Convergent functional genomics of cocaine misuse in humans and animal models

References

• Degenhardt L, Charlson F, Ferrari A, Santomauro D, Erskine H, Mantilla-Herrara A, Whiteford H, Leung J, Naghavi M, Griswold M, et al. The global burden of disease attributable to alcohol and drug use in 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Psychiatry. 2018;5:987–1012.
   PubMed Web of Science ®Google Scholar
• Kendler KS, Prescott CA. Cocaine use, abuse and dependence in a population-based sample of female twins. Br J Psychiatry. 1998 Oct;173:345–50. PubMed PMID: 9926041.
   PubMed Web of Science ®Google Scholar
• Kendler KS, Karkowski LM, Neale MC, Prescott CA. Illicit psychoactive substance use, heavy use, abuse, and dependence in a US population-based sample of male twins. Arch Gen Psychiatry. 2000 Mar;57:261–69. PubMed PMID: 10711912.
   PubMed Web of Science ®Google Scholar
• Verhulst B, Neale MC, Kendler KS. The heritability of alcohol use disorders: a meta-analysis of twin and adoption studies. Psychol Med. Apr 2015;45:1061–72. doi: 10.1017/S0033291714002165. PubMed PMID: 25171596. PMCID: PMC4345133. Epub 2014/ 08/30.
   PubMed Web of Science ®Google Scholar
• Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA.Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009 Jun 9;106:9362–67. doi:10.1073/pnas.0903103106. PubMed PMID: 19474294. PMCID: PMC2687147. Epub 2009/05/29.
   PubMed Web of Science ®Google Scholar
• Gelernter J, Sherva R, Koesterer R, Almasy L, Zhao H, Kranzler HR, Farrer L. Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene. Mol Psychiatry. Jun 2014;19:717–23. doi: 10.1038/mp.2013.99. PubMed PMID: 23958962. PMCID: 3865158.
   PubMed Web of Science ®Google Scholar
• Bannon MJ, Johnson MM, Michelhaugh SK, Hartley ZJ, Halter SD, David JA, Kapatos G, Schmidt CJ. A molecular profile of cocaine abuse includes the differential expression of genes that regulate transcription, chromatin, and dopamine cell phenotype. Neuropsychopharmacol. Aug 2014;39:2191–99. doi: 10.1038/npp.2014.70. PubMed PMID: 24642598. PMCID: Pmc4104338. Epub 2014/ 03/20.eng.
   PubMed Web of Science ®Google Scholar
• Ribeiro EA, Scarpa JR, Garamszegi SP, Kasarskis A, Mash DC, Nestler EJ.Gene network dysregulation in dorsolateral prefrontal cortex neurons of humans with cocaine use disorder. Sci Rep. 2017 Jul 14;7:5412. doi:10.1038/s41598-017-05720-3. PubMed PMID: 28710498. PMCID: Pmc5511210. Epub 2017/07/16. eng.
   PubMed Web of Science ®Google Scholar
• Albertson DN, Schmidt CJ, Kapatos G, Bannon MJ. Distinctive profiles of gene expression in the human nucleus accumbens associated with cocaine and heroin abuse. Neuropsychopharmacol. Oct 2006;31:2304–12. doi: 10.1038/sj.npp.1301089. PubMed PMID: 16710320. PMCID: Pmc2239258. Epub 2006/ 05/20.eng.
   PubMed Web of Science ®Google Scholar
• Mash DC, auffrench-Mullen J, Adi N, Qin Y, Buck A, Pablo J.Gene expression in human hippocampus from cocaine abusers identifies genes which regulate extracellular matrix remodeling. PLoS One. 2007 Nov 14;2:e1187. doi:10.1371/journal.pone.0001187. PubMed PMID: 18000554. PMCID: Pmc2063513. Epub 2007/ 11/15. eng.
   PubMed Web of Science ®Google Scholar
• Zhou Z, Yuan Q, Mash DC, Goldman D.Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol. Proc Natl Acad Sci U S A. 2011 Apr 19;108:6626–31. doi:10.1073/pnas.1018514108. PubMed PMID: 21464311. PMCID: Pmc3081016. Epub 2011/04/06.eng.
