Co-expression network of neural-differentiation genes shows specific pattern in schizophrenia Bioinformatic and algorithmical studies

BMC Medical Genomics

Volumn 8, Issue 1, 2015, Pages

  Maschietto, Mariana ^a   Tahira, Ana C ^a   Puga, Renato ^b   Lima, Leandro ^a   Mariani, Daniel ^a   Da Silveira Paulsen, Bruna ^c   Belmonte De Abreu, Paulo ^d   Vieira, Henrique ^a   Krepischi, Ana Cv ^a   Carraro, Dirce M ^e   Palha, Joana A ^f,g   Rehen, Stevens ^c,h   Brentani, Helena ^a,i  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b HOSPITAL ISRAELITA ALBERT EINSTEIN   (Brazil)

^c FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^d FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^e A C CAMARGO CANCER CENTER   (Brazil)

^f UNIVERSITY OF MINHO   (Portugal)

^g UNIVERSITY OF MINHO   (Portugal)

^h D OR INSTITUTE FOR RESEARCH AND EDUCATION IDOR   (Brazil)

ⁱ National Institute of Developmental Psychiatry for Children and Adolescents (INPD/Brazil)   (Brazil)

Author keywords

Gene network; Module analyses; Neuronal differentiation; Oxidative stress; Schizophrenia

Indexed keywords

CLOZAPINE;

ADULT; ARTICLE; BRAIN TISSUE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CLINICAL ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA METHYLATION; FEMALE; FIBROBLAST; FRONTAL CORTEX; GENE CLUSTER; GENE DISRUPTION; GENE EXPRESSION; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; HUMAN TISSUE; MIDDLE AGED; NERVE CELL DIFFERENTIATION; NERVOUS SYSTEM DEVELOPMENT; OXIDATIVE STRESS; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; SCHIZOPHRENIA; SIGNAL TRANSDUCTION; BIOPSY; BRAIN; CASE CONTROL STUDY; CELL DIFFERENTIATION; COMPARATIVE GENOMIC HYBRIDIZATION; FRONTAL LOBE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; METABOLISM; NERVE CELL; PATHOLOGY;

BIOPSY; BRAIN; CASE-CONTROL STUDIES; CELL DIFFERENTIATION; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; DNA METHYLATION; FEMALE; FIBROBLASTS; FRONTAL LOBE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MIDDLE AGED; NEUROGENESIS; NEURONS; OXIDATIVE STRESS; SCHIZOPHRENIA; SIGNAL TRANSDUCTION;

EID: 84929438629     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/s12920-015-0098-9     Document Type: Article

References (69)

