Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report

Translational Psychiatry

Volumn 6, Issue 5, 2016, Pages

  Breen, M S ^a   Uhlmann, A ^b   Nday, C M ^c   Glatt, S J ^d   Mitt, M ^e   Metsalpu, A ^e   Stein, D J ^b   Illing, N ^c  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

^c UNIVERSITY OF CAPE TOWN   (South Africa)

^d SUNY UPSTATE MEDICAL UNIVERSITY   (United States)

^e UNIVERSITY OF TARTU   (Estonia)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; METHAMPHETAMINE;

ADULT; AMPHETAMINE DEPENDENCE; BLOOD; BRAIN; COMPLICATION; FEMALE; GENE REGULATORY NETWORK; HUMAN; MALE; NUCLEAR MAGNETIC RESONANCE IMAGING; PATHOPHYSIOLOGY; PHYSIOLOGY; PSYCHOSES, SUBSTANCE-INDUCED; SEQUENCE ANALYSIS; STATISTICS AND NUMERICAL DATA; YOUNG ADULT;

ADULT; AMPHETAMINE-RELATED DISORDERS; BIOMARKERS; BRAIN; FEMALE; GENE REGULATORY NETWORKS; HUMANS; MAGNETIC RESONANCE IMAGING; MALE; METHAMPHETAMINE; PSYCHOSES, SUBSTANCE-INDUCED; SEQUENCE ANALYSIS, RNA; YOUNG ADULT;

EID: 85016119798     PISSN: None     EISSN: 21583188     Source Type: Journal    
DOI: 10.1038/TP.2016.67     Document Type: Article

References (77)