   PubMed Web of Science ®Google Scholar
• Eipper-Mains JE, Kiraly DD, Duff MO, Horowitz MJ, McManus CJ, Eipper BA, Graveley BR, Mains RE. Effects of cocaine and withdrawal on the mouse nucleus accumbens transcriptome. Genes Brain Behav. 2013 Feb;12:21–33. doi:10.1111/j.1601-183X.2012.00873.x. PubMed PMID: 23094851. PMCID: Pmc3553295. Epub 2012/ 10/26.eng.
   PubMed Web of Science ®Google Scholar
• Li M, Xu P, Xu Y, Teng H, Tian W, Du Q, Zhao M. Dynamic expression changes in the transcriptome of the prefrontal cortex after repeated exposure to cocaine in mice. Front Pharmacol. 2017;8:142. PubMed PMID: 28386228. PMCID: Pmc5362609. Epub 2017/04/08.eng.
   PubMed Web of Science ®Google Scholar
• Korostynski M, Piechota M, Dzbek J, Mlynarski W, Szklarczyk K, Ziolkowska B, Przewlocki R. Novel drug-regulated transcriptional networks in brain reveal pharmacological properties of psychotropic drugs. BMC Genomics. 2013 Sep 8;14:606. doi:10.1186/1471-2164-14-181. PubMed PMID: 24010892. PMCID: Pmc3844597. Epub 2013/09/10.eng.
   PubMed Web of Science ®Google Scholar
• Freeman WM, Lull ME, Patel KM, Brucklacher RM, Morgan D, Roberts DC, Vrana KE. Gene expression changes in the medial prefrontal cortex and nucleus accumbens following abstinence from cocaine self-administration. BMC Neurosci. 2010 Feb 26;11:29. doi:10.1186/1471-2202-11-105. PubMed PMID: 20187946. PMCID: Pmc2837051. Epub 2010/03/02.eng.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Kong F, Crofton EJ, Dragosljvich SN, Sinha M, Li D, Fan X, Koshy S, Hommel JD, Spratt HM, et al. Transcriptomics of environmental enrichment reveals a role for retinoic acid signaling in addiction. Front Mol Neurosci. 2016;9:119. doi:10.3389/fnmol.2016.00119. PubMed PMID: 27899881. PMCID: Pmc5110542. Epub 2016/12/03.eng.
   PubMed Web of Science ®Google Scholar
• Massart R, Barnea R, Dikshtein Y, Suderman M, Meir O, Hallett M, Kennedy P, Nestler EJ, Szyf M, Yadid G.Role of DNA methylation in the nucleus accumbens in incubation of cocaine craving. J Neurosci. 2015 May 27;35:8042–58. doi:10.1523/JNEUROSCI.3053-14.2015. PubMed PMID: 26019323. Epub 2015/ 05/29.eng.
   PubMed Web of Science ®Google Scholar
• Kontou PI, Pavlopoulou A, Bagos PG. Methods of analysis and meta-analysis for identifying differentially expressed genes. Methods Mol Biol. 2018;1793:183–210. doi:10.1007/978-1-4939-7868-7_12. PubMed PMID: 29876898. Epub 2018/ 06/08.
   PubMedGoogle Scholar
• Forero DA, Lopez-Leon S, Gonzalez-Giraldo Y, Bagos PG. Ten simple rules for carrying out and writing meta-analyses. PLoS Comput Biol. May 2019;15:e1006922. doi: 10.1371/journal.pcbi.1006791. PubMed PMID: 31095553. Epub 2019/05/17.
   PubMed Web of Science ®Google Scholar
• Ramasamy A, Mondry A, Holmes CC, Altman DG.Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med. 2008 Sep 30;5:e184. doi:10.1371/journal.pmed.0050184. PubMed PMID: 18767902. PMCID: 2528050.
   PubMed Web of Science ®Google Scholar
• Niculescu AB. Convergent functional genomics of psychiatric disorders. Am J Med Genet B Neuropsychiatr Genet. 2013 Oct;162B:587–94. doi: 10.1002/ajmg.b.32163. PubMed PMID: 23728881. Epub 2013/ 06/04.