1. Sullivan PF, Kendler KS, Neale MC. Schizophrenia as a complex trait: evidence from a meta-analysis of twin studies. Arch Gen Psychiatry. 2003;60(12):11871192.
2. Tsuang MT, Stone WS, Faraone SV. Genes, environment and schizophrenia. Br J Psychiatry Suppl. 2001;40:s18-24.
3. Palha JA, Goodman AB. Thyroid hormones and retinoids: a possible link between genes and environment in schizophrenia. Brain Res Rev. 2006;51(1):61-71.
4. Sun J, Jia P, Fanous AH, van den Oord E, Chen X, Riley BP, et al. Schizophrenia gene networks and pathways and their applications for novel candidate gene selection. PLoS One. 2010;5(6):e11351.
5. Christian K, Song H, Ming GL. Adult neurogenesis as a cellular model to study schizophrenia. Cell Cycle. 2010;9(4):636-7.
6. Clapcote SJ, Lipina TV, Millar JK, Mackie S, Christie S, Ogawa F, et al. Behavioral phenotypes of Disc1 missense mutations in mice. Neuron. 2007;54(3):387-402.
7. Hikida T, Jaaro-Peled H, Seshadri S, Oishi K, Hookway C, Kong S, et al. Dominant-negative DISC1 transgenic mice display schizophrenia-associated phenotypes detected by measures translatable to humans. Proc Natl Acad Sci U S A. 2007;104(36):14501-6.
8. Brennand KJ, Gage FH. Modeling psychiatric disorders through reprogramming. Dis Model Mech. 2012;5(1):26-32.
9. Shao L, Vawter MP. Shared gene expression alterations in schizophrenia and bipolar disorder. Biol Psychiatry. 2008;64(2):89-97.
10. Zhan L, Kerr JR, Lafuente MJ, Maclean A, Chibalina MV, Liu B, et al. Altered expression and coregulation of dopamine signalling genes in schizophrenia and bipolar disorder. Neuropathol Appl Neurobiol. 2011;37(2):206219.
11. Iwamoto K, Kato T. Gene expression profiling in schizophrenia and related mental disorders. Neuroscientist. 2006;12(4):349-61.
12. Arion D, Unger T, Lewis DA, Levitt P, Mirnics K. Molecular evidence for increased expression of genes related to immune and chaperone function in the prefrontal cortex in schizophrenia. Biol Psychiatry. 2007;62(7):711-21.
13. Haroutunian V, Katsel P, Dracheva S, Stewart DG, Davis KL. Variations in oligodendrocyte-related gene expression across multiple cortical regions: implications for the pathophysiology of schizophrenia. Int J Neuropsychopharmacol. 2007;10(4):565-73.
14. Torkamani A, Dean B, Schork NJ, Thomas EA. Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia. Genome Res. 2010;20(4):403-12.
15. Mistry M, Gillis J, Pavlidis P. Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls. BMC Neurosci. 2013;14:105.
16. Middleton FA, Pato CN, Gentile KL, McGann L, Brown AM, Trauzzi M, et al. Gene expression analysis of peripheral blood leukocytes from discordant sib-pairs with schizophrenia and bipolar disorder reveals points of convergence between genetic and functional genomic approaches. Am J Med Genet B Neuropsychiatr Genet. 2005;136B(1):12-25.
17. Domenici E, Willé DR, Tozzi F, Prokopenko I, Miller S, McKeown A, et al. Plasma protein biomarkers for depression and schizophrenia by multi analyte profiling of case-control collections. PLoS One. 2010;5(2):e9166.
18. Bowden NA, Weidenhofer J, Scott RJ, Schall U, Todd J, Michie PT, et al. Preliminary investigation of gene expression profiles in peripheral blood lymphocytes in schizophrenia. Schizophr Res. 2006;82(2-3):175-83.
19. Maschietto M, Silva AR, Puga RD, Lima L, Pereira CB, Nakano EY, et al. Gene expression of peripheral blood lymphocytes may discriminate patients with schizophrenia from controls. Psychiatry Res. 2012;200(2-3):1018-21.
20. Benitez-King G, Riquelme A, Ortiz-Lopez L, Berlanga C, Rodriguez-Verdugo MS, Romo F, et al. A noninvasive method to isolate the neuronal linage from the nasal epithelium from schizophrenic and bipolar diseases. J Neurosci Methods. 2011;201(1):35-45.
21. Pedrosa E, Sandler V, Shah A, Carroll R, Chang C, Rockowitz S, et al. Development of patient-specific neurons in schizophrenia using induced pluripotent stem cells. J Neurogenet. 2011;25(3):88-103.
22. Brennand KJ, Simone A, Jou J, Gelboin-Burkhart C, Tran N, Sangar S, et al. Modelling schizophrenia using human induced pluripotent stem cells. Nature. 2011;473(7346):221-5.