1. Yang MH, Jung MS, Lee MJ, Yoo KH, Yook YJ, Park EY et al. Gene expression profiling of the rewarding effect caused by methamphetamine in the mesolimbic dopamine system. Mol Cells 2008; 26: 121–130.
2. United Nations Office on Drugs and Crime. World Drug Report 2004. UN Office on Drugs and Crime: Vienna, Austria.
3. Kapp C. Crystal meth boom adds to South Africa’s health challenges. Lancet 2008; 371: 193–194.
4. Nutt DJ, King LA, Phillips LD. Drug harms in the UK: a multicriteria decision analysis. Lancet 2010; 376: 1558–1565.
5. Srisurapanont M, Ali R, Marsden J, Sunga A, Wada K, Monteiro M. Psychotic symptoms in methamphetamine psychotic in-patients. Int J Neuropsychopharmacol 2003; 6: 347–352.
6. Smith MJ, Thirthalli J, Abdallah AB, Murray RM, Cottler LB. Prevalence of psychotic symptoms in substance users: a comparison across substances. Compr Psychiatry 2009; 50: 245–250.
7. Bousman CA, Glatt SJ, Everall IP, Tsuang MT. Genetic association studies of methamphetamine use disorders: a systematic review and synthesis. Am J Med Genet B Neuropsychiatr Genet 2009; 150B: 1025–1049.
8. Hsieh JH, Stein DJ, Howells FM. The neurobiology of methamphetamine induced psychosis. Front Hum Neurosci 2014; 8: 537.
9. Srisurapanont M, Arunpongpaisal S, Wada K, Marsden J, Ali R, Kongsakon R. Comparisons of methamphetamine psychotic and schizophrenic symptoms: a differential item functioning analysis. Prog Neuropsychopharmacol Biol Psychiatry 2011; 35: 959–964.
10. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008; 9: 559.
11. Simon R, Lam A, Li M-C, Ngan M, Menenzes S, Zhao Y. Analysis of gene expression data using BRB-Array tools. Cancer Inform 2007; 2: 11–17.
12. Niculescu A, Segal D, Kuczenski R, Barrett T, Hauger R, Kelsoe J. Identifying a series of candidate genes for mania and psychosis: a convergent functional genomics approach. Physiol Genomics 2000; 4: 83–91.
13. Ogden CA, Rich ME, Schork NJ, Paulus MP, Geyer MA, Lohr JB et al. Candidate genes, pathways and mechanisms for bipolar (manic-depressive) and related disorders: an expanded convergent functional genomics approach. Mol Psychiatr 2004; 9: 1007–1029.
14. Patel SD, Le-Niculescu H, Koller DL, Green SD, Lahiri DK, McMahon FJ et al. Coming to grips with complex disorders: genetic risk prediction in bipolar disorder using panels of genes identified through convergent functional genomics. Am J Med Genet B Neuropsychiatr Genet 2010; 153B: 850–877.
15. Le-Niculescu H, Patel SD, Bhat M, Kuczenski R, Faraone SV, Tsuang MT et al. 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; 150B: 155–181.
16. Rodd ZA, Bertsch BA, Strother WN, Le-Niculescu H, Balaraman Y, Hayden E et al. Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach. Pharmacogenomics J 2007; 7: 222–256.
17. Le-Niculescu H, Balaraman Y, Patel SD, Ayalew M, Gupta J, Kuczenski R et al. Convergent functional genomics of anxiety disorders: translational identification of genes, biomarkers, pathways and mechanisms. Transl Psychiatr 2011; 1: e9.
18. Ayalew M, Le-Niculescu H, Levey DF, Jain N, Changala B, Patel SD et al. Convergent functional genomics of schizophrenia: from comprehensive understanding to genetic risk prediction. Mol Psychiatry 2012; 17: 887–905.
19. Le-Niculescu H, Levey DF, Ayalew M, Palmer L, Gavrin LM, Jain N et al. Discovery and validation of blood biomarkers for suicidality. Mol Psychiatry 2013; 18: 1249–1264.
20. Kurian SM, Le-Niculescu H, Patel SD, Bertram D, Davis J, Dike C et al. Identification of blood biomarkers for psychosis using convergent functional genomics. Mol Psychiatry 2009; 16: 37–58.
21. First MB, Gibbon M, Spitzer RL, Williams JBW. User’s Guide for the Structured Clinical Interview for DSM-IV-TR Axis I Disorders—Research Version—(SCID-I for DSM-IV-TR, November 2002 Revision).
22. Brugha TS, Cragg D. The List of Threatening Experiences: the reliability and validity of a brief life events questionnaire. Acta Psychiatr Scand 1990; 82: 77–81.
23. Kessler RC, Andrews G, Colpe LJ, Hiripi E, Mroczek DK, Normand SL et al. Short screening scales to monitor population prevalences and trends in non-specific psychological distress. Psychol Med 2002; 32: 959–976.
24. Beck AT, Steer RA, Brown GK. Manual for the Beck Depression Inventory-II. Psychological Corporation: San Antonio, TX, USA, 1996.
25. Carver C, White T. Behavioral inhibition, behavioral activation, and affective responses to impending reward and punishment: the BIS/BAS scales. J Pers Soc Psychol 1994; 67: 319–333.
26. Eysenck S, Eysenck H, Barrett P. A revised version of the psychoticism scale. Pers Individ Diff 1985; 6: 21–29.
