Microarray profiling and co-expression network analysis of circulating lncRNAs and mRNAs associated with major depressive disorder

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Liu, Zhifen ^a   Li, Xinrong ^a   Sun, Ning ^a   Xu, Yong ^a   Meng, Yaqin ^a   Yang, Chunxia ^a   Wang, Yanfang ^a   Zhang, Kerang ^a  

^a SHANXI MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; MESSENGER RNA;

ADULT; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; DISEASE ASSOCIATION; FEMALE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETIC CORRELATION; GENETIC SUSCEPTIBILITY; HUMAN; MAJOR DEPRESSION; MALE; MICROARRAY ANALYSIS; MOLECULAR PATHOLOGY; NUCLEOTIDE SEQUENCE; RNA ANALYSIS; RNA GENE; BLOOD; CASE CONTROL STUDY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; MIDDLE AGED; MOLECULAR GENETICS; PATHOLOGY;

ADULT; CASE-CONTROL STUDIES; DEPRESSIVE DISORDER, MAJOR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, LONG NONCODING; RNA, MESSENGER;

EID: 84899854471     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093388     Document Type: Article

References (63)

1. Tsuang MT, Taylor L, Faraone SV (2004) An overview of the genetics of psychotic mood disorders. J Psychiatr Res 38: 3-15. (Pubitemid 38018985)
2. Levinson DF (2006) The genetics of depression: a review. Biol Psychiatry 60: 84-92.
3. Lohoff FW (2010) Overview of the genetics of major depressive disorder. Curr Psychiatry Rep 12: 539-546.
4. Vialou V, Feng J, Robison AJ, Nestler EJ (2013) Epigenetic mechanisms of depression and antidepressant action. Annu Rev Pharmacol Toxicol 53:59-87.
5. Marques AC, Ponting CP (2009) Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol 10: R124.
6. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, et al. (2010) Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 40: 939-953.
7. Aravin AA, Hannon GJ, Brennecke J (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318: 761-764. (Pubitemid 351411762)
8. Huang Y, Shen XJ, Zou Q, Wang SP, Tang SM, et al. (2011) Biological functions of microRNAs: a review. J Physiol Biochem 67: 129-139.
9. Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20: 515-524. (Pubitemid 43345317)
10. Nagano T, Fraser P (2011) No-nonsense functions for long noncoding RNAs. Cell 145:178-181.
11. Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, et al. (2006) Experimental validation of the regulated expression of large numbers of noncoding RNAs from the mouse genome. Genome Res 16:11-19. (Pubitemid 43048929)
12. Ng SY, Lin L, Soh BS, Stanton LW (2013) Long noncoding RNAs in development and disease of the central nervous system. Trends Genet 29: 461-468.
13. Bhartiya D, Kapoor S, Jalali S, Sati S, Kaushik K (2012) Conceptual approaches for lncRNA drug discovery and future strategies. Expert Opin Drug Discov 7: 503-513.
14. Hall J, Thomas KL, Everitt BJ (2000) Rapid and selective induction of BDNF expression in the hippocampus during contextual learning. Nat Neurosci 3: 533-535. (Pubitemid 30332069)
15. Rattiner LM, Davis M, French CT, Ressler KJ (2004) Brain-derived neurotrophic factor and tyrosine kinase receptor B involvement in amygdala-dependent fear conditioning. J Neurosci 24: 4796-4806. (Pubitemid 38668204)
16. Bredy TW, Wu H, Crego C, Zellhoefer J, Sun YE, et al. (2007) Histone modifications around individual BDNF gene promoters in prefrontal cortex are associated with extinction of conditioned fear. Learn Mem 14: 268-276. (Pubitemid 46625629)
17. Millar JK, Wilson-Annan JC, Anderson S, Christie S, Taylor MS, et al. (2000) Disruption of two novel genes by a translocation co-segregating with schizophrenia. Hum Mol Genet 9: 1415-1423. (Pubitemid 30312490)
18. Chubb JE, Bradshaw NJ, Soares DC, Porteous DJ, Millar JK (2008) The DISC locus in psychiatric illness. Mol Psychiatry 13: 36-64.