23. Chen J, Lin M, Foxe JJ, Pedrosa E, Hrabovsky A, Carroll R, et al. Transcriptome comparison of human neurons generated using induced pluripotent stem cells derived from dental pulp and skin fibroblasts. PLoS One. 2013;8(10):e75682.
24. Paulsen BD, Maciel RD, Galina A, da Silveira MS, Souza CD, Drummond H, et al. Altered oxygen metabolism associated to neurogenesis of induced pluripotent stem cells derived from a schizophrenic patient. Cell Transplant. 2011;21(7):1547-59.
25. Robicsek O, Karry R, Petit I, Salman-Kesner N, Muller FJ, Klein E, et al. Abnormal neuronal differentiation and mitochondrial dysfunction in hair follicle-derived induced pluripotent stem cells of schizophrenia patients. Mol Psychiatry. 2013;18(10):1067-76.
26. Brennand K, Savas JN, Kim Y, Tran N, Simone A, Hashimoto-Torii K, et al. Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. Mol Psychiatry. 2014;20(3):361-8.
27. de Baumont A, Maschietto M, Lima L, Carraro DM, Olivieri EH, Fiorini A, et al. Innate immune response is differentially dysregulated between bipolar disease and schizophrenia. Schizophr Res. 2015;161(2-3):215-21.
28. Vêncio RZ, Koide T. HTself: self-self based statistical test for low replication microarray studies. DNA Res. 2005;12(3):211-4.
29. Sunkin SM, Ng L, Lau C, Dolbeare T, Gilbert TL, Thompson CL, et al. Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. Nucleic Acids Res. 2013;41(Database issue):D996-1008.
30. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, et al. TM4: a free, open-source system for microarray data management and analysis. BioTechniques. 2003;34(2):374-8.
31. Parikshak NN, Luo R, Zhang A, Won H, Lowe JK, Chandran V, et al. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell. 2013;155(5):1008-21.
32. Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, et al. GO-Elite: a flexible solution for pathway and ontology overrepresentation. Bioinformatics. 2012;28(16):2209-10.
33. Eisinger BE, Saul MC, Driessen TM, Gammie SC. Development of a versatile enrichment analysis tool reveals associations between the maternal brain and mental health disorders, including autism. BMC Neurosci. 2013;14:147.
34. Langfelder P, Horvath S. Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol. 2007;1:54.
35. Langfelder P, Zhang B, Horvath S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics. 2008;24(5):719-20.
36. Langfelder P, Luo R, Oldham MC, Horvath S. Is my network module preserved and reproducible? PLoS Comput Biol. 2011;7(1):e1001057.
37. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498-504.
38. Zhang B, Kirov S, Snoddy J. WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005;33(Web Server issue):W741-8.
39. Zeng L, Zhang Q, Li S, Plotnikov AN, Walsh MJ, Zhou MM. Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature. 2010;466(7303):258-62.
40. Betous R, Mason AC, Rambo RP, Bansbach CE, Badu-Nkansah A, Sirbu BM, et al. SMARCAL1 catalyzes fork regression and Holliday junction migration to maintain genome stability during DNA replication. Genes Dev. 2012;26(2):151-62.
41. Wang L, Charroux B, Kerridge S, Tsai CC. Atrophin recruits HDAC1/2 and G9a to modify histone H3K9 and to determine cell fates. EMBO Rep. 2008;9(6):555562.
42. Fleck D, Garratt AN, Haass C, Willem M. BACE1 dependent neuregulin processing: review. Curr Alzheimer Res. 2012;9(2):178-83.
43. Luo X, He W, Hu X, Yan R. Reversible overexpression of bace1-cleaved neuregulin-1 N-terminal fragment induces schizophrenia-like phenotypes in mice. Biol Psychiatry. 2014;76(2):120-7.
44. Lee KY, Ahn YM, Joo EJ, Chang JS, Kim YS. The association of DUSP6 gene with schizophrenia and bipolar disorder: its possible role in the development of bipolar disorder. Mol Psychiatry. 2006;11(5):425-6.
45. Grant P, Gabriel F, Kuepper Y, Wielpuetz C, Hennig J. Psychosis-proneness correlates with expression levels of dopaminergic genes. Eur Psychiatry. 2014;29(5):304-6.
46. Kubota-Sakashita M, Iwamoto K, Bundo M, Kato T. A role of ADAR2 and RNA editing of glutamate receptors in mood disorders and schizophrenia. Mol Brain. 2014;7:5.
47. Blaveri E, Kalsi G, Lawrence J, Quested D, Moorey H, Lamb G, et al. Genetic association studies of schizophrenia using the 8p21-22 genes: prepronociceptin (PNOC), neuronal nicotinic cholinergic receptor alpha polypeptide 2 (CHRNA2) and arylamine Nacetyltransferase 1 (NAT1). Eur J Hum Genet. 2001;9(6):469-72.