27. Kay SR, Fiszbein A, Opler LA. The Positive and Negative Syndrome Scale (PANSS) for schizophrenia. Schizophr Bull 1987; 13: 261–276.
28. van der Kouwe AJ, Benner T, Salat DH, Fischl B. Brain morphometry with multiecho MPRAGE. Neuroimage 2008; 40: 559–569.
29. Fischl B, Salat DH, van der Kouwe AJ, Makris N, Segonne F, Quinn BT et al. Sequence-independent segmentation of magnetic resonance images. Neuroimage 2004; 23: S69–S84.
30. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina Sequence Data. Bioinformatics 2014; 30: 2114–2120.
31. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25: 1105–1111.
32. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10: R25.
33. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 2009; 25: 2078–2079.
34. Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with highthroughput sequencing data. Bioinformatics 2015; 31: 166–169.
35. Law CW, Chen Y, Shi W, Smyth GK. Voom Precision Weights Unlock Linear Model Analysis Tools for RNA-Seq Read Counts. Technical Report Bioinformatics Division. Walter and Eliza Hall Institute of Medical Research: Melbourne, VIC, Australia, 2013; [http://www.statsci.org/smyth/pubs/13 5 1-voom-techreport].
36. Breen MS, Beliakova-Bethell N, Mujica-Parodi LR, Carlson JM, Ensign WY, Woelk CH et al. Acute psychological stress induces short-term variable immune response. Brain Behav Immun 2015; 53: 172–182.
37. Breen MS, Maihofer AX, Glatt SJ, Tylee DS, Chandler SD, Tsuang MT et al. Gene networks specific for innate immunity define post-traumatic stress disorder. Mol Psychiatry 2015; 20: 1538–1545.
38. Kayala MA, Baldi P. Cyber-T web server: differential analysis of highthroughput data. Nucleic Acids Res 2012; 40: W553–W559.
39. Smyth GK. Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer: New York, NY, USA, 2005, pp 397–420.
40. Chen J, Bardes EE, Aronow BJ, Jegga AG. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res 2009; 37: W305–W311.
41. Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL et al. The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. Nucleic Acids Res 2015; 43, (Database issue) D914–D920.
42. Shoemaker JE, Fukuyama S, Sakabe S, Kitano H, Kawaoka Y. CTen: a web-based platform for identifying enriched cell types from heterogenous microarray data. BMC Genomics 2011; 13: 460.
43. Breen MS, Stein DJ, Baldwin DS. A systematic review of blood transcriptomics and complex brain disorders: moving beyond ‘surrogate marker’ status. Hum Psychopharmacol 2015 (in review).
44. Piñero J, Queralt-Rosinach N, Bravo A, Deu-Pons J, Bauer-Mehren A, Baron M et al. DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database 2015; 2015: abav028.
45. Lee J, Goh L-K, Chen G, Verma S, Tan C-H, Lee T-S. Analysis of blood-based gene expression signature in first-episode psychosis. Psychiatry Res 2012; 200: 52–54.
46. Ciechanover A, Orian A, Schwartz AL. Ubiquitin-mediated proteolysis: biological regulation via destruction. Bioessays 2000; 22: 442–451.
47. Bousman CA, Chana G, Glatt SJ, Chandler SD, May T, Lohr J et al. Positive symptoms of psychosis correlate with expression of ubiquitin proteasome genes in peripheral blood. Am J Med Genet Part B 2010; 153B: 1336–1341.
48. Bousman CA, Chana G, Glatt SJ, Chandler SD, Lucero GR, Tatro E et al. Preliminary evidence of ubiquitin proteasome system dysregulation in schizophrenia and bipolar disorder: convergent pathway analysis findings from two independent samples. Am J Med Genet Part B 2010; 153B: 494–502.
49. Vawter MP, Barrett T, Cheadle C, Sokolov BP, Wood WH III, Donovan DM et al. Application of cDNA microarrays to examine gene expression differences in schizophrenia. Brain Res Bull 2001; 55: 641–650.
50. Vawter MP, Crook JM, Hyde TM, Kleinman JE, Weinberger DR, Becker KG et al. Microarray analysis of gene expression in the prefrontal cortex in schizophrenia: a preliminary study. Schizophr Res 2002; 58: 11–20.
51. Middleton FA, Mirnics K, Pierri JN, Lewis DA, Levitt P. Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia. J Neurosci 2002; 22: 2718–2729.
52. Altar CA, Jurata LW, Charles V, Lemire A, Liu P, Bukhman Y et al. Deficient hippocampal neuron expression of proteasome, ubiquitin, and mitochondrial genes in multiple schizophrenia cohorts. Biol Psychiatry 2005; 58: 85–96.
53. Konradi C, Eaton M, MacDonald ML, Walsh J, Benes FM, Heckers S. Molecular evidence for mitochondrial dysfunction in bipolar disorder. Arch Gen Psychiatry 2004; 61: 300–308.