   PubMed Web of Science ®Google Scholar
• Bertsch B, Ogden CA, Sidhu K, Le-Niculescu H, Kuczenski R, Niculescu AB. Convergent functional genomics: a Bayesian candidate gene identification approach for complex disorders. Methods. Nov 2005;37:274–79. doi: 10.1016/j.ymeth.2005.03.012. PubMed PMID: 16308156. Epub 2005/ 11/26.
   PubMed Web of Science ®Google Scholar
• Niculescu AB 3rd, Segal DS, Kuczenski R, Barrett T, Hauger RL, Kelsoe JR.Identifying a series of candidate genes for mania and psychosis: a convergent functional genomics approach. Physiol Genomics. 2000 Nov 9;4:83–91. doi:10.1152/physiolgenomics.2000.4.1.83. PubMed PMID: 11074017.
   PubMed Web of Science ®Google Scholar
• Le-Niculescu H, Patel SD, Bhat M, Kuczenski R, Faraone SV, Tsuang MT, McMahon FJ, Schork NJ, Nurnberger JI, Niculescu AB.Convergent functional genomics of genome-wide association data for bipolar disorder: comprehensive identification of candidate genes, pathways and mechanisms. Am J Med Genet B Neuropsychiatr Genet. 2009 Mar 5;150B:155–81. doi:10.1002/ajmg.b.30887. PubMed PMID: 19025758. Epub 2008/ 11/26.
   PubMed Web of Science ®Google Scholar
• Rodd ZA, Bertsch BA, Strother WN, Le-Niculescu H, Balaraman Y, Hayden E, Jerome RE, Lumeng L, Nurnberger JI, Edenberg HJ, et al. Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach. Pharmacogenomics J. Aug 2007;7:222–56. doi: 10.1038/sj.tpj.6500420. PubMed PMID: 17033615.
   PubMed Web of Science ®Google Scholar
• Levey DF, Le-Niculescu H, Frank J, Ayalew M, Jain N, Kirlin B, Learman R, Winiger E, Rodd Z, Shekhar A, et al.Genetic risk prediction and neurobiological understanding of alcoholism. Transl Psychiatry. 2014 May 20;4:e391. doi:10.1038/tp.2014.29. PubMed PMID: 24844177. PMCID: PMC4035721. Epub 2014/05/23.
   PubMed Web of Science ®Google Scholar
• Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, et al. NCBI GEO: archive for functional genomics data sets–update. Nucleic Acids Res. Jan 2013;41:D991–5. doi: 10.1093/nar/gks1193. PubMed PMID: 23193258. PMCID: 3531084.
   PubMed Web of Science ®Google Scholar
• Falagas ME, Pitsouni EI, Malietzis GA, Pappas G. Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses. FASEB J. Feb 2008;22:338–42. doi: 10.1096/fj.07-9492LSF. PubMed PMID: 17884971.
   PubMed Web of Science ®Google Scholar
• Xia J, Benner MJ, Hancock RE. NetworkAnalyst–integrative approaches for protein-protein interaction network analysis and visual exploration. Nucleic Acids Res. Jul 2014;42:W167–74. doi: 10.1093/nar/gku443. PubMed PMID: 24861621. PMCID: 4086107.
   PubMed Web of Science ®Google Scholar
• Tseng GC, Ghosh D, Feingold E. Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res. May 2012;40:3785–99. doi: 10.1093/nar/gkr1265. PubMed PMID: 22262733. PMCID: 3351145.
   PubMed Web of Science ®Google Scholar
• Walsh CJ, Hu P, Batt J, Santos CC.Microarray meta-analysis and cross-platform normalization: integrative genomics for robust biomarker discovery. Microarrays (Basel). 2015 Aug 21;4:389–406. doi:10.3390/microarrays4030389. PubMed PMID: 27600230. PMCID: PMC4996376. Epub 2015/ 01/01.
   PubMedGoogle Scholar
• Forero DA. Available software for meta-analyses of genome-wide expression studies. PeerJ Preprints. 2019 May;7:e27708v1.
   Google Scholar
• Fernandez-Castillo N, Cabana-Dominguez J, Soriano J, Sanchez-Mora C, Roncero C, Grau-Lopez L, Ros-Cucurull E, Daigre C, van Donkelaar MMJ, Franke B, et al.Transcriptomic and genetic studies identify NFAT5 as a candidate gene for cocaine dependence. Transl Psychiatry. 2015 Oct 27;5:e667. doi:10.1038/tp.2015.158. PubMed PMID: 26506053. PMCID: 4930134.
