Identifiying gene networks underlying the neurobiology of ethanol and alcoholism

Alcohol Research and Health

Volumn 34, Issue 3, 2011, Pages 306-317

  Wolen, Aaron R ^a   Miles, Michael F ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Alcohol use disorders (AUDs); Alcoholism; Animal models; Gene networks; Genetic association studies; Genetic basis of alcoholism; Genetic mapping; Genetic technology; Genetical genomics; Genetics; Genomes; Human studies; Quantitative trait loci (QTLS)

Indexed keywords

EID: 84870222231     PISSN: 15357414     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (64)

1. Albert, R., and Jeong, H. Internet: Diameter of the WorldWide Web. Nature 401:130-131, 1999.
2. Bailey, D.W. Recombinant-inbred strains: An aid to fnd-ing identity, linkage, and function of histocompatibility and other genes. Transplantation 11(3):325-327, 1971. PMID: 5558564
3. Baldwin, N.E., Chesler, E.J., Kiro, V.S. et al. Computational, integrative, and comparative methods for the elucidation of genetic coexpression networks. Journal of Biomedicine & Biotechnology 2005(2):172-180, 2005. PMID: 16046823
4. Belknap, J.K., and Atkins, A.L. The replicability of QTLs for murine alcohol preference drinking behavior across eight independent studies. Mammalian Genome 12(12):893-899, 2001. PMID: 11707775
5. Bennett, B., Beeson, M., Gordon, L., and Johnson, T.E. Reciprocal congenics defning individual quantitative trait loci for sedative/hypnotic sensitivity to ethanol. Alcoholism: Clinical and Experimental Research 26(2):149-157, 2002. PMID: 11964553
6. Bierut, L.J., Agrawal, A., Bucholz, K.K., et al. A genome-wide association study of alcohol dependence. Proceedings of the National Academy of Sciences of the United States of America 107(11):5082-5087, 2010. PMID: 20202923
7. Botstein, D.; White, R.L.; Skolnick, M.; and Davis, R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32(3):314-331, 1980. PMID: 6247908
8. Bottomly, D.; Walter, N.A.; Hunter, J.E. et al. Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays. PLoS One 6(3):e17820, 2011. PMID: 21455293
9. Brem, R.B.; yvert, G.; Clinton, R.; And Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast Science 296(5568):752-755, 2002. PMID: 11923494
10. Butte, A.J.; Tamayo, P.; Slonim, D. et al. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proceedings of the National Academy of Sciences of the United States of America 97(22): 12182-12186, 2000. PMID: 11027309
11. Carter, S.L.; Brechbühler, C.M.; Griffin, M.; and Bond, A.T. Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 20(14): 2242-2250, 2004. PMID: 15130938
12. Chen, H., and Sharp, B.M. Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics 5:147, 2004. PMID: 15473905
13. Chesler, E.J.; Lu, L.; Shou, S. et al. Complex trait analysi of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nature Genetics 37(3):233-242, 2005. PMID: 15711545
14. Chesler, E.J.; Lu, L.; Wang, J. et al. WebQTL: Rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nature Neuroscience 7(5):485-486, 2004. PMID: 15114364
15. Chesler, E.J.; Wang, J.; Lu, L., et al. Genetic correlates of gene expression in recombinant inbred strains: A relational model system to explore neurobehavioral pheno-types. Neuroinformatics 1(4):343-357, 2003. PMID: 15043220
16. Daniels, G.M., and Buck, K.J. Expression profling identi-fes strain-specifc changes associated with ethanol withdrawal in mice. Genes, Brain, and Behavior 1(1):35-45, 2002. PMID: 12886948
17. Defries, J.C.; Wilson, J.R.; Erwin, V.G.; and Petersen, D.R. LS × SS recombinant inbred strains of mice: Initial characterization. Alcoholism: Clinical and Experimental Research 13(2):196-200, 1989. PMID: 2658655
18. Eisen, M.B.; Spellman, P.T.; Brown, P.o.; and Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America 95(25): 14863-14868, 1998. PMID: 9843981
19. Girvan, M., and Newman, M.E. Community structure in social and biological networks. Proceedings of the National Academy of Sciences of the United States of America 99(12):7821-7826, 2002. PMID: 12060727
20. Grahame, N.J.; Li, T.K.; and Lumeng, L. Limited access alcohol drinking in high- and low-alcohol preferring selected lines of mice. Alcoholism: Clinical and Experimental Research 23(6):1015-1022, 1999. PMID: 10397285
