Type I interferon signaling genes in recurrent major depression: Increased expression detected by whole-blood RNA sequencing

Molecular Psychiatry

Volumn 19, Issue 12, 2014, Pages 1267-1274

  Mostafavi, S ^a   Battle, A ^a   Zhu, X ^b   Potash, J B ^c   Weissman, M M ^d   Shi, J ^e   Beckman, K ^f   Haudenschild, C ^g   Mccormick, C ^h   Mei, R ⁱ   Gameroff, M J ^d   Gindes, H ^c   Adams, P ^d   Goes, F S ^j   Mondimore, F M ^j   Mackinnon, D F ^j   Notes, L ^k   Schweizer, B ^j   Furman, D ^b   Montgomery, S B ^b,l   Urban, A E ^b   Koller, D ^a   Levinson, D F ^b   more..

^a Stanford University   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF IOWA HOSPITALS AND CLINICS   (United States)

^d NEW YORK STATE PSYCHIATRIC INSTITUTE   (United States)

^e NATIONAL CANCER INSTITUTE   (United States)

^f UNIVERSITY OF MINNESOTA   (United States)

^g Personalis   (United States)

^h ILLUMINA INC   (United States)

ⁱ Centrillion Biosciences Inc ^*  (United States)

^j JOHNS HOPKINS UNIVERSITY   (United States)

^k AMERICAN UNIVERSITY   (United States)

^l STANFORD UNIVERSITY   (United States)

more..

Author keywords

interferon I signaling; major depressive disorder; MDD; pathway expression signature; RNA sequencing; transcriptomic

Indexed keywords

ALPHA INTERFERON; ANTIDEPRESSANT AGENT; BETA INTERFERON; INTERFERON; RNA;

ADULT; ALCOHOL CONSUMPTION; ARTICLE; CAUCASIAN; CELL CYCLE ARREST; CHILDHOOD TRAUMA QUESTIONNAIRE; CONTROLLED STUDY; FEMALE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; LEUKOCYTE; MAJOR CLINICAL STUDY; MAJOR DEPRESSION; MALE; MEDICAL HISTORY; MENTAL STRESS; PATHOGENESIS; PHYSIOLOGICAL STRESS; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA SEQUENCE; SIGNAL TRANSDUCTION; SMOKING; SUBSTANCE ABUSE; DEPRESSIVE DISORDER, MAJOR; GENE EXPRESSION; GENETICS; INTERVIEW; MIDDLE AGED; PROCEDURES; RECURRENT DISEASE; SELF REPORT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; YOUNG ADULT;

ADULT; DEPRESSIVE DISORDER, MAJOR; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENE EXPRESSION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INTERFERON TYPE I; INTERVIEWS AS TOPIC; MALE; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; RECURRENCE; SELF REPORT; SEQUENCE ANALYSIS, RNA; SIGNAL TRANSDUCTION; YOUNG ADULT;

EID: 84927176211     PISSN: 13594184     EISSN: 14765578     Source Type: Journal    
DOI: 10.1038/mp.2013.161     Document Type: Article

References (55)