54. Lam YA, Pickart CM, Alban A, Landon M, Jamieson C, Ramage R et al. Inhibition of the ubiquitin-proteasome system in Alzheimer’s disease. Proc Natl Acad Sci USA 2000; 97: 9902–9906.
55. Shimura H, Schlossmacher MG, Hattori N, Frosch MP, Trockenbacher A, Schneider R et al. Ubiquitination of a new form of alpha-synuclein by Parkin from human brain: implications for Parkinson’s disease. Science 2001; 293: 263–269.
56. Rubio M, Wood K, Haroutunian V, Meador-Woodruff J. Dysfunction of the Ubiquitin Proteasome and Ubiquitin-Like Systems in Schizophrenia. Neuropsychopharmacology 2013; 38: 1910–1920.
57. White T, Nelson M, Lim KO. Diffusion tensor imaging in psychiatric disorders. Top Magn Reson Imaging 2008; 19: 97–109.
58. Whitford TJ, Kubicki M, Schneiderman JS, O'Donnell LJ, King R, Alvarado JL et al. Corpus callosum abnormalities and their association with psychotic symptoms in patients with schizophrenia. Biol Psychiatry 2010; 68: 70–77.
59. Price G, Cercignani M, Parker GJ, Altmann DR, Barnes TR, Barker GJ et al. Abnormal brain connectivity in first-episode psychosis: a diffusion MRI tractography study of the corpus callosum. Neuroimage 2007; 35: 458–466.
60. Friston KJ, Frith CD. Schizophrenia: a disconnection syndrome? Clin Neurosci 1995; 3: 89–97.
61. Kubicki M, McCarley R, Westin CF, Park HJ, Maier S, Kikinis R et al. A review of diffusion tensor imaging studies in schizophrenia. J Psychiatr Res 2007; 41: 15–30.
62. Orikabe L, Yamasue H, Inoue H, Takayanagi Y, Mozue Y, Sudo Y et al. Reduced amygdala and hippocampal volumes in patients with methamphetamine psychosis. Schizophr Res 2011; 132: 183–189.
63. Velakoulis D, Wood SJ, Wong MT, McGorry PD, Yung A, Phillips L et al. Hippocampal and amygdala volumes according to psychosis stage and diagnosis: a magnetic resonance imaging study of chronic schizophrenia, first-episode psychosis, and ultra-high-risk individuals. Arch Gen Psychiatry 2006; 63: 139–149.
64. Fusar-Poli P, Howes OD, Allen P, Broome M, Valli I, Asselin M-C et al. Abnormal prefrontal activation directly related to pre-synaptic striatal dopamine dysfunction in people at clinical high risk for psychosis. Mol Psychiatry 2009; 16: 67–75.
65. Schenk VW, Stolk PJ. Psychosis following arsenic (possibly thalium) poisoning. Psychiatr Neurol Neurochir 1967; 70: 31–37.
66. Lebrun AH, Storch S, Pohl S, Streichert T, Mole SE, Ullrich K et al. Identification of potential biomarkers and modifiers of CLN3-disease progression. Neuropediatrics 2010; 41: V1240.
67. Ratnaike RN. Acute and chronic arsenic toxicity. Postgrad Med J 2003; 79:391–396.
68. Mitchison HM, Taschner PEM, O'Rawe AM, De Vos N, Phillips HA, Thompson AD et al. Genetic mapping of the batten disease locus (CLN3) to the interval D16S288-D16S383 by analysis of haplotypes and allelic association. Genomics 1994; 22: 465–468.
69. Olsen L, Hansen T, Jakobsen KD, Djurovic S, Melle I, Agartz I et al. The estrogen hypothesis of schizophrenia implicates glucose metabolism: association study in three independent samples. BMC Med Genet 2008; 9: 39.
70. Le-Niculescu H, Balaraman Y, Patel S, Tan J, Sidhu K, Jerome RE et al. Towards understanding the schizophrenia code: an expanded convergent functional genomics approach. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:129–158.
71. Duong HA, Robles MS, Knutti D, Weitz CJ. A molecular mechanism for circadian clock negative feedback. Science 2011; 332: 1446–1449.
72. Monti JM, BaHammam AS, Pandi-Perumal SR, Bromundt V, Spence DW, Cardinali DP et al. Sleep and circadian rhythm dysregulation in schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2013; 43: 209–216.
73. van Venrooij JA, Fluitman SB, Lijmer JG, Kavelaars A, Heijnen CJ, Westenberg HG et al. Impaired neuroendocrine and immune response to acute stress in medication-naive patients with a first episode of psychosis. Schizophr Bull 2012; 38: 272–279.
74. Mondelli V, Ciufonlini S, Murri MB, Bonaccorso S, Di Fortio M, Giordano A et al. Cortisol and inflammatory biomarkers predict poor treatment response in first episode psychosis. Schizophr Bull 2015; 41: 1162–1170.
75. Le Moal M, Koob GF. Drug addiction: pathways to the disease and pathophysiological perspectives. Eur Neuropsychopharmacol 2007; 17: 377–393.
76. Qiu MH, Liu W, Qu WM, Urade Y, Lu J, Huang ZL. The role of nucleus accumbens core/shell in sleep-wake regulation and their involvement in modafinil-induced arousal. PLoS One 2012; 7: e45471.
77. Felger JC, Miller AH. Cytokine effects on the basal ganglia and dopamine function: the subcortical source of inflammatory malais. Front Neuroendocrinol 2012; 33: 315–327.