   PubMed Web of Science ®Google Scholar
• Ribeiro EA, Salery M, Scarpa JR, Calipari ES, Hamilton PJ, Ku SM, Kronman H, Purushothaman I, Juarez B, Heshmati M, et al. Transcriptional and physiological adaptations in nucleus accumbens somatostatin interneurons that regulate behavioral responses to cocaine. Nat Commun. 2018 Aug 8;9:3149. PubMed PMID: 30089879. PMCID: 6082848.
   PubMed Web of Science ®Google Scholar
• Walker DM, Cates HM, Loh YE, Purushothaman I, Ramakrishnan A, Cahill KM, Lardner CK, Godino A, Kronman HG, Rabkin J, et al. Cocaine self-administration alters transcriptome-wide responses in the brain’s reward circuitry. Biol Psychiatry. 2018 Dec 15;84:867–80. doi:10.1016/j.biopsych.2018.04.009. PubMed PMID: 29861096. PMCID: 6202276.
   PubMed Web of Science ®Google Scholar
• Hawrylycz M, Miller JA, Menon V, Feng D, Dolbeare T, Guillozet-Bongaarts AL, Jegga AG, Aronow BJ, Lee C-K, Bernard A, et al. Canonical genetic signatures of the adult human brain. Nat Neurosci. Dec 2015;18:1832–44. doi: 10.1038/nn.4171. PubMed PMID: 26571460. PMCID: 4700510.
   PubMed Web of Science ®Google Scholar
• Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57. doi:10.1038/nprot.2008.211. PubMed PMID: 19131956.
   PubMed Web of Science ®Google Scholar
• Rolland T, Tasan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, et al.A proteome-scale map of the human interactome network. Cell. 2014 Nov 20;159:1212–26. doi:10.1016/j.cell.2014.10.050. PubMed PMID: 25416956. PMCID: 4266588.
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. Nov 2003;13:2498–504. doi: 10.1101/gr.1239303. PubMed PMID: 14597658. PMCID: 403769.
   PubMed Web of Science ®Google Scholar
• Forero DA, Guio-Vega GP, Gonzalez-Giraldo Y. A comprehensive regional analysis of genome-wide expression profiles for major depressive disorder. J Affect Disord. Aug 2017;15:86–92. doi: 10.1016/j.jad.2017.04.061. PubMed PMID: 28460316.
   Web of Science ®Google Scholar
• Guio-Vega GP, Forero DA. Functional genomics of candidate genes derived from genome-wide association studies for five common neurological diseases. Int J Neurosci. Feb 2017;127:118–23. doi: 10.3109/00207454.2016.1149172. PubMed PMID: 26829381.
   PubMed Web of Science ®Google Scholar
• Eipper-Mains JE, Kiraly DD, Palakodeti D, Mains RE, Eipper BA, Graveley BR. microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs. RNA (New York, NY). Aug 2011;17:1529–43. doi: 10.1261/rna.2775511. PubMed PMID: 21708909. PMCID: Pmc3153976. Epub 2011/ 06/29.eng.
   PubMed Web of Science ®Google Scholar
• Karagkouni D, Paraskevopoulou MD, Chatzopoulos S, Vlachos IS, Tastsoglou S, Kanellos I, Papadimitriou D, Kavakiotis I, Maniou S, Skoufos G, et al.DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. Nucleic Acids Res. 2018 Jan 4;46:D239–D45. doi:10.1093/nar/gkx1141. PubMed PMID: 29156006. PMCID: 5753203.
   PubMed Web of Science ®Google Scholar
• Russ AP, Lampel S. The druggable genome: an update. Drug Discov Today. Dec 2005;10:1607–10. doi: 10.1016/S1359-6446(05)03666-4. PubMed PMID: 16376820.
   PubMed Web of Science ®Google Scholar
• Pierce RC, Fant B, Swinford-Jackson SE, Heller EA, Berrettini WH, Wimmer ME. Environmental, genetic and epigenetic contributions to cocaine addiction. Neuropsychopharmacol. Jun 2018;43:1471–80. doi: 10.1038/s41386-018-0008-x. PubMed PMID: 29453446. PMCID: 5983541.