1. Sullivan PF, Neale MC, Kendler KS. Genetic epidemiology of major depression: review and meta-analysis. Am J Psychiatry 2000; 157: 1552-1562
2. Poulsen P, Kyvik KO, Vaag A, Beck-Nielsen H. Heritability of type II (non-insulindependent) diabetes mellitus and abnormal glucose tolerance-a populationbased twin study. Diabetologia 1999; 42: 139-145
3. Ripke S, Wray NR, Lewis CM, Hamilton SP, Weissman MM, Breen G., et al. A megaanalysis of genome-wide association studies for major depressive disorder. Mol Psychiatry 2013; 18: 497-511
4. Rush AJ. The varied clinical presentations of major depressive disorder. J Clin Psychiatry 2007; 68(Suppl 8): 4-10
5. Sullivan PF, de Geus EJ, Willemsen G, James MR, Smit JH, Zandbelt T., et al. Genome-wide association for major depressive disorder: a possible role for the presynaptic protein piccolo. Mol Psychiatry 2009; 14: 359-375
6. Ripke S, Wray NR, Lewis CM, Hamilton SP, Weissman MM, Breen G., et al. A megaanalysis of genome-wide association studies for major depressive disorder. Mol Psychiatry 2013; 18: 497-511
7. Klengel T, Binder EB. Gene-environment interactions in major depressive disorder. Can J Psychiatry 2013; 58: 76-83
8. Grishina I, Lattes B. A novel Cdk2 interactor is phosphorylated by Cdc7 and associates with components of the replication complexes. Cell Cycle 2005; 4: 1120-1126
9. Sangfelt O, Erickson S, Castro J, Heiden T, Gustafsson A, Einhorn S., et al. Molecular mechanisms underlying interferon-alpha-induced G0/G1 arrest: CKI-mediated regulation of G1 Cdk-complexes and activation of pocket proteins. Oncogene 1999; 18: 2798-2810
10. Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MW, McCormick C., et al. Characterizing the genetic basis of transcriptome diversity through RNAsequencing of 922 individuals. Genome Research 2013; doi:10.1101/gr.155192.113
11. Kessler RC, Andrews G, Mroczek D, Ustun B, Wittchen H. The World Health Organization Composite International Diagnostic Interview short-form (CIDI-SF). Int J Methods Psychiatric Res 1998; 7: 171-185
12. Kroenke K, Spitzer RL, Williams JB. The PHQ-9: validity of a brief depression severity measure. J Gen Int Medi 2001; 16: 606-613
13. Spitzer RL, Kroenke K, Williams JB, Lowe B. A brief measure for assessing generalized anxiety disorder: the GAD-7. Arch Int Medi 2006; 166: 1092-1097
14. Debey-Pascher S, Hofmann A, Kreusch F, Schuler G, Schuler-Thurner B, Schultze JL., et al. RNA-stabilized whole blood samples but not peripheral blood mononuclear cells can be stored for prolonged time periods prior to transcriptome analysis. J Mol Diagn 2011; 13: 452-460
15. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25: 1105-1111
16. Anders S HTSeq: Analysing high-throughput sequencing data with Python http://www-huberemblde/users/anders/HTSeq/doc/overviewhtml. 2010
17. Abbas AR, Wolslegel K, Seshasayee D, Modrusan Z, Clark HF. Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PloS ONE 2009; 4: e6098
18. Abbas AR, Baldwin D, Ma Y, Ouyang W, Gurney A, Martin F., et al. Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data. Genes Immun 2005; 6: 319-331
19. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc 1995; 57: 289-300
20. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genet 2006; 38: 904-909
21. Stegle O, Parts L, Durbin R, Winn J. A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLoS Comput Biol 2010; 6: e1000770
22. Furlotte NA, Kang HM, Ye C, Eskin E. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity. Bioinformatics 2011; 27: i288-i294
23. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003; 100: 9440-9445
24. Liberzon A, Subramanian A, Pinchback R, Thorvaldsdottir H, Tamayo P, Mesirov JP. Molecular signatures database (MSigDB) 3.0. Bioinformatics 2011; 27: 1739-1740
25. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Nati Acad Sci USA 2005; 102: 15545-15550
26. Shieh G. On power and sample size calculations for likelihood ratio tests in generalized linear models. Biometrics 2000; 56: 1192-1196
27. Platanias LC. Mechanisms of type-I- and type-II-interferon-mediated signalling. Nat Rev Immunol 2005; 5: 375-386
28. Taniguchi T, Takaoka A. A weak signal for strong responses: interferon-alpha/beta revisited. Nat Rev Mol Cell Biol 2001; 2: 378-386
29. Wang BX, Fish EN. The yin and yang of viruses and interferons. Trends Immunol 2012; 33: 190-197
30. Udina M, Castellvi P, Moreno-Espana J, Navines R, Valdes M, Forns X., et al. Interferon-induced depression in chronic hepatitis C: a systematic review and meta-analysis. J Clin Psychiatry 2012; 73: 1128-1138
31. Schaefer M, Engelbrecht MA, Gut O, Fiebich BL, Bauer J, Schmidt F., et al. Interferon alpha (IFNalpha) and psychiatric syndromes: a review. Prog Neuro-psychopharmacol Biol Psychiatry 2002; 26: 731-746
