-3506.
8. Christian DT, Alexander NJ, Diaz MR, Robinson S, McCool BA (2012) Chronic intermittent ethanol and withdrawal differentially modulate basolateral amygdala AMPA-type glutamate receptor function and trafficking. Neuropharmacology 62:2430-2439.
9. Crabbe JC, Harris RA, Koob GF (2011a) Preclinical studies of alcohol binge drinking. Ann N Y Acad Sci 1216:24-40.
10. Crabbe JC, Metten P, Huang LC, Schlumbohm JP, Spence SE, Barkley-Levenson AM, Finn DA, Rhodes JS, Cameron AJ (in press) Ethanol withdrawal-associated drinking and drinking in the dark: common and discrete genetic contributions. Addiction Genetics.
11. Crabbe JC, Metten P, Rhodes JS, Yu CH, Brown LL, Phillips TJ, Finn DA (2009) A line of mice selected for high blood ethanol concentrations shows drinking in the dark to intoxication. Biol Psychiatry 65:662-670.
12. Crabbe JC, Phillips TJ, Harris RA, Arends MA, Koob GF (2006) Alcohol-related genes: contributions from studies with genetically engineered mice. Addict Biol 11:195-269.
13. Crabbe JC, Spence SE, Brown LL, Metten P (2011b) Alcohol preference drinking in a mouse line selectively bred for high drinking in the dark. Alcohol 45:427-440.
14. Davies DL, Crawford DK, Trudell JR, Mihic SJ, Alkana RL (2004) Multiple sites of ethanol action in alpha1 and alpha2 glycine receptors suggested by sensitivity to pressure antagonism. J Neurochem 89:1175-1185.
15. Devaud LL, Purdy RH, Finn DA, Morrow AL (1996) Sensitization of gamma-aminobutyric acidA receptors to neuroactive steroids in rats during ethanol withdrawal. J Pharmacol Exp Ther 278:510-517.
16. Du P, Kibbe WA, Lin SM (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics 24:1547-1548.
17. Ehlers CL, Somes C, Li TK, Lumeng L, Kinkead B, Owens MJ, Nemeroff CB (1999) Neurontensin studies in alcohol naive, preferring and non-preferring rats. Neuroscience 93:227-236.
18. Enoch MA, Hodgkinson CA, Yuan Q, Albaugh B, Virkkunen M, Goldman D (2009) GABRG1 and GABRA2 as independent predictors for alcoholism in two populations. Neuropsychopharmacology 34:1245-1254.
19. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491.
20. Fidler TL, Powers MS, Ramirez JJ, Crane A, Mulgrew J, Smitasin P, Cunningham CL (2012) Dependence induced increases in intragastric alcohol consumption in mice. Addict Biol 17:13-32.
21. Finn DA, Belknap JK, Cronise K, Yoneyama N, Murillo A, Crabbe JC (2005) A procedure to produce high alcohol intake in mice. Psychopharmacology 178:471-480.
22. Grahame NJ, Li TK, Lumeng L (1999) Selective breeding for high and low alcohol preference in mice. Behav Genet 29:47-57.
23. Hitzemann B, Dains K, Kanes S, Hitzemann R (1994) Further studies on the relationship between dopamine cell density and haloperidol-induced catalepsy. J Pharmacol Exp Ther 271:969-976.
24. Hitzemann R, Edmunds S, Wu W, Malmanger B, Walter N, Belknap J, Darakjian P, McWeeney S (2009) Detection of reciprocal quantitative trait loci for acute ethanol withdrawal and ethanol consumption in heterogeneous stock mice. Psychopharmacology 203:713-722.
25. Howard RJ, Murail S, Ondricek KE, Corringer PJ, Lindahl E, Trudell JR, Harris RA (2011) Structural basis for alcohol modulation of a pentameric ligand-gated ion channel. Proc Natl Acad Sci USA 108:12149-12154.
26. Iancu OD, Darakjian P, Malmanger B, Walter NA, McWeeney S, Hitzemann R (2012a) Gene networks and haloperidol-induced catalepsy. Genes Brain Behav 11:29-37.
27. Iancu OD, Darakjian P, Walter NA, Malmanger B, Oberbeck D, Belknap J, McWeeney S, Hitzemann R (2010) Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse. BMC Genomics 11:585.
28. Iancu OD, Kawane S, Bottomly D, Searles R, Hitzemann R, McWeeney S (2012b) Utilizing RNA-Seq data for de novo coexpression network inference. Bioinformatics 28:1592-1597.
29. Johnson BA, Rosenthal N, Capece JA, Wiegand F, Mao L, Beyers K, McKay A, Ait-Daoud N, Anton RF, Ciraulo DA, Kranzler HR, Mann K, O'Malley SS, Swift RM (2007) Topiramate for treating alcohol dependence: a randomized controlled trial. JAMA 298:1641-1651.
30. Jonsson S, Kerekes N, Hyytia P, Ericson M, Soderpalm B (2009) Glycine receptor expression in the forebrain of male AA/ANA rats. Brain Res 1305:S27-S36.