48. Shimo H, Nakamura M, Tomiyasu A, Ichiba M, Ueno S, Sano A. Comprehensive analysis of the genes responsible for neuroacanthocytosis in mood disorder and schizophrenia. Neurosci Res. 2011;69(3):196-202.
49. Lochman J, Balcar VJ, Stastny F, Sery O. Preliminary evidence for association between schizophrenia and polymorphisms in the regulatory Regions of the ADRA2A, DRD3 and SNAP-25 Genes. Psychiatry Res. 2013;205(1-2):7-12.
50. Nicodemus KK, Callicott JH, Higier RG, Luna A, Nixon DC, Lipska BK, et al. Evidence of statistical epistasis between DISC1, CIT and NDEL1 impacting risk for schizophrenia: biological validation with functional neuroimaging. Hum Genet. 2010;127(4):441-52.
51. Matsumoto A, Mizuno M, Hamada N, Nozaki Y, Jimbo EF, Momoi MY, et al. LIN7A depletion disrupts cerebral cortex development, contributing to intellectual disability in 12q21-deletion syndrome. PLoS One. 2014;9(3):e92695.
52. Mizuno M, Matsumoto A, Hamada N, Ito H, Miyauchi A, Jimbo EF, et al. Role of an adaptor protein Lin-7B in brain development: possible involvement in autism spectrum disorders. J Neurochem. 2015;132(1):61-9.
53. Lanktree M, Squassina A, Krinsky M, Strauss J, Jain U, Macciardi F, et al. Association study of brain-derived neurotrophic factor (BDNF) and LIN-7 homolog (LIN-7) genes with adult attention-deficit/hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet. 2008;147B(6):945-51.
54. Mayshar Y, Ben-David U, Lavon N, Biancotti JC, Yakir B, Clark AT, et al. Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell. 2010;7(4):521-31.
55. Laurent LC, Ulitsky I, Slavin I, Tran H, Schork A, Morey R, et al. Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture. Cell Stem Cell. 2011;8(1):106-18.
56. Vestin A, Mills AA. The tumor suppressor Chd5 is induced during neuronal differentiation in the developing mouse brain. Gene Expression Patterns: GEP. 2013;13(8):482-9.
57. Bushe CJ, Hodgson R. Schizophrenia and cancer: in 2010 do we understand the connection? Can J Psychiatry. 2010;55(12):761-7.
58. Ward PS, Thompson CB. Metabolic reprogramming: a cancer hallmark even warburg did not anticipate. Cancer Cell. 2012;21(3):297-308.
59. Rafalski VA, Mancini E, Brunet A. Energy metabolism and energy-sensing pathways in mammalian embryonic and adult stem cell fate. J Cell Sci. 2012;125(Pt 23):5597-608.
60. Wasch R, Robbins JA, Cross FR. The emerging role of APC/CCdh1 in controlling differentiation, genomic stability and tumor suppression. Oncogene. 2010;29(1):1-10.
61. Spiegel S, Milstien S. Sphingosine-1-phosphate: signaling inside and out. FEBS Lett. 2000;476(1-2):55-7.
62. Lou CH, Shao A, Shum EY, Espinoza JL, Huang L, Karam R, et al. Posttranscriptional control of the stem cell and neurogenic programs by the nonsense-mediated RNA decay pathway. Cell Reports. 2014;6(4):748-64.
63. Shiizaki S, Naguro I, Ichijo H. Activation mechanisms of ASK1 in response to various stresses and its significance in intracellular signaling. Advances in Biological Regulation. 2013;53(1):135-44.
64. Vedrenne V, Gowher A, De Lonlay P, Nitschke P, Serre V, Boddaert N, et al. Mutation in PNPT1, which encodes a polyribonucleotide nucleotidyltransferase, impairs RNA import into mitochondria and causes respiratory-chain deficiency. Am J Hum Genet. 2012;91(5):912-8.
65. Carrier JL, Javadi P, Bourrier E, Camus C, Segal-Bendirdjian E, Karniguian A. cFos mediates cAMP-dependent generation of ROS and rescue of maturation program in retinoid-resistant acute promyelocytic leukemia cell line NB4-LR1. PLoS One. 2012;7(11):e50408.
66. Folmes CD, Dzeja PP, Nelson TJ, Terzic A. Metabolic plasticity in stem cell homeostasis and differentiation. Cell Stem Cell. 2012;11(5):596-606.
67. Folmes CD, Dzeja PP, Nelson TJ, Terzic A. Mitochondria in control of cell fate. Circ Res. 2012;110(4):526-9.
68. Ochocki JD, Simon MC. Nutrient-sensing pathways and metabolic regulation in stem cells. J Cell Biol. 2013;203(1):23-33.
69. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a pratical and powerful approach to multiple testing. J R Statist Soc B. 1995;57(1):289-300.