32. Schlaak JF, Trippler M, Hoyo-Becerra C, Erim Y, Kis B, Wang B., et al. Selective hyperresponsiveness of the interferon system in major depressive disorders and depression induced by interferon therapy. PloS ONE 2012; 7: e38668
33. Felger JC, Cole SW, Pace TW, Hu F, Woolwine BJ, Doho GH., et al. Molecular signatures of peripheral blood mononuclear cells during chronic interferon-alpha treatment: relationship with depression and fatigue. Psychological Med 2012; 42: 1591-1603
34. Raison CL, Borisov AS, Woolwine BJ, Massung B, Vogt G, Miller AH. Interferonalpha effects on diurnal hypothalamic-pituitary-adrenal axis activity: relationship with proinflammatory cytokines and behavior. Mol Psychiatry 2010; 15: 535-547
35. Raison CL, Borisov AS, Majer M, Drake DF, Pagnoni G, Woolwine BJ., et al. Activation of central nervous system inflammatory pathways by interferon-alpha: relationship to monoamines and depression. Biol Psychiatry 2009; 65: 296-303
36. Hughes MM, Carballedo A, McLoughlin DM, Amico F, Harkin A, Frodl T., et al. Tryptophan depletion in depressed patients occurs independent of kynurenine pathway activation. Brain Behav Immun 2012; 26: 979-987
37. Zunszain PA, Anacker C, Cattaneo A, Carvalho LA, Pariante CM. Glucocorticoids, cytokines and brain abnormalities in depression. Prog Neuro-psychopharmacol Biol Psychiatry 2011; 35: 722-729
38. Dowlati Y, Herrmann N, Swardfager W, Liu H, Sham L, Reim EK., et al. A metaanalysis of cytokines in major depression. Biol Psychiatry 2010; 67: 446-457
39. Dantzer R, O'Connor JC, Freund GG, Johnson RW, Kelley KW. From inflammation to sickness and depression: when the immune system subjugates the brain. Nat Rev Neurosci 2008; 9: 46-56
40. Miller AH, Maletic V, Raison CL. Inflammation and its discontents: the role of cytokines in the pathophysiology of major depression. Biol Psychiatry 2009; 65: 732-741
41. Wium-Andersen MK, Orsted DD, Nielsen SF, Nordestgaard BG. Elevated C-reactive protein levels, psychological distress, and depression in 73, 131 individuals. JAMA Psychiatry 2013; 70: 176-184
42. McKinnon MC, Yucel K, Nazarov A, MacQueen GM. A meta-analysis examining clinical predictors of hippocampal volume in patients with major depressive disorder. J Psychiatry Neurosci 2009; 34: 41-54
43. Nadeau S, Rivest S. Glucocorticoids play a fundamental role in protecting the brain during innate immune response. J Neurosci 2003; 23: 5536-5544
44. Heim C, Newport DJ, Mletzko T, Miller AH, Nemeroff CB. The link between childhood trauma and depression: insights from HPA axis studies in humans. Psychoneuroendocrinology 2008; 33: 693-710
45. Leonard B, Maes M. Mechanistic explanations how cell-mediated immune activation, inflammation and oxidative and nitrosative stress pathways and their sequels and concomitants play a role in the pathophysiology of unipolar depression. Neurosci Biobehav Rev 2012; 36: 764-785
46. Raison CL, Miller AH. The evolutionary significance of depression in Pathogen Host Defense (PATHOS-D). Mol Psychiatry 2013; 18: 15-37
47. Sequeira A, Mamdani F, Ernst C, Vawter MP, Bunney WE, Lebel V., et al. Global brain gene expression analysis links glutamatergic and GABAergic alterations to suicide and major depression. PloS ONE 2009; 4: e6585
48. Kang HJ, Voleti B, Hajszan T, Rajkowska G, Stockmeier CA, Licznerski P., et al. Decreased expression of synapse-related genes and loss of synapses in major depressive disorder. Nat Med 2012; 18: 1413-1417
49. Hepgul N, Cattaneo A, Zunszain PA, Pariante CM. Depression pathogenesis and treatment: what can we learn from blood mRNA expression?. BMC Med 2013; 11: 28
50. Glahn DC, Curran JE, Winkler AM, Carless MA, Kent JW Jr., Charlesworth JC., et al. High dimensional endophenotype ranking in the search for major depression risk genes. Biol Psychiatry 2012; 71: 6-14
51. Carless MA, Glahn DC, Johnson MP, Curran JE, Bozaoglu K, Dyer TD., et al. Impact of DISC1 variation on neuroanatomical and neurocognitive phenotypes. Mol Psychiatry 2011; 16, 1096-1104
52. Cole SW, Hawkley LC, Arevalo JM, Cacioppo JT. Transcript origin analysis identifies antigen-presenting cells as primary targets of socially regulated gene expression in leukocytes. Proc Nati Acad Sci USA 2011; 108: 3080-3085
53. Cole SW, Hawkley LC, Arevalo JM, Sung CY, Rose RM, Cacioppo JT. Social regulation of gene expression in human leukocytes. Genome Biol 2007; 8: R189
54. Xie RL, Gupta S, Miele A, Shiffman D, Stein JL, Stein GS., et al. The tumor suppressor interferon regulatory factor 1 interferes with SP1 activation to repress the human CDK2 promoter. J Biol Chem 2003; 278: 26589-26596
55. Nica AC, Parts L, Glass D, Nisbet J, Barrett A, Sekowska M., et al. The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet 2011; 7: e1002003