31. Kim K, Yang J, Zhong XP, Kim MH, Kim YS, Lee HW, Han S, Choi J, Han K, Seo J, Prescott SM, Topham MK, Bae YC, Koretzky G, Choi SY, Kim E (2009) Synaptic removal of diacylglycerol by DGKzeta and PSD-95 regulates dendritic spine maintenance. EMBO J 28:1170-1179.
32. Kranzler HR, Edenberg HJ (2010) Pharmacogenetics of alcohol and alcohol dependence treatment. Curr Pharm Des 16:2141-2148.
33. Langfelder P, Horvath S (2007) Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol 1:54.
34. Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559.
35. Langfelder P, Luo R, Oldham MC, Horvath S (2011) Is my network module preserved and reproducible? PLoS Comput Biol 7:e1001057.
36. Langfelder P, Zhang B, Horvath S (2008) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24:719-720.
37. Lee MR, Hinton DJ, Unal SS, Richelson E, Choi DS (2011) Increased ethanol consumption and preference in mice lacking neurotensin receptor type 2. Alcohol Clin Exp Res 35:99-107.
38. Lewohl JM, Wang L, Miles MF, Zhang L, Dodd PR, Harris RA (2000) Gene expression in human alcoholism: microarray analysis of frontal cortex. Alcohol Clin Exp Res 24:1873-1882.
39. Lisman J, Yasuda R, Raghavachari S (2012) Mechanisms of CaMKII action in long-term potentiation. Nat Rev Neurosci 13:169-182.
40. Lyons AM, Lowery EG, Sparta DR, Thiele TE (2008) Effects of food availability and administration of orexigenic and anorectic agents on elevated ethanol drinking associated with drinking in the dark procedures. Alcohol Clin Exp Res 32:1962-1968.
41. Malmanger B, Lawler M, Coulombe S, Murray R, Cooper S, Polyakov Y, Belknap J, Hitzemann R (2006) Further studies on using multiple-cross mapping (MCM) to map quantitative trait loci. Mamm Genome 17:1193-1204.
42. Moonat S, Sakharkar AJ, Zhang H, Pandey SC (2011) The role of amygdaloid brain-derived neurotrophic factor, activity-regulated cytoskeleton-associated protein and dendritic spines in anxiety and alcoholism. Addict Biol 16:238-250.
43. Mulligan MK, Ponomarev I, Hitzemann RJ, Belknap JK, Tabakoff B, Harris RA, Crabbe JC, Blednov YA, Grahame NJ, Phillips TJ, Finn DA, Hoffman PL, Iyer VR, Koob GF, Bergeson SE (2006) Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. Proc Natl Acad Sci USA 103:6368-6373.
44. Mulligan MK, Rhodes JS, Crabbe JC, Mayfield RD, Adron Harris R, Ponomarev I (2011) Molecular profiles of drinking alcohol to intoxication in C57BL/6J mice. Alcohol Clin Exp Res 35:659-670.
45. 2+/calmodulin kinase kinase beta affects the formation of some, but not all, types of hippocampus-dependent long-term memory. J Neurosci 23:9752-9760.
46. Ray LA, Hutchison KE (2009) Associations among GABRG1, level of response to alcohol, and drinking behaviors. Alcohol Clin Exp Res 33:1382-1390.
47. Rhodes JS, Best K, Belknap JK, Finn DA, Crabbe JC (2005) Evaluation of a simple model of ethanol drinking to intoxication in C57BL/6J mice. Physiol Behav 84:53-63.
48. Rhodes JS, Ford MM, Yu CH, Brown LL, Finn DA, Garland T Jr, Crabbe JC (2007) Mouse inbred strain differences in ethanol drinking to intoxication. Genes Brain Behav 6:1-18.
49. Roberts A, Pardo-Manuel de Villena F, Wang W, McMillan L, Threadgill DW (2007) The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics. Mamm Genome 18:473-481.
50. Saba LM, Bennett B, Hoffman PL, Barcomb K, Ishii T, Kechris K, Tabakoff B (2011) A systems genetic analysis of alcohol drinking by mice, rats and men: influence of brain GABAergic transmission. Neuropharmacology 60:1269-1280.
51. Sparrow AM, Lowery-Gionta EG, Pleil KE, Li C, Sprow GM, Cox BR, Rinker JA, Jijon AM, Pena J, Navarro M, Kash TL, Thiele TE (2012) Central neuropeptide Y modulates binge-like ethanol drinking in C57BL/6J mice via Y1 and Y2 receptors. Neuropsychopharmacology 37:1409-1421.
52. Sprow GM, Thiele TE (2012) The neurobiology of binge-like ethanol drinking: evidence from rodent models. Physiol Behav 106:325-331.
53. Wang KS, Liu X, Zhang Q, Wu LY, Zeng M (2012) Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms. J Neural Transm 119:425-433.
54. Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4:Article17.
55. Zhou FC, Anthony B, Dunn KW, Lindquist WB, Xu ZC, Deng P (2007) Chronic alcohol drinking alters neuronal dendritic spines in the brain reward center nucleus accumbens. Brain Res 1134:148-161.