21. Grieve, S.J., and Littleton, J.M. Age and strain differences in the rate of development of functional tolerance to ethanol by mice. Journal of Pharmacy and Pharmacology 31(10):696-700, 1979. PMID: 41043
22. Horvath, S., and Dong, J. Geometric interpretation of gene coexpression network analysis. PLoS Computational Biology 4(8):e1000117, 2008. PMID: 18704157
23. Inoue, M.; Rashid, M.H.; Fujita, R. et al. Initiation of neuropathic pain requires lysophosphatidic acid receptor signaling. Nature Medicine 10(7):712-718, 2004. PMID: 15195086
24. Jansen, R.C., and Nap, J.P. Genetical genomics: The added value from segregation. Trends in Genetics 17(7):388-391, 2001. PMID: 11418218
25. Jeong, H.; Tombor, B.; Albert, R.X.; et al. The large-scale organization of metabolic networks. Nature 407(6804): 651-654, 2000. PMID: 11034217
26. Kerns, R.T.; Ravindranathan, A.; Hassan, S.; et al. Ethanol-responsive brain region expression networks: Implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25(9): 2255-2266, 2005. PMID: 15745951
27. Kirstein, S.L.; Davidson, K.L.; Ehringer, M.A.; et al. Quantitative trait loci affecting initial sensitivity and acute functional tolerance to ethanol-induced ataxia and brain cAMP signaling in BXD recombinant inbred mice. Journal of Pharmacology and Experimental Therapeutics 302(3):1238-1245, 2002. PMID: 12183685
28. Kril, J.J., and HALLIDAy, G.M. Brain shrinkage in alcoholics: A decade on and what have we learned? Progress in Neurobiology 58(4):381-387, 1999. PMID: 10368034
29. Langfelder, P., and HORVATH, S. WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics 9:559, 2008. PMID: 19114008
30. LEWOHL, J.M.; Wang, L.; Miles, M.F.; et al. Gene expression in human alcoholism: Microarray analysis of frontal cortex. Alcoholism: Clinical and Experimental Research 24(12):1873-1882, 2000. PMID: 11141048
31. Markel, P.D.; Bennett, B.; BEESON, M.; et al. Confrmation of quantitative trait loci for ethanol sensitivity in long-sleep and short-sleep mice. Genome Research 7(2):92-99, 1997. PMID: 9049627
32. MATAS-RICo, E.; GARCIA-DIAz, B.; LLEBREZZAYAS, P.; et al. Deletion of lysophosphatidic acid receptor LPA1 reduces neurogenesis in the mouse dentate gyrus. Molecular and Cellular Neurosciences 39(3):342-355, 2008. PMID: 18708146
33. MAYFIELD, R.D.; LEWOHL, J.M.; DODD, P.R.; et al. Patterns of gene expression are altered in the frontal and motor cortices of human alcoholics. Journal of Neurochemistry 81(4):802-813, 2002. PMID: 12065639
34. Metten, P., and Crabbe, J.C. Common genetic determinants of severity of acute withdrawal from ethanol, pen-tobarbital and diazepam in inbred mice. Behavioural Pharmacology 5(4 and 5):533-547, 1994. PMID: 11224305
35. MOROZOVA, T.V.; MACKAY, T.F.; and ANHOLT, R.R. Transcriptional networks for alcohol sensitivity in Drosophila melanogaster. Genetics 187(4): 1193-1205, 2011. PMID: 21270389
36. MOZHUI, K.; CIOBANU, D.C.; SCHIKORSKI, T.; et al. Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression. PLoS Genetics 4(11): e1000260, 2008. PMID: 19008955
37. MULLIGAN, M.K.; PONOMAREV, I.; HITZEMANN, R.J.; et al. Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. Proceedings of the National Academy of Sciences of the United States of America 103(16):6368-6373, 2006. PMID: 16618939
38. MULLIGAN, M.K.; RHODES, J.S.; CRABBE, J.C.; et al. Molecular profles of drinking alcohol to intoxication in C57BL/6J mice. Alcoholism: Clinical and Experimental Research 35(4):659-670, 2011. PMID: 21223303
39. NICOLAE, D.L.; GAMAZON, E.; ZHANG, W.; et al. Trait-associated SNPs are more likely to be eQTLs: Annotation to enhance discovery from GWASs. PLoS Genetics 6(4): e1000888, 2010. PMID: 20369019
40. Phillips, T.J.; BROWN, K.J.; BURCKHARTKASCH, S.; et al. Alcohol preference and sensitivity are markedly reduced in mice lacking dopamine D2 receptors. Nature Neuroscience 1(7):610-615, 1998. PMID: 10196569
41. Rask, E.; Walker, B.R.; SÖDERBERG, S.; et al. Tissue-specifc changes in peripheral cortisol metabolism in obese women: Increased adipose 11beta-hydroxysteroid dehydrogenase type 1 activity. Journal of Clinical Endocrinology and Metabolism 87(7):3330-3336, 2002. PMID: 12107245