19. Williams JM, Beck TF, Pearson DM, Proud MB, Cheung SW, et al. (2009) A 1q42 deletion involving DISC1, DISC2, and TSNAX in an autism spectrum disorder. Am J Med Genet A 149A: 1758-1762.
20. Sullivan PF, Fan C, Perou CM (2006) Evaluating the comparability of gene expression in blood and brain. Am J Med Genet B Neuropsychiatr Genet 141B: 261-268.
21. First MB, Spitzer RL, Gibbon M, Williams JBW, Davies M, et al. (1995) The Structured Clinical Interview for DSM-III-R Personality Disorders (SCID-II). Part II: Multi-site Test-retest Reliability Study. Journal of Personality Disorders 9: 92-104.
22. Xu W, Seok J, Mindrinos MN, Schweitzer AC, Jiang H, et al. (2011) Human transcriptome array for high-throughput clinical studies. Proc Natl Acad SciUS A 108: 3707-3712.
23. Wright GW, Simon RM (2003) A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 19: 2448-2455. (Pubitemid 38016644)
24. The Gene Ontology (GO) project in 2006. Nucleic Acids Res 34: D322-326.
25. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29. (Pubitemid 30257031)
26. Dupuy D, Bertin N, Hidalgo CA, Venkatesan K, Tu D, et al. (2007) Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nat Biotechnol 25: 663-668. (Pubitemid 46897203)
27. Yi M, Horton JD, Cohen JC, Hobbs HH, Stephens RM (2006) Whole-PathwayScope: a comprehensive pathway-based analysis tool for high-throughput data. BMC Bioinformatics 7: 30.
28. Draghici S, Khatri P, Tarca AL, Amin K, Done A, et al. (2007) A systems biology approach for pathway level analysis. Genome Res 17: 1537-1545. (Pubitemid 47529438)
29. Pujana MA, Han JD, Starita LM, Stevens KN, Tewari M, et al. (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 39: 1338-1349. (Pubitemid 350035000)
30. Prieto C, Risueno A, Fontanillo C, De las Rivas J (2008) Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS One 3: e3911.
31. Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
32. Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, et al. (2003) From gene networks to gene function. Genome Res 13: 2568-2576. (Pubitemid 37541145)
33. Dong C, Wong ML, Licinio J (2009) Sequence variations of ABCB1, SLC6A2, SLC6A3, SLC6A4, CREB1, CRHR1 and NTRK2: association with major depression and antidepressant response in Mexican-Americans. Mol Psychiatry 14: 1105-1118.
34. Shyn SI, Shi J, Kraft JB, Potash JB, Knowles JA, et al. (2011) Novel loci for major depression identified by genome-wide association study of Sequenced Treatment Alternatives to Relieve Depression and meta-analysis of three studies. Mol Psychiatry 16: 202-215.
35. Lewis CM, Ng MY, Butler AW, Cohen-Woods S, Uher R, et al. (2010) Genome-wide association study of major recurrent depression in the U.K. population. Am J Psychiatry 167: 949-957.
36. Shi J, Potash JB, Knowles JA, Weissman MM, Coryell W, et al. (2011) Genome-wide association study of recurrent early-onset major depressive disorder. Mol Psychiatry 16: 193-201.
37. Lee PH, Perlis RH, Jung JY, Byrne EM, Rueckert E, et al. (2012) Multi-locus genome-wide association analysis supports the role of glutamatergic synaptic transmission in the etiology of major depressive disorder. Transl Psychiatry 2: e184.
38. Henningsen K, Palmfeldt J, Christiansen S, Baiges I, Bak S, et al. (2012) Candidate hippocampal biomarkers of susceptibility and resilience to stress in a rat model of depression. Mol Cell Proteomics 11: M111 016428.
39. Teyssier JR, Ragot S, Chauvet-Gelinier JC, Trojak B, Bonin B (2011) Expression of oxidative stress-response genes is not activated in the prefrontal cortex of patients with depressive disorder. Psychiatry Res 186: 244-247.
40. Tordera RM, Garcia-Garcia AL, Elizalde N, Segura V, Aso E, et al. (2011) Chronic stress and impaired glutamate function elicit a depressive-like phenotype and common changes in gene expression in the mouse frontal cortex. Eur Neuropsychopharmacol 21: 23-32.