   PubMed Web of Science ®Google Scholar
• Hu R, Dai Y, Jia P. ANCO-GeneDB: zhao Z.annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence. Database. 2018 Jan 1. doi:10.1093/database/bay121. PubMed PMID: 30403795.
   Google Scholar
• Wolf ME. Synaptic mechanisms underlying persistent cocaine craving. Nat Rev Neurosci. Jun 2016;17:351–65. doi: 10.1038/nrn.2016.39. PubMed PMID: 27150400. PMCID: 5466704.
   PubMed Web of Science ®Google Scholar
• Korpi ER, Den Hollander B, Farooq U, Vashchinkina E, Rajkumar R, Nutt DJ, Hyytiä P, Dawe GS. Mechanisms of action and persistent neuroplasticity by drugs of abuse. Pharmacol Rev. Oct 2015;67:872–1004. doi: 10.1124/pr.115.010967. PubMed PMID: 26403687.
   PubMed Web of Science ®Google Scholar
• Ortinski PI. Cocaine-induced changes in NMDA receptor signaling. Mol Neurobiol. Oct 2014;50:494–506. doi: 10.1007/s12035-014-8636-6. PubMed PMID: 24445951. PMCID: 4105334.
   PubMed Web of Science ®Google Scholar
• Most D, Workman E, Harris RA. Synaptic adaptations by alcohol and drugs of abuse: changes in microRNA expression and mRNA regulation. Front Mol Neurosci. 2014;7:85. doi:10.3389/fnmol.2014.00085. PubMed PMID: 25565954. PMCID: 4267177.
   PubMed Web of Science ®Google Scholar
• Forero DA, Lopez-Leon S, Shin HD, Park BL, Kim DJ. Meta-analysis of six genes (BDNF, DRD1, DRD3, DRD4, GRIN2B and MAOA) involved in neuroplasticity and the risk for alcohol dependence. Drug Alcohol Depend. Apr 2015;1:259–63. doi: 10.1016/j.drugalcdep.2015.01.017. PubMed PMID: 25660313.
   Web of Science ®Google Scholar
• Xu M. c-Fos is an intracellular regulator of cocaine-induced long-term changes. Ann N Y Acad Sci. Oct 2008;1139:1–9. doi: 10.1196/annals.1432.049. PubMed PMID: 18991842. PMCID: 2596070.
   PubMed Web of Science ®Google Scholar
• Forero DA, van der Ven K, Callaerts P, Del-Favero J. miRNA genes and the brain: implications for psychiatric disorders. Hum Mutat. Nov 2010;31:1195–204. doi: 10.1002/humu.21344. PubMed PMID: 20725930.
   PubMed Web of Science ®Google Scholar
• Lopez-Bellido R, Barreto-Valer K, Sanchez-Simon FM, Rodriguez RE. Cocaine modulates the expression of opioid receptors and miR-let-7d in zebrafish embryos. PLoS One. 2012;7:e50885. doi:10.1371/journal.pone.0050885. PubMed PMID: 23226419. PMCID: 3511421.
   PubMed Web of Science ®Google Scholar
• Huggett SB, Stallings MC. Cocaine’omics: genome-wide and transcriptome-wide analyses provide biological insight into cocaine use and dependence. Addict Biol. 2019 Feb 8. doi:10.1111/adb.12719. PubMed PMID: 30734435.
   PubMed Web of Science ®Google Scholar
• Chen J, Ma Y, Fan R, Yang Z, Li MD. Implication of genes for the N-methyl-D-aspartate (NMDA) receptor in substance addictions. Mol Neurobiol. Sep 2018;55:7567–78. doi: 10.1007/s12035-018-0877-3. PubMed PMID: 29429049. Epub 2018/ 02/13.
   PubMed Web of Science ®Google Scholar
• Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. Dec 2001;29:365–71. doi: 10.1038/ng1201-365. PubMed PMID: 11726920.
   PubMed Web of Science ®Google Scholar
• Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, et al. Repeatability of published microarray gene expression analyses. Nat Genet. Feb 2009;41:149–55. doi: 10.1038/ng.295. PubMed PMID: 19174838.
   PubMed Web of Science ®Google Scholar