42. Reimers, M. A.; RILEY, B. P.; Kalsi, G.; et al. Pathway based analysis of genotypes in relation to alcohol dependence. Pharmacogenomics Journal, 2011, April 5 [Epub ahead of print]. PMID: 21468025
43. RIMONDINI, R.; Arlinde, C.; SOMMER, W.; and Heilig, M. Long-lasting increase in voluntary ethanol consumption and transcriptional regulation in the rat brain after intermittent exposure to alcohol. FASEB Journal 16(1):27-35, 2002. PMID: 11772933
44. RUANO, D.; Abecasis, G.R.; Glaser, B.; et al. Functional gene group analysis reveals a role of synaptic het-erotrimeric G proteins in cognitive ability. American Journal of Human Genetics 86(2):113-125, 2010. PMID: 20060087
45. Saba, L.; Bhave, S.V.; Grahame, N.; et al. Candidate genes and their regulatory elements: Alcohol preference and tolerance. Mammalian Genome 17(6):669-688, 2006. PMID: 16783646
46. SAITO, M.; SZAKALL, I.; TOTH, R.; et al. Mouse striatal tran-scriptome analysis: Effects of oral self-administration of alcohol. Alcohol 32(3):223-241, 2004. PMID: 15282116
47. Schadt, E.E.; Lamb, J.; YANG, X.; et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genetics 37(7):710-717, 2005. PMID: 15965475
48. Schadt, E.E.; MONKS, S.A.; Drake, T.A.; et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422(6929):297-302, 2003. PMID: 12646919
49. SCHUCKIT, M. A. Subjective responses to alcohol in sons of alcoholics and control subjects. Archives of General Psychiatry 41(9):879-884, 1984. PMID: 6466047
50. SCHUCKIT, M.A. Low level of response to alcohol as a predictor of future alcoholism. American Journal of Psychiatry 151(2):184-189, 1994. PMID: 8296886
51. SCOTT, R.E.; WHITE-GRINDLEY, E.; RULEY, H.E.; et al. P2P-R expression is genetically coregulated with components of the translation machinery and with PuM2, a transla-tional repressor that associates with the P2P-R mRNA. Journal of Cellular Physiology 204(1):99-105, 2005. PMID: 15617101
52. STUART, J.M.; Segal, E.; KOLLER, D.; and Kim, S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302 (5643):249-255, 2003. PMID: 12934013
53. TABAKOFF, B.; Saba, L.; PRINTZ, M.; et al. Genetical genomic determinants of alcohol consumption in rats and humans. BMC Biology 7:70, 2009. PMID: 19874574
54. Treadwell, J.A., and Singh, S.M. Microarray analysis of mouse brain gene expression following acute ethanol treatment. Neurochemical Research 29(2):357-369, 2004. PMID: 15002731
55. van'T veer, L.J.; Dai, H.; van de Vijver, M.J.; et al. Gene expression profling predicts clinical outcome of breast cancer. Nature 415(6871): 530-536, 2002. PMID: 14654526
56. van NOORT, V.; Snel, B.; and HUYNEN, M.A. The yeast coex-pression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Reports 5(3):280-284, 2004. PMID: 14968131
57. Watts, D.J., and STROGATZ, S. H. Collective dynamics of "small-world" networks. Nature 393(6684): 440-442, 1998. PMID: 9623998
58. Wickham, H. ggplot2: Elegant Graphics for Data Analysis. New york: Springer, 2009.
59. Williams, R.W.; Bennett, B.; Lu, L.; et al. Genetic structure of the LXS panel of recombinant inbred mouse strains: A powerful resource for complex trait analysis. Mammalian Genome 15(8):637-647, 2004. PMID: 15457343
60. Williams, R.W.; Gu, J.; Qi, S.; and Lu, L. The genetic structure of recombinant inbred mice: High-resolution consensus maps for complex trait analysis. Genome Biology 2(11):RESEARCH0046, 2001. PMID: 11737945
61. WOLEN, A.R.; Phillips, C.A.; LANGSTON, M.A.; et al. Genetic dissection of acute ethanol respoonsive gene networks in prefrontal cortex; Functional and mechanistic implications. PLoS, in press.
62. YORK, T.P.; Miles, M.F.; Kendler, K.S.; et al. Epistatic and environmental control of genome-wide gene expression. Twin Research and Human Genetics 8(1):5-15, 2005. PMID: 15836804
63. ZHANG, B., and HORVATH, S. A general framework for weighted gene co-expression network analysis. Statistical Applications in Genetics and Molecular Biology 4:Article17, 2005. PMID: 16646834
64. ZHU, J.; LUM, P.Y.; LAMB, J.; et al. An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenetic and Genome Research 105(2-4):363-374, 2004. PMID: 15237224