41. Wong ML, Dong C, Maestre-Mesa J, Licinio J (2008) Polymorphisms in inflammation-related genes are associated with susceptibility to major depression and antidepressant response. Mol Psychiatry 13: 800-812.
42. Yamada S, Yamamoto M, Ozawa H, Riederer P, Saito T (2003) Reduced phosphorylation of cyclic AMP-responsive element binding protein in the postmortem orbitofrontal cortex of patients with major depressive disorder. J Neural Transm 110: 671-680. (Pubitemid 36683520)
43. Seifuddin F, Pirooznia M, Judy JT, Goes FS, Potash JB, et al. (2013) Systematic review of genome-wide gene expression studies of bipolar disorder. BMC Psychiatry 13: 213.
44. Consortium MDDWGotPG (2013) A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry 18: 497-511.
45. Tiwary BK (2012) The severity of mental disorders is linked to interaction among candidate genes. Integr Biol (Camb) 4: 1096-1101.
46. Segman RH, Goltser-Dubner T, Weiner I, Canetti L, Galili-Weisstub E, et al. (2010) Blood mononuclear cell gene expression signature of postpartum depression. Mol Psychiatry15: 93-100.
47. Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, et al. (2013) Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing. Mol Psychiatry [Epub ahead of print].
48. Mehta D, Menke A, Binder EB (2010) Gene expression studies in major depression. Curr Psychiatry Rep 12: 135-144.
49. Ansorge MS, Hen R, Gingrich JA (2007) Neurodevelopmental origins of depressive disorders. Curr Opin Pharmacol 7: 8-17. (Pubitemid 46238045)
50. D. Enache, B. Winblad, D. (2011) Aarsland Depression in dementia: epidemiology, mechanisms, and treatment. Curr. Opin. Psychiatry 24: 461-472.
51. Wuwongse S, Cheng SS, Wong GT, Hung CH, Zhang NQ, et al. (2013) Effects of corticosterone and amyloid-beta on proteins essential for synaptic function: Implications for depression and Alzheimer's disease. Biochim Biophys Acta 1832: 2245-2256.
52. Marsh L (2013) Depression and Parkinson's disease: current knowledge. Curr Neurol Neurosci Rep 13: 409.
53. Hult Lundh S, Nilsson N, Soylu R, Kirik D, Petersén Å (2013) Hypothalamic expression of mutant huntingtin contributes to the development of depressive-like behavior in the BAC transgenic mouse model of Huntington's disease. Hum Mol Genet 22: 3485-3497.
54. Hauser SR, Getachew B, Taylor RE, Tizabi Y (2011) Alcohol induced depressive-like behavior is associated with a reduction in hippocampal BDNF. Pharmacol Biochem Behav 100: 253-258.
55. Schroeder M, Hillemacher T, Bleich S, Frieling H (2012) The epigenetic code in depression: implications for treatment. Clin Pharmacol Ther 91: 310-314.
56. Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136: 629-641.
57. Spadaro PA, Bredy TW (2012) Emerging role of non-coding RNA in neural plasticity, cognitive function, and neuropsychiatric disorders. Front Genet 3: 132.
58. Barry G, Briggs JA, Vanichkina DP, Poth EM, Beveridge NJ, et al. (2013) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry 1-9.
59. Sanchez Y, Huarte M (2013) Long non-coding RNAs: challenges for diagnosis and therapies. Nucleic Acid Ther 23: 15-20.
60. Liew CC, Ma J, Tang HC, Zheng R, Dempsey AA (2006) The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool. J Lab Clin Med 147:126-132. (Pubitemid 43288168)
61. Sullivan PF, Fan C, Perou CM (2006) Evaluating the comparability of gene expression in blood and brain. Am J Med Genet B Neuropsychiatr Genet 141B:261-268.
62. Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, et al. (2012) Genome-wide analysis of long noncoding RNA stability. Genome Res 22: 885-898.
63. Lee GL, Dobi A, Srivastava S (2011) Prostate cancer: diagnostic performance of the PCA3 urine test. Nat Rev Urol 8